=== START 2026-09-17T14:19:46Z ===
git --git-dir /Users/mvandenb/src/worktrees/.planemo-home/.planemo/gx_repo config remote.origin.fetch '+refs/*:refs/*'
git --git-dir /Users/mvandenb/src/worktrees/.planemo-home/.planemo/gx_repo config remote.origin.mirror true
git --git-dir /Users/mvandenb/src/worktrees/.planemo-home/.planemo/gx_repo remote update >/dev/null 2>&1
galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input
git clone --branch release_26.1 --depth 1 file:///Users/mvandenb/src/worktrees/.planemo-home/.planemo/gx_repo /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/galaxy-dev
Cloning into '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/galaxy-dev'...
if [ -d .venv ]; then GALAXY_VIRTUAL_ENV=.venv; else GALAXY_VIRTUAL_ENV=/Users/mvandenb/src/worktrees/.planemo-home/.planemo/gx_venv_3.12_release_26.1; fi && export GALAXY_VIRTUAL_ENV && if [ ! -e "$GALAXY_VIRTUAL_ENV" ]; then /Users/mvandenb/.local/bin/virtualenv $GALAXY_VIRTUAL_ENV -p /opt/homebrew/bin/python3.12; echo "Created virtualenv"; fi && if [ -e "$GALAXY_VIRTUAL_ENV" ]; then . "$GALAXY_VIRTUAL_ENV"/bin/activate; echo "Activated a virtualenv for Galaxy"; echo "$VIRTUAL_ENV"; else echo "Failed to activate virtualenv."; fi && ./scripts/common_startup.sh ${COMMON_STARTUP_ARGS}
galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input
Activated a virtualenv for Galaxy
/Users/mvandenb/src/worktrees/.planemo-home/.planemo/gx_venv_3.12_release_26.1
Initializing tool-data/shared/ucsc/builds.txt from builds.txt.sample
Initializing tool-data/shared/ucsc/manual_builds.txt from manual_builds.txt.sample
Activating virtualenv at /Users/mvandenb/src/worktrees/.planemo-home/.planemo/gx_venv_3.12_release_26.1
Using Python 3.12.13 environment at: /Users/mvandenb/src/worktrees/.planemo-home/.planemo/gx_venv_3.12_release_26.1
Checked 313 packages in 133ms
Trying to resolve path for the 'email_ban_file' option but it's empty/None
The Galaxy client build is being skipped due to the SKIP_CLIENT_BUILD environment variable.
Starting Galaxy with command [cd /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/galaxy-dev && if [ -d .venv ]; then GALAXY_VIRTUAL_ENV=.venv; else GALAXY_VIRTUAL_ENV=/Users/mvandenb/src/worktrees/.planemo-home/.planemo/gx_venv_3.12_release_26.1; fi && export GALAXY_VIRTUAL_ENV && if [ ! -e "$GALAXY_VIRTUAL_ENV" ]; then /Users/mvandenb/.local/bin/virtualenv $GALAXY_VIRTUAL_ENV -p /opt/homebrew/bin/python3.12; echo "Created virtualenv"; fi && if [ -e "$GALAXY_VIRTUAL_ENV" ]; then . "$GALAXY_VIRTUAL_ENV"/bin/activate; echo "Activated a virtualenv for Galaxy"; echo "$VIRTUAL_ENV"; else echo "Failed to activate virtualenv."; fi && /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/galaxy-dev/run.sh $COMMON_STARTUP_ARGS --daemon]
galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input
Activated a virtualenv for Galaxy
/Users/mvandenb/src/worktrees/.planemo-home/.planemo/gx_venv_3.12_release_26.1
Activating virtualenv at /Users/mvandenb/src/worktrees/.planemo-home/.planemo/gx_venv_3.12_release_26.1
Using Python 3.12.13 environment at: /Users/mvandenb/src/worktrees/.planemo-home/.planemo/gx_venv_3.12_release_26.1
Checked 313 packages in 16ms
Option master_api_key has been deprecated in favor of bootstrap_admin_api_key
Trying to resolve path for the 'email_ban_file' option but it's empty/None
Trying to resolve path for the 'data_manager_config_file' option but it's empty/None
Using Python 3.12.13 environment at: /Users/mvandenb/src/worktrees/.planemo-home/.planemo/gx_venv_3.12_release_26.1
Using Python 3.12.13 environment at: /Users/mvandenb/src/worktrees/.planemo-home/.planemo/gx_venv_3.12_release_26.1
Checked 1 package in 6ms
The Galaxy client build is being skipped due to the SKIP_CLIENT_BUILD environment variable.
Activating virtualenv at /Users/mvandenb/src/worktrees/.planemo-home/.planemo/gx_venv_3.12_release_26.1
Executing: galaxyctl start
Adding service gunicorn
supervisord is not running
Adding service celery
supervisord is not running
Adding service celery-beat
supervisord is not running
Adding service gx-it-proxy
supervisord is not running
celery                           STARTING  
celery-beat                      STARTING  
gunicorn                         STARTING  
gx-it-proxy                      STARTING  
Log files are in /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/gravity/log
galaxy.util WARNING 2026-09-17 16:20:09,748 [pN:main.1,p:70319,tN:MainThread] directory not found: /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/galaxy-dev/config/plugins/activities
galaxy.tools WARNING 2026-09-17 16:20:09,749 [pN:main.1,p:70319,tN:MainThread] The default shed tool config file (/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file
galaxy.tool_util.toolbox.base INFO 2026-09-17 16:20:09,749 [pN:main.1,p:70319,tN:MainThread] Parsing the tool configuration /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/tool_conf.xml
galaxy.tool_util.toolbox.base DEBUG 2026-09-17 16:20:09,750 [pN:main.1,p:70319,tN:MainThread] Tool path for tool configuration /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/tool_conf.xml is None
galaxy.tools DEBUG 2026-09-17 16:20:09,751 [pN:main.1,p:70319,tN:MainThread] No parameter model for tool 'upload1': Cannot generate a tool parameter model for upload_dataset inputs
galaxy.tool_util.toolbox.base DEBUG 2026-09-17 16:20:09,763 [pN:main.1,p:70319,tN:MainThread] Loaded tool id: upload1, version: 1.1.7 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2026-09-17 16:20:09,765 [pN:main.1,p:70319,tN:MainThread] Loaded tool id: __SAMPLE_SHEET_TO_TABULAR__, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2026-09-17 16:20:09,766 [pN:main.1,p:70319,tN:MainThread] Loaded tool id: __FLATTEN__, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2026-09-17 16:20:09,769 [pN:main.1,p:70319,tN:MainThread] Loaded tool id: Cut1, version: 1.0.2 into tool panel..
galaxy.tool_util.parser.factory INFO 2026-09-17 16:20:09,769 [pN:main.1,p:70319,tN:MainThread] Loading tool from YAML - this is experimental - tool will not function in future.
galaxy.tool_util.toolbox.base ERROR 2026-09-17 16:20:09,773 [pN:main.1,p:70319,tN:MainThread] Error reading tool from path: /Users/mvandenb/src/worktrees/foundry/brc-c-auris/.foundry-runs/auris-scf1/galaxy-workflow.gxwf.yml
Traceback (most recent call last):
  File "/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/galaxy-dev/lib/galaxy/tool_util/toolbox/base.py", line 967, in _load_tool_tag_set
    tool = self.load_tool(concrete_path, use_cached=False)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/galaxy-dev/lib/galaxy/tool_util/toolbox/base.py", line 1222, in load_tool
    tool = self.create_tool(
           ^^^^^^^^^^^^^^^^^
  File "/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/galaxy-dev/lib/galaxy/tools/__init__.py", line 619, in create_tool
    return self._create_tool_from_source(tool_source, config_file=config_file, **kwds)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/galaxy-dev/lib/galaxy/tools/__init__.py", line 634, in _create_tool_from_source
    return create_tool_from_source(self.app, tool_source, **kwds)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/galaxy-dev/lib/galaxy/tools/__init__.py", line 448, in create_tool_from_source
    tool = ToolClass(config_file, tool_source, app, **kwds)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/galaxy-dev/lib/galaxy/tools/__init__.py", line 1099, in __init__
    raise e
  File "/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/galaxy-dev/lib/galaxy/tools/__init__.py", line 1096, in __init__
    self.parse(tool_source, guid=guid, dynamic=dynamic)
  File "/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/galaxy-dev/lib/galaxy/tools/__init__.py", line 1329, in parse
    raise Exception(f"Missing tool 'id' for tool at '{tool_source}'")
Exception: Missing tool 'id' for tool at 'YamlToolSource[/Users/mvandenb/src/worktrees/foundry/brc-c-auris/.foundry-runs/auris-scf1/galaxy-workflow.gxwf.yml]'
galaxy.tool_util.toolbox.base DEBUG 2026-09-17 16:20:09,776 [pN:main.1,p:70319,tN:MainThread] Loaded tool id: __FILTER_FROM_FILE__, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2026-09-17 16:20:09,784 [pN:main.1,p:70319,tN:MainThread] Loaded tool id: Filter1, version: 1.1.1 into tool panel..
galaxy.tools WARNING 2026-09-17 16:20:09,785 [pN:main.1,p:70319,tN:MainThread] The default shed tool config file (/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file
galaxy.tool_util.toolbox.base INFO 2026-09-17 16:20:09,785 [pN:main.1,p:70319,tN:MainThread] Parsing the tool configuration /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/shed_tools_conf.xml
galaxy.tool_util.toolbox.base DEBUG 2026-09-17 16:20:09,786 [pN:main.1,p:70319,tN:MainThread] Tool path for shed tool configuration /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/shed_tools_conf.xml is /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/shed_tools
galaxy.tools WARNING 2026-09-17 16:20:09,786 [pN:main.1,p:70319,tN:MainThread] The default shed tool config file (/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file
galaxy.tool_util.toolbox.base INFO 2026-09-17 16:20:09,786 [pN:main.1,p:70319,tN:MainThread] Parsing the tool configuration /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/empty_tool_conf.xml
galaxy.tool_util.toolbox.base DEBUG 2026-09-17 16:20:09,787 [pN:main.1,p:70319,tN:MainThread] Tool path for tool configuration /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/empty_tool_conf.xml is None
galaxy.tool_util.toolbox.base DEBUG 2026-09-17 16:20:09,787 [pN:main.1,p:70319,tN:MainThread] Reading tools from config files finished (38.252 ms)
galaxy.tool_util.toolbox.base DEBUG 2026-09-17 16:20:09,788 [pN:main.1,p:70319,tN:MainThread] Loaded tool id: upload1, version: 1.1.7 into tool panel..
galaxy.tool_util.toolbox.views.edam DEBUG 2026-09-17 16:20:09,788 [pN:main.1,p:70319,tN:MainThread] Loading EDAM tool panel finished (0.683 ms)
galaxy.tool_util.toolbox.base DEBUG 2026-09-17 16:20:09,788 [pN:main.1,p:70319,tN:MainThread] Loaded tool id: upload1, version: 1.1.7 into tool panel..
galaxy.tool_util.toolbox.views.edam DEBUG 2026-09-17 16:20:09,788 [pN:main.1,p:70319,tN:MainThread] Loading EDAM tool panel finished (0.545 ms)
galaxy.tool_util.toolbox.integrated_panel DEBUG 2026-09-17 16:20:09,789 [pN:main.1,p:70319,tN:MainThread] Writing integrated tool panel config file to '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/integrated_tool_panel_conf.xml'
galaxy.tool_util.toolbox.base DEBUG 2026-09-17 16:20:09,789 [pN:main.1,p:70319,tN:MainThread] Loaded tool id: upload1, version: 1.1.7 into tool panel..
galaxy.tool_util.toolbox.views.edam DEBUG 2026-09-17 16:20:09,790 [pN:main.1,p:70319,tN:MainThread] Loading EDAM tool panel finished (0.571 ms)
galaxy.tool_util.toolbox.base DEBUG 2026-09-17 16:20:09,790 [pN:main.1,p:70319,tN:MainThread] Loaded tool id: upload1, version: 1.1.7 into tool panel..
galaxy.tool_util.toolbox.views.edam DEBUG 2026-09-17 16:20:09,790 [pN:main.1,p:70319,tN:MainThread] Loading EDAM tool panel finished (0.535 ms)
galaxy.tools.search WARNING 2026-09-17 16:20:11,434 [pN:main.1,p:70319,tN:MainThread] Index at '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/galaxy-dev/database/tool_search_index/default' uses outdated schema, creating a new index
galaxy.tools.search WARNING 2026-09-17 16:20:11,439 [pN:main.1,p:70319,tN:MainThread] Index at '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/galaxy-dev/database/tool_search_index/my_panel' uses outdated schema, creating a new index
galaxy.tools.search WARNING 2026-09-17 16:20:11,443 [pN:main.1,p:70319,tN:MainThread] Index at '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/galaxy-dev/database/tool_search_index/ontology:edam_operations' uses outdated schema, creating a new index
galaxy.tools.search WARNING 2026-09-17 16:20:11,445 [pN:main.1,p:70319,tN:MainThread] Index at '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/galaxy-dev/database/tool_search_index/ontology:edam_topics' uses outdated schema, creating a new index
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,452 [pN:main.1,p:70319,tN:MainThread] Loaded display application 'ucsc_bam' for datatype 'bam', inherit=False.
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,454 [pN:main.1,p:70319,tN:MainThread] Loaded display application 'ensembl_bam' for datatype 'bam', inherit=False.
galaxy.datatypes.display_applications.application ERROR 2026-09-17 16:20:11,455 [pN:main.1,p:70319,tN:MainThread] Error loading a set of Dynamic Display Application links: Unable to find data table named "igv_broad_genomes".
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,457 [pN:main.1,p:70319,tN:MainThread] Loaded display application 'igv_bam' for datatype 'bam', inherit=False.
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,458 [pN:main.1,p:70319,tN:MainThread] Loaded display application 'igb_bam' for datatype 'bam', inherit=False.
galaxy.datatypes.display_applications.application ERROR 2026-09-17 16:20:11,459 [pN:main.1,p:70319,tN:MainThread] Error loading a set of Dynamic Display Application links: Unable to find data table named "bam_iobio".
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,460 [pN:main.1,p:70319,tN:MainThread] Loaded display application 'iobio_bam' for datatype 'bam', inherit=False.
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,461 [pN:main.1,p:70319,tN:MainThread] Loaded display application 'igb_cram' for datatype 'cram', inherit=False.
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,462 [pN:main.1,p:70319,tN:MainThread] Loaded display application 'igb_bed' for datatype 'bed', inherit=False.
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,462 [pN:main.1,p:70319,tN:MainThread] Loaded display application 'igb_bedgraph' for datatype 'bedgraph', inherit=False.
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,463 [pN:main.1,p:70319,tN:MainThread] Loaded display application 'ucsc_bigbed' for datatype 'bigbed', inherit=False.
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,464 [pN:main.1,p:70319,tN:MainThread] Loaded display application 'igb_bb' for datatype 'bigbed', inherit=False.
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,465 [pN:main.1,p:70319,tN:MainThread] Loaded display application 'ucsc_bigwig' for datatype 'bigwig', inherit=False.
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,466 [pN:main.1,p:70319,tN:MainThread] Loaded display application 'igb_bigwig' for datatype 'bigwig', inherit=False.
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,467 [pN:main.1,p:70319,tN:MainThread] Loaded display application 'igv_bigwig' for datatype 'bigwig', inherit=False.
galaxy.datatypes.display_applications.application ERROR 2026-09-17 16:20:11,468 [pN:main.1,p:70319,tN:MainThread] Error loading a set of Dynamic Display Application links: Unable to find data table named "intermine_simple_display".
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,468 [pN:main.1,p:70319,tN:MainThread] Loaded display application 'intermine_simple' for datatype 'intermine_tabular', inherit=False.
galaxy.datatypes.display_applications.application ERROR 2026-09-17 16:20:11,469 [pN:main.1,p:70319,tN:MainThread] Error loading a set of Dynamic Display Application links: Unable to find data table named "igv_broad_genomes".
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,470 [pN:main.1,p:70319,tN:MainThread] Loaded display application 'igv_fasta' for datatype 'fasta', inherit=True.
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,472 [pN:main.1,p:70319,tN:MainThread] Loaded display application 'ensembl_gff' for datatype 'gff', inherit=True.
galaxy.datatypes.display_applications.application ERROR 2026-09-17 16:20:11,473 [pN:main.1,p:70319,tN:MainThread] Error loading a set of Dynamic Display Application links: Unable to find data table named "igv_broad_genomes".
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,473 [pN:main.1,p:70319,tN:MainThread] Loaded display application 'igv_gff' for datatype 'gff', inherit=True.
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,474 [pN:main.1,p:70319,tN:MainThread] Loaded display application 'igb_gtf' for datatype 'gtf', inherit=False.
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,475 [pN:main.1,p:70319,tN:MainThread] Loaded display application 'ensembl_interval' for datatype 'interval', inherit=True.
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,476 [pN:main.1,p:70319,tN:MainThread] Loaded display application 'gbrowse_interval_as_bed' for datatype 'interval', inherit=True.
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,477 [pN:main.1,p:70319,tN:MainThread] Loaded display application 'rviewer_interval' for datatype 'interval', inherit=True.
galaxy.datatypes.display_applications.application ERROR 2026-09-17 16:20:11,478 [pN:main.1,p:70319,tN:MainThread] Error loading a set of Dynamic Display Application links: Unable to find data table named "igv_broad_genomes".
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,478 [pN:main.1,p:70319,tN:MainThread] Loaded display application 'igv_interval_as_bed' for datatype 'interval', inherit=True.
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,479 [pN:main.1,p:70319,tN:MainThread] Loaded display application 'avivator' for datatype 'tiff', inherit=False.
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,479 [pN:main.1,p:70319,tN:MainThread] Loaded display application 'avivator' for datatype 'ome.tiff', inherit=False.
galaxy.datatypes.display_applications.application ERROR 2026-09-17 16:20:11,480 [pN:main.1,p:70319,tN:MainThread] Error loading a set of Dynamic Display Application links: Unable to find data table named "q2view_display".
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,480 [pN:main.1,p:70319,tN:MainThread] Loaded display application 'q2view' for datatype 'qza', inherit=False.
galaxy.datatypes.display_applications.application ERROR 2026-09-17 16:20:11,481 [pN:main.1,p:70319,tN:MainThread] Error loading a set of Dynamic Display Application links: Unable to find data table named "q2view_display".
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,481 [pN:main.1,p:70319,tN:MainThread] Loaded display application 'q2view' for datatype 'qzv', inherit=False.
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,482 [pN:main.1,p:70319,tN:MainThread] Loaded display application 'ucsc_maf_customtrack' for datatype 'mafcustomtrack', inherit=False.
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,483 [pN:main.1,p:70319,tN:MainThread] Loaded display application 'minerva_tabular' for datatype 'tabular', inherit=False.
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,483 [pN:main.1,p:70319,tN:MainThread] Loaded display application 'ucsc_vcf' for datatype 'vcf', inherit=False.
galaxy.datatypes.display_applications.application ERROR 2026-09-17 16:20:11,484 [pN:main.1,p:70319,tN:MainThread] Error loading a set of Dynamic Display Application links: Unable to find data table named "igv_broad_genomes".
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,485 [pN:main.1,p:70319,tN:MainThread] Loaded display application 'igv_vcf' for datatype 'vcf', inherit=False.
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,485 [pN:main.1,p:70319,tN:MainThread] Loaded display application 'rviewer_vcf' for datatype 'vcf', inherit=True.
galaxy.datatypes.display_applications.application ERROR 2026-09-17 16:20:11,486 [pN:main.1,p:70319,tN:MainThread] Error loading a set of Dynamic Display Application links: Unable to find data table named "vcf_iobio".
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,486 [pN:main.1,p:70319,tN:MainThread] Loaded display application 'iobio_vcf' for datatype 'vcf', inherit=False.
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,487 [pN:main.1,p:70319,tN:MainThread] Loaded display application 'igb_wig' for datatype 'wig', inherit=False.
galaxy.datatypes.display_applications.application ERROR 2026-09-17 16:20:11,488 [pN:main.1,p:70319,tN:MainThread] Error loading a set of Dynamic Display Application links: Unable to find data table named "igv_broad_genomes".
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,488 [pN:main.1,p:70319,tN:MainThread] Loaded display application 'igv_vcf' for datatype 'vcf_bgzip', inherit=False.
galaxy.datatypes.display_applications.application ERROR 2026-09-17 16:20:11,489 [pN:main.1,p:70319,tN:MainThread] Error loading a set of Dynamic Display Application links: Unable to find data table named "igv_broad_genomes".
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,489 [pN:main.1,p:70319,tN:MainThread] Loaded display application 'igv_genbank' for datatype 'genbank', inherit=False.
galaxy.datatypes.display_applications.application ERROR 2026-09-17 16:20:11,490 [pN:main.1,p:70319,tN:MainThread] Error loading a set of Dynamic Display Application links: Unable to find data table named "biom_simple_display".
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,490 [pN:main.1,p:70319,tN:MainThread] Loaded display application 'biom_simple' for datatype 'biom1', inherit=False.
galaxy.datatypes.display_applications.application ERROR 2026-09-17 16:20:11,491 [pN:main.1,p:70319,tN:MainThread] Error loading a set of Dynamic Display Application links: Unable to find data table named "icn3d_simple_display".
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,491 [pN:main.1,p:70319,tN:MainThread] Loaded display application 'icn3d_simple' for datatype 'sdf', inherit=False.
galaxy.datatypes.display_applications.application ERROR 2026-09-17 16:20:11,492 [pN:main.1,p:70319,tN:MainThread] Error loading a set of Dynamic Display Application links: Unable to find data table named "icn3d_simple_display".
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,492 [pN:main.1,p:70319,tN:MainThread] Loaded display application 'icn3d_simple' for datatype 'mol2', inherit=False.
galaxy.datatypes.display_applications.application ERROR 2026-09-17 16:20:11,492 [pN:main.1,p:70319,tN:MainThread] Error loading a set of Dynamic Display Application links: Unable to find data table named "icn3d_simple_display".
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,493 [pN:main.1,p:70319,tN:MainThread] Loaded display application 'icn3d_simple' for datatype 'pdb', inherit=False.
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,493 [pN:main.1,p:70319,tN:MainThread] Loaded display application 'ucsc_trackhub' for datatype 'trackhub', inherit=False.
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,494 [pN:main.1,p:70319,tN:MainThread] Adding inherited display application 'igv_fasta' to datatype 'a2m'
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,494 [pN:main.1,p:70319,tN:MainThread] Adding inherited display application 'ensembl_interval' to datatype 'bed'
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,494 [pN:main.1,p:70319,tN:MainThread] Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bed'
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,494 [pN:main.1,p:70319,tN:MainThread] Adding inherited display application 'rviewer_interval' to datatype 'bed'
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,495 [pN:main.1,p:70319,tN:MainThread] Adding inherited display application 'igv_interval_as_bed' to datatype 'bed'
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,495 [pN:main.1,p:70319,tN:MainThread] Adding inherited display application 'ensembl_interval' to datatype 'bedgraph'
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,495 [pN:main.1,p:70319,tN:MainThread] Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bedgraph'
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,495 [pN:main.1,p:70319,tN:MainThread] Adding inherited display application 'rviewer_interval' to datatype 'bedgraph'
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,495 [pN:main.1,p:70319,tN:MainThread] Adding inherited display application 'igv_interval_as_bed' to datatype 'bedgraph'
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,495 [pN:main.1,p:70319,tN:MainThread] Adding inherited display application 'ensembl_interval' to datatype 'bedstrict'
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,496 [pN:main.1,p:70319,tN:MainThread] Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bedstrict'
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,496 [pN:main.1,p:70319,tN:MainThread] Adding inherited display application 'rviewer_interval' to datatype 'bedstrict'
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,496 [pN:main.1,p:70319,tN:MainThread] Adding inherited display application 'igv_interval_as_bed' to datatype 'bedstrict'
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,496 [pN:main.1,p:70319,tN:MainThread] Adding inherited display application 'ensembl_interval' to datatype 'bed6'
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,496 [pN:main.1,p:70319,tN:MainThread] Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bed6'
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,497 [pN:main.1,p:70319,tN:MainThread] Adding inherited display application 'rviewer_interval' to datatype 'bed6'
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,497 [pN:main.1,p:70319,tN:MainThread] Adding inherited display application 'igv_interval_as_bed' to datatype 'bed6'
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,497 [pN:main.1,p:70319,tN:MainThread] Adding inherited display application 'ensembl_interval' to datatype 'bed12'
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,497 [pN:main.1,p:70319,tN:MainThread] Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bed12'
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,497 [pN:main.1,p:70319,tN:MainThread] Adding inherited display application 'rviewer_interval' to datatype 'bed12'
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,498 [pN:main.1,p:70319,tN:MainThread] Adding inherited display application 'igv_interval_as_bed' to datatype 'bed12'
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,498 [pN:main.1,p:70319,tN:MainThread] Adding inherited display application 'ensembl_interval' to datatype 'probed'
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,498 [pN:main.1,p:70319,tN:MainThread] Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'probed'
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,498 [pN:main.1,p:70319,tN:MainThread] Adding inherited display application 'rviewer_interval' to datatype 'probed'
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,498 [pN:main.1,p:70319,tN:MainThread] Adding inherited display application 'igv_interval_as_bed' to datatype 'probed'
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,499 [pN:main.1,p:70319,tN:MainThread] Adding inherited display application 'ensembl_interval' to datatype 'chrint'
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,499 [pN:main.1,p:70319,tN:MainThread] Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'chrint'
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,499 [pN:main.1,p:70319,tN:MainThread] Adding inherited display application 'rviewer_interval' to datatype 'chrint'
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,499 [pN:main.1,p:70319,tN:MainThread] Adding inherited display application 'igv_interval_as_bed' to datatype 'chrint'
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,499 [pN:main.1,p:70319,tN:MainThread] Adding inherited display application 'igv_fasta' to datatype 'fasta.gz'
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,500 [pN:main.1,p:70319,tN:MainThread] Adding inherited display application 'igv_fasta' to datatype 'fasta.bz2'
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,500 [pN:main.1,p:70319,tN:MainThread] Adding inherited display application 'igv_fasta' to datatype 'a3m'
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,500 [pN:main.1,p:70319,tN:MainThread] Adding inherited display application 'ensembl_gff' to datatype 'gff3'
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,500 [pN:main.1,p:70319,tN:MainThread] Adding inherited display application 'igv_gff' to datatype 'gff3'
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,500 [pN:main.1,p:70319,tN:MainThread] Adding inherited display application 'ensembl_gff' to datatype 'gff3.gz'
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,501 [pN:main.1,p:70319,tN:MainThread] Adding inherited display application 'igv_gff' to datatype 'gff3.gz'
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,501 [pN:main.1,p:70319,tN:MainThread] Adding inherited display application 'ensembl_gff' to datatype 'gff3.bz2'
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,501 [pN:main.1,p:70319,tN:MainThread] Adding inherited display application 'igv_gff' to datatype 'gff3.bz2'
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,501 [pN:main.1,p:70319,tN:MainThread] Adding inherited display application 'ensembl_gff' to datatype 'gtf'
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,501 [pN:main.1,p:70319,tN:MainThread] Adding inherited display application 'igv_gff' to datatype 'gtf'
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,502 [pN:main.1,p:70319,tN:MainThread] Adding inherited display application 'ensembl_gff' to datatype 'gtf.gz'
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,502 [pN:main.1,p:70319,tN:MainThread] Adding inherited display application 'igv_gff' to datatype 'gtf.gz'
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,502 [pN:main.1,p:70319,tN:MainThread] Adding inherited display application 'ensembl_interval' to datatype 'encodepeak'
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,503 [pN:main.1,p:70319,tN:MainThread] Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'encodepeak'
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,503 [pN:main.1,p:70319,tN:MainThread] Adding inherited display application 'rviewer_interval' to datatype 'encodepeak'
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,503 [pN:main.1,p:70319,tN:MainThread] Adding inherited display application 'igv_interval_as_bed' to datatype 'encodepeak'
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,503 [pN:main.1,p:70319,tN:MainThread] Adding inherited display application 'igv_fasta' to datatype 'sequences'
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,503 [pN:main.1,p:70319,tN:MainThread] Adding inherited display application 'ensembl_interval' to datatype 'interval_tabix.gz'
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,504 [pN:main.1,p:70319,tN:MainThread] Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'interval_tabix.gz'
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,504 [pN:main.1,p:70319,tN:MainThread] Adding inherited display application 'rviewer_interval' to datatype 'interval_tabix.gz'
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,504 [pN:main.1,p:70319,tN:MainThread] Adding inherited display application 'igv_interval_as_bed' to datatype 'interval_tabix.gz'
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,504 [pN:main.1,p:70319,tN:MainThread] Adding inherited display application 'ensembl_interval' to datatype 'juicer_medium_tabix.gz'
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,504 [pN:main.1,p:70319,tN:MainThread] Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'juicer_medium_tabix.gz'
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,505 [pN:main.1,p:70319,tN:MainThread] Adding inherited display application 'rviewer_interval' to datatype 'juicer_medium_tabix.gz'
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,505 [pN:main.1,p:70319,tN:MainThread] Adding inherited display application 'igv_interval_as_bed' to datatype 'juicer_medium_tabix.gz'
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,505 [pN:main.1,p:70319,tN:MainThread] Adding inherited display application 'ensembl_interval' to datatype 'bed_tabix.gz'
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,505 [pN:main.1,p:70319,tN:MainThread] Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bed_tabix.gz'
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,505 [pN:main.1,p:70319,tN:MainThread] Adding inherited display application 'rviewer_interval' to datatype 'bed_tabix.gz'
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,505 [pN:main.1,p:70319,tN:MainThread] Adding inherited display application 'igv_interval_as_bed' to datatype 'bed_tabix.gz'
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,506 [pN:main.1,p:70319,tN:MainThread] Adding inherited display application 'ensembl_interval' to datatype 'gff_tabix.gz'
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,506 [pN:main.1,p:70319,tN:MainThread] Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'gff_tabix.gz'
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,506 [pN:main.1,p:70319,tN:MainThread] Adding inherited display application 'rviewer_interval' to datatype 'gff_tabix.gz'
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,506 [pN:main.1,p:70319,tN:MainThread] Adding inherited display application 'igv_interval_as_bed' to datatype 'gff_tabix.gz'
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,507 [pN:main.1,p:70319,tN:MainThread] Adding inherited display application 'igv_fasta' to datatype 'mothur.align'
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,509 [pN:main.1,p:70319,tN:MainThread] Loaded converter: CONVERTER_uncompressed_to_gz
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,510 [pN:main.1,p:70319,tN:MainThread] Loaded converter: CONVERTER_gz_to_uncompressed
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,511 [pN:main.1,p:70319,tN:MainThread] Loaded converter: CONVERTER_uncompressed_to_gz
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,512 [pN:main.1,p:70319,tN:MainThread] Loaded converter: CONVERTER_gz_to_uncompressed
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,513 [pN:main.1,p:70319,tN:MainThread] Loaded converter: CONVERTER_uncompressed_to_gz
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,514 [pN:main.1,p:70319,tN:MainThread] Loaded converter: CONVERTER_gz_to_uncompressed
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,515 [pN:main.1,p:70319,tN:MainThread] Loaded converter: CONVERTER_uncompressed_to_gz
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,516 [pN:main.1,p:70319,tN:MainThread] Loaded converter: CONVERTER_gz_to_uncompressed
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,517 [pN:main.1,p:70319,tN:MainThread] Loaded converter: CONVERTER_uncompressed_to_gz
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,518 [pN:main.1,p:70319,tN:MainThread] Loaded converter: CONVERTER_gz_to_uncompressed
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,519 [pN:main.1,p:70319,tN:MainThread] Loaded converter: CONVERTER_bz2_to_uncompressed
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,520 [pN:main.1,p:70319,tN:MainThread] Loaded converter: CONVERTER_Bam_Bai_0
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,521 [pN:main.1,p:70319,tN:MainThread] Loaded converter: CONVERTER_bam_to_bigwig_0
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,521 [pN:main.1,p:70319,tN:MainThread] Loaded converter: CONVERTER_bam_to_qname_sorted_bam
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,522 [pN:main.1,p:70319,tN:MainThread] Loaded converter: CONVERTER_bam_to_bigwig_0
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,523 [pN:main.1,p:70319,tN:MainThread] Loaded converter: CONVERTER_bam_to_coodinate_sorted_bam
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,523 [pN:main.1,p:70319,tN:MainThread] Loaded converter: CONVERTER_bam_to_qname_sorted_bam
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,524 [pN:main.1,p:70319,tN:MainThread] Loaded converter: CONVERTER_cram_to_bam_0
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,525 [pN:main.1,p:70319,tN:MainThread] Loaded converter: CONVERTER_bed_to_gff_0
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,527 [pN:main.1,p:70319,tN:MainThread] Loaded converter: CONVERTER_interval_to_bgzip_0
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,528 [pN:main.1,p:70319,tN:MainThread] Loaded converter: CONVERTER_interval_to_tabix_0
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,528 [pN:main.1,p:70319,tN:MainThread] Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,529 [pN:main.1,p:70319,tN:MainThread] Loaded converter: CONVERTER_bed_to_fli_0
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,530 [pN:main.1,p:70319,tN:MainThread] Loaded converter: CONVERTER_bedgraph_to_bigwig
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,531 [pN:main.1,p:70319,tN:MainThread] Loaded converter: CONVERTER_len_to_linecount
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,531 [pN:main.1,p:70319,tN:MainThread] Loaded converter: CONVERTER_parquet_to_csv
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,533 [pN:main.1,p:70319,tN:MainThread] Loaded converter: ucsc_bigbedtobed
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,534 [pN:main.1,p:70319,tN:MainThread] Loaded converter: bigwigtowig
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,536 [pN:main.1,p:70319,tN:MainThread] Loaded converter: CONVERTER_interval_to_bgzip_0
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,537 [pN:main.1,p:70319,tN:MainThread] Loaded converter: CONVERTER_interval_to_tabix_0
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,538 [pN:main.1,p:70319,tN:MainThread] Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,538 [pN:main.1,p:70319,tN:MainThread] Loaded converter: csv_to_tabular
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,539 [pN:main.1,p:70319,tN:MainThread] Loaded converter: tabular_to_csv
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,540 [pN:main.1,p:70319,tN:MainThread] Loaded converter: CONVERTER_fasta_to_tabular
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,540 [pN:main.1,p:70319,tN:MainThread] Loaded converter: CONVERTER_fasta_to_bowtie_base_index
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,541 [pN:main.1,p:70319,tN:MainThread] Loaded converter: CONVERTER_fasta_to_bowtie_color_index
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,542 [pN:main.1,p:70319,tN:MainThread] Loaded converter: CONVERTER_fasta_to_2bit
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,542 [pN:main.1,p:70319,tN:MainThread] Loaded converter: CONVERTER_fasta_to_len
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,543 [pN:main.1,p:70319,tN:MainThread] Loaded converter: CONVERTER_fasta_to_fai
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,544 [pN:main.1,p:70319,tN:MainThread] Loaded converter: CONVERTER_uncompressed_to_gz
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,545 [pN:main.1,p:70319,tN:MainThread] Loaded converter: CONVERTER_gz_to_uncompressed
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,545 [pN:main.1,p:70319,tN:MainThread] Loaded converter: CONVERTER_bz2_to_uncompressed
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,546 [pN:main.1,p:70319,tN:MainThread] Loaded converter: CONVERTER_fastq_to_fqtoc0
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,547 [pN:main.1,p:70319,tN:MainThread] Loaded converter: CONVERTER_uncompressed_to_gz
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,548 [pN:main.1,p:70319,tN:MainThread] Loaded converter: CONVERTER_gz_to_uncompressed
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,548 [pN:main.1,p:70319,tN:MainThread] Loaded converter: CONVERTER_bz2_to_uncompressed
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,549 [pN:main.1,p:70319,tN:MainThread] Loaded converter: CONVERTER_fastq_to_fqtoc0
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,550 [pN:main.1,p:70319,tN:MainThread] Loaded converter: CONVERTER_uncompressed_to_gz
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,551 [pN:main.1,p:70319,tN:MainThread] Loaded converter: CONVERTER_gz_to_uncompressed
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,551 [pN:main.1,p:70319,tN:MainThread] Loaded converter: CONVERTER_bz2_to_uncompressed
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,552 [pN:main.1,p:70319,tN:MainThread] Loaded converter: CONVERTER_fastq_to_fqtoc0
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,553 [pN:main.1,p:70319,tN:MainThread] Loaded converter: CONVERTER_uncompressed_to_gz
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,554 [pN:main.1,p:70319,tN:MainThread] Loaded converter: CONVERTER_gz_to_uncompressed
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,554 [pN:main.1,p:70319,tN:MainThread] Loaded converter: CONVERTER_bz2_to_uncompressed
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,555 [pN:main.1,p:70319,tN:MainThread] Loaded converter: CONVERTER_fastq_to_fqtoc0
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,556 [pN:main.1,p:70319,tN:MainThread] Loaded converter: CONVERTER_uncompressed_to_gz
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,557 [pN:main.1,p:70319,tN:MainThread] Loaded converter: CONVERTER_gz_to_uncompressed
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,557 [pN:main.1,p:70319,tN:MainThread] Loaded converter: CONVERTER_bz2_to_uncompressed
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,558 [pN:main.1,p:70319,tN:MainThread] Loaded converter: CONVERTER_fastq_to_fqtoc0
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,559 [pN:main.1,p:70319,tN:MainThread] Loaded converter: CONVERTER_uncompressed_to_gz
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,560 [pN:main.1,p:70319,tN:MainThread] Loaded converter: CONVERTER_gz_to_uncompressed
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,560 [pN:main.1,p:70319,tN:MainThread] Loaded converter: CONVERTER_bz2_to_uncompressed
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,561 [pN:main.1,p:70319,tN:MainThread] Loaded converter: CONVERTER_gff_to_bed_0
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,562 [pN:main.1,p:70319,tN:MainThread] Loaded converter: CONVERTER_gff_to_interval_index_0
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,562 [pN:main.1,p:70319,tN:MainThread] Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,563 [pN:main.1,p:70319,tN:MainThread] Loaded converter: CONVERTER_gff_to_fli_0
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,565 [pN:main.1,p:70319,tN:MainThread] Loaded converter: CONVERTER_interval_to_bgzip_0
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,566 [pN:main.1,p:70319,tN:MainThread] Loaded converter: CONVERTER_interval_to_tabix_0
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,567 [pN:main.1,p:70319,tN:MainThread] Loaded converter: CONVERTER_uncompressed_to_gz
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,567 [pN:main.1,p:70319,tN:MainThread] Loaded converter: CONVERTER_gz_to_uncompressed
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,568 [pN:main.1,p:70319,tN:MainThread] Loaded converter: CONVERTER_bz2_to_uncompressed
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,569 [pN:main.1,p:70319,tN:MainThread] Loaded converter: CONVERTER_gff_to_interval_index_0
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,569 [pN:main.1,p:70319,tN:MainThread] Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,570 [pN:main.1,p:70319,tN:MainThread] Loaded converter: CONVERTER_uncompressed_to_gz
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,571 [pN:main.1,p:70319,tN:MainThread] Loaded converter: CONVERTER_gz_to_uncompressed
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,572 [pN:main.1,p:70319,tN:MainThread] Loaded converter: CONVERTER_interval_to_bed_0
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,572 [pN:main.1,p:70319,tN:MainThread] Loaded converter: CONVERTER_interval_to_bedstrict_0
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,573 [pN:main.1,p:70319,tN:MainThread] Loaded converter: CONVERTER_interval_to_bed6_0
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,574 [pN:main.1,p:70319,tN:MainThread] Loaded converter: CONVERTER_interval_to_bed12_0
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,575 [pN:main.1,p:70319,tN:MainThread] Loaded converter: CONVERTER_interval_to_bgzip_0
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,576 [pN:main.1,p:70319,tN:MainThread] Loaded converter: CONVERTER_interval_to_tabix_0
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,577 [pN:main.1,p:70319,tN:MainThread] Loaded converter: CONVERTER_interval_to_bigwig_0
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,578 [pN:main.1,p:70319,tN:MainThread] Loaded converter: CONVERTER_picard_interval_list_to_bed6
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,579 [pN:main.1,p:70319,tN:MainThread] Loaded converter: CONVERTER_archive_to_directory
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,580 [pN:main.1,p:70319,tN:MainThread] Loaded converter: CONVERTER_archive_to_directory
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,581 [pN:main.1,p:70319,tN:MainThread] Loaded converter: CONVERTER_archive_to_directory
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,582 [pN:main.1,p:70319,tN:MainThread] Loaded converter: CONVERTER_archive_to_directory
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,582 [pN:main.1,p:70319,tN:MainThread] Loaded converter: CONVERTER_uncompressed_to_gz
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,583 [pN:main.1,p:70319,tN:MainThread] Loaded converter: CONVERTER_gz_to_uncompressed
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,584 [pN:main.1,p:70319,tN:MainThread] Loaded converter: CONVERTER_bz2_to_uncompressed
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,585 [pN:main.1,p:70319,tN:MainThread] Loaded converter: CONVERTER_uncompressed_to_gz
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,586 [pN:main.1,p:70319,tN:MainThread] Loaded converter: CONVERTER_gz_to_uncompressed
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,587 [pN:main.1,p:70319,tN:MainThread] Loaded converter: CONVERTER_uncompressed_to_gz
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,587 [pN:main.1,p:70319,tN:MainThread] Loaded converter: CONVERTER_gz_to_uncompressed
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,588 [pN:main.1,p:70319,tN:MainThread] Loaded converter: CONVERTER_uncompressed_to_gz
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,589 [pN:main.1,p:70319,tN:MainThread] Loaded converter: CONVERTER_gz_to_uncompressed
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,590 [pN:main.1,p:70319,tN:MainThread] Loaded converter: CONVERTER_uncompressed_to_gz
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,591 [pN:main.1,p:70319,tN:MainThread] Loaded converter: CONVERTER_gz_to_uncompressed
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,591 [pN:main.1,p:70319,tN:MainThread] Loaded converter: CONVERTER_maf_to_fasta_0
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,592 [pN:main.1,p:70319,tN:MainThread] Loaded converter: CONVERTER_maf_to_interval_0
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,593 [pN:main.1,p:70319,tN:MainThread] Loaded converter: CONVERTER_uncompressed_to_gz
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,594 [pN:main.1,p:70319,tN:MainThread] Loaded converter: CONVERTER_gz_to_uncompressed
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,594 [pN:main.1,p:70319,tN:MainThread] Loaded converter: CONVERTER_bz2_to_uncompressed
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,595 [pN:main.1,p:70319,tN:MainThread] Loaded converter: CONVERTER_interval_to_tabix_0
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,597 [pN:main.1,p:70319,tN:MainThread] Loaded converter: CONVERTER_interval_to_bgzip_0
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,597 [pN:main.1,p:70319,tN:MainThread] Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,598 [pN:main.1,p:70319,tN:MainThread] Loaded converter: CONVERTER_uncompressed_to_gz
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,599 [pN:main.1,p:70319,tN:MainThread] Loaded converter: CONVERTER_gz_to_uncompressed
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,600 [pN:main.1,p:70319,tN:MainThread] Loaded converter: CONVERTER_uncompressed_to_gz
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,601 [pN:main.1,p:70319,tN:MainThread] Loaded converter: CONVERTER_gz_to_uncompressed
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,602 [pN:main.1,p:70319,tN:MainThread] Loaded converter: CONVERTER_interval_to_bgzip_0
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,603 [pN:main.1,p:70319,tN:MainThread] Loaded converter: CONVERTER_interval_to_tabix_0
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,604 [pN:main.1,p:70319,tN:MainThread] Loaded converter: CONVERTER_sam_to_unsorted_bam
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,604 [pN:main.1,p:70319,tN:MainThread] Loaded converter: CONVERTER_bam_to_coodinate_sorted_bam
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,605 [pN:main.1,p:70319,tN:MainThread] Loaded converter: CONVERTER_bam_to_qname_sorted_bam
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,606 [pN:main.1,p:70319,tN:MainThread] Loaded converter: CONVERTER_sam_to_bigwig_0
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,606 [pN:main.1,p:70319,tN:MainThread] Loaded converter: tabular_to_dbnsfp
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,607 [pN:main.1,p:70319,tN:MainThread] Loaded converter: tabular_to_csv
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,608 [pN:main.1,p:70319,tN:MainThread] Loaded converter: CONVERTER_uncompressed_to_gz
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,609 [pN:main.1,p:70319,tN:MainThread] Loaded converter: CONVERTER_gz_to_uncompressed
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,610 [pN:main.1,p:70319,tN:MainThread] Loaded converter: CONVERTER_interval_to_bgzip_0
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,611 [pN:main.1,p:70319,tN:MainThread] Loaded converter: CONVERTER_vcf_to_vcf_bgzip_0
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,612 [pN:main.1,p:70319,tN:MainThread] Loaded converter: CONVERTER_interval_to_tabix_0
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,612 [pN:main.1,p:70319,tN:MainThread] Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,613 [pN:main.1,p:70319,tN:MainThread] Loaded converter: CONVERTER_uncompressed_to_gz
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,614 [pN:main.1,p:70319,tN:MainThread] Loaded converter: CONVERTER_bcf_uncompressed_to_bcf
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,615 [pN:main.1,p:70319,tN:MainThread] Loaded converter: CONVERTER_bcf_uncompressed_to_bcf
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,616 [pN:main.1,p:70319,tN:MainThread] Loaded converter: CONVERTER_wig_to_bigwig
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,617 [pN:main.1,p:70319,tN:MainThread] Loaded converter: CONVERTER_wiggle_to_interval_0
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,617 [pN:main.1,p:70319,tN:MainThread] Loaded converter: CONVERTER_vcf_bgzip_to_tabix_0
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,618 [pN:main.1,p:70319,tN:MainThread] Loaded converter: CONVERTER_gz_to_uncompressed
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,619 [pN:main.1,p:70319,tN:MainThread] Loaded converter: lped2fpedconvert
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,619 [pN:main.1,p:70319,tN:MainThread] Loaded converter: lped2pbedconvert
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,620 [pN:main.1,p:70319,tN:MainThread] Loaded converter: pbed2lpedconvert
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,621 [pN:main.1,p:70319,tN:MainThread] Loaded converter: pbed2ldindepconvert
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,621 [pN:main.1,p:70319,tN:MainThread] Loaded converter: CONVERTER_uncompressed_to_gz
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,622 [pN:main.1,p:70319,tN:MainThread] Loaded converter: CONVERTER_gz_to_uncompressed
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,623 [pN:main.1,p:70319,tN:MainThread] Loaded converter: CONVERTER_biom
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,624 [pN:main.1,p:70319,tN:MainThread] Loaded converter: CONVERTER_biom
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,628 [pN:main.1,p:70319,tN:MainThread] Loaded converter: CONVERTER_molecules
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,631 [pN:main.1,p:70319,tN:MainThread] Loaded converter: CONVERTER_molecules
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,634 [pN:main.1,p:70319,tN:MainThread] Loaded converter: CONVERTER_molecules
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,634 [pN:main.1,p:70319,tN:MainThread] Loaded converter: CONVERTER_SMILES_to_MOL
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,638 [pN:main.1,p:70319,tN:MainThread] Loaded converter: CONVERTER_molecules
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,639 [pN:main.1,p:70319,tN:MainThread] Loaded converter: CONVERTER_smiles_to_smiles
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,642 [pN:main.1,p:70319,tN:MainThread] Loaded converter: CONVERTER_molecules
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,645 [pN:main.1,p:70319,tN:MainThread] Loaded converter: CONVERTER_molecules
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,648 [pN:main.1,p:70319,tN:MainThread] Loaded converter: CONVERTER_molecules
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,651 [pN:main.1,p:70319,tN:MainThread] Loaded converter: CONVERTER_molecules
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,654 [pN:main.1,p:70319,tN:MainThread] Loaded converter: CONVERTER_molecules
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,657 [pN:main.1,p:70319,tN:MainThread] Loaded converter: CONVERTER_molecules
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,658 [pN:main.1,p:70319,tN:MainThread] Loaded converter: CONVERTER_inchi_to_mol
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,661 [pN:main.1,p:70319,tN:MainThread] Loaded converter: CONVERTER_molecules
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,664 [pN:main.1,p:70319,tN:MainThread] Loaded converter: CONVERTER_molecules
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,667 [pN:main.1,p:70319,tN:MainThread] Loaded converter: CONVERTER_molecules
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,670 [pN:main.1,p:70319,tN:MainThread] Loaded converter: CONVERTER_molecules
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,673 [pN:main.1,p:70319,tN:MainThread] Loaded converter: CONVERTER_molecules
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,676 [pN:main.1,p:70319,tN:MainThread] Loaded converter: CONVERTER_molecules
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,679 [pN:main.1,p:70319,tN:MainThread] Loaded converter: CONVERTER_molecules
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,682 [pN:main.1,p:70319,tN:MainThread] Loaded converter: CONVERTER_molecules
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,685 [pN:main.1,p:70319,tN:MainThread] Loaded converter: CONVERTER_molecules
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,688 [pN:main.1,p:70319,tN:MainThread] Loaded converter: CONVERTER_molecules
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,689 [pN:main.1,p:70319,tN:MainThread] Loaded converter: CONVERTER_mol2_to_mol
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,692 [pN:main.1,p:70319,tN:MainThread] Loaded converter: CONVERTER_molecules
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,693 [pN:main.1,p:70319,tN:MainThread] Loaded converter: CONVERTER_cml_to_smiles
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,696 [pN:main.1,p:70319,tN:MainThread] Loaded converter: CONVERTER_molecules
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,699 [pN:main.1,p:70319,tN:MainThread] Loaded converter: CONVERTER_molecules
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,702 [pN:main.1,p:70319,tN:MainThread] Loaded converter: CONVERTER_molecules
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,703 [pN:main.1,p:70319,tN:MainThread] Loaded converter: CONVERTER_Pdb_to_Gro_0
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,704 [pN:main.1,p:70319,tN:MainThread] Loaded converter: CONVERTER_mdconvert
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,705 [pN:main.1,p:70319,tN:MainThread] Loaded converter: CONVERTER_mdconvert
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,707 [pN:main.1,p:70319,tN:MainThread] Loaded converter: CONVERTER_mdconvert
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,708 [pN:main.1,p:70319,tN:MainThread] Loaded converter: CONVERTER_mdconvert
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,709 [pN:main.1,p:70319,tN:MainThread] Loaded converter: CONVERTER_mdconvert
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,710 [pN:main.1,p:70319,tN:MainThread] Loaded converter: CONVERTER_mdconvert
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,711 [pN:main.1,p:70319,tN:MainThread] Loaded converter: CONVERTER_Gro_to_Pdb_0
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,712 [pN:main.1,p:70319,tN:MainThread] Loaded converter: CONVERTER_ref_to_seq_taxomony
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,712 [pN:main.1,p:70319,tN:MainThread] Loaded converter: CONVERTER_neostorezip_to_neostore
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:11,715 [pN:main.1,p:70319,tN:MainThread] Loaded external metadata tool: __SET_METADATA__
galaxy.tools.special_tools DEBUG 2026-09-17 16:20:11,717 [pN:main.1,p:70319,tN:MainThread] Loaded history export tool: __EXPORT_HISTORY__
galaxy.tools.special_tools DEBUG 2026-09-17 16:20:11,718 [pN:main.1,p:70319,tN:MainThread] Loaded history export to uri tool: __EXPORT_HISTORY_TO_URI__
galaxy.tools.special_tools DEBUG 2026-09-17 16:20:11,718 [pN:main.1,p:70319,tN:MainThread] Loaded history import tool: __IMPORT_HISTORY__
galaxy.tools DEBUG 2026-09-17 16:20:11,719 [pN:main.1,p:70319,tN:MainThread] No parameter model for tool '__DATA_FETCH__': Cannot generate a tool parameter model for upload_dataset inputs
galaxy.tools.special_tools DEBUG 2026-09-17 16:20:11,719 [pN:main.1,p:70319,tN:MainThread] Loaded data fetch tool: __DATA_FETCH__
galaxy.visualization.plugins.registry INFO 2026-09-17 16:20:11,720 [pN:main.1,p:70319,tN:MainThread] VisualizationsRegistry, loaded plugin: example
galaxy.tours._impl INFO 2026-09-17 16:20:11,726 [pN:main.1,p:70319,tN:MainThread] Loaded tour 'core.galaxy_ui'
galaxy.tours._impl INFO 2026-09-17 16:20:11,731 [pN:main.1,p:70319,tN:MainThread] Loaded tour 'core.deferred'
galaxy.tours._impl INFO 2026-09-17 16:20:11,734 [pN:main.1,p:70319,tN:MainThread] Loaded tour 'core.windows'
galaxy.tours._impl INFO 2026-09-17 16:20:11,736 [pN:main.1,p:70319,tN:MainThread] Loaded tour 'core.visualizations'
galaxy.tours._impl INFO 2026-09-17 16:20:11,740 [pN:main.1,p:70319,tN:MainThread] Loaded tour 'core.history'
galaxy.workflow.scheduling_manager INFO 2026-09-17 16:20:11,753 [pN:main.1,p:70319,tN:MainThread] No workflow schedulers plugin config file defined, using default scheduler.
galaxy.web_stack.handlers INFO 2026-09-17 16:20:11,753 [pN:main.1,p:70319,tN:MainThread] WorkflowSchedulingManager: No job handler assignment method is set, defaulting to 'HANDLER_ASSIGNMENT_METHODS.DB_TRANSACTION_ISOLATION', set the `assign_with` attribute on <handlers> to override the default
galaxy.workflow.scheduling_manager DEBUG 2026-09-17 16:20:11,753 [pN:main.1,p:70319,tN:MainThread] Starting workflow schedulers
galaxy.jobs.handler INFO 2026-09-17 16:20:11,756 [pN:main.1,p:70319,tN:WorkflowRequestMonitor.monitor_thread] Handler job grabber initialized with 'HANDLER_ASSIGNMENT_METHODS.DB_TRANSACTION_ISOLATION' assignment method for handler 'main.1', tag(s): None, _default_
galaxy.workflow.completion_hooks INFO 2026-09-17 16:20:11,760 [pN:main.1,p:70319,tN:MainThread] Enabling workflow completion hook: send_notification
galaxy.workflow.completion_hooks INFO 2026-09-17 16:20:11,760 [pN:main.1,p:70319,tN:MainThread] Enabling workflow completion hook: export_to_file_source
galaxy.workflow.completion_monitor INFO 2026-09-17 16:20:11,761 [pN:main.1,p:70319,tN:MainThread] Starting workflow completion monitor
galaxy.jobs.manager DEBUG 2026-09-17 16:20:11,762 [pN:main.1,p:70319,tN:MainThread] Initializing job handler
galaxy.jobs INFO 2026-09-17 16:20:11,763 [pN:main.1,p:70319,tN:MainThread] Handler 'main.1' will load all configured runner plugins
galaxy.jobs.runners.state_handler_factory DEBUG 2026-09-17 16:20:11,768 [pN:main.1,p:70319,tN:MainThread] Loaded 'failure' state handler from module galaxy.jobs.runners.state_handlers.resubmit
galaxy.jobs DEBUG 2026-09-17 16:20:11,768 [pN:main.1,p:70319,tN:MainThread] Loaded job runner 'galaxy.jobs.runners.local:LocalJobRunner' as 'local'
galaxy.jobs.handler DEBUG 2026-09-17 16:20:11,768 [pN:main.1,p:70319,tN:MainThread] Loaded job runners plugins: local
galaxy.jobs.runners DEBUG 2026-09-17 16:20:11,768 [pN:main.1,p:70319,tN:MainThread] Starting 1 LocalRunner workers
galaxy.jobs.handler DEBUG 2026-09-17 16:20:11,768 [pN:main.1,p:70319,tN:MainThread] Handler queue starting for jobs assigned to handler: main.1
galaxy.jobs.handler INFO 2026-09-17 16:20:11,772 [pN:main.1,p:70319,tN:JobHandlerQueue.monitor_thread] Handler job grabber initialized with 'HANDLER_ASSIGNMENT_METHODS.DB_TRANSACTION_ISOLATION' assignment method for handler 'main.1', tag(s): 
galaxy.jobs.handler INFO 2026-09-17 16:20:11,772 [pN:main.1,p:70319,tN:MainThread] job handler queue started
galaxy.jobs.handler INFO 2026-09-17 16:20:11,773 [pN:main.1,p:70319,tN:MainThread] job handler stop queue started
galaxy.queue_worker INFO 2026-09-17 16:20:11,774 [pN:main.1,p:70319,tN:MainThread] Binding and starting galaxy control worker for main.1
galaxy.queue_worker INFO 2026-09-17 16:20:11,776 [pN:main.1,p:70319,tN:MainThread] Queuing async task rebuild_toolbox_search_index for main.1.
galaxy.model.database_heartbeat DEBUG 2026-09-17 16:20:11,793 [pN:main.1,p:70319,tN:database_heartbeart_main.1.thread] main.1 is config watcher
galaxy.app INFO 2026-09-17 16:20:11,794 [pN:main.1,p:70319,tN:MainThread] Galaxy app startup finished (3482.985 ms)
galaxy.model.database_heartbeat DEBUG 2026-09-17 16:20:11,797 [pN:main.1,p:70319,tN:database_heartbeart_main.1.thread] main.1 is history audit monitor
galaxy.queue_worker INFO 2026-09-17 16:20:11,798 [pN:main.1,p:70319,tN:Thread-2] Instance 'main.1' received 'rebuild_toolbox_search_index' task, executing now.
galaxy.tools.search DEBUG 2026-09-17 16:20:11,798 [pN:main.1,p:70319,tN:Thread-2] Starting to build toolbox index of panel default.
galaxy.web.framework.base DEBUG 2026-09-17 16:20:11,801 [pN:main.1,p:70319,tN:MainThread] Enabling 'user' controller, class: User
galaxy.web.framework.base DEBUG 2026-09-17 16:20:11,807 [pN:main.1,p:70319,tN:MainThread] Enabling 'page' controller, class: PageController
galaxy.web.framework.base DEBUG 2026-09-17 16:20:11,809 [pN:main.1,p:70319,tN:MainThread] Enabling 'visualization' controller, class: VisualizationController
galaxy.web.framework.base DEBUG 2026-09-17 16:20:11,837 [pN:main.1,p:70319,tN:MainThread] Enabling 'dataset' controller, class: DatasetInterface
galaxy.web.framework.base DEBUG 2026-09-17 16:20:11,840 [pN:main.1,p:70319,tN:MainThread] Enabling 'forms' controller, class: Forms
galaxy.web.framework.base DEBUG 2026-09-17 16:20:11,852 [pN:main.1,p:70319,tN:MainThread] Enabling 'admin' controller, class: AdminGalaxy
galaxy.web.framework.base DEBUG 2026-09-17 16:20:11,853 [pN:main.1,p:70319,tN:MainThread] Enabling 'shed_tool_static' controller, class: ShedToolStatic
galaxy.web.framework.base DEBUG 2026-09-17 16:20:11,854 [pN:main.1,p:70319,tN:MainThread] Enabling 'tool_runner' controller, class: ToolRunner
galaxy.web.framework.base DEBUG 2026-09-17 16:20:11,860 [pN:main.1,p:70319,tN:MainThread] Enabling 'admin_toolshed' controller, class: AdminGalaxy
galaxy.web.framework.base DEBUG 2026-09-17 16:20:11,861 [pN:main.1,p:70319,tN:MainThread] Enabling 'admin_toolshed' controller, class: AdminToolshed
galaxy.web.framework.base DEBUG 2026-09-17 16:20:11,862 [pN:main.1,p:70319,tN:MainThread] Enabling 'workflow' controller, class: WorkflowController
galaxy.web.framework.base DEBUG 2026-09-17 16:20:11,864 [pN:main.1,p:70319,tN:MainThread] Enabling 'async' controller, class: ASync
galaxy.web.framework.base DEBUG 2026-09-17 16:20:11,865 [pN:main.1,p:70319,tN:MainThread] Enabling 'data_manager' controller, class: DataManager
galaxy.web.framework.base DEBUG 2026-09-17 16:20:11,868 [pN:main.1,p:70319,tN:MainThread] Enabling 'root' controller, class: RootController
galaxy.web.framework.base DEBUG 2026-09-17 16:20:11,868 [pN:main.1,p:70319,tN:MainThread] Enabling 'authnz' controller, class: OIDC
galaxy.web.framework.base DEBUG 2026-09-17 16:20:11,887 [pN:main.1,p:70319,tN:MainThread] Enabling 'history' controller, class: HistoryController
galaxy.tools.search DEBUG 2026-09-17 16:20:11,903 [pN:main.1,p:70319,tN:Thread-2] Toolbox index of panel default finished (104.779 ms)
galaxy.tools.search DEBUG 2026-09-17 16:20:11,903 [pN:main.1,p:70319,tN:Thread-2] Starting to build toolbox index of panel my_panel.
galaxy.tools.search DEBUG 2026-09-17 16:20:11,906 [pN:main.1,p:70319,tN:Thread-2] Toolbox index of panel my_panel finished (2.292 ms)
galaxy.tools.search DEBUG 2026-09-17 16:20:11,906 [pN:main.1,p:70319,tN:Thread-2] Starting to build toolbox index of panel ontology:edam_operations.
galaxy.web.framework.base DEBUG 2026-09-17 16:20:11,999 [pN:main.1,p:70319,tN:MainThread] Enabling 'container_resolution' API controller, class: ContainerResolutionAPIController
galaxy.web.framework.base DEBUG 2026-09-17 16:20:12,404 [pN:main.1,p:70319,tN:MainThread] Enabling 'tool_entry_points' API controller, class: ToolEntryPointsAPIController
galaxy.web.framework.base DEBUG 2026-09-17 16:20:12,569 [pN:main.1,p:70319,tN:MainThread] Enabling 'users' API controller, class: UserAPIController
galaxy.web.framework.base DEBUG 2026-09-17 16:20:12,571 [pN:main.1,p:70319,tN:MainThread] Enabling 'toolshed' API controller, class: ToolShedController
galaxy.tools.search DEBUG 2026-09-17 16:20:12,652 [pN:main.1,p:70319,tN:Thread-2] Toolbox index of panel ontology:edam_operations finished (745.460 ms)
galaxy.tools.search DEBUG 2026-09-17 16:20:12,660 [pN:main.1,p:70319,tN:Thread-2] Starting to build toolbox index of panel ontology:edam_topics.
galaxy.web.framework.base DEBUG 2026-09-17 16:20:12,805 [pN:main.1,p:70319,tN:MainThread] Enabling 'tools' API controller, class: ToolsController
galaxy.web.framework.base DEBUG 2026-09-17 16:20:12,810 [pN:main.1,p:70319,tN:MainThread] Enabling 'library_datasets' API controller, class: LibraryDatasetsController
galaxy.web.framework.base DEBUG 2026-09-17 16:20:13,343 [pN:main.1,p:70319,tN:MainThread] Enabling 'page_revisions' API controller, class: PageRevisionsController
galaxy.web.framework.base DEBUG 2026-09-17 16:20:13,632 [pN:main.1,p:70319,tN:MainThread] Enabling 'forms' API controller, class: FormDefinitionAPIController
galaxy.tools.search DEBUG 2026-09-17 16:20:13,673 [pN:main.1,p:70319,tN:Thread-2] Toolbox index of panel ontology:edam_topics finished (1009.142 ms)
galaxy.web.framework.base DEBUG 2026-09-17 16:20:13,813 [pN:main.1,p:70319,tN:MainThread] Enabling 'jobs' API controller, class: JobController
galaxy.web.framework.base DEBUG 2026-09-17 16:20:13,816 [pN:main.1,p:70319,tN:MainThread] Enabling 'job_ports' API controller, class: JobPortsAPIController
galaxy.web.framework.base DEBUG 2026-09-17 16:20:13,816 [pN:main.1,p:70319,tN:MainThread] Enabling 'trs_search' API controller, class: TrsSearchAPIController
galaxy.web.framework.base DEBUG 2026-09-17 16:20:14,336 [pN:main.1,p:70319,tN:MainThread] Enabling 'tool_dependencies' API controller, class: ToolDependenciesAPIController
galaxy.web.framework.base DEBUG 2026-09-17 16:20:14,360 [pN:main.1,p:70319,tN:MainThread] Enabling 'history_dataset_extended_metadata' API controller, class: HistoryDatasetExtendMetadataController
galaxy.web.framework.base DEBUG 2026-09-17 16:20:14,360 [pN:main.1,p:70319,tN:MainThread] Enabling 'library_dataset_extended_metadata' API controller, class: LibraryDatasetExtendMetadataController
galaxy.web.framework.base DEBUG 2026-09-17 16:20:14,361 [pN:main.1,p:70319,tN:MainThread] Enabling 'trs_consumer' API controller, class: TrsConsumeAPIController
galaxy.web.framework.base DEBUG 2026-09-17 16:20:14,872 [pN:main.1,p:70319,tN:MainThread] Enabling 'workflows' API controller, class: WorkflowsAPIController
galaxy.web.framework.base DEBUG 2026-09-17 16:20:14,988 [pN:main.1,p:70319,tN:MainThread] Enabling 'sanitize_allow' API controller, class: SanitizeAllowController
galaxy.web.framework.base DEBUG 2026-09-17 16:20:14,990 [pN:main.1,p:70319,tN:MainThread] Enabling 'job_files' API controller, class: JobFilesAPIController
galaxy.web.framework.base DEBUG 2026-09-17 16:20:14,994 [pN:main.1,p:70319,tN:MainThread] Enabling 'uploads' API controller, class: UploadsAPIController
galaxy.web.framework.base DEBUG 2026-09-17 16:20:15,008 [pN:main.1,p:70319,tN:MainThread] Enabling 'tool_shed_repositories' API controller, class: ToolShedRepositoriesController
galaxy.web.framework.base DEBUG 2026-09-17 16:20:15,009 [pN:main.1,p:70319,tN:MainThread] Enabling 'history_content_provenance' API controller, class: HDAProvenanceController
galaxy.web.framework.base DEBUG 2026-09-17 16:20:15,009 [pN:main.1,p:70319,tN:MainThread] Enabling 'ldda_provenance' API controller, class: LDDAProvenanceController
galaxy.web.framework.base DEBUG 2026-09-17 16:20:15,010 [pN:main.1,p:70319,tN:MainThread] Enabling 'webhooks' API controller, class: WebhooksController
galaxy.web.framework.base DEBUG 2026-09-17 16:20:15,247 [pN:main.1,p:70319,tN:MainThread] Enabling 'authenticate' API controller, class: AuthenticationController
galaxy.web.framework.base DEBUG 2026-09-17 16:20:15,263 [pN:main.1,p:70319,tN:MainThread] Enabling 'history_annotations' API controller, class: HistoryAnnotationsController
galaxy.web.framework.base DEBUG 2026-09-17 16:20:15,263 [pN:main.1,p:70319,tN:MainThread] Enabling 'history_content_annotations' API controller, class: HistoryContentAnnotationsController
galaxy.web.framework.base DEBUG 2026-09-17 16:20:15,264 [pN:main.1,p:70319,tN:MainThread] Enabling 'workflow_annotations' API controller, class: WorkflowAnnotationsController
galaxy.webapps.util DEBUG 2026-09-17 16:20:16,143 [pN:main.1,p:70319,tN:MainThread] Enabling 'paste.httpexceptions' middleware
galaxy.webapps.util DEBUG 2026-09-17 16:20:16,146 [pN:main.1,p:70319,tN:MainThread] Enabling 'RemoteUser' middleware
galaxy.webapps.util DEBUG 2026-09-17 16:20:16,146 [pN:main.1,p:70319,tN:MainThread] Enabling 'ErrorMiddleware' middleware
galaxy.webapps.util DEBUG 2026-09-17 16:20:16,146 [pN:main.1,p:70319,tN:MainThread] Enabling 'XForwardedHostMiddleware' middleware
galaxy.webapps.util DEBUG 2026-09-17 16:20:16,146 [pN:main.1,p:70319,tN:MainThread] Enabling 'RequestIDMiddleware' middleware
galaxy.webapps.util DEBUG 2026-09-17 16:20:16,146 [pN:main.1,p:70319,tN:MainThread] Enabling 'build_url_map' middleware
galaxy.web_stack INFO 2026-09-17 16:20:16,147 [pN:main.1,p:70319,tN:MainThread] Galaxy server instance 'main.1' is running

Serving on http://127.0.0.1:57725

galaxy.webapps.galaxy.buildapp DEBUG 2026-09-17 16:20:16,147 [pN:main.1,p:70319,tN:MainThread] Prior to webapp return, Galaxy thread <_MainThread(MainThread, started 8427134336)> is alive.
galaxy.webapps.galaxy.buildapp DEBUG 2026-09-17 16:20:16,147 [pN:main.1,p:70319,tN:MainThread] Prior to webapp return, Galaxy thread <Thread(WorkflowRequestMonitor.monitor_thread, started daemon 6174502912)> is alive.
galaxy.webapps.galaxy.buildapp DEBUG 2026-09-17 16:20:16,148 [pN:main.1,p:70319,tN:MainThread] Prior to webapp return, Galaxy thread <Thread(WorkflowCompletionMonitor.monitor_thread, started daemon 6191329280)> is alive.
galaxy.webapps.galaxy.buildapp DEBUG 2026-09-17 16:20:16,148 [pN:main.1,p:70319,tN:MainThread] Prior to webapp return, Galaxy thread <Thread(LocalRunner.work_thread-0, started daemon 6208155648)> is alive.
galaxy.webapps.galaxy.buildapp DEBUG 2026-09-17 16:20:16,148 [pN:main.1,p:70319,tN:MainThread] Prior to webapp return, Galaxy thread <Thread(JobHandlerQueue.monitor_thread, started daemon 6224982016)> is alive.
galaxy.webapps.galaxy.buildapp DEBUG 2026-09-17 16:20:16,148 [pN:main.1,p:70319,tN:MainThread] Prior to webapp return, Galaxy thread <Thread(JobHandlerStopQueue.monitor_thread, started daemon 6241808384)> is alive.
galaxy.webapps.galaxy.buildapp DEBUG 2026-09-17 16:20:16,148 [pN:main.1,p:70319,tN:MainThread] Prior to webapp return, Galaxy thread <Thread(database_heartbeart_main.1.thread, started daemon 6258634752)> is alive.
galaxy.webapps.galaxy.buildapp DEBUG 2026-09-17 16:20:16,149 [pN:main.1,p:70319,tN:MainThread] Prior to webapp return, Galaxy thread <GalaxyQueueWorker(Thread-2, started daemon 6275461120)> is alive.
galaxy.webapps.galaxy.buildapp DEBUG 2026-09-17 16:20:16,149 [pN:main.1,p:70319,tN:MainThread] Prior to webapp return, Galaxy thread <FSEventsObserver(Thread-3, started daemon 6292287488)> is alive.
galaxy.webapps.galaxy.buildapp DEBUG 2026-09-17 16:20:16,149 [pN:main.1,p:70319,tN:MainThread] Prior to webapp return, Galaxy thread <Thread(Thread-4 (check), started daemon 6309113856)> is alive.
galaxy.webapps.galaxy.buildapp DEBUG 2026-09-17 16:20:16,149 [pN:main.1,p:70319,tN:MainThread] Prior to webapp return, Galaxy thread <Thread(Thread-5 (check), started daemon 6325940224)> is alive.
ephemeris.shed_tools WARNING: 'tool_shed' not a valid key. Will be skipped during parsing
ephemeris.shed_tools WARNING: 'tool_shed' not a valid key. Will be skipped during parsing
ephemeris.shed_tools WARNING: 'tool_shed' not a valid key. Will be skipped during parsing
ephemeris.shed_tools WARNING: 'tool_shed' not a valid key. Will be skipped during parsing
ephemeris.shed_tools WARNING: 'tool_shed' not a valid key. Will be skipped during parsing
ephemeris.shed_tools WARNING: 'tool_shed' not a valid key. Will be skipped during parsing
ephemeris.shed_tools WARNING: 'tool_shed' not a valid key. Will be skipped during parsing
ephemeris.shed_tools WARNING: 'tool_shed' not a valid key. Will be skipped during parsing
ephemeris.shed_tools WARNING: 'tool_shed' not a valid key. Will be skipped during parsing
ephemeris.shed_tools WARNING: 'tool_shed' not a valid key. Will be skipped during parsing
ephemeris.shed_tools WARNING: 'tool_shed' not a valid key. Will be skipped during parsing
ephemeris.shed_tools WARNING: 'tool_shed' not a valid key. Will be skipped during parsing
galaxy.tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager DEBUG 2026-09-17 16:20:21,195 [pN:main.1,p:70319,tN:WSGI_0] Creating repository dependency objects...
galaxy.tool_util.toolbox.base DEBUG 2026-09-17 16:20:22,563 [pN:main.1,p:70319,tN:WSGI_0] Loading new tool panel section: Tools from workflows
galaxy.tool_util.toolbox.integrated_panel DEBUG 2026-09-17 16:20:22,564 [pN:main.1,p:70319,tN:WSGI_0] Writing integrated tool panel config file to '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/integrated_tool_panel_conf.xml'
galaxy.tool_shed.util.repository_util DEBUG 2026-09-17 16:20:22,566 [pN:main.1,p:70319,tN:WSGI_0] Adding new row for repository 'fastqc' in the tool_shed_repository table, status set to 'installation_status.NEW'.
galaxy.tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager DEBUG 2026-09-17 16:20:22,569 [pN:main.1,p:70319,tN:WSGI_0] Building repository dependency relationships...
galaxy.tool_util.toolbox.base DEBUG 2026-09-17 16:20:22,569 [pN:main.1,p:70319,tN:WSGI_0] Appending to tool panel section: Tools from workflows
galaxy.tool_util.toolbox.base DEBUG 2026-09-17 16:20:22,576 [pN:main.1,p:70319,tN:WSGI_0] Appending to tool panel section: Tools from workflows
galaxy.tool_shed.galaxy_install.install_manager INFO 2026-09-17 16:20:22,582 [pN:main.1,p:70319,tN:WSGI_0] Cloning repository 'https://toolshed.g2.bx.psu.edu/repos/devteam/fastqc' at 24:2c64fded1286
PIL.Image DEBUG 2026-09-17 16:20:29,082 [pN:main.1,p:70319,tN:WSGI_0] Importing AvifImagePlugin
PIL.Image DEBUG 2026-09-17 16:20:29,368 [pN:main.1,p:70319,tN:WSGI_0] Importing BlpImagePlugin
PIL.Image DEBUG 2026-09-17 16:20:29,379 [pN:main.1,p:70319,tN:WSGI_0] Importing BmpImagePlugin
PIL.Image DEBUG 2026-09-17 16:20:29,380 [pN:main.1,p:70319,tN:WSGI_0] Importing BufrStubImagePlugin
PIL.Image DEBUG 2026-09-17 16:20:29,382 [pN:main.1,p:70319,tN:WSGI_0] Importing CurImagePlugin
PIL.Image DEBUG 2026-09-17 16:20:29,383 [pN:main.1,p:70319,tN:WSGI_0] Importing DcxImagePlugin
PIL.Image DEBUG 2026-09-17 16:20:29,386 [pN:main.1,p:70319,tN:WSGI_0] Importing DdsImagePlugin
PIL.Image DEBUG 2026-09-17 16:20:29,391 [pN:main.1,p:70319,tN:WSGI_0] Importing EpsImagePlugin
PIL.Image DEBUG 2026-09-17 16:20:29,394 [pN:main.1,p:70319,tN:WSGI_0] Importing FitsImagePlugin
PIL.Image DEBUG 2026-09-17 16:20:29,396 [pN:main.1,p:70319,tN:WSGI_0] Importing FliImagePlugin
PIL.Image DEBUG 2026-09-17 16:20:29,397 [pN:main.1,p:70319,tN:WSGI_0] Importing FpxImagePlugin
PIL.Image DEBUG 2026-09-17 16:20:29,399 [pN:main.1,p:70319,tN:WSGI_0] Image: failed to import FpxImagePlugin: No module named 'olefile'
PIL.Image DEBUG 2026-09-17 16:20:29,400 [pN:main.1,p:70319,tN:WSGI_0] Importing FtexImagePlugin
PIL.Image DEBUG 2026-09-17 16:20:29,401 [pN:main.1,p:70319,tN:WSGI_0] Importing GbrImagePlugin
PIL.Image DEBUG 2026-09-17 16:20:29,402 [pN:main.1,p:70319,tN:WSGI_0] Importing GifImagePlugin
PIL.Image DEBUG 2026-09-17 16:20:29,402 [pN:main.1,p:70319,tN:WSGI_0] Importing GribStubImagePlugin
PIL.Image DEBUG 2026-09-17 16:20:29,403 [pN:main.1,p:70319,tN:WSGI_0] Importing Hdf5StubImagePlugin
PIL.Image DEBUG 2026-09-17 16:20:29,404 [pN:main.1,p:70319,tN:WSGI_0] Importing IcnsImagePlugin
PIL.Image DEBUG 2026-09-17 16:20:29,409 [pN:main.1,p:70319,tN:WSGI_0] Importing IcoImagePlugin
PIL.Image DEBUG 2026-09-17 16:20:29,412 [pN:main.1,p:70319,tN:WSGI_0] Importing ImImagePlugin
PIL.Image DEBUG 2026-09-17 16:20:29,415 [pN:main.1,p:70319,tN:WSGI_0] Importing ImtImagePlugin
PIL.Image DEBUG 2026-09-17 16:20:29,416 [pN:main.1,p:70319,tN:WSGI_0] Importing IptcImagePlugin
PIL.Image DEBUG 2026-09-17 16:20:29,418 [pN:main.1,p:70319,tN:WSGI_0] Importing JpegImagePlugin
PIL.Image DEBUG 2026-09-17 16:20:29,418 [pN:main.1,p:70319,tN:WSGI_0] Importing Jpeg2KImagePlugin
PIL.Image DEBUG 2026-09-17 16:20:29,418 [pN:main.1,p:70319,tN:WSGI_0] Importing McIdasImagePlugin
PIL.Image DEBUG 2026-09-17 16:20:29,419 [pN:main.1,p:70319,tN:WSGI_0] Importing MicImagePlugin
PIL.Image DEBUG 2026-09-17 16:20:29,420 [pN:main.1,p:70319,tN:WSGI_0] Image: failed to import MicImagePlugin: No module named 'olefile'
PIL.Image DEBUG 2026-09-17 16:20:29,420 [pN:main.1,p:70319,tN:WSGI_0] Importing MpegImagePlugin
PIL.Image DEBUG 2026-09-17 16:20:29,422 [pN:main.1,p:70319,tN:WSGI_0] Importing MpoImagePlugin
PIL.Image DEBUG 2026-09-17 16:20:29,437 [pN:main.1,p:70319,tN:WSGI_0] Importing MspImagePlugin
PIL.Image DEBUG 2026-09-17 16:20:29,438 [pN:main.1,p:70319,tN:WSGI_0] Importing PalmImagePlugin
PIL.Image DEBUG 2026-09-17 16:20:29,441 [pN:main.1,p:70319,tN:WSGI_0] Importing PcdImagePlugin
PIL.Image DEBUG 2026-09-17 16:20:29,442 [pN:main.1,p:70319,tN:WSGI_0] Importing PcxImagePlugin
PIL.Image DEBUG 2026-09-17 16:20:29,442 [pN:main.1,p:70319,tN:WSGI_0] Importing PdfImagePlugin
PIL.Image DEBUG 2026-09-17 16:20:29,450 [pN:main.1,p:70319,tN:WSGI_0] Importing PixarImagePlugin
PIL.Image DEBUG 2026-09-17 16:20:29,451 [pN:main.1,p:70319,tN:WSGI_0] Importing PngImagePlugin
PIL.Image DEBUG 2026-09-17 16:20:29,451 [pN:main.1,p:70319,tN:WSGI_0] Importing PpmImagePlugin
PIL.Image DEBUG 2026-09-17 16:20:29,451 [pN:main.1,p:70319,tN:WSGI_0] Importing PsdImagePlugin
PIL.Image DEBUG 2026-09-17 16:20:29,453 [pN:main.1,p:70319,tN:WSGI_0] Importing QoiImagePlugin
PIL.Image DEBUG 2026-09-17 16:20:29,455 [pN:main.1,p:70319,tN:WSGI_0] Importing SgiImagePlugin
PIL.Image DEBUG 2026-09-17 16:20:29,456 [pN:main.1,p:70319,tN:WSGI_0] Importing SpiderImagePlugin
PIL.Image DEBUG 2026-09-17 16:20:29,457 [pN:main.1,p:70319,tN:WSGI_0] Importing SunImagePlugin
PIL.Image DEBUG 2026-09-17 16:20:29,458 [pN:main.1,p:70319,tN:WSGI_0] Importing TgaImagePlugin
PIL.Image DEBUG 2026-09-17 16:20:29,460 [pN:main.1,p:70319,tN:WSGI_0] Importing TiffImagePlugin
PIL.Image DEBUG 2026-09-17 16:20:29,460 [pN:main.1,p:70319,tN:WSGI_0] Importing WebPImagePlugin
PIL.Image DEBUG 2026-09-17 16:20:30,070 [pN:main.1,p:70319,tN:WSGI_0] Importing WmfImagePlugin
PIL.Image DEBUG 2026-09-17 16:20:30,078 [pN:main.1,p:70319,tN:WSGI_0] Importing XbmImagePlugin
PIL.Image DEBUG 2026-09-17 16:20:30,081 [pN:main.1,p:70319,tN:WSGI_0] Importing XpmImagePlugin
PIL.Image DEBUG 2026-09-17 16:20:30,083 [pN:main.1,p:70319,tN:WSGI_0] Importing XVThumbImagePlugin
charset_normalizer DEBUG 2026-09-17 16:20:30,564 [pN:main.1,p:70319,tN:WSGI_0] Encoding detection: ascii is most likely the one.
galaxy.tool_util.toolbox.base DEBUG 2026-09-17 16:20:30,576 [pN:main.1,p:70319,tN:WSGI_0] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy1, version: 0.74+galaxy1 into tool panel....
galaxy.tool_util.toolbox.integrated_panel DEBUG 2026-09-17 16:20:30,576 [pN:main.1,p:70319,tN:WSGI_0] Writing integrated tool panel config file to '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/integrated_tool_panel_conf.xml'
galaxy.app DEBUG 2026-09-17 16:20:30,579 [pN:main.1,p:70319,tN:WSGI_0] Waiting for toolbox reload
galaxy.tool_util.toolbox.watcher DEBUG 2026-09-17 16:20:31,392 [pN:main.1,p:70319,tN:Thread-4 (check)] The file '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/shed_tools_conf.xml' has changes.
galaxy.queue_worker INFO 2026-09-17 16:20:31,393 [pN:main.1,p:70319,tN:Thread-4 (check)] Queuing sync task reload_toolbox for main.1.
galaxy.queue_worker INFO 2026-09-17 16:20:32,099 [pN:main.1,p:70319,tN:Thread-2] Instance 'main.1' received 'reload_toolbox' task, executing now.
galaxy.queue_worker DEBUG 2026-09-17 16:20:32,100 [pN:main.1,p:70319,tN:Thread-2] Executing toolbox reload on 'main.1'
galaxy.util WARNING 2026-09-17 16:20:32,102 [pN:main.1,p:70319,tN:Thread-2] directory not found: /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/galaxy-dev/config/plugins/activities
galaxy.tools WARNING 2026-09-17 16:20:32,104 [pN:main.1,p:70319,tN:Thread-2] The default shed tool config file (/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file
galaxy.tool_util.toolbox.base INFO 2026-09-17 16:20:32,105 [pN:main.1,p:70319,tN:Thread-2] Parsing the tool configuration /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/tool_conf.xml
galaxy.tool_util.toolbox.base DEBUG 2026-09-17 16:20:32,106 [pN:main.1,p:70319,tN:Thread-2] Tool path for tool configuration /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/tool_conf.xml is None
galaxy.tool_util.parser.factory INFO 2026-09-17 16:20:32,107 [pN:main.1,p:70319,tN:Thread-2] Loading tool from YAML - this is experimental - tool will not function in future.
galaxy.tool_util.toolbox.base ERROR 2026-09-17 16:20:32,120 [pN:main.1,p:70319,tN:Thread-2] Error reading tool from path: /Users/mvandenb/src/worktrees/foundry/brc-c-auris/.foundry-runs/auris-scf1/galaxy-workflow.gxwf.yml
Traceback (most recent call last):
  File "/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/galaxy-dev/lib/galaxy/tool_util/toolbox/base.py", line 967, in _load_tool_tag_set
    tool = self.load_tool(concrete_path, use_cached=False)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/galaxy-dev/lib/galaxy/tool_util/toolbox/base.py", line 1222, in load_tool
    tool = self.create_tool(
           ^^^^^^^^^^^^^^^^^
  File "/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/galaxy-dev/lib/galaxy/tools/__init__.py", line 619, in create_tool
    return self._create_tool_from_source(tool_source, config_file=config_file, **kwds)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/galaxy-dev/lib/galaxy/tools/__init__.py", line 634, in _create_tool_from_source
    return create_tool_from_source(self.app, tool_source, **kwds)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/galaxy-dev/lib/galaxy/tools/__init__.py", line 448, in create_tool_from_source
    tool = ToolClass(config_file, tool_source, app, **kwds)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/galaxy-dev/lib/galaxy/tools/__init__.py", line 1099, in __init__
    raise e
  File "/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/galaxy-dev/lib/galaxy/tools/__init__.py", line 1096, in __init__
    self.parse(tool_source, guid=guid, dynamic=dynamic)
  File "/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/galaxy-dev/lib/galaxy/tools/__init__.py", line 1329, in parse
    raise Exception(f"Missing tool 'id' for tool at '{tool_source}'")
Exception: Missing tool 'id' for tool at 'YamlToolSource[/Users/mvandenb/src/worktrees/foundry/brc-c-auris/.foundry-runs/auris-scf1/galaxy-workflow.gxwf.yml]'
galaxy.tools WARNING 2026-09-17 16:20:32,121 [pN:main.1,p:70319,tN:Thread-2] The default shed tool config file (/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file
galaxy.tool_util.toolbox.base INFO 2026-09-17 16:20:32,122 [pN:main.1,p:70319,tN:Thread-2] Parsing the tool configuration /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/shed_tools_conf.xml
galaxy.tool_util.toolbox.base DEBUG 2026-09-17 16:20:32,123 [pN:main.1,p:70319,tN:Thread-2] Tool path for shed tool configuration /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/shed_tools_conf.xml is /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/shed_tools
galaxy.tools WARNING 2026-09-17 16:20:32,123 [pN:main.1,p:70319,tN:Thread-2] The default shed tool config file (/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file
galaxy.tool_util.toolbox.base INFO 2026-09-17 16:20:32,124 [pN:main.1,p:70319,tN:Thread-2] Parsing the tool configuration /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/empty_tool_conf.xml
galaxy.tool_util.toolbox.base DEBUG 2026-09-17 16:20:32,125 [pN:main.1,p:70319,tN:Thread-2] Tool path for tool configuration /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/empty_tool_conf.xml is None
galaxy.tool_util.toolbox.base DEBUG 2026-09-17 16:20:32,125 [pN:main.1,p:70319,tN:Thread-2] Reading tools from config files finished (21.163 ms)
galaxy.tool_util.toolbox.base DEBUG 2026-09-17 16:20:32,126 [pN:main.1,p:70319,tN:Thread-2] Loading section: Built-in Converters
galaxy.tool_util.toolbox.base DEBUG 2026-09-17 16:20:32,126 [pN:main.1,p:70319,tN:Thread-2] Loading section: Tools from workflows
galaxy.tool_util.toolbox.base DEBUG 2026-09-17 16:20:32,126 [pN:main.1,p:70319,tN:Thread-2] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy1, version: 0.74+galaxy1 into tool panel....
galaxy.tool_util.toolbox.base DEBUG 2026-09-17 16:20:32,126 [pN:main.1,p:70319,tN:Thread-2] Loading tool panel finished (0.982 ms)
galaxy.tool_util.toolbox.base DEBUG 2026-09-17 16:20:32,128 [pN:main.1,p:70319,tN:Thread-2] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy1, version: 0.74+galaxy1 into tool panel....
galaxy.tool_util.toolbox.views.edam DEBUG 2026-09-17 16:20:32,128 [pN:main.1,p:70319,tN:Thread-2] Loading EDAM tool panel finished (1.253 ms)
galaxy.tool_util.toolbox.base DEBUG 2026-09-17 16:20:32,129 [pN:main.1,p:70319,tN:Thread-2] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy1, version: 0.74+galaxy1 into tool panel....
galaxy.tool_util.toolbox.views.edam DEBUG 2026-09-17 16:20:32,129 [pN:main.1,p:70319,tN:Thread-2] Loading EDAM tool panel finished (0.981 ms)
galaxy.tool_util.toolbox.integrated_panel DEBUG 2026-09-17 16:20:32,130 [pN:main.1,p:70319,tN:Thread-2] Writing integrated tool panel config file to '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/integrated_tool_panel_conf.xml'
galaxy.tool_util.toolbox.base DEBUG 2026-09-17 16:20:32,132 [pN:main.1,p:70319,tN:Thread-2] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy1, version: 0.74+galaxy1 into tool panel....
galaxy.tool_util.toolbox.views.edam DEBUG 2026-09-17 16:20:32,132 [pN:main.1,p:70319,tN:Thread-2] Loading EDAM tool panel finished (1.088 ms)
galaxy.tool_util.toolbox.base DEBUG 2026-09-17 16:20:32,133 [pN:main.1,p:70319,tN:Thread-2] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy1, version: 0.74+galaxy1 into tool panel....
galaxy.tool_util.toolbox.views.edam DEBUG 2026-09-17 16:20:32,133 [pN:main.1,p:70319,tN:Thread-2] Loading EDAM tool panel finished (0.921 ms)
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:32,137 [pN:main.1,p:70319,tN:Thread-2] Loaded external metadata tool: __SET_METADATA__
galaxy.tools.special_tools DEBUG 2026-09-17 16:20:32,138 [pN:main.1,p:70319,tN:Thread-2] Loaded history export tool: __EXPORT_HISTORY__
galaxy.tools.special_tools DEBUG 2026-09-17 16:20:32,139 [pN:main.1,p:70319,tN:Thread-2] Loaded history export to uri tool: __EXPORT_HISTORY_TO_URI__
galaxy.tools.special_tools DEBUG 2026-09-17 16:20:32,141 [pN:main.1,p:70319,tN:Thread-2] Loaded history import tool: __IMPORT_HISTORY__
galaxy.tools DEBUG 2026-09-17 16:20:32,141 [pN:main.1,p:70319,tN:Thread-2] No parameter model for tool '__DATA_FETCH__': Cannot generate a tool parameter model for upload_dataset inputs
galaxy.tools.special_tools DEBUG 2026-09-17 16:20:32,142 [pN:main.1,p:70319,tN:Thread-2] Loaded data fetch tool: __DATA_FETCH__
galaxy.queue_worker INFO 2026-09-17 16:20:32,142 [pN:main.1,p:70319,tN:Thread-2] Queuing async task rebuild_toolbox_search_index for main.1.
galaxy.queue_worker DEBUG 2026-09-17 16:20:32,144 [pN:main.1,p:70319,tN:Thread-2] Toolbox reload (44.292 ms)
galaxy.queue_worker INFO 2026-09-17 16:20:32,147 [pN:main.1,p:70319,tN:Thread-2] Instance 'main.1' received 'rebuild_toolbox_search_index' task, executing now.
galaxy.tools.search DEBUG 2026-09-17 16:20:32,147 [pN:main.1,p:70319,tN:Thread-2] Starting to build toolbox index of panel default.
galaxy.tools.search DEBUG 2026-09-17 16:20:32,176 [pN:main.1,p:70319,tN:Thread-2] Toolbox index of panel default finished (28.806 ms)
galaxy.tools.search DEBUG 2026-09-17 16:20:32,177 [pN:main.1,p:70319,tN:Thread-2] Starting to build toolbox index of panel my_panel.
galaxy.tools.search DEBUG 2026-09-17 16:20:32,179 [pN:main.1,p:70319,tN:Thread-2] Toolbox index of panel my_panel finished (1.858 ms)
galaxy.tools.search DEBUG 2026-09-17 16:20:32,179 [pN:main.1,p:70319,tN:Thread-2] Starting to build toolbox index of panel ontology:edam_operations.
galaxy.app DEBUG 2026-09-17 16:20:32,187 [pN:main.1,p:70319,tN:WSGI_0] Finished waiting for toolbox reload (1607.540 ms)
galaxy.tools.search DEBUG 2026-09-17 16:20:32,232 [pN:main.1,p:70319,tN:Thread-2] Toolbox index of panel ontology:edam_operations finished (53.218 ms)
galaxy.tools.search DEBUG 2026-09-17 16:20:32,233 [pN:main.1,p:70319,tN:Thread-2] Starting to build toolbox index of panel ontology:edam_topics.
galaxy.tools.search DEBUG 2026-09-17 16:20:32,257 [pN:main.1,p:70319,tN:Thread-2] Toolbox index of panel ontology:edam_topics finished (24.088 ms)
galaxy.queue_worker INFO 2026-09-17 16:20:32,414 [pN:main.1,p:70319,tN:Thread-4 (check)] Sending reload_toolbox control task.
galaxy.tool_util.deps.conda_util DEBUG 2026-09-17 16:20:32,890 [pN:main.1,p:70319,tN:WSGI_0] Executing command: /Users/mvandenb/src/worktrees/.planemo-home/conda/bin/conda list -f --json conda-libmamba-solver > '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/tmp/tmp3ooimik7'
galaxy.tool_util.deps.conda_util DEBUG 2026-09-17 16:20:33,417 [pN:main.1,p:70319,tN:WSGI_0] Executing command: /Users/mvandenb/src/worktrees/.planemo-home/conda/bin/conda create -y --quiet --strict-channel-priority --solver libmamba --override-channels --channel conda-forge --channel bioconda --name __fastqc@0.12.1 fastqc=0.12.1
galaxy.tool_util.deps DEBUG 2026-09-17 16:20:39,606 [pN:main.1,p:70319,tN:WSGI_0] Using dependency fastqc version 0.12.1 of type conda
galaxy.tool_util.deps DEBUG 2026-09-17 16:20:39,607 [pN:main.1,p:70319,tN:WSGI_0] Using dependency fastqc version 0.12.1 of type conda
galaxy.tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager DEBUG 2026-09-17 16:20:40,706 [pN:main.1,p:70319,tN:WSGI_0] Creating repository dependency objects...
galaxy.tool_util.toolbox.base DEBUG 2026-09-17 16:20:42,135 [pN:main.1,p:70319,tN:WSGI_0] Appending to tool panel section: Tools from workflows
galaxy.tool_shed.util.repository_util DEBUG 2026-09-17 16:20:42,138 [pN:main.1,p:70319,tN:WSGI_0] Adding new row for repository 'cutadapt' in the tool_shed_repository table, status set to 'installation_status.NEW'.
galaxy.tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager DEBUG 2026-09-17 16:20:42,146 [pN:main.1,p:70319,tN:WSGI_0] Building repository dependency relationships...
galaxy.tool_util.toolbox.base DEBUG 2026-09-17 16:20:42,147 [pN:main.1,p:70319,tN:WSGI_0] Appending to tool panel section: Tools from workflows
galaxy.tool_util.toolbox.base DEBUG 2026-09-17 16:20:42,156 [pN:main.1,p:70319,tN:WSGI_0] Appending to tool panel section: Tools from workflows
galaxy.tool_shed.galaxy_install.install_manager INFO 2026-09-17 16:20:42,169 [pN:main.1,p:70319,tN:WSGI_0] Cloning repository 'https://toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt' at 46:f6168dd17f82
galaxy.tool_util.data DEBUG 2026-09-17 16:20:43,811 [pN:main.1,p:70319,tN:WSGI_0] Loaded 1 lines from '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/tmp/tmp-toolshed-gmfcr9l551irc/adapters.loc' for 'adapters'
galaxy.tool_util.data DEBUG 2026-09-17 16:20:43,811 [pN:main.1,p:70319,tN:WSGI_0] Loaded tool data table 'adapters' from file '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/shed_tools/toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/f6168dd17f82/cutadapt/tool_data_table_conf.xml.sample'
galaxy.tool_util.data DEBUG 2026-09-17 16:20:47,227 [pN:main.1,p:70319,tN:WSGI_0] Loaded 1 lines from '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/tmp/tmp-toolshed-gmfcr9l551irc/adapters.loc' for 'adapters'
galaxy.tool_util.data DEBUG 2026-09-17 16:20:47,227 [pN:main.1,p:70319,tN:WSGI_0] Loading another instance of data table 'adapters' from file '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/shed_tools/toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/f6168dd17f82/cutadapt/tool_data_table_conf.xml.sample', attempting to merge content.
galaxy.tool_util.data WARNING 2026-09-17 16:20:47,227 [pN:main.1,p:70319,tN:WSGI_0] Attempted to add fields (['TGTAGGCC', 'Dummy-Adapter (do not use me)']) to data table 'adapters', but this entry already exists and allow_duplicates is False.
galaxy.tool_util.data DEBUG 2026-09-17 16:20:47,228 [pN:main.1,p:70319,tN:WSGI_0] Loaded 1 lines from '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/tmp/tmp-toolshed-gmfcr9l551irc/adapters.loc' for 'adapters'
galaxy.tool_util.data DEBUG 2026-09-17 16:20:47,228 [pN:main.1,p:70319,tN:WSGI_0] Loading another instance of data table 'adapters' from file '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/shed_tools/toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/f6168dd17f82/cutadapt/tool_data_table_conf.xml.sample', attempting to merge content.
galaxy.tool_util.data WARNING 2026-09-17 16:20:47,228 [pN:main.1,p:70319,tN:WSGI_0] Attempted to add fields (['TGTAGGCC', 'Dummy-Adapter (do not use me)']) to data table 'adapters', but this entry already exists and allow_duplicates is False.
galaxy.tool_util.data DEBUG 2026-09-17 16:20:47,229 [pN:main.1,p:70319,tN:WSGI_0] Loaded 1 lines from '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/tmp/tmp-toolshed-gmfcr9l551irc/adapters.loc' for 'adapters'
galaxy.tool_util.data DEBUG 2026-09-17 16:20:47,229 [pN:main.1,p:70319,tN:WSGI_0] Loading another instance of data table 'adapters' from file '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/shed_tools/toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/f6168dd17f82/cutadapt/tool_data_table_conf.xml.sample', attempting to merge content.
galaxy.tool_util.data WARNING 2026-09-17 16:20:47,229 [pN:main.1,p:70319,tN:WSGI_0] Attempted to add fields (['TGTAGGCC', 'Dummy-Adapter (do not use me)']) to data table 'adapters', but this entry already exists and allow_duplicates is False.
galaxy.tool_util.data DEBUG 2026-09-17 16:20:47,230 [pN:main.1,p:70319,tN:WSGI_0] Loaded 1 lines from '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/tmp/tmp-toolshed-gmfcr9l551irc/adapters.loc' for 'adapters'
galaxy.tool_util.data DEBUG 2026-09-17 16:20:47,230 [pN:main.1,p:70319,tN:WSGI_0] Loading another instance of data table 'adapters' from file '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/shed_tools/toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/f6168dd17f82/cutadapt/tool_data_table_conf.xml.sample', attempting to merge content.
galaxy.tool_util.data WARNING 2026-09-17 16:20:47,230 [pN:main.1,p:70319,tN:WSGI_0] Attempted to add fields (['TGTAGGCC', 'Dummy-Adapter (do not use me)']) to data table 'adapters', but this entry already exists and allow_duplicates is False.
galaxy.tool_util.data DEBUG 2026-09-17 16:20:47,231 [pN:main.1,p:70319,tN:WSGI_0] Loaded 1 lines from '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/tmp/tmp-toolshed-gmfcr9l551irc/adapters.loc' for 'adapters'
galaxy.tool_util.data DEBUG 2026-09-17 16:20:47,231 [pN:main.1,p:70319,tN:WSGI_0] Loading another instance of data table 'adapters' from file '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/shed_tools/toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/f6168dd17f82/cutadapt/tool_data_table_conf.xml.sample', attempting to merge content.
galaxy.tool_util.data WARNING 2026-09-17 16:20:47,231 [pN:main.1,p:70319,tN:WSGI_0] Attempted to add fields (['TGTAGGCC', 'Dummy-Adapter (do not use me)']) to data table 'adapters', but this entry already exists and allow_duplicates is False.
galaxy.tool_util.data DEBUG 2026-09-17 16:20:47,232 [pN:main.1,p:70319,tN:WSGI_0] Loaded 1 lines from '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/tmp/tmp-toolshed-gmfcr9l551irc/adapters.loc' for 'adapters'
galaxy.tool_util.data DEBUG 2026-09-17 16:20:47,232 [pN:main.1,p:70319,tN:WSGI_0] Loading another instance of data table 'adapters' from file '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/shed_tools/toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/f6168dd17f82/cutadapt/tool_data_table_conf.xml.sample', attempting to merge content.
galaxy.tool_util.data WARNING 2026-09-17 16:20:47,232 [pN:main.1,p:70319,tN:WSGI_0] Attempted to add fields (['TGTAGGCC', 'Dummy-Adapter (do not use me)']) to data table 'adapters', but this entry already exists and allow_duplicates is False.
galaxy.tool_util.data DEBUG 2026-09-17 16:20:47,232 [pN:main.1,p:70319,tN:WSGI_0] Loaded 1 lines from '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/tmp/tmp-toolshed-gmfcr9l551irc/adapters.loc' for 'adapters'
galaxy.tool_util.data DEBUG 2026-09-17 16:20:47,233 [pN:main.1,p:70319,tN:WSGI_0] Loading another instance of data table 'adapters' from file '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/shed_tools/toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/f6168dd17f82/cutadapt/tool_data_table_conf.xml.sample', attempting to merge content.
galaxy.tool_util.data WARNING 2026-09-17 16:20:47,233 [pN:main.1,p:70319,tN:WSGI_0] Attempted to add fields (['TGTAGGCC', 'Dummy-Adapter (do not use me)']) to data table 'adapters', but this entry already exists and allow_duplicates is False.
galaxy.tool_util.data DEBUG 2026-09-17 16:20:47,233 [pN:main.1,p:70319,tN:WSGI_0] Loaded 1 lines from '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/tmp/tmp-toolshed-gmfcr9l551irc/adapters.loc' for 'adapters'
galaxy.tool_util.data DEBUG 2026-09-17 16:20:47,233 [pN:main.1,p:70319,tN:WSGI_0] Loading another instance of data table 'adapters' from file '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/shed_tools/toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/f6168dd17f82/cutadapt/tool_data_table_conf.xml.sample', attempting to merge content.
galaxy.tool_util.data WARNING 2026-09-17 16:20:47,234 [pN:main.1,p:70319,tN:WSGI_0] Attempted to add fields (['TGTAGGCC', 'Dummy-Adapter (do not use me)']) to data table 'adapters', but this entry already exists and allow_duplicates is False.
galaxy.tool_util.data DEBUG 2026-09-17 16:20:47,234 [pN:main.1,p:70319,tN:WSGI_0] Loaded 1 lines from '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/tmp/tmp-toolshed-gmfcr9l551irc/adapters.loc' for 'adapters'
galaxy.tool_util.data DEBUG 2026-09-17 16:20:47,234 [pN:main.1,p:70319,tN:WSGI_0] Loading another instance of data table 'adapters' from file '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/shed_tools/toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/f6168dd17f82/cutadapt/tool_data_table_conf.xml.sample', attempting to merge content.
galaxy.tool_util.data WARNING 2026-09-17 16:20:47,235 [pN:main.1,p:70319,tN:WSGI_0] Attempted to add fields (['TGTAGGCC', 'Dummy-Adapter (do not use me)']) to data table 'adapters', but this entry already exists and allow_duplicates is False.
galaxy.tool_util.data DEBUG 2026-09-17 16:20:47,235 [pN:main.1,p:70319,tN:WSGI_0] Loaded 1 lines from '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/tmp/tmp-toolshed-gmfcr9l551irc/adapters.loc' for 'adapters'
galaxy.tool_util.data DEBUG 2026-09-17 16:20:47,235 [pN:main.1,p:70319,tN:WSGI_0] Loading another instance of data table 'adapters' from file '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/shed_tools/toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/f6168dd17f82/cutadapt/tool_data_table_conf.xml.sample', attempting to merge content.
galaxy.tool_util.data WARNING 2026-09-17 16:20:47,235 [pN:main.1,p:70319,tN:WSGI_0] Attempted to add fields (['TGTAGGCC', 'Dummy-Adapter (do not use me)']) to data table 'adapters', but this entry already exists and allow_duplicates is False.
galaxy.tool_util.data DEBUG 2026-09-17 16:20:47,236 [pN:main.1,p:70319,tN:WSGI_0] Loaded 1 lines from '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/tmp/tmp-toolshed-gmfcr9l551irc/adapters.loc' for 'adapters'
galaxy.tool_util.data DEBUG 2026-09-17 16:20:47,236 [pN:main.1,p:70319,tN:WSGI_0] Loading another instance of data table 'adapters' from file '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/shed_tools/toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/f6168dd17f82/cutadapt/tool_data_table_conf.xml.sample', attempting to merge content.
galaxy.tool_util.data WARNING 2026-09-17 16:20:47,236 [pN:main.1,p:70319,tN:WSGI_0] Attempted to add fields (['TGTAGGCC', 'Dummy-Adapter (do not use me)']) to data table 'adapters', but this entry already exists and allow_duplicates is False.
galaxy.tool_util.data DEBUG 2026-09-17 16:20:47,237 [pN:main.1,p:70319,tN:WSGI_0] Loaded 1 lines from '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/tmp/tmp-toolshed-gmfcr9l551irc/adapters.loc' for 'adapters'
galaxy.tool_util.data DEBUG 2026-09-17 16:20:47,237 [pN:main.1,p:70319,tN:WSGI_0] Loading another instance of data table 'adapters' from file '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/shed_tools/toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/f6168dd17f82/cutadapt/tool_data_table_conf.xml.sample', attempting to merge content.
galaxy.tool_util.data WARNING 2026-09-17 16:20:47,237 [pN:main.1,p:70319,tN:WSGI_0] Attempted to add fields (['TGTAGGCC', 'Dummy-Adapter (do not use me)']) to data table 'adapters', but this entry already exists and allow_duplicates is False.
galaxy.tool_util.data DEBUG 2026-09-17 16:20:47,238 [pN:main.1,p:70319,tN:WSGI_0] Loaded 1 lines from '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/tmp/tmp-toolshed-gmfcr9l551irc/adapters.loc' for 'adapters'
galaxy.tool_util.data DEBUG 2026-09-17 16:20:47,238 [pN:main.1,p:70319,tN:WSGI_0] Loading another instance of data table 'adapters' from file '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/shed_tools/toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/f6168dd17f82/cutadapt/tool_data_table_conf.xml.sample', attempting to merge content.
galaxy.tool_util.data WARNING 2026-09-17 16:20:47,238 [pN:main.1,p:70319,tN:WSGI_0] Attempted to add fields (['TGTAGGCC', 'Dummy-Adapter (do not use me)']) to data table 'adapters', but this entry already exists and allow_duplicates is False.
galaxy.tool_util.data DEBUG 2026-09-17 16:20:47,239 [pN:main.1,p:70319,tN:WSGI_0] Loaded 1 lines from '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/tmp/tmp-toolshed-gmfcr9l551irc/adapters.loc' for 'adapters'
galaxy.tool_util.data DEBUG 2026-09-17 16:20:47,239 [pN:main.1,p:70319,tN:WSGI_0] Loading another instance of data table 'adapters' from file '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/shed_tools/toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/f6168dd17f82/cutadapt/tool_data_table_conf.xml.sample', attempting to merge content.
galaxy.tool_util.data WARNING 2026-09-17 16:20:47,239 [pN:main.1,p:70319,tN:WSGI_0] Attempted to add fields (['TGTAGGCC', 'Dummy-Adapter (do not use me)']) to data table 'adapters', but this entry already exists and allow_duplicates is False.
galaxy.tool_util.data DEBUG 2026-09-17 16:20:47,239 [pN:main.1,p:70319,tN:WSGI_0] Loaded 1 lines from '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/tmp/tmp-toolshed-gmfcr9l551irc/adapters.loc' for 'adapters'
galaxy.tool_util.data DEBUG 2026-09-17 16:20:47,240 [pN:main.1,p:70319,tN:WSGI_0] Loading another instance of data table 'adapters' from file '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/shed_tools/toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/f6168dd17f82/cutadapt/tool_data_table_conf.xml.sample', attempting to merge content.
galaxy.tool_util.data WARNING 2026-09-17 16:20:47,240 [pN:main.1,p:70319,tN:WSGI_0] Attempted to add fields (['TGTAGGCC', 'Dummy-Adapter (do not use me)']) to data table 'adapters', but this entry already exists and allow_duplicates is False.
charset_normalizer DEBUG 2026-09-17 16:20:47,757 [pN:main.1,p:70319,tN:WSGI_0] Encoding detection: ascii is most likely the one.
galaxy.tool_util.data DEBUG 2026-09-17 16:20:47,796 [pN:main.1,p:70319,tN:WSGI_0] Loaded 1 lines from '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/galaxy-dev/tool-data/shed/adapters.loc' for 'adapters'
galaxy.tool_util.data DEBUG 2026-09-17 16:20:47,797 [pN:main.1,p:70319,tN:WSGI_0] Loaded tool data table 'adapters' from file '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/galaxy-dev/tool-data/toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/f6168dd17f82/tool_data_table_conf.xml'
galaxy.tool_util.toolbox.base DEBUG 2026-09-17 16:20:54,517 [pN:main.1,p:70319,tN:WSGI_0] Loaded tool id: toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/5.2+galaxy2, version: 5.2+galaxy2 into tool panel....
galaxy.tool_util.toolbox.integrated_panel DEBUG 2026-09-17 16:20:54,517 [pN:main.1,p:70319,tN:WSGI_0] Writing integrated tool panel config file to '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/integrated_tool_panel_conf.xml'
galaxy.app DEBUG 2026-09-17 16:20:54,519 [pN:main.1,p:70319,tN:WSGI_0] Waiting for toolbox reload
galaxy.tool_util.toolbox.watcher DEBUG 2026-09-17 16:20:55,525 [pN:main.1,p:70319,tN:Thread-4 (check)] The file '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/shed_tools_conf.xml' has changes.
galaxy.queue_worker INFO 2026-09-17 16:20:55,527 [pN:main.1,p:70319,tN:Thread-4 (check)] Queuing sync task reload_toolbox for main.1.
galaxy.queue_worker INFO 2026-09-17 16:20:55,616 [pN:main.1,p:70319,tN:Thread-2] Instance 'main.1' received 'reload_toolbox' task, executing now.
galaxy.queue_worker DEBUG 2026-09-17 16:20:55,618 [pN:main.1,p:70319,tN:Thread-2] Executing toolbox reload on 'main.1'
galaxy.util WARNING 2026-09-17 16:20:55,621 [pN:main.1,p:70319,tN:Thread-2] directory not found: /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/galaxy-dev/config/plugins/activities
galaxy.tools WARNING 2026-09-17 16:20:55,624 [pN:main.1,p:70319,tN:Thread-2] The default shed tool config file (/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file
galaxy.tool_util.toolbox.base INFO 2026-09-17 16:20:55,625 [pN:main.1,p:70319,tN:Thread-2] Parsing the tool configuration /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/tool_conf.xml
galaxy.tool_util.toolbox.base DEBUG 2026-09-17 16:20:55,626 [pN:main.1,p:70319,tN:Thread-2] Tool path for tool configuration /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/tool_conf.xml is None
galaxy.tool_util.parser.factory INFO 2026-09-17 16:20:55,627 [pN:main.1,p:70319,tN:Thread-2] Loading tool from YAML - this is experimental - tool will not function in future.
galaxy.tool_util.toolbox.base ERROR 2026-09-17 16:20:55,642 [pN:main.1,p:70319,tN:Thread-2] Error reading tool from path: /Users/mvandenb/src/worktrees/foundry/brc-c-auris/.foundry-runs/auris-scf1/galaxy-workflow.gxwf.yml
Traceback (most recent call last):
  File "/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/galaxy-dev/lib/galaxy/tool_util/toolbox/base.py", line 967, in _load_tool_tag_set
    tool = self.load_tool(concrete_path, use_cached=False)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/galaxy-dev/lib/galaxy/tool_util/toolbox/base.py", line 1222, in load_tool
    tool = self.create_tool(
           ^^^^^^^^^^^^^^^^^
  File "/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/galaxy-dev/lib/galaxy/tools/__init__.py", line 619, in create_tool
    return self._create_tool_from_source(tool_source, config_file=config_file, **kwds)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/galaxy-dev/lib/galaxy/tools/__init__.py", line 634, in _create_tool_from_source
    return create_tool_from_source(self.app, tool_source, **kwds)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/galaxy-dev/lib/galaxy/tools/__init__.py", line 448, in create_tool_from_source
    tool = ToolClass(config_file, tool_source, app, **kwds)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/galaxy-dev/lib/galaxy/tools/__init__.py", line 1099, in __init__
    raise e
  File "/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/galaxy-dev/lib/galaxy/tools/__init__.py", line 1096, in __init__
    self.parse(tool_source, guid=guid, dynamic=dynamic)
  File "/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/galaxy-dev/lib/galaxy/tools/__init__.py", line 1329, in parse
    raise Exception(f"Missing tool 'id' for tool at '{tool_source}'")
Exception: Missing tool 'id' for tool at 'YamlToolSource[/Users/mvandenb/src/worktrees/foundry/brc-c-auris/.foundry-runs/auris-scf1/galaxy-workflow.gxwf.yml]'
galaxy.tools WARNING 2026-09-17 16:20:55,644 [pN:main.1,p:70319,tN:Thread-2] The default shed tool config file (/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file
galaxy.tool_util.toolbox.base INFO 2026-09-17 16:20:55,645 [pN:main.1,p:70319,tN:Thread-2] Parsing the tool configuration /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/shed_tools_conf.xml
galaxy.tool_util.toolbox.base DEBUG 2026-09-17 16:20:55,646 [pN:main.1,p:70319,tN:Thread-2] Tool path for shed tool configuration /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/shed_tools_conf.xml is /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/shed_tools
galaxy.tools WARNING 2026-09-17 16:20:55,647 [pN:main.1,p:70319,tN:Thread-2] The default shed tool config file (/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file
galaxy.tool_util.toolbox.base INFO 2026-09-17 16:20:55,647 [pN:main.1,p:70319,tN:Thread-2] Parsing the tool configuration /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/empty_tool_conf.xml
galaxy.tool_util.toolbox.base DEBUG 2026-09-17 16:20:55,648 [pN:main.1,p:70319,tN:Thread-2] Tool path for tool configuration /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/empty_tool_conf.xml is None
galaxy.tool_util.toolbox.base DEBUG 2026-09-17 16:20:55,649 [pN:main.1,p:70319,tN:Thread-2] Reading tools from config files finished (25.185 ms)
galaxy.tool_util.toolbox.base DEBUG 2026-09-17 16:20:55,649 [pN:main.1,p:70319,tN:Thread-2] Loading section: Built-in Converters
galaxy.tool_util.toolbox.base DEBUG 2026-09-17 16:20:55,650 [pN:main.1,p:70319,tN:Thread-2] Loading section: Tools from workflows
galaxy.tool_util.toolbox.base DEBUG 2026-09-17 16:20:55,650 [pN:main.1,p:70319,tN:Thread-2] Loaded tool id: toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/5.2+galaxy2, version: 5.2+galaxy2 into tool panel....
galaxy.tool_util.toolbox.base DEBUG 2026-09-17 16:20:55,651 [pN:main.1,p:70319,tN:Thread-2] Loading tool panel finished (1.251 ms)
galaxy.tool_util.toolbox.base DEBUG 2026-09-17 16:20:55,652 [pN:main.1,p:70319,tN:Thread-2] Loaded tool id: toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/5.2+galaxy2, version: 5.2+galaxy2 into tool panel....
galaxy.tool_util.toolbox.views.edam DEBUG 2026-09-17 16:20:55,652 [pN:main.1,p:70319,tN:Thread-2] Loading EDAM tool panel finished (1.277 ms)
galaxy.tool_util.toolbox.base DEBUG 2026-09-17 16:20:55,653 [pN:main.1,p:70319,tN:Thread-2] Loaded tool id: toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/5.2+galaxy2, version: 5.2+galaxy2 into tool panel....
galaxy.tool_util.toolbox.views.edam DEBUG 2026-09-17 16:20:55,654 [pN:main.1,p:70319,tN:Thread-2] Loading EDAM tool panel finished (1.036 ms)
galaxy.tool_util.toolbox.integrated_panel DEBUG 2026-09-17 16:20:55,654 [pN:main.1,p:70319,tN:Thread-2] Writing integrated tool panel config file to '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/integrated_tool_panel_conf.xml'
galaxy.tool_util.toolbox.base DEBUG 2026-09-17 16:20:55,656 [pN:main.1,p:70319,tN:Thread-2] Loaded tool id: toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/5.2+galaxy2, version: 5.2+galaxy2 into tool panel....
galaxy.tool_util.toolbox.views.edam DEBUG 2026-09-17 16:20:55,656 [pN:main.1,p:70319,tN:Thread-2] Loading EDAM tool panel finished (1.158 ms)
galaxy.tool_util.toolbox.base DEBUG 2026-09-17 16:20:55,657 [pN:main.1,p:70319,tN:Thread-2] Loaded tool id: toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/5.2+galaxy2, version: 5.2+galaxy2 into tool panel....
galaxy.tool_util.toolbox.views.edam DEBUG 2026-09-17 16:20:55,658 [pN:main.1,p:70319,tN:Thread-2] Loading EDAM tool panel finished (1.059 ms)
galaxy.datatypes.registry DEBUG 2026-09-17 16:20:55,661 [pN:main.1,p:70319,tN:Thread-2] Loaded external metadata tool: __SET_METADATA__
galaxy.tools.special_tools DEBUG 2026-09-17 16:20:55,662 [pN:main.1,p:70319,tN:Thread-2] Loaded history export tool: __EXPORT_HISTORY__
galaxy.tools.special_tools DEBUG 2026-09-17 16:20:55,663 [pN:main.1,p:70319,tN:Thread-2] Loaded history export to uri tool: __EXPORT_HISTORY_TO_URI__
galaxy.tools.special_tools DEBUG 2026-09-17 16:20:55,664 [pN:main.1,p:70319,tN:Thread-2] Loaded history import tool: __IMPORT_HISTORY__
galaxy.tools DEBUG 2026-09-17 16:20:55,665 [pN:main.1,p:70319,tN:Thread-2] No parameter model for tool '__DATA_FETCH__': Cannot generate a tool parameter model for upload_dataset inputs
galaxy.tools.special_tools DEBUG 2026-09-17 16:20:55,666 [pN:main.1,p:70319,tN:Thread-2] Loaded data fetch tool: __DATA_FETCH__
galaxy.queue_worker INFO 2026-09-17 16:20:55,666 [pN:main.1,p:70319,tN:Thread-2] Queuing async task rebuild_toolbox_search_index for main.1.
galaxy.queue_worker DEBUG 2026-09-17 16:20:55,668 [pN:main.1,p:70319,tN:Thread-2] Toolbox reload (50.055 ms)
galaxy.queue_worker INFO 2026-09-17 16:20:55,671 [pN:main.1,p:70319,tN:Thread-2] Instance 'main.1' received 'rebuild_toolbox_search_index' task, executing now.
galaxy.tools.search DEBUG 2026-09-17 16:20:55,672 [pN:main.1,p:70319,tN:Thread-2] Starting to build toolbox index of panel default.
galaxy.app DEBUG 2026-09-17 16:20:55,694 [pN:main.1,p:70319,tN:WSGI_0] Finished waiting for toolbox reload (1175.270 ms)
galaxy.tool_util.deps.conda_util DEBUG 2026-09-17 16:20:55,697 [pN:main.1,p:70319,tN:WSGI_0] Executing command: /Users/mvandenb/src/worktrees/.planemo-home/conda/bin/conda create -y --quiet --strict-channel-priority --solver libmamba --override-channels --channel conda-forge --channel bioconda --name __cutadapt@5.2 cutadapt=5.2
galaxy.tools.search DEBUG 2026-09-17 16:20:55,746 [pN:main.1,p:70319,tN:Thread-2] Toolbox index of panel default finished (74.250 ms)
galaxy.tools.search DEBUG 2026-09-17 16:20:55,747 [pN:main.1,p:70319,tN:Thread-2] Starting to build toolbox index of panel my_panel.
galaxy.tools.search DEBUG 2026-09-17 16:20:55,749 [pN:main.1,p:70319,tN:Thread-2] Toolbox index of panel my_panel finished (1.810 ms)
galaxy.tools.search DEBUG 2026-09-17 16:20:55,749 [pN:main.1,p:70319,tN:Thread-2] Starting to build toolbox index of panel ontology:edam_operations.
galaxy.tools.search DEBUG 2026-09-17 16:20:55,779 [pN:main.1,p:70319,tN:Thread-2] Toolbox index of panel ontology:edam_operations finished (29.683 ms)
galaxy.tools.search DEBUG 2026-09-17 16:20:55,780 [pN:main.1,p:70319,tN:Thread-2] Starting to build toolbox index of panel ontology:edam_topics.
galaxy.tools.search DEBUG 2026-09-17 16:20:55,808 [pN:main.1,p:70319,tN:Thread-2] Toolbox index of panel ontology:edam_topics finished (28.505 ms)
galaxy.queue_worker INFO 2026-09-17 16:20:56,554 [pN:main.1,p:70319,tN:Thread-4 (check)] Sending reload_toolbox control task.
galaxy.tool_util.deps DEBUG 2026-09-17 16:21:03,051 [pN:main.1,p:70319,tN:WSGI_0] Using dependency cutadapt version 5.2 of type conda
galaxy.tool_util.deps DEBUG 2026-09-17 16:21:03,052 [pN:main.1,p:70319,tN:WSGI_0] Using dependency cutadapt version 5.2 of type conda
galaxy.tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager DEBUG 2026-09-17 16:21:03,806 [pN:main.1,p:70319,tN:WSGI_0] Creating repository dependency objects...
galaxy.tool_util.toolbox.base DEBUG 2026-09-17 16:21:05,338 [pN:main.1,p:70319,tN:WSGI_0] Appending to tool panel section: Tools from workflows
galaxy.tool_shed.util.repository_util DEBUG 2026-09-17 16:21:05,340 [pN:main.1,p:70319,tN:WSGI_0] Adding new row for repository 'rgrnastar' in the tool_shed_repository table, status set to 'installation_status.NEW'.
galaxy.tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager DEBUG 2026-09-17 16:21:05,346 [pN:main.1,p:70319,tN:WSGI_0] Building repository dependency relationships...
galaxy.tool_util.toolbox.base DEBUG 2026-09-17 16:21:05,346 [pN:main.1,p:70319,tN:WSGI_0] Appending to tool panel section: Tools from workflows
galaxy.tool_util.toolbox.base DEBUG 2026-09-17 16:21:05,353 [pN:main.1,p:70319,tN:WSGI_0] Appending to tool panel section: Tools from workflows
galaxy.tool_shed.galaxy_install.install_manager INFO 2026-09-17 16:21:05,363 [pN:main.1,p:70319,tN:WSGI_0] Cloning repository 'https://toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar' at 34:d8d32326fbfb
galaxy.tool_util.data DEBUG 2026-09-17 16:21:18,369 [pN:main.1,p:70319,tN:WSGI_0] Loaded 0 lines from '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/tmp/tmp-toolshed-gmfcrgelpt5dx/rnastar_index2x_versioned.loc' for 'rnastar_index2x_versioned'
galaxy.tool_util.data DEBUG 2026-09-17 16:21:18,370 [pN:main.1,p:70319,tN:WSGI_0] Loaded tool data table 'rnastar_index2x_versioned' from file '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/shed_tools/toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/d8d32326fbfb/rgrnastar/tool_data_table_conf.xml.sample'
galaxy.tool_util.data DEBUG 2026-09-17 16:21:18,417 [pN:main.1,p:70319,tN:WSGI_0] Loaded 0 lines from '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/tmp/tmp-toolshed-gmfcrgelpt5dx/rnastar_index2x_versioned.loc' for 'rnastar_index2x_versioned'
galaxy.tool_util.data DEBUG 2026-09-17 16:21:18,417 [pN:main.1,p:70319,tN:WSGI_0] Loading another instance of data table 'rnastar_index2x_versioned' from file '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/shed_tools/toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/d8d32326fbfb/rgrnastar/tool_data_table_conf.xml.sample', attempting to merge content.
galaxy.tool_util.data DEBUG 2026-09-17 16:21:18,418 [pN:main.1,p:70319,tN:WSGI_0] Loaded 0 lines from '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/tmp/tmp-toolshed-gmfcrgelpt5dx/rnastar_index2x_versioned.loc' for 'rnastar_index2x_versioned'
galaxy.tool_util.data DEBUG 2026-09-17 16:21:18,418 [pN:main.1,p:70319,tN:WSGI_0] Loading another instance of data table 'rnastar_index2x_versioned' from file '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/shed_tools/toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/d8d32326fbfb/rgrnastar/tool_data_table_conf.xml.sample', attempting to merge content.
galaxy.tool_util.data DEBUG 2026-09-17 16:21:18,418 [pN:main.1,p:70319,tN:WSGI_0] Loaded 0 lines from '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/tmp/tmp-toolshed-gmfcrgelpt5dx/rnastar_index2x_versioned.loc' for 'rnastar_index2x_versioned'
galaxy.tool_util.data DEBUG 2026-09-17 16:21:18,419 [pN:main.1,p:70319,tN:WSGI_0] Loading another instance of data table 'rnastar_index2x_versioned' from file '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/shed_tools/toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/d8d32326fbfb/rgrnastar/tool_data_table_conf.xml.sample', attempting to merge content.
charset_normalizer DEBUG 2026-09-17 16:21:18,926 [pN:main.1,p:70319,tN:WSGI_0] Encoding detection: ascii is most likely the one.
galaxy.tool_util.data DEBUG 2026-09-17 16:21:18,959 [pN:main.1,p:70319,tN:WSGI_0] Loaded 0 lines from '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/galaxy-dev/tool-data/shed/rnastar_index2x_versioned.loc' for 'rnastar_index2x_versioned'
galaxy.tool_util.data DEBUG 2026-09-17 16:21:18,959 [pN:main.1,p:70319,tN:WSGI_0] Loaded tool data table 'rnastar_index2x_versioned' from file '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/galaxy-dev/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/d8d32326fbfb/tool_data_table_conf.xml'
galaxy.tool_util.toolbox.base DEBUG 2026-09-17 16:21:19,067 [pN:main.1,p:70319,tN:WSGI_0] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.11b+galaxy1, version: 2.7.11b+galaxy1 into tool panel....
galaxy.tool_util.toolbox.integrated_panel DEBUG 2026-09-17 16:21:19,068 [pN:main.1,p:70319,tN:WSGI_0] Writing integrated tool panel config file to '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/integrated_tool_panel_conf.xml'
galaxy.app DEBUG 2026-09-17 16:21:19,069 [pN:main.1,p:70319,tN:WSGI_0] Waiting for toolbox reload
galaxy.tool_util.toolbox.watcher DEBUG 2026-09-17 16:21:19,784 [pN:main.1,p:70319,tN:Thread-4 (check)] The file '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/shed_tools_conf.xml' has changes.
galaxy.queue_worker INFO 2026-09-17 16:21:19,786 [pN:main.1,p:70319,tN:Thread-4 (check)] Queuing sync task reload_toolbox for main.1.
galaxy.queue_worker INFO 2026-09-17 16:21:20,120 [pN:main.1,p:70319,tN:Thread-2] Instance 'main.1' received 'reload_toolbox' task, executing now.
galaxy.queue_worker DEBUG 2026-09-17 16:21:20,122 [pN:main.1,p:70319,tN:Thread-2] Executing toolbox reload on 'main.1'
galaxy.util WARNING 2026-09-17 16:21:20,125 [pN:main.1,p:70319,tN:Thread-2] directory not found: /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/galaxy-dev/config/plugins/activities
galaxy.tools WARNING 2026-09-17 16:21:20,128 [pN:main.1,p:70319,tN:Thread-2] The default shed tool config file (/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file
galaxy.tool_util.toolbox.base INFO 2026-09-17 16:21:20,129 [pN:main.1,p:70319,tN:Thread-2] Parsing the tool configuration /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/tool_conf.xml
galaxy.tool_util.toolbox.base DEBUG 2026-09-17 16:21:20,131 [pN:main.1,p:70319,tN:Thread-2] Tool path for tool configuration /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/tool_conf.xml is None
galaxy.tool_util.parser.factory INFO 2026-09-17 16:21:20,132 [pN:main.1,p:70319,tN:Thread-2] Loading tool from YAML - this is experimental - tool will not function in future.
galaxy.tool_util.toolbox.base ERROR 2026-09-17 16:21:20,146 [pN:main.1,p:70319,tN:Thread-2] Error reading tool from path: /Users/mvandenb/src/worktrees/foundry/brc-c-auris/.foundry-runs/auris-scf1/galaxy-workflow.gxwf.yml
Traceback (most recent call last):
  File "/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/galaxy-dev/lib/galaxy/tool_util/toolbox/base.py", line 967, in _load_tool_tag_set
    tool = self.load_tool(concrete_path, use_cached=False)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/galaxy-dev/lib/galaxy/tool_util/toolbox/base.py", line 1222, in load_tool
    tool = self.create_tool(
           ^^^^^^^^^^^^^^^^^
  File "/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/galaxy-dev/lib/galaxy/tools/__init__.py", line 619, in create_tool
    return self._create_tool_from_source(tool_source, config_file=config_file, **kwds)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/galaxy-dev/lib/galaxy/tools/__init__.py", line 634, in _create_tool_from_source
    return create_tool_from_source(self.app, tool_source, **kwds)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/galaxy-dev/lib/galaxy/tools/__init__.py", line 448, in create_tool_from_source
    tool = ToolClass(config_file, tool_source, app, **kwds)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/galaxy-dev/lib/galaxy/tools/__init__.py", line 1099, in __init__
    raise e
  File "/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/galaxy-dev/lib/galaxy/tools/__init__.py", line 1096, in __init__
    self.parse(tool_source, guid=guid, dynamic=dynamic)
  File "/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/galaxy-dev/lib/galaxy/tools/__init__.py", line 1329, in parse
    raise Exception(f"Missing tool 'id' for tool at '{tool_source}'")
Exception: Missing tool 'id' for tool at 'YamlToolSource[/Users/mvandenb/src/worktrees/foundry/brc-c-auris/.foundry-runs/auris-scf1/galaxy-workflow.gxwf.yml]'
galaxy.tools WARNING 2026-09-17 16:21:20,148 [pN:main.1,p:70319,tN:Thread-2] The default shed tool config file (/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file
galaxy.tool_util.toolbox.base INFO 2026-09-17 16:21:20,149 [pN:main.1,p:70319,tN:Thread-2] Parsing the tool configuration /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/shed_tools_conf.xml
galaxy.tool_util.toolbox.base DEBUG 2026-09-17 16:21:20,150 [pN:main.1,p:70319,tN:Thread-2] Tool path for shed tool configuration /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/shed_tools_conf.xml is /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/shed_tools
galaxy.tools WARNING 2026-09-17 16:21:20,151 [pN:main.1,p:70319,tN:Thread-2] The default shed tool config file (/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file
galaxy.tool_util.toolbox.base INFO 2026-09-17 16:21:20,151 [pN:main.1,p:70319,tN:Thread-2] Parsing the tool configuration /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/empty_tool_conf.xml
galaxy.tool_util.toolbox.base DEBUG 2026-09-17 16:21:20,152 [pN:main.1,p:70319,tN:Thread-2] Tool path for tool configuration /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/empty_tool_conf.xml is None
galaxy.tool_util.toolbox.base DEBUG 2026-09-17 16:21:20,152 [pN:main.1,p:70319,tN:Thread-2] Reading tools from config files finished (24.514 ms)
galaxy.tool_util.toolbox.base DEBUG 2026-09-17 16:21:20,153 [pN:main.1,p:70319,tN:Thread-2] Loading section: Built-in Converters
galaxy.tool_util.toolbox.base DEBUG 2026-09-17 16:21:20,153 [pN:main.1,p:70319,tN:Thread-2] Loading section: Tools from workflows
galaxy.tool_util.toolbox.base DEBUG 2026-09-17 16:21:20,154 [pN:main.1,p:70319,tN:Thread-2] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.11b+galaxy1, version: 2.7.11b+galaxy1 into tool panel....
galaxy.tool_util.toolbox.base DEBUG 2026-09-17 16:21:20,154 [pN:main.1,p:70319,tN:Thread-2] Loading tool panel finished (1.150 ms)
galaxy.tool_util.toolbox.base DEBUG 2026-09-17 16:21:20,155 [pN:main.1,p:70319,tN:Thread-2] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.11b+galaxy1, version: 2.7.11b+galaxy1 into tool panel....
galaxy.tool_util.toolbox.views.edam DEBUG 2026-09-17 16:21:20,156 [pN:main.1,p:70319,tN:Thread-2] Loading EDAM tool panel finished (1.785 ms)
galaxy.tool_util.toolbox.base DEBUG 2026-09-17 16:21:20,157 [pN:main.1,p:70319,tN:Thread-2] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.11b+galaxy1, version: 2.7.11b+galaxy1 into tool panel....
galaxy.tool_util.toolbox.base DEBUG 2026-09-17 16:21:20,158 [pN:main.1,p:70319,tN:Thread-2] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.11b+galaxy1, version: 2.7.11b+galaxy1 into tool panel....
galaxy.tool_util.toolbox.views.edam DEBUG 2026-09-17 16:21:20,158 [pN:main.1,p:70319,tN:Thread-2] Loading EDAM tool panel finished (1.629 ms)
galaxy.tool_util.toolbox.integrated_panel DEBUG 2026-09-17 16:21:20,158 [pN:main.1,p:70319,tN:Thread-2] Writing integrated tool panel config file to '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/integrated_tool_panel_conf.xml'
galaxy.tool_util.toolbox.base DEBUG 2026-09-17 16:21:20,160 [pN:main.1,p:70319,tN:Thread-2] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.11b+galaxy1, version: 2.7.11b+galaxy1 into tool panel....
galaxy.tool_util.toolbox.views.edam DEBUG 2026-09-17 16:21:20,161 [pN:main.1,p:70319,tN:Thread-2] Loading EDAM tool panel finished (1.231 ms)
galaxy.tool_util.toolbox.base DEBUG 2026-09-17 16:21:20,162 [pN:main.1,p:70319,tN:Thread-2] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.11b+galaxy1, version: 2.7.11b+galaxy1 into tool panel....
galaxy.tool_util.toolbox.base DEBUG 2026-09-17 16:21:20,162 [pN:main.1,p:70319,tN:Thread-2] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.11b+galaxy1, version: 2.7.11b+galaxy1 into tool panel....
galaxy.tool_util.toolbox.views.edam DEBUG 2026-09-17 16:21:20,163 [pN:main.1,p:70319,tN:Thread-2] Loading EDAM tool panel finished (1.414 ms)
galaxy.datatypes.registry DEBUG 2026-09-17 16:21:20,167 [pN:main.1,p:70319,tN:Thread-2] Loaded external metadata tool: __SET_METADATA__
galaxy.tools.special_tools DEBUG 2026-09-17 16:21:20,168 [pN:main.1,p:70319,tN:Thread-2] Loaded history export tool: __EXPORT_HISTORY__
galaxy.tools.special_tools DEBUG 2026-09-17 16:21:20,169 [pN:main.1,p:70319,tN:Thread-2] Loaded history export to uri tool: __EXPORT_HISTORY_TO_URI__
galaxy.tools.special_tools DEBUG 2026-09-17 16:21:20,171 [pN:main.1,p:70319,tN:Thread-2] Loaded history import tool: __IMPORT_HISTORY__
galaxy.tools DEBUG 2026-09-17 16:21:20,171 [pN:main.1,p:70319,tN:Thread-2] No parameter model for tool '__DATA_FETCH__': Cannot generate a tool parameter model for upload_dataset inputs
galaxy.tools.special_tools DEBUG 2026-09-17 16:21:20,172 [pN:main.1,p:70319,tN:Thread-2] Loaded data fetch tool: __DATA_FETCH__
galaxy.queue_worker INFO 2026-09-17 16:21:20,172 [pN:main.1,p:70319,tN:Thread-2] Queuing async task rebuild_toolbox_search_index for main.1.
galaxy.queue_worker DEBUG 2026-09-17 16:21:20,174 [pN:main.1,p:70319,tN:Thread-2] Toolbox reload (52.856 ms)
galaxy.queue_worker INFO 2026-09-17 16:21:20,177 [pN:main.1,p:70319,tN:Thread-2] Instance 'main.1' received 'rebuild_toolbox_search_index' task, executing now.
galaxy.tools.search DEBUG 2026-09-17 16:21:20,178 [pN:main.1,p:70319,tN:Thread-2] Starting to build toolbox index of panel default.
galaxy.tools.search DEBUG 2026-09-17 16:21:20,210 [pN:main.1,p:70319,tN:Thread-2] Toolbox index of panel default finished (31.574 ms)
galaxy.tools.search DEBUG 2026-09-17 16:21:20,210 [pN:main.1,p:70319,tN:Thread-2] Starting to build toolbox index of panel my_panel.
galaxy.tools.search DEBUG 2026-09-17 16:21:20,212 [pN:main.1,p:70319,tN:Thread-2] Toolbox index of panel my_panel finished (1.698 ms)
galaxy.tools.search DEBUG 2026-09-17 16:21:20,212 [pN:main.1,p:70319,tN:Thread-2] Starting to build toolbox index of panel ontology:edam_operations.
galaxy.tools.search DEBUG 2026-09-17 16:21:20,240 [pN:main.1,p:70319,tN:Thread-2] Toolbox index of panel ontology:edam_operations finished (27.668 ms)
galaxy.tools.search DEBUG 2026-09-17 16:21:20,241 [pN:main.1,p:70319,tN:Thread-2] Starting to build toolbox index of panel ontology:edam_topics.
galaxy.app DEBUG 2026-09-17 16:21:20,261 [pN:main.1,p:70319,tN:WSGI_0] Finished waiting for toolbox reload (1192.421 ms)
galaxy.tool_util.deps.conda_util DEBUG 2026-09-17 16:21:20,263 [pN:main.1,p:70319,tN:WSGI_0] Executing command: /Users/mvandenb/src/worktrees/.planemo-home/conda/bin/conda create -y --quiet --strict-channel-priority --solver libmamba --override-channels --channel conda-forge --channel bioconda --name mulled-v1-2587c2c4c73f06c66693919d27659bb7b97e119c8d24463373752affcf535671 star=2.7.11b samtools=1.18 gzip=1.13
galaxy.tools.search DEBUG 2026-09-17 16:21:20,302 [pN:main.1,p:70319,tN:Thread-2] Toolbox index of panel ontology:edam_topics finished (61.839 ms)
galaxy.queue_worker INFO 2026-09-17 16:21:20,818 [pN:main.1,p:70319,tN:Thread-4 (check)] Sending reload_toolbox control task.
galaxy.tool_util.deps.conda_util DEBUG 2026-09-17 16:21:21,389 [pN:main.1,p:70319,tN:WSGI_0] Executing command: /Users/mvandenb/src/worktrees/.planemo-home/conda/bin/conda create -y --quiet --solver libmamba --override-channels --channel conda-forge --channel bioconda --name mulled-v1-2587c2c4c73f06c66693919d27659bb7b97e119c8d24463373752affcf535671 star=2.7.11b samtools=1.18 gzip=1.13
galaxy.tool_util.deps.resolvers.conda DEBUG 2026-09-17 16:21:22,027 [pN:main.1,p:70319,tN:WSGI_0] Removing failed conda install of [CondaTarget[package=star,version=2.7.11b], CondaTarget[package=samtools,version=1.18], CondaTarget[package=gzip,version=1.13]]
galaxy.tool_util.deps.conda_util DEBUG 2026-09-17 16:21:22,028 [pN:main.1,p:70319,tN:WSGI_0] Executing command: /Users/mvandenb/src/worktrees/.planemo-home/conda/bin/conda create -y --quiet --strict-channel-priority --solver libmamba --override-channels --channel conda-forge --channel bioconda --name __star@2.7.11b star=2.7.11b
galaxy.tool_util.deps DEBUG 2026-09-17 16:21:24,558 [pN:main.1,p:70319,tN:WSGI_0] Using dependency star version 2.7.11b of type conda
galaxy.tool_util.deps.conda_util DEBUG 2026-09-17 16:21:24,559 [pN:main.1,p:70319,tN:WSGI_0] Executing command: /Users/mvandenb/src/worktrees/.planemo-home/conda/bin/conda create -y --quiet --strict-channel-priority --solver libmamba --override-channels --channel conda-forge --channel bioconda --name __samtools@1.18 samtools=1.18
galaxy.tool_util.deps.conda_util DEBUG 2026-09-17 16:21:25,543 [pN:main.1,p:70319,tN:WSGI_0] Executing command: /Users/mvandenb/src/worktrees/.planemo-home/conda/bin/conda create -y --quiet --solver libmamba --override-channels --channel conda-forge --channel bioconda --name __samtools@1.18 samtools=1.18
galaxy.tool_util.deps.resolvers.conda DEBUG 2026-09-17 16:21:26,112 [pN:main.1,p:70319,tN:WSGI_0] Removing failed conda install of samtools, version '1.18'
galaxy.tool_util.deps.conda_util DEBUG 2026-09-17 16:21:26,113 [pN:main.1,p:70319,tN:WSGI_0] Executing command: /Users/mvandenb/src/worktrees/.planemo-home/conda/bin/conda create -y --quiet --strict-channel-priority --solver libmamba --override-channels --channel conda-forge --channel bioconda --name __gzip@1.13 gzip=1.13
galaxy.tool_util.deps DEBUG 2026-09-17 16:21:27,280 [pN:main.1,p:70319,tN:WSGI_0] Using dependency gzip version 1.13 of type conda
galaxy.tool_util.deps.conda_util DEBUG 2026-09-17 16:21:27,715 [pN:main.1,p:70319,tN:WSGI_0] Executing command: /Users/mvandenb/src/worktrees/.planemo-home/conda/bin/conda list -f --json conda-libmamba-solver > '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/tmp/tmpbcrtayzr'
galaxy.tool_util.deps.conda_util DEBUG 2026-09-17 16:21:28,207 [pN:main.1,p:70319,tN:WSGI_0] Executing command: /Users/mvandenb/src/worktrees/.planemo-home/conda/bin/conda create -y --quiet --strict-channel-priority --solver libmamba --override-channels --channel conda-forge --channel bioconda --name __samtools@_uv_ 'samtools=*'
galaxy.tool_util.deps DEBUG 2026-09-17 16:21:30,543 [pN:main.1,p:70319,tN:WSGI_0] Using dependency samtools version None of type conda
galaxy.tool_util.deps.conda_util DEBUG 2026-09-17 16:21:30,544 [pN:main.1,p:70319,tN:WSGI_0] Executing command: /Users/mvandenb/src/worktrees/.planemo-home/conda/bin/conda create -y --quiet --strict-channel-priority --solver libmamba --override-channels --channel conda-forge --channel bioconda --name mulled-v1-2587c2c4c73f06c66693919d27659bb7b97e119c8d24463373752affcf535671 star=2.7.11b samtools=1.18 gzip=1.13
galaxy.tool_util.deps.conda_util DEBUG 2026-09-17 16:21:31,547 [pN:main.1,p:70319,tN:WSGI_0] Executing command: /Users/mvandenb/src/worktrees/.planemo-home/conda/bin/conda create -y --quiet --solver libmamba --override-channels --channel conda-forge --channel bioconda --name mulled-v1-2587c2c4c73f06c66693919d27659bb7b97e119c8d24463373752affcf535671 star=2.7.11b samtools=1.18 gzip=1.13
galaxy.tool_util.deps.resolvers.conda DEBUG 2026-09-17 16:21:32,179 [pN:main.1,p:70319,tN:WSGI_0] Removing failed conda install of [CondaTarget[package=star,version=2.7.11b], CondaTarget[package=samtools,version=1.18], CondaTarget[package=gzip,version=1.13]]
galaxy.tool_util.deps DEBUG 2026-09-17 16:21:32,180 [pN:main.1,p:70319,tN:WSGI_0] Using dependency star version 2.7.11b of type conda
galaxy.tool_util.deps.conda_util DEBUG 2026-09-17 16:21:32,180 [pN:main.1,p:70319,tN:WSGI_0] Executing command: /Users/mvandenb/src/worktrees/.planemo-home/conda/bin/conda create -y --quiet --strict-channel-priority --solver libmamba --override-channels --channel conda-forge --channel bioconda --name __samtools@1.18 samtools=1.18
galaxy.tool_util.deps.conda_util DEBUG 2026-09-17 16:21:32,793 [pN:main.1,p:70319,tN:WSGI_0] Executing command: /Users/mvandenb/src/worktrees/.planemo-home/conda/bin/conda create -y --quiet --solver libmamba --override-channels --channel conda-forge --channel bioconda --name __samtools@1.18 samtools=1.18
galaxy.tool_util.deps.resolvers.conda DEBUG 2026-09-17 16:21:33,356 [pN:main.1,p:70319,tN:WSGI_0] Removing failed conda install of samtools, version '1.18'
galaxy.tool_util.deps DEBUG 2026-09-17 16:21:33,357 [pN:main.1,p:70319,tN:WSGI_0] Using dependency gzip version 1.13 of type conda
galaxy.tool_util.deps DEBUG 2026-09-17 16:21:33,357 [pN:main.1,p:70319,tN:WSGI_0] Using dependency samtools version None of type conda
galaxy.tool_util.deps.conda_util DEBUG 2026-09-17 16:21:33,357 [pN:main.1,p:70319,tN:WSGI_0] Executing command: /Users/mvandenb/src/worktrees/.planemo-home/conda/bin/conda list --name __star@2.7.11b --export > '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/tmp/jobdeps6ucw_gyoc050b36be0996747a28b73bfd6b802b81b06580abdb09bcc585df744f846f9a5/__star@2.7.11b'
galaxy.tool_util.deps.conda_util DEBUG 2026-09-17 16:21:33,789 [pN:main.1,p:70319,tN:WSGI_0] Executing command: /Users/mvandenb/src/worktrees/.planemo-home/conda/bin/conda create -y --quiet --strict-channel-priority --solver libmamba --override-channels --channel conda-forge --channel bioconda --unknown --offline --prefix /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/deps/_cache/f0eb3b2c --file /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/tmp/jobdeps6ucw_gyoc050b36be0996747a28b73bfd6b802b81b06580abdb09bcc585df744f846f9a5/__star@2.7.11b
galaxy.tool_util.deps.conda_util DEBUG 2026-09-17 16:21:35,885 [pN:main.1,p:70319,tN:WSGI_0] Executing command: /Users/mvandenb/src/worktrees/.planemo-home/conda/bin/conda clean --tarballs -y
galaxy.tool_util.deps.conda_util DEBUG 2026-09-17 16:21:36,737 [pN:main.1,p:70319,tN:WSGI_0] Executing command: /Users/mvandenb/src/worktrees/.planemo-home/conda/bin/conda list --name __gzip@1.13 --export > '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/tmp/jobdepsde29ov2m3886499b5cdedeb5cad0d2661fc7992519aa7a3f8b33e7359587a29b73ba1c38/__gzip@1.13'
galaxy.tool_util.deps.conda_util DEBUG 2026-09-17 16:21:37,133 [pN:main.1,p:70319,tN:WSGI_0] Executing command: /Users/mvandenb/src/worktrees/.planemo-home/conda/bin/conda install -y --strict-channel-priority --solver libmamba --override-channels --channel conda-forge --channel bioconda --unknown --offline --prefix /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/deps/_cache/f0eb3b2c --file /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/tmp/jobdepsde29ov2m3886499b5cdedeb5cad0d2661fc7992519aa7a3f8b33e7359587a29b73ba1c38/__gzip@1.13
galaxy.tool_util.deps.conda_util DEBUG 2026-09-17 16:21:37,719 [pN:main.1,p:70319,tN:WSGI_0] Executing command: /Users/mvandenb/src/worktrees/.planemo-home/conda/bin/conda clean --tarballs -y
galaxy.tool_util.deps.conda_util DEBUG 2026-09-17 16:21:38,123 [pN:main.1,p:70319,tN:WSGI_0] Executing command: /Users/mvandenb/src/worktrees/.planemo-home/conda/bin/conda list --name __samtools@_uv_ --export > '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/tmp/jobdepsd07bmom6373e7bbee36e032187809f77033895b78158b1575365caf0cada674b44d010b8/__samtools@_uv_'
galaxy.tool_util.deps.conda_util DEBUG 2026-09-17 16:21:38,557 [pN:main.1,p:70319,tN:WSGI_0] Executing command: /Users/mvandenb/src/worktrees/.planemo-home/conda/bin/conda install -y --strict-channel-priority --solver libmamba --override-channels --channel conda-forge --channel bioconda --unknown --offline --prefix /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/deps/_cache/f0eb3b2c --file /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/tmp/jobdepsd07bmom6373e7bbee36e032187809f77033895b78158b1575365caf0cada674b44d010b8/__samtools@_uv_
galaxy.tool_util.deps.conda_util DEBUG 2026-09-17 16:21:39,085 [pN:main.1,p:70319,tN:WSGI_0] Executing command: /Users/mvandenb/src/worktrees/.planemo-home/conda/bin/conda install -y --solver libmamba --override-channels --channel conda-forge --channel bioconda --unknown --offline --prefix /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/deps/_cache/f0eb3b2c --file /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/tmp/jobdepsd07bmom6373e7bbee36e032187809f77033895b78158b1575365caf0cada674b44d010b8/__samtools@_uv_
galaxy.tool_util.deps.conda_util DEBUG 2026-09-17 16:21:39,615 [pN:main.1,p:70319,tN:WSGI_0] Executing command: /Users/mvandenb/src/worktrees/.planemo-home/conda/bin/conda clean --tarballs -y
galaxy.tool_shed.galaxy_install.install_manager ERROR 2026-09-17 16:21:40,015 [pN:main.1,p:70319,tN:WSGI_0] Error installing repository 'rgrnastar'
Traceback (most recent call last):
  File "/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/galaxy-dev/lib/galaxy/tool_shed/galaxy_install/install_manager.py", line 520, in install_repositories
    self.install_tool_shed_repository(
  File "/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/galaxy-dev/lib/galaxy/tool_shed/galaxy_install/install_manager.py", line 652, in install_tool_shed_repository
    [dependency_manager.build_cache(r) for r in new_requirements]
     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/galaxy-dev/lib/galaxy/tool_util/deps/__init__.py", line 418, in build_cache
    [dep.build_cache(hashed_dependencies_dir) for dep in cacheable_dependencies]
     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/galaxy-dev/lib/galaxy/tool_util/deps/resolvers/conda.py", line 495, in build_cache
    self.build_environment()
  File "/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/galaxy-dev/lib/galaxy/tool_util/deps/resolvers/conda.py", line 511, in build_environment
    raise DependencyException(
galaxy.tool_util.deps.resolvers.DependencyException: Conda dependency failed to build job environment. This is most likely a limitation in conda. You can try to shorten the path to the job_working_directory.
galaxy.tool_shed.util.repository_util DEBUG 2026-09-17 16:21:40,031 [pN:main.1,p:70319,tN:WSGI_0] Removed repository installation directory: /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/shed_tools/toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/d8d32326fbfb
galaxy.tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager DEBUG 2026-09-17 16:21:40,743 [pN:main.1,p:70319,tN:WSGI_0] Creating repository dependency objects...
galaxy.tools.cache DEBUG 2026-09-17 16:21:41,012 [pN:main.1,p:70319,tN:Thread-4 (check)] Removed the following tools from cache: ['toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.11b+galaxy1', 'toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star', 'rna_star']
galaxy.queue_worker INFO 2026-09-17 16:21:41,015 [pN:main.1,p:70319,tN:Thread-4 (check)] Queuing sync task reload_toolbox for main.1.
galaxy.queue_worker INFO 2026-09-17 16:21:41,557 [pN:main.1,p:70319,tN:Thread-2] Instance 'main.1' received 'reload_toolbox' task, executing now.
galaxy.queue_worker DEBUG 2026-09-17 16:21:41,558 [pN:main.1,p:70319,tN:Thread-2] Executing toolbox reload on 'main.1'
galaxy.util WARNING 2026-09-17 16:21:41,560 [pN:main.1,p:70319,tN:Thread-2] directory not found: /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/galaxy-dev/config/plugins/activities
galaxy.tools WARNING 2026-09-17 16:21:41,562 [pN:main.1,p:70319,tN:Thread-2] The default shed tool config file (/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file
galaxy.tool_util.toolbox.base INFO 2026-09-17 16:21:41,563 [pN:main.1,p:70319,tN:Thread-2] Parsing the tool configuration /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/tool_conf.xml
galaxy.tool_util.toolbox.base DEBUG 2026-09-17 16:21:41,564 [pN:main.1,p:70319,tN:Thread-2] Tool path for tool configuration /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/tool_conf.xml is None
galaxy.tool_util.parser.factory INFO 2026-09-17 16:21:41,565 [pN:main.1,p:70319,tN:Thread-2] Loading tool from YAML - this is experimental - tool will not function in future.
galaxy.tool_util.toolbox.base ERROR 2026-09-17 16:21:41,577 [pN:main.1,p:70319,tN:Thread-2] Error reading tool from path: /Users/mvandenb/src/worktrees/foundry/brc-c-auris/.foundry-runs/auris-scf1/galaxy-workflow.gxwf.yml
Traceback (most recent call last):
  File "/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/galaxy-dev/lib/galaxy/tool_util/toolbox/base.py", line 967, in _load_tool_tag_set
    tool = self.load_tool(concrete_path, use_cached=False)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/galaxy-dev/lib/galaxy/tool_util/toolbox/base.py", line 1222, in load_tool
    tool = self.create_tool(
           ^^^^^^^^^^^^^^^^^
  File "/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/galaxy-dev/lib/galaxy/tools/__init__.py", line 619, in create_tool
    return self._create_tool_from_source(tool_source, config_file=config_file, **kwds)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/galaxy-dev/lib/galaxy/tools/__init__.py", line 634, in _create_tool_from_source
    return create_tool_from_source(self.app, tool_source, **kwds)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/galaxy-dev/lib/galaxy/tools/__init__.py", line 448, in create_tool_from_source
    tool = ToolClass(config_file, tool_source, app, **kwds)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/galaxy-dev/lib/galaxy/tools/__init__.py", line 1099, in __init__
    raise e
  File "/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/galaxy-dev/lib/galaxy/tools/__init__.py", line 1096, in __init__
    self.parse(tool_source, guid=guid, dynamic=dynamic)
  File "/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/galaxy-dev/lib/galaxy/tools/__init__.py", line 1329, in parse
    raise Exception(f"Missing tool 'id' for tool at '{tool_source}'")
Exception: Missing tool 'id' for tool at 'YamlToolSource[/Users/mvandenb/src/worktrees/foundry/brc-c-auris/.foundry-runs/auris-scf1/galaxy-workflow.gxwf.yml]'
galaxy.tools WARNING 2026-09-17 16:21:41,578 [pN:main.1,p:70319,tN:Thread-2] The default shed tool config file (/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file
galaxy.tool_util.toolbox.base INFO 2026-09-17 16:21:41,579 [pN:main.1,p:70319,tN:Thread-2] Parsing the tool configuration /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/shed_tools_conf.xml
galaxy.tool_util.toolbox.base DEBUG 2026-09-17 16:21:41,580 [pN:main.1,p:70319,tN:Thread-2] Tool path for shed tool configuration /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/shed_tools_conf.xml is /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/shed_tools
galaxy.tool_util.toolbox.base ERROR 2026-09-17 16:21:41,580 [pN:main.1,p:70319,tN:Thread-2] Error reading tool configuration file from path 'toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/d8d32326fbfb/rgrnastar/rg_rnaStar.xml': [Errno 2] No such file or directory
galaxy.tools WARNING 2026-09-17 16:21:41,581 [pN:main.1,p:70319,tN:Thread-2] The default shed tool config file (/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file
galaxy.tool_util.toolbox.base INFO 2026-09-17 16:21:41,581 [pN:main.1,p:70319,tN:Thread-2] Parsing the tool configuration /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/empty_tool_conf.xml
galaxy.tool_util.toolbox.base DEBUG 2026-09-17 16:21:41,582 [pN:main.1,p:70319,tN:Thread-2] Tool path for tool configuration /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/empty_tool_conf.xml is None
galaxy.tool_util.toolbox.base DEBUG 2026-09-17 16:21:41,582 [pN:main.1,p:70319,tN:Thread-2] Reading tools from config files finished (20.092 ms)
galaxy.tool_util.toolbox.base DEBUG 2026-09-17 16:21:41,583 [pN:main.1,p:70319,tN:Thread-2] Loading section: Built-in Converters
galaxy.tool_util.toolbox.base DEBUG 2026-09-17 16:21:41,583 [pN:main.1,p:70319,tN:Thread-2] Loading section: Tools from workflows
galaxy.tool_util.toolbox.base DEBUG 2026-09-17 16:21:41,583 [pN:main.1,p:70319,tN:Thread-2] Loading tool panel finished (0.705 ms)
galaxy.tool_util.toolbox.views.edam DEBUG 2026-09-17 16:21:41,585 [pN:main.1,p:70319,tN:Thread-2] Loading EDAM tool panel finished (1.113 ms)
galaxy.tool_util.toolbox.views.edam DEBUG 2026-09-17 16:21:41,586 [pN:main.1,p:70319,tN:Thread-2] Loading EDAM tool panel finished (0.754 ms)
galaxy.tool_util.toolbox.integrated_panel DEBUG 2026-09-17 16:21:41,586 [pN:main.1,p:70319,tN:Thread-2] Writing integrated tool panel config file to '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/integrated_tool_panel_conf.xml'
galaxy.tool_util.toolbox.views.edam DEBUG 2026-09-17 16:21:41,588 [pN:main.1,p:70319,tN:Thread-2] Loading EDAM tool panel finished (0.749 ms)
galaxy.tool_util.toolbox.views.edam DEBUG 2026-09-17 16:21:41,589 [pN:main.1,p:70319,tN:Thread-2] Loading EDAM tool panel finished (0.715 ms)
galaxy.datatypes.registry DEBUG 2026-09-17 16:21:41,593 [pN:main.1,p:70319,tN:Thread-2] Loaded external metadata tool: __SET_METADATA__
galaxy.tools.special_tools DEBUG 2026-09-17 16:21:41,594 [pN:main.1,p:70319,tN:Thread-2] Loaded history export tool: __EXPORT_HISTORY__
galaxy.tools.special_tools DEBUG 2026-09-17 16:21:41,595 [pN:main.1,p:70319,tN:Thread-2] Loaded history export to uri tool: __EXPORT_HISTORY_TO_URI__
galaxy.tools.special_tools DEBUG 2026-09-17 16:21:41,596 [pN:main.1,p:70319,tN:Thread-2] Loaded history import tool: __IMPORT_HISTORY__
galaxy.tools DEBUG 2026-09-17 16:21:41,597 [pN:main.1,p:70319,tN:Thread-2] No parameter model for tool '__DATA_FETCH__': Cannot generate a tool parameter model for upload_dataset inputs
galaxy.tools.special_tools DEBUG 2026-09-17 16:21:41,597 [pN:main.1,p:70319,tN:Thread-2] Loaded data fetch tool: __DATA_FETCH__
galaxy.queue_worker INFO 2026-09-17 16:21:41,598 [pN:main.1,p:70319,tN:Thread-2] Queuing async task rebuild_toolbox_search_index for main.1.
galaxy.queue_worker DEBUG 2026-09-17 16:21:41,600 [pN:main.1,p:70319,tN:Thread-2] Toolbox reload (41.599 ms)
galaxy.queue_worker INFO 2026-09-17 16:21:41,603 [pN:main.1,p:70319,tN:Thread-2] Instance 'main.1' received 'rebuild_toolbox_search_index' task, executing now.
galaxy.tools.search DEBUG 2026-09-17 16:21:41,603 [pN:main.1,p:70319,tN:Thread-2] Starting to build toolbox index of panel default.
galaxy.tools.search DEBUG 2026-09-17 16:21:41,632 [pN:main.1,p:70319,tN:Thread-2] Toolbox index of panel default finished (28.282 ms)
galaxy.tools.search DEBUG 2026-09-17 16:21:41,632 [pN:main.1,p:70319,tN:Thread-2] Starting to build toolbox index of panel my_panel.
galaxy.tools.search DEBUG 2026-09-17 16:21:41,634 [pN:main.1,p:70319,tN:Thread-2] Toolbox index of panel my_panel finished (2.126 ms)
galaxy.tools.search DEBUG 2026-09-17 16:21:41,635 [pN:main.1,p:70319,tN:Thread-2] Starting to build toolbox index of panel ontology:edam_operations.
galaxy.tools.search DEBUG 2026-09-17 16:21:41,651 [pN:main.1,p:70319,tN:Thread-2] Toolbox index of panel ontology:edam_operations finished (16.462 ms)
galaxy.tools.search DEBUG 2026-09-17 16:21:41,652 [pN:main.1,p:70319,tN:Thread-2] Starting to build toolbox index of panel ontology:edam_topics.
galaxy.tools.search DEBUG 2026-09-17 16:21:41,668 [pN:main.1,p:70319,tN:Thread-2] Toolbox index of panel ontology:edam_topics finished (15.636 ms)
galaxy.queue_worker INFO 2026-09-17 16:21:42,039 [pN:main.1,p:70319,tN:Thread-4 (check)] Sending reload_toolbox control task.
galaxy.tool_util.toolbox.base DEBUG 2026-09-17 16:21:42,114 [pN:main.1,p:70319,tN:WSGI_0] Appending to tool panel section: Tools from workflows
galaxy.tool_shed.util.repository_util DEBUG 2026-09-17 16:21:42,115 [pN:main.1,p:70319,tN:WSGI_0] Adding new row for repository 'map_param_value' in the tool_shed_repository table, status set to 'installation_status.NEW'.
galaxy.tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager DEBUG 2026-09-17 16:21:42,118 [pN:main.1,p:70319,tN:WSGI_0] Building repository dependency relationships...
galaxy.tool_util.toolbox.base DEBUG 2026-09-17 16:21:42,119 [pN:main.1,p:70319,tN:WSGI_0] Appending to tool panel section: Tools from workflows
galaxy.tool_util.toolbox.base DEBUG 2026-09-17 16:21:42,125 [pN:main.1,p:70319,tN:WSGI_0] Appending to tool panel section: Tools from workflows
galaxy.tool_shed.galaxy_install.install_manager INFO 2026-09-17 16:21:42,134 [pN:main.1,p:70319,tN:WSGI_0] Cloning repository 'https://toolshed.g2.bx.psu.edu/repos/iuc/map_param_value' at 3:022a635f2283
charset_normalizer DEBUG 2026-09-17 16:21:43,757 [pN:main.1,p:70319,tN:WSGI_0] Encoding detection: ascii is most likely the one.
galaxy.tool_util.toolbox.base DEBUG 2026-09-17 16:21:43,815 [pN:main.1,p:70319,tN:WSGI_0] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.2.0, version: 0.2.0 into tool panel....
galaxy.tool_util.toolbox.integrated_panel DEBUG 2026-09-17 16:21:43,815 [pN:main.1,p:70319,tN:WSGI_0] Writing integrated tool panel config file to '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/integrated_tool_panel_conf.xml'
galaxy.app DEBUG 2026-09-17 16:21:43,817 [pN:main.1,p:70319,tN:WSGI_0] Waiting for toolbox reload
galaxy.tool_util.toolbox.watcher DEBUG 2026-09-17 16:21:44,069 [pN:main.1,p:70319,tN:Thread-4 (check)] The file '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/shed_tools_conf.xml' has changes.
galaxy.queue_worker INFO 2026-09-17 16:21:44,071 [pN:main.1,p:70319,tN:Thread-4 (check)] Queuing sync task reload_toolbox for main.1.
galaxy.queue_worker INFO 2026-09-17 16:21:44,722 [pN:main.1,p:70319,tN:Thread-2] Instance 'main.1' received 'reload_toolbox' task, executing now.
galaxy.queue_worker DEBUG 2026-09-17 16:21:44,724 [pN:main.1,p:70319,tN:Thread-2] Executing toolbox reload on 'main.1'
galaxy.util WARNING 2026-09-17 16:21:44,727 [pN:main.1,p:70319,tN:Thread-2] directory not found: /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/galaxy-dev/config/plugins/activities
galaxy.tools WARNING 2026-09-17 16:21:44,729 [pN:main.1,p:70319,tN:Thread-2] The default shed tool config file (/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file
galaxy.tool_util.toolbox.base INFO 2026-09-17 16:21:44,730 [pN:main.1,p:70319,tN:Thread-2] Parsing the tool configuration /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/tool_conf.xml
galaxy.tool_util.toolbox.base DEBUG 2026-09-17 16:21:44,731 [pN:main.1,p:70319,tN:Thread-2] Tool path for tool configuration /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/tool_conf.xml is None
galaxy.tool_util.parser.factory INFO 2026-09-17 16:21:44,732 [pN:main.1,p:70319,tN:Thread-2] Loading tool from YAML - this is experimental - tool will not function in future.
galaxy.tool_util.toolbox.base ERROR 2026-09-17 16:21:44,747 [pN:main.1,p:70319,tN:Thread-2] Error reading tool from path: /Users/mvandenb/src/worktrees/foundry/brc-c-auris/.foundry-runs/auris-scf1/galaxy-workflow.gxwf.yml
Traceback (most recent call last):
  File "/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/galaxy-dev/lib/galaxy/tool_util/toolbox/base.py", line 967, in _load_tool_tag_set
    tool = self.load_tool(concrete_path, use_cached=False)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/galaxy-dev/lib/galaxy/tool_util/toolbox/base.py", line 1222, in load_tool
    tool = self.create_tool(
           ^^^^^^^^^^^^^^^^^
  File "/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/galaxy-dev/lib/galaxy/tools/__init__.py", line 619, in create_tool
    return self._create_tool_from_source(tool_source, config_file=config_file, **kwds)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/galaxy-dev/lib/galaxy/tools/__init__.py", line 634, in _create_tool_from_source
    return create_tool_from_source(self.app, tool_source, **kwds)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/galaxy-dev/lib/galaxy/tools/__init__.py", line 448, in create_tool_from_source
    tool = ToolClass(config_file, tool_source, app, **kwds)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/galaxy-dev/lib/galaxy/tools/__init__.py", line 1099, in __init__
    raise e
  File "/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/galaxy-dev/lib/galaxy/tools/__init__.py", line 1096, in __init__
    self.parse(tool_source, guid=guid, dynamic=dynamic)
  File "/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/galaxy-dev/lib/galaxy/tools/__init__.py", line 1329, in parse
    raise Exception(f"Missing tool 'id' for tool at '{tool_source}'")
Exception: Missing tool 'id' for tool at 'YamlToolSource[/Users/mvandenb/src/worktrees/foundry/brc-c-auris/.foundry-runs/auris-scf1/galaxy-workflow.gxwf.yml]'
galaxy.tools WARNING 2026-09-17 16:21:44,749 [pN:main.1,p:70319,tN:Thread-2] The default shed tool config file (/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file
galaxy.tool_util.toolbox.base INFO 2026-09-17 16:21:44,749 [pN:main.1,p:70319,tN:Thread-2] Parsing the tool configuration /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/shed_tools_conf.xml
galaxy.tool_util.toolbox.base DEBUG 2026-09-17 16:21:44,751 [pN:main.1,p:70319,tN:Thread-2] Tool path for shed tool configuration /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/shed_tools_conf.xml is /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/shed_tools
galaxy.tool_util.toolbox.base ERROR 2026-09-17 16:21:44,751 [pN:main.1,p:70319,tN:Thread-2] Error reading tool configuration file from path 'toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/d8d32326fbfb/rgrnastar/rg_rnaStar.xml': [Errno 2] No such file or directory
galaxy.tools WARNING 2026-09-17 16:21:44,752 [pN:main.1,p:70319,tN:Thread-2] The default shed tool config file (/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file
galaxy.tool_util.toolbox.base INFO 2026-09-17 16:21:44,752 [pN:main.1,p:70319,tN:Thread-2] Parsing the tool configuration /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/empty_tool_conf.xml
galaxy.tool_util.toolbox.base DEBUG 2026-09-17 16:21:44,753 [pN:main.1,p:70319,tN:Thread-2] Tool path for tool configuration /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/empty_tool_conf.xml is None
galaxy.tool_util.toolbox.base DEBUG 2026-09-17 16:21:44,754 [pN:main.1,p:70319,tN:Thread-2] Reading tools from config files finished (24.659 ms)
galaxy.tool_util.toolbox.base DEBUG 2026-09-17 16:21:44,754 [pN:main.1,p:70319,tN:Thread-2] Loading section: Built-in Converters
galaxy.tool_util.toolbox.base DEBUG 2026-09-17 16:21:44,754 [pN:main.1,p:70319,tN:Thread-2] Loading section: Tools from workflows
galaxy.tool_util.toolbox.base DEBUG 2026-09-17 16:21:44,755 [pN:main.1,p:70319,tN:Thread-2] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.2.0, version: 0.2.0 into tool panel....
galaxy.tool_util.toolbox.base DEBUG 2026-09-17 16:21:44,755 [pN:main.1,p:70319,tN:Thread-2] Loading tool panel finished (1.140 ms)
galaxy.tool_util.toolbox.base DEBUG 2026-09-17 16:21:44,757 [pN:main.1,p:70319,tN:Thread-2] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.2.0, version: 0.2.0 into tool panel....
galaxy.tool_util.toolbox.views.edam DEBUG 2026-09-17 16:21:44,757 [pN:main.1,p:70319,tN:Thread-2] Loading EDAM tool panel finished (1.645 ms)
galaxy.tool_util.toolbox.base DEBUG 2026-09-17 16:21:44,758 [pN:main.1,p:70319,tN:Thread-2] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.2.0, version: 0.2.0 into tool panel....
galaxy.tool_util.toolbox.views.edam DEBUG 2026-09-17 16:21:44,759 [pN:main.1,p:70319,tN:Thread-2] Loading EDAM tool panel finished (1.211 ms)
galaxy.tool_util.toolbox.integrated_panel DEBUG 2026-09-17 16:21:44,759 [pN:main.1,p:70319,tN:Thread-2] Writing integrated tool panel config file to '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/integrated_tool_panel_conf.xml'
galaxy.tool_util.toolbox.base DEBUG 2026-09-17 16:21:44,761 [pN:main.1,p:70319,tN:Thread-2] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.2.0, version: 0.2.0 into tool panel....
galaxy.tool_util.toolbox.views.edam DEBUG 2026-09-17 16:21:44,762 [pN:main.1,p:70319,tN:Thread-2] Loading EDAM tool panel finished (1.204 ms)
galaxy.tool_util.toolbox.base DEBUG 2026-09-17 16:21:44,763 [pN:main.1,p:70319,tN:Thread-2] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.2.0, version: 0.2.0 into tool panel....
galaxy.tool_util.toolbox.views.edam DEBUG 2026-09-17 16:21:44,763 [pN:main.1,p:70319,tN:Thread-2] Loading EDAM tool panel finished (1.061 ms)
galaxy.datatypes.registry DEBUG 2026-09-17 16:21:44,766 [pN:main.1,p:70319,tN:Thread-2] Loaded external metadata tool: __SET_METADATA__
galaxy.tools.special_tools DEBUG 2026-09-17 16:21:44,768 [pN:main.1,p:70319,tN:Thread-2] Loaded history export tool: __EXPORT_HISTORY__
galaxy.tools.special_tools DEBUG 2026-09-17 16:21:44,769 [pN:main.1,p:70319,tN:Thread-2] Loaded history export to uri tool: __EXPORT_HISTORY_TO_URI__
galaxy.tools.special_tools DEBUG 2026-09-17 16:21:44,770 [pN:main.1,p:70319,tN:Thread-2] Loaded history import tool: __IMPORT_HISTORY__
galaxy.tools DEBUG 2026-09-17 16:21:44,771 [pN:main.1,p:70319,tN:Thread-2] No parameter model for tool '__DATA_FETCH__': Cannot generate a tool parameter model for upload_dataset inputs
galaxy.tools.special_tools DEBUG 2026-09-17 16:21:44,772 [pN:main.1,p:70319,tN:Thread-2] Loaded data fetch tool: __DATA_FETCH__
galaxy.queue_worker INFO 2026-09-17 16:21:44,772 [pN:main.1,p:70319,tN:Thread-2] Queuing async task rebuild_toolbox_search_index for main.1.
galaxy.queue_worker DEBUG 2026-09-17 16:21:44,774 [pN:main.1,p:70319,tN:Thread-2] Toolbox reload (50.295 ms)
galaxy.queue_worker INFO 2026-09-17 16:21:44,777 [pN:main.1,p:70319,tN:Thread-2] Instance 'main.1' received 'rebuild_toolbox_search_index' task, executing now.
galaxy.tools.search DEBUG 2026-09-17 16:21:44,778 [pN:main.1,p:70319,tN:Thread-2] Starting to build toolbox index of panel default.
galaxy.tools.search DEBUG 2026-09-17 16:21:44,804 [pN:main.1,p:70319,tN:Thread-2] Toolbox index of panel default finished (25.799 ms)
galaxy.tools.search DEBUG 2026-09-17 16:21:44,804 [pN:main.1,p:70319,tN:Thread-2] Starting to build toolbox index of panel my_panel.
galaxy.tools.search DEBUG 2026-09-17 16:21:44,806 [pN:main.1,p:70319,tN:Thread-2] Toolbox index of panel my_panel finished (1.785 ms)
galaxy.tools.search DEBUG 2026-09-17 16:21:44,806 [pN:main.1,p:70319,tN:Thread-2] Starting to build toolbox index of panel ontology:edam_operations.
galaxy.tools.search DEBUG 2026-09-17 16:21:44,830 [pN:main.1,p:70319,tN:Thread-2] Toolbox index of panel ontology:edam_operations finished (23.297 ms)
galaxy.tools.search DEBUG 2026-09-17 16:21:44,830 [pN:main.1,p:70319,tN:Thread-2] Starting to build toolbox index of panel ontology:edam_topics.
galaxy.tools.search DEBUG 2026-09-17 16:21:44,853 [pN:main.1,p:70319,tN:Thread-2] Toolbox index of panel ontology:edam_topics finished (22.503 ms)
galaxy.app DEBUG 2026-09-17 16:21:44,872 [pN:main.1,p:70319,tN:WSGI_0] Finished waiting for toolbox reload (1054.892 ms)
galaxy.queue_worker INFO 2026-09-17 16:21:45,101 [pN:main.1,p:70319,tN:Thread-4 (check)] Sending reload_toolbox control task.
galaxy.tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager DEBUG 2026-09-17 16:21:45,599 [pN:main.1,p:70319,tN:WSGI_0] Creating repository dependency objects...
galaxy.tool_util.toolbox.base DEBUG 2026-09-17 16:21:46,996 [pN:main.1,p:70319,tN:WSGI_0] Appending to tool panel section: Tools from workflows
galaxy.tool_shed.util.repository_util DEBUG 2026-09-17 16:21:46,997 [pN:main.1,p:70319,tN:WSGI_0] Adding new row for repository 'featurecounts' in the tool_shed_repository table, status set to 'installation_status.NEW'.
galaxy.tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager DEBUG 2026-09-17 16:21:47,000 [pN:main.1,p:70319,tN:WSGI_0] Building repository dependency relationships...
galaxy.tool_util.toolbox.base DEBUG 2026-09-17 16:21:47,001 [pN:main.1,p:70319,tN:WSGI_0] Appending to tool panel section: Tools from workflows
galaxy.tool_util.toolbox.base DEBUG 2026-09-17 16:21:47,006 [pN:main.1,p:70319,tN:WSGI_0] Appending to tool panel section: Tools from workflows
galaxy.tool_shed.galaxy_install.install_manager INFO 2026-09-17 16:21:47,013 [pN:main.1,p:70319,tN:WSGI_0] Cloning repository 'https://toolshed.g2.bx.psu.edu/repos/iuc/featurecounts' at 36:37d067694d40
galaxy.tool_util.data DEBUG 2026-09-17 16:21:49,459 [pN:main.1,p:70319,tN:WSGI_0] Loaded 0 lines from '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/tmp/tmp-toolshed-gmfcrqmxia50a/gene_sets.loc' for 'gene_sets'
galaxy.tool_util.data DEBUG 2026-09-17 16:21:49,459 [pN:main.1,p:70319,tN:WSGI_0] Loaded tool data table 'gene_sets' from file '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/shed_tools/toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/37d067694d40/featurecounts/tool_data_table_conf.xml.sample'
galaxy.tool_util.data DEBUG 2026-09-17 16:21:49,459 [pN:main.1,p:70319,tN:WSGI_0] Loaded 4 lines from '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/tmp/tmp-toolshed-gmfcrqmxia50a/featurecounts_anno.loc' for 'featurecounts_anno'
galaxy.tool_util.data DEBUG 2026-09-17 16:21:49,460 [pN:main.1,p:70319,tN:WSGI_0] Loaded tool data table 'featurecounts_anno' from file '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/shed_tools/toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/37d067694d40/featurecounts/tool_data_table_conf.xml.sample'
galaxy.tool_util.data DEBUG 2026-09-17 16:21:49,558 [pN:main.1,p:70319,tN:WSGI_0] Loaded 0 lines from '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/tmp/tmp-toolshed-gmfcrqmxia50a/gene_sets.loc' for 'gene_sets'
galaxy.tool_util.data DEBUG 2026-09-17 16:21:49,558 [pN:main.1,p:70319,tN:WSGI_0] Loading another instance of data table 'gene_sets' from file '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/shed_tools/toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/37d067694d40/featurecounts/tool_data_table_conf.xml.sample', attempting to merge content.
galaxy.tool_util.data DEBUG 2026-09-17 16:21:49,558 [pN:main.1,p:70319,tN:WSGI_0] Loaded 4 lines from '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/tmp/tmp-toolshed-gmfcrqmxia50a/featurecounts_anno.loc' for 'featurecounts_anno'
galaxy.tool_util.data DEBUG 2026-09-17 16:21:49,558 [pN:main.1,p:70319,tN:WSGI_0] Loading another instance of data table 'featurecounts_anno' from file '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/shed_tools/toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/37d067694d40/featurecounts/tool_data_table_conf.xml.sample', attempting to merge content.
galaxy.tool_util.data WARNING 2026-09-17 16:21:49,559 [pN:main.1,p:70319,tN:WSGI_0] Attempted to add fields (['hg38', 'hg38']) to data table 'featurecounts_anno', but this entry already exists and allow_duplicates is False.
galaxy.tool_util.data WARNING 2026-09-17 16:21:49,559 [pN:main.1,p:70319,tN:WSGI_0] Attempted to add fields (['hg19', 'hg19']) to data table 'featurecounts_anno', but this entry already exists and allow_duplicates is False.
galaxy.tool_util.data WARNING 2026-09-17 16:21:49,559 [pN:main.1,p:70319,tN:WSGI_0] Attempted to add fields (['mm10', 'mm10']) to data table 'featurecounts_anno', but this entry already exists and allow_duplicates is False.
galaxy.tool_util.data WARNING 2026-09-17 16:21:49,560 [pN:main.1,p:70319,tN:WSGI_0] Attempted to add fields (['mm9', 'mm9']) to data table 'featurecounts_anno', but this entry already exists and allow_duplicates is False.
galaxy.tool_util.data DEBUG 2026-09-17 16:21:49,560 [pN:main.1,p:70319,tN:WSGI_0] Loaded 0 lines from '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/tmp/tmp-toolshed-gmfcrqmxia50a/gene_sets.loc' for 'gene_sets'
galaxy.tool_util.data DEBUG 2026-09-17 16:21:49,560 [pN:main.1,p:70319,tN:WSGI_0] Loading another instance of data table 'gene_sets' from file '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/shed_tools/toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/37d067694d40/featurecounts/tool_data_table_conf.xml.sample', attempting to merge content.
galaxy.tool_util.data DEBUG 2026-09-17 16:21:49,560 [pN:main.1,p:70319,tN:WSGI_0] Loaded 4 lines from '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/tmp/tmp-toolshed-gmfcrqmxia50a/featurecounts_anno.loc' for 'featurecounts_anno'
galaxy.tool_util.data DEBUG 2026-09-17 16:21:49,561 [pN:main.1,p:70319,tN:WSGI_0] Loading another instance of data table 'featurecounts_anno' from file '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/shed_tools/toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/37d067694d40/featurecounts/tool_data_table_conf.xml.sample', attempting to merge content.
galaxy.tool_util.data WARNING 2026-09-17 16:21:49,561 [pN:main.1,p:70319,tN:WSGI_0] Attempted to add fields (['hg38', 'hg38']) to data table 'featurecounts_anno', but this entry already exists and allow_duplicates is False.
galaxy.tool_util.data WARNING 2026-09-17 16:21:49,561 [pN:main.1,p:70319,tN:WSGI_0] Attempted to add fields (['hg19', 'hg19']) to data table 'featurecounts_anno', but this entry already exists and allow_duplicates is False.
galaxy.tool_util.data WARNING 2026-09-17 16:21:49,561 [pN:main.1,p:70319,tN:WSGI_0] Attempted to add fields (['mm10', 'mm10']) to data table 'featurecounts_anno', but this entry already exists and allow_duplicates is False.
galaxy.tool_util.data WARNING 2026-09-17 16:21:49,562 [pN:main.1,p:70319,tN:WSGI_0] Attempted to add fields (['mm9', 'mm9']) to data table 'featurecounts_anno', but this entry already exists and allow_duplicates is False.
charset_normalizer DEBUG 2026-09-17 16:21:50,028 [pN:main.1,p:70319,tN:WSGI_0] Encoding detection: ascii is most likely the one.
galaxy.tool_util.data DEBUG 2026-09-17 16:21:50,057 [pN:main.1,p:70319,tN:WSGI_0] Loaded 0 lines from '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/galaxy-dev/tool-data/shed/gene_sets.loc' for 'gene_sets'
galaxy.tool_util.data DEBUG 2026-09-17 16:21:50,057 [pN:main.1,p:70319,tN:WSGI_0] Loaded tool data table 'gene_sets' from file '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/galaxy-dev/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/37d067694d40/tool_data_table_conf.xml'
galaxy.tool_util.data DEBUG 2026-09-17 16:21:50,058 [pN:main.1,p:70319,tN:WSGI_0] Loaded 4 lines from '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/galaxy-dev/tool-data/shed/featurecounts_anno.loc' for 'featurecounts_anno'
galaxy.tool_util.data DEBUG 2026-09-17 16:21:50,058 [pN:main.1,p:70319,tN:WSGI_0] Loaded tool data table 'featurecounts_anno' from file '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/galaxy-dev/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/37d067694d40/tool_data_table_conf.xml'
galaxy.tool_util.toolbox.base DEBUG 2026-09-17 16:21:50,259 [pN:main.1,p:70319,tN:WSGI_0] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/2.1.1+galaxy1, version: 2.1.1+galaxy1 into tool panel....
galaxy.tool_util.toolbox.integrated_panel DEBUG 2026-09-17 16:21:50,259 [pN:main.1,p:70319,tN:WSGI_0] Writing integrated tool panel config file to '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/integrated_tool_panel_conf.xml'
galaxy.app DEBUG 2026-09-17 16:21:50,260 [pN:main.1,p:70319,tN:WSGI_0] Waiting for toolbox reload
galaxy.tool_util.toolbox.watcher DEBUG 2026-09-17 16:21:51,177 [pN:main.1,p:70319,tN:Thread-4 (check)] The file '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/shed_tools_conf.xml' has changes.
galaxy.queue_worker INFO 2026-09-17 16:21:51,179 [pN:main.1,p:70319,tN:Thread-4 (check)] Queuing sync task reload_toolbox for main.1.
galaxy.queue_worker INFO 2026-09-17 16:21:51,981 [pN:main.1,p:70319,tN:Thread-2] Instance 'main.1' received 'reload_toolbox' task, executing now.
galaxy.queue_worker DEBUG 2026-09-17 16:21:51,983 [pN:main.1,p:70319,tN:Thread-2] Executing toolbox reload on 'main.1'
galaxy.util WARNING 2026-09-17 16:21:51,987 [pN:main.1,p:70319,tN:Thread-2] directory not found: /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/galaxy-dev/config/plugins/activities
galaxy.tools WARNING 2026-09-17 16:21:51,990 [pN:main.1,p:70319,tN:Thread-2] The default shed tool config file (/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file
galaxy.tool_util.toolbox.base INFO 2026-09-17 16:21:51,991 [pN:main.1,p:70319,tN:Thread-2] Parsing the tool configuration /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/tool_conf.xml
galaxy.tool_util.toolbox.base DEBUG 2026-09-17 16:21:51,993 [pN:main.1,p:70319,tN:Thread-2] Tool path for tool configuration /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/tool_conf.xml is None
galaxy.tool_util.parser.factory INFO 2026-09-17 16:21:51,993 [pN:main.1,p:70319,tN:Thread-2] Loading tool from YAML - this is experimental - tool will not function in future.
galaxy.tool_util.toolbox.base ERROR 2026-09-17 16:21:52,009 [pN:main.1,p:70319,tN:Thread-2] Error reading tool from path: /Users/mvandenb/src/worktrees/foundry/brc-c-auris/.foundry-runs/auris-scf1/galaxy-workflow.gxwf.yml
Traceback (most recent call last):
  File "/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/galaxy-dev/lib/galaxy/tool_util/toolbox/base.py", line 967, in _load_tool_tag_set
    tool = self.load_tool(concrete_path, use_cached=False)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/galaxy-dev/lib/galaxy/tool_util/toolbox/base.py", line 1222, in load_tool
    tool = self.create_tool(
           ^^^^^^^^^^^^^^^^^
  File "/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/galaxy-dev/lib/galaxy/tools/__init__.py", line 619, in create_tool
    return self._create_tool_from_source(tool_source, config_file=config_file, **kwds)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/galaxy-dev/lib/galaxy/tools/__init__.py", line 634, in _create_tool_from_source
    return create_tool_from_source(self.app, tool_source, **kwds)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/galaxy-dev/lib/galaxy/tools/__init__.py", line 448, in create_tool_from_source
    tool = ToolClass(config_file, tool_source, app, **kwds)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/galaxy-dev/lib/galaxy/tools/__init__.py", line 1099, in __init__
    raise e
  File "/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/galaxy-dev/lib/galaxy/tools/__init__.py", line 1096, in __init__
    self.parse(tool_source, guid=guid, dynamic=dynamic)
  File "/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/galaxy-dev/lib/galaxy/tools/__init__.py", line 1329, in parse
    raise Exception(f"Missing tool 'id' for tool at '{tool_source}'")
Exception: Missing tool 'id' for tool at 'YamlToolSource[/Users/mvandenb/src/worktrees/foundry/brc-c-auris/.foundry-runs/auris-scf1/galaxy-workflow.gxwf.yml]'
galaxy.tools WARNING 2026-09-17 16:21:52,011 [pN:main.1,p:70319,tN:Thread-2] The default shed tool config file (/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file
galaxy.tool_util.toolbox.base INFO 2026-09-17 16:21:52,012 [pN:main.1,p:70319,tN:Thread-2] Parsing the tool configuration /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/shed_tools_conf.xml
galaxy.tool_util.toolbox.base DEBUG 2026-09-17 16:21:52,013 [pN:main.1,p:70319,tN:Thread-2] Tool path for shed tool configuration /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/shed_tools_conf.xml is /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/shed_tools
galaxy.tool_util.toolbox.base ERROR 2026-09-17 16:21:52,014 [pN:main.1,p:70319,tN:Thread-2] Error reading tool configuration file from path 'toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/d8d32326fbfb/rgrnastar/rg_rnaStar.xml': [Errno 2] No such file or directory
galaxy.tools WARNING 2026-09-17 16:21:52,014 [pN:main.1,p:70319,tN:Thread-2] The default shed tool config file (/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file
galaxy.tool_util.toolbox.base INFO 2026-09-17 16:21:52,015 [pN:main.1,p:70319,tN:Thread-2] Parsing the tool configuration /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/empty_tool_conf.xml
galaxy.tool_util.toolbox.base DEBUG 2026-09-17 16:21:52,016 [pN:main.1,p:70319,tN:Thread-2] Tool path for tool configuration /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/empty_tool_conf.xml is None
galaxy.tool_util.toolbox.base DEBUG 2026-09-17 16:21:52,016 [pN:main.1,p:70319,tN:Thread-2] Reading tools from config files finished (26.396 ms)
galaxy.tool_util.toolbox.base DEBUG 2026-09-17 16:21:52,017 [pN:main.1,p:70319,tN:Thread-2] Loading section: Built-in Converters
galaxy.tool_util.toolbox.base DEBUG 2026-09-17 16:21:52,017 [pN:main.1,p:70319,tN:Thread-2] Loading section: Tools from workflows
galaxy.tool_util.toolbox.base DEBUG 2026-09-17 16:21:52,017 [pN:main.1,p:70319,tN:Thread-2] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/2.1.1+galaxy1, version: 2.1.1+galaxy1 into tool panel....
galaxy.tool_util.toolbox.base DEBUG 2026-09-17 16:21:52,018 [pN:main.1,p:70319,tN:Thread-2] Loading tool panel finished (1.189 ms)
galaxy.tool_util.toolbox.base DEBUG 2026-09-17 16:21:52,020 [pN:main.1,p:70319,tN:Thread-2] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/2.1.1+galaxy1, version: 2.1.1+galaxy1 into tool panel....
galaxy.tool_util.toolbox.views.edam DEBUG 2026-09-17 16:21:52,020 [pN:main.1,p:70319,tN:Thread-2] Loading EDAM tool panel finished (1.715 ms)
galaxy.tool_util.toolbox.base DEBUG 2026-09-17 16:21:52,021 [pN:main.1,p:70319,tN:Thread-2] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/2.1.1+galaxy1, version: 2.1.1+galaxy1 into tool panel....
galaxy.tool_util.toolbox.views.edam DEBUG 2026-09-17 16:21:52,021 [pN:main.1,p:70319,tN:Thread-2] Loading EDAM tool panel finished (1.087 ms)
galaxy.tool_util.toolbox.integrated_panel DEBUG 2026-09-17 16:21:52,022 [pN:main.1,p:70319,tN:Thread-2] Writing integrated tool panel config file to '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/integrated_tool_panel_conf.xml'
galaxy.tool_util.toolbox.base DEBUG 2026-09-17 16:21:52,024 [pN:main.1,p:70319,tN:Thread-2] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/2.1.1+galaxy1, version: 2.1.1+galaxy1 into tool panel....
galaxy.tool_util.toolbox.views.edam DEBUG 2026-09-17 16:21:52,024 [pN:main.1,p:70319,tN:Thread-2] Loading EDAM tool panel finished (1.168 ms)
galaxy.tool_util.toolbox.base DEBUG 2026-09-17 16:21:52,025 [pN:main.1,p:70319,tN:Thread-2] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/2.1.1+galaxy1, version: 2.1.1+galaxy1 into tool panel....
galaxy.tool_util.toolbox.views.edam DEBUG 2026-09-17 16:21:52,026 [pN:main.1,p:70319,tN:Thread-2] Loading EDAM tool panel finished (1.081 ms)
galaxy.datatypes.registry DEBUG 2026-09-17 16:21:52,029 [pN:main.1,p:70319,tN:Thread-2] Loaded external metadata tool: __SET_METADATA__
galaxy.tools.special_tools DEBUG 2026-09-17 16:21:52,030 [pN:main.1,p:70319,tN:Thread-2] Loaded history export tool: __EXPORT_HISTORY__
galaxy.tools.special_tools DEBUG 2026-09-17 16:21:52,032 [pN:main.1,p:70319,tN:Thread-2] Loaded history export to uri tool: __EXPORT_HISTORY_TO_URI__
galaxy.tools.special_tools DEBUG 2026-09-17 16:21:52,033 [pN:main.1,p:70319,tN:Thread-2] Loaded history import tool: __IMPORT_HISTORY__
galaxy.tools DEBUG 2026-09-17 16:21:52,034 [pN:main.1,p:70319,tN:Thread-2] No parameter model for tool '__DATA_FETCH__': Cannot generate a tool parameter model for upload_dataset inputs
galaxy.tools.special_tools DEBUG 2026-09-17 16:21:52,034 [pN:main.1,p:70319,tN:Thread-2] Loaded data fetch tool: __DATA_FETCH__
galaxy.queue_worker INFO 2026-09-17 16:21:52,034 [pN:main.1,p:70319,tN:Thread-2] Queuing async task rebuild_toolbox_search_index for main.1.
galaxy.queue_worker DEBUG 2026-09-17 16:21:52,037 [pN:main.1,p:70319,tN:Thread-2] Toolbox reload (53.861 ms)
galaxy.queue_worker INFO 2026-09-17 16:21:52,040 [pN:main.1,p:70319,tN:Thread-2] Instance 'main.1' received 'rebuild_toolbox_search_index' task, executing now.
galaxy.tools.search DEBUG 2026-09-17 16:21:52,041 [pN:main.1,p:70319,tN:Thread-2] Starting to build toolbox index of panel default.
galaxy.app DEBUG 2026-09-17 16:21:52,058 [pN:main.1,p:70319,tN:WSGI_0] Finished waiting for toolbox reload (1797.567 ms)
galaxy.tools.search DEBUG 2026-09-17 16:21:52,178 [pN:main.1,p:70319,tN:Thread-2] Toolbox index of panel default finished (137.341 ms)
galaxy.tools.search DEBUG 2026-09-17 16:21:52,179 [pN:main.1,p:70319,tN:Thread-2] Starting to build toolbox index of panel my_panel.
galaxy.tools.search DEBUG 2026-09-17 16:21:52,182 [pN:main.1,p:70319,tN:Thread-2] Toolbox index of panel my_panel finished (2.243 ms)
galaxy.tools.search DEBUG 2026-09-17 16:21:52,182 [pN:main.1,p:70319,tN:Thread-2] Starting to build toolbox index of panel ontology:edam_operations.
galaxy.queue_worker INFO 2026-09-17 16:21:52,221 [pN:main.1,p:70319,tN:Thread-4 (check)] Sending reload_toolbox control task.
galaxy.tools.search DEBUG 2026-09-17 16:21:52,266 [pN:main.1,p:70319,tN:Thread-2] Toolbox index of panel ontology:edam_operations finished (83.954 ms)
galaxy.tools.search DEBUG 2026-09-17 16:21:52,266 [pN:main.1,p:70319,tN:Thread-2] Starting to build toolbox index of panel ontology:edam_topics.
galaxy.tools.search DEBUG 2026-09-17 16:21:52,344 [pN:main.1,p:70319,tN:Thread-2] Toolbox index of panel ontology:edam_topics finished (77.101 ms)
galaxy.tool_util.deps.conda_util DEBUG 2026-09-17 16:21:52,535 [pN:main.1,p:70319,tN:WSGI_0] Executing command: /Users/mvandenb/src/worktrees/.planemo-home/conda/bin/conda list -f --json conda-libmamba-solver > '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/tmp/tmp7k_pu5m9'
galaxy.tool_util.deps.conda_util DEBUG 2026-09-17 16:21:53,031 [pN:main.1,p:70319,tN:WSGI_0] Executing command: /Users/mvandenb/src/worktrees/.planemo-home/conda/bin/conda create -y --quiet --strict-channel-priority --solver libmamba --override-channels --channel conda-forge --channel bioconda --name mulled-v1-8a9871e65826613f7c0e728aefef9703f3193e097a88a93c1297988cf953d598 subread=2.1.1 samtools=1.21
galaxy.tool_util.deps DEBUG 2026-09-17 16:21:57,153 [pN:main.1,p:70319,tN:WSGI_0] Using dependency subread version 2.1.1 of type conda
galaxy.tool_util.deps DEBUG 2026-09-17 16:21:57,153 [pN:main.1,p:70319,tN:WSGI_0] Using dependency samtools version 1.21 of type conda
galaxy.tool_util.deps DEBUG 2026-09-17 16:21:57,154 [pN:main.1,p:70319,tN:WSGI_0] Using dependency subread version 2.1.1 of type conda
galaxy.tool_util.deps DEBUG 2026-09-17 16:21:57,154 [pN:main.1,p:70319,tN:WSGI_0] Using dependency samtools version 1.21 of type conda
galaxy.tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager DEBUG 2026-09-17 16:21:58,073 [pN:main.1,p:70319,tN:WSGI_0] Creating repository dependency objects...
galaxy.tool_util.toolbox.base DEBUG 2026-09-17 16:21:59,463 [pN:main.1,p:70319,tN:WSGI_0] Appending to tool panel section: Tools from workflows
galaxy.tool_shed.util.repository_util DEBUG 2026-09-17 16:21:59,466 [pN:main.1,p:70319,tN:WSGI_0] Adding new row for repository 'compose_text_param' in the tool_shed_repository table, status set to 'installation_status.NEW'.
galaxy.tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager DEBUG 2026-09-17 16:21:59,473 [pN:main.1,p:70319,tN:WSGI_0] Building repository dependency relationships...
galaxy.tool_util.toolbox.base DEBUG 2026-09-17 16:21:59,474 [pN:main.1,p:70319,tN:WSGI_0] Appending to tool panel section: Tools from workflows
galaxy.tool_util.toolbox.base DEBUG 2026-09-17 16:21:59,483 [pN:main.1,p:70319,tN:WSGI_0] Appending to tool panel section: Tools from workflows
galaxy.tool_shed.galaxy_install.install_manager INFO 2026-09-17 16:21:59,496 [pN:main.1,p:70319,tN:WSGI_0] Cloning repository 'https://toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param' at 1:e188c9826e0f
charset_normalizer DEBUG 2026-09-17 16:22:01,084 [pN:main.1,p:70319,tN:WSGI_0] Encoding detection: ascii is most likely the one.
galaxy.tool_util.toolbox.base DEBUG 2026-09-17 16:22:01,095 [pN:main.1,p:70319,tN:WSGI_0] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1, version: 0.1.1 into tool panel....
galaxy.tool_util.toolbox.integrated_panel DEBUG 2026-09-17 16:22:01,096 [pN:main.1,p:70319,tN:WSGI_0] Writing integrated tool panel config file to '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/integrated_tool_panel_conf.xml'
galaxy.app DEBUG 2026-09-17 16:22:01,098 [pN:main.1,p:70319,tN:WSGI_0] Waiting for toolbox reload
galaxy.tool_util.toolbox.watcher DEBUG 2026-09-17 16:22:01,294 [pN:main.1,p:70319,tN:Thread-4 (check)] The file '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/shed_tools_conf.xml' has changes.
galaxy.queue_worker INFO 2026-09-17 16:22:01,295 [pN:main.1,p:70319,tN:Thread-4 (check)] Queuing sync task reload_toolbox for main.1.
galaxy.queue_worker INFO 2026-09-17 16:22:01,461 [pN:main.1,p:70319,tN:Thread-2] Instance 'main.1' received 'reload_toolbox' task, executing now.
galaxy.queue_worker DEBUG 2026-09-17 16:22:01,463 [pN:main.1,p:70319,tN:Thread-2] Executing toolbox reload on 'main.1'
galaxy.util WARNING 2026-09-17 16:22:01,466 [pN:main.1,p:70319,tN:Thread-2] directory not found: /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/galaxy-dev/config/plugins/activities
galaxy.tools WARNING 2026-09-17 16:22:01,469 [pN:main.1,p:70319,tN:Thread-2] The default shed tool config file (/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file
galaxy.tool_util.toolbox.base INFO 2026-09-17 16:22:01,471 [pN:main.1,p:70319,tN:Thread-2] Parsing the tool configuration /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/tool_conf.xml
galaxy.tool_util.toolbox.base DEBUG 2026-09-17 16:22:01,472 [pN:main.1,p:70319,tN:Thread-2] Tool path for tool configuration /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/tool_conf.xml is None
galaxy.tool_util.parser.factory INFO 2026-09-17 16:22:01,473 [pN:main.1,p:70319,tN:Thread-2] Loading tool from YAML - this is experimental - tool will not function in future.
galaxy.tool_util.toolbox.base ERROR 2026-09-17 16:22:01,486 [pN:main.1,p:70319,tN:Thread-2] Error reading tool from path: /Users/mvandenb/src/worktrees/foundry/brc-c-auris/.foundry-runs/auris-scf1/galaxy-workflow.gxwf.yml
Traceback (most recent call last):
  File "/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/galaxy-dev/lib/galaxy/tool_util/toolbox/base.py", line 967, in _load_tool_tag_set
    tool = self.load_tool(concrete_path, use_cached=False)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/galaxy-dev/lib/galaxy/tool_util/toolbox/base.py", line 1222, in load_tool
    tool = self.create_tool(
           ^^^^^^^^^^^^^^^^^
  File "/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/galaxy-dev/lib/galaxy/tools/__init__.py", line 619, in create_tool
    return self._create_tool_from_source(tool_source, config_file=config_file, **kwds)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/galaxy-dev/lib/galaxy/tools/__init__.py", line 634, in _create_tool_from_source
    return create_tool_from_source(self.app, tool_source, **kwds)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/galaxy-dev/lib/galaxy/tools/__init__.py", line 448, in create_tool_from_source
    tool = ToolClass(config_file, tool_source, app, **kwds)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/galaxy-dev/lib/galaxy/tools/__init__.py", line 1099, in __init__
    raise e
  File "/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/galaxy-dev/lib/galaxy/tools/__init__.py", line 1096, in __init__
    self.parse(tool_source, guid=guid, dynamic=dynamic)
  File "/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/galaxy-dev/lib/galaxy/tools/__init__.py", line 1329, in parse
    raise Exception(f"Missing tool 'id' for tool at '{tool_source}'")
Exception: Missing tool 'id' for tool at 'YamlToolSource[/Users/mvandenb/src/worktrees/foundry/brc-c-auris/.foundry-runs/auris-scf1/galaxy-workflow.gxwf.yml]'
galaxy.tools WARNING 2026-09-17 16:22:01,488 [pN:main.1,p:70319,tN:Thread-2] The default shed tool config file (/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file
galaxy.tool_util.toolbox.base INFO 2026-09-17 16:22:01,489 [pN:main.1,p:70319,tN:Thread-2] Parsing the tool configuration /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/shed_tools_conf.xml
galaxy.tool_util.toolbox.base DEBUG 2026-09-17 16:22:01,490 [pN:main.1,p:70319,tN:Thread-2] Tool path for shed tool configuration /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/shed_tools_conf.xml is /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/shed_tools
galaxy.tool_util.toolbox.base ERROR 2026-09-17 16:22:01,491 [pN:main.1,p:70319,tN:Thread-2] Error reading tool configuration file from path 'toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/d8d32326fbfb/rgrnastar/rg_rnaStar.xml': [Errno 2] No such file or directory
galaxy.tools WARNING 2026-09-17 16:22:01,491 [pN:main.1,p:70319,tN:Thread-2] The default shed tool config file (/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file
galaxy.tool_util.toolbox.base INFO 2026-09-17 16:22:01,491 [pN:main.1,p:70319,tN:Thread-2] Parsing the tool configuration /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/empty_tool_conf.xml
galaxy.tool_util.toolbox.base DEBUG 2026-09-17 16:22:01,492 [pN:main.1,p:70319,tN:Thread-2] Tool path for tool configuration /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/empty_tool_conf.xml is None
galaxy.tool_util.toolbox.base DEBUG 2026-09-17 16:22:01,492 [pN:main.1,p:70319,tN:Thread-2] Reading tools from config files finished (22.892 ms)
galaxy.tool_util.toolbox.base DEBUG 2026-09-17 16:22:01,492 [pN:main.1,p:70319,tN:Thread-2] Loading section: Built-in Converters
galaxy.tool_util.toolbox.base DEBUG 2026-09-17 16:22:01,493 [pN:main.1,p:70319,tN:Thread-2] Loading section: Tools from workflows
galaxy.tool_util.toolbox.base DEBUG 2026-09-17 16:22:01,493 [pN:main.1,p:70319,tN:Thread-2] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1, version: 0.1.1 into tool panel....
galaxy.tool_util.toolbox.base DEBUG 2026-09-17 16:22:01,493 [pN:main.1,p:70319,tN:Thread-2] Loading tool panel finished (0.699 ms)
galaxy.tool_util.toolbox.base DEBUG 2026-09-17 16:22:01,494 [pN:main.1,p:70319,tN:Thread-2] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1, version: 0.1.1 into tool panel....
galaxy.tool_util.toolbox.views.edam DEBUG 2026-09-17 16:22:01,494 [pN:main.1,p:70319,tN:Thread-2] Loading EDAM tool panel finished (0.975 ms)
galaxy.tool_util.toolbox.base DEBUG 2026-09-17 16:22:01,495 [pN:main.1,p:70319,tN:Thread-2] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1, version: 0.1.1 into tool panel....
galaxy.tool_util.toolbox.views.edam DEBUG 2026-09-17 16:22:01,495 [pN:main.1,p:70319,tN:Thread-2] Loading EDAM tool panel finished (0.676 ms)
galaxy.tool_util.toolbox.integrated_panel DEBUG 2026-09-17 16:22:01,495 [pN:main.1,p:70319,tN:Thread-2] Writing integrated tool panel config file to '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/integrated_tool_panel_conf.xml'
galaxy.tool_util.toolbox.base DEBUG 2026-09-17 16:22:01,497 [pN:main.1,p:70319,tN:Thread-2] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1, version: 0.1.1 into tool panel....
galaxy.tool_util.toolbox.views.edam DEBUG 2026-09-17 16:22:01,497 [pN:main.1,p:70319,tN:Thread-2] Loading EDAM tool panel finished (0.723 ms)
galaxy.tool_util.toolbox.base DEBUG 2026-09-17 16:22:01,498 [pN:main.1,p:70319,tN:Thread-2] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1, version: 0.1.1 into tool panel....
galaxy.tool_util.toolbox.views.edam DEBUG 2026-09-17 16:22:01,498 [pN:main.1,p:70319,tN:Thread-2] Loading EDAM tool panel finished (0.680 ms)
galaxy.datatypes.registry DEBUG 2026-09-17 16:22:01,500 [pN:main.1,p:70319,tN:Thread-2] Loaded external metadata tool: __SET_METADATA__
galaxy.tools.special_tools DEBUG 2026-09-17 16:22:01,501 [pN:main.1,p:70319,tN:Thread-2] Loaded history export tool: __EXPORT_HISTORY__
galaxy.tools.special_tools DEBUG 2026-09-17 16:22:01,502 [pN:main.1,p:70319,tN:Thread-2] Loaded history export to uri tool: __EXPORT_HISTORY_TO_URI__
galaxy.tools.special_tools DEBUG 2026-09-17 16:22:01,502 [pN:main.1,p:70319,tN:Thread-2] Loaded history import tool: __IMPORT_HISTORY__
galaxy.tools DEBUG 2026-09-17 16:22:01,503 [pN:main.1,p:70319,tN:Thread-2] No parameter model for tool '__DATA_FETCH__': Cannot generate a tool parameter model for upload_dataset inputs
galaxy.tools.special_tools DEBUG 2026-09-17 16:22:01,503 [pN:main.1,p:70319,tN:Thread-2] Loaded data fetch tool: __DATA_FETCH__
galaxy.queue_worker INFO 2026-09-17 16:22:01,504 [pN:main.1,p:70319,tN:Thread-2] Queuing async task rebuild_toolbox_search_index for main.1.
galaxy.queue_worker DEBUG 2026-09-17 16:22:01,505 [pN:main.1,p:70319,tN:Thread-2] Toolbox reload (42.464 ms)
galaxy.queue_worker INFO 2026-09-17 16:22:01,508 [pN:main.1,p:70319,tN:Thread-2] Instance 'main.1' received 'rebuild_toolbox_search_index' task, executing now.
galaxy.tools.search DEBUG 2026-09-17 16:22:01,508 [pN:main.1,p:70319,tN:Thread-2] Starting to build toolbox index of panel default.
galaxy.app DEBUG 2026-09-17 16:22:01,523 [pN:main.1,p:70319,tN:WSGI_0] Finished waiting for toolbox reload (425.469 ms)
galaxy.tools.search DEBUG 2026-09-17 16:22:01,531 [pN:main.1,p:70319,tN:Thread-2] Toolbox index of panel default finished (22.474 ms)
galaxy.tools.search DEBUG 2026-09-17 16:22:01,531 [pN:main.1,p:70319,tN:Thread-2] Starting to build toolbox index of panel my_panel.
galaxy.tools.search DEBUG 2026-09-17 16:22:01,534 [pN:main.1,p:70319,tN:Thread-2] Toolbox index of panel my_panel finished (2.409 ms)
galaxy.tools.search DEBUG 2026-09-17 16:22:01,534 [pN:main.1,p:70319,tN:Thread-2] Starting to build toolbox index of panel ontology:edam_operations.
galaxy.tools.search DEBUG 2026-09-17 16:22:01,557 [pN:main.1,p:70319,tN:Thread-2] Toolbox index of panel ontology:edam_operations finished (22.724 ms)
galaxy.tools.search DEBUG 2026-09-17 16:22:01,558 [pN:main.1,p:70319,tN:Thread-2] Starting to build toolbox index of panel ontology:edam_topics.
galaxy.tools.search DEBUG 2026-09-17 16:22:01,575 [pN:main.1,p:70319,tN:Thread-2] Toolbox index of panel ontology:edam_topics finished (16.638 ms)
galaxy.tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager DEBUG 2026-09-17 16:22:02,270 [pN:main.1,p:70319,tN:WSGI_0] Creating repository dependency objects...
galaxy.queue_worker INFO 2026-09-17 16:22:02,320 [pN:main.1,p:70319,tN:Thread-4 (check)] Sending reload_toolbox control task.
galaxy.tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager INFO 2026-09-17 16:22:03,305 [pN:main.1,p:70319,tN:WSGI_0] Skipping installation of revision e188c9826e0f of repository 'compose_text_param' because it was installed with the (possibly updated) revision e188c9826e0f and its current installation status is 'Installed'.
galaxy.tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager DEBUG 2026-09-17 16:22:03,307 [pN:main.1,p:70319,tN:WSGI_0] Building repository dependency relationships...
galaxy.tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager DEBUG 2026-09-17 16:22:04,114 [pN:main.1,p:70319,tN:WSGI_0] Creating repository dependency objects...
galaxy.tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager INFO 2026-09-17 16:22:05,172 [pN:main.1,p:70319,tN:WSGI_0] Skipping installation of revision e188c9826e0f of repository 'compose_text_param' because it was installed with the (possibly updated) revision e188c9826e0f and its current installation status is 'Installed'.
galaxy.tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager DEBUG 2026-09-17 16:22:05,174 [pN:main.1,p:70319,tN:WSGI_0] Building repository dependency relationships...
galaxy.tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager DEBUG 2026-09-17 16:22:05,945 [pN:main.1,p:70319,tN:WSGI_0] Creating repository dependency objects...
galaxy.tool_util.toolbox.base DEBUG 2026-09-17 16:22:07,463 [pN:main.1,p:70319,tN:WSGI_0] Appending to tool panel section: Tools from workflows
galaxy.tool_shed.util.repository_util DEBUG 2026-09-17 16:22:07,467 [pN:main.1,p:70319,tN:WSGI_0] Adding new row for repository 'deseq2' in the tool_shed_repository table, status set to 'installation_status.NEW'.
galaxy.tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager DEBUG 2026-09-17 16:22:07,473 [pN:main.1,p:70319,tN:WSGI_0] Building repository dependency relationships...
galaxy.tool_util.toolbox.base DEBUG 2026-09-17 16:22:07,474 [pN:main.1,p:70319,tN:WSGI_0] Appending to tool panel section: Tools from workflows
galaxy.tool_util.toolbox.base DEBUG 2026-09-17 16:22:07,482 [pN:main.1,p:70319,tN:WSGI_0] Appending to tool panel section: Tools from workflows
galaxy.tool_shed.galaxy_install.install_manager INFO 2026-09-17 16:22:07,504 [pN:main.1,p:70319,tN:WSGI_0] Cloning repository 'https://toolshed.g2.bx.psu.edu/repos/iuc/deseq2' at 35:05f9e54d7e81
charset_normalizer DEBUG 2026-09-17 16:22:10,740 [pN:main.1,p:70319,tN:WSGI_0] Encoding detection: ascii is most likely the one.
galaxy.tool_util.toolbox.base DEBUG 2026-09-17 16:22:10,844 [pN:main.1,p:70319,tN:WSGI_0] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.8+galaxy4, version: 2.11.40.8+galaxy4 into tool panel....
galaxy.tool_util.toolbox.integrated_panel DEBUG 2026-09-17 16:22:10,845 [pN:main.1,p:70319,tN:WSGI_0] Writing integrated tool panel config file to '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/integrated_tool_panel_conf.xml'
galaxy.app DEBUG 2026-09-17 16:22:10,846 [pN:main.1,p:70319,tN:WSGI_0] Waiting for toolbox reload
galaxy.tool_util.toolbox.watcher DEBUG 2026-09-17 16:22:11,433 [pN:main.1,p:70319,tN:Thread-4 (check)] The file '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/shed_tools_conf.xml' has changes.
galaxy.queue_worker INFO 2026-09-17 16:22:11,435 [pN:main.1,p:70319,tN:Thread-4 (check)] Queuing sync task reload_toolbox for main.1.
galaxy.queue_worker INFO 2026-09-17 16:22:11,739 [pN:main.1,p:70319,tN:Thread-2] Instance 'main.1' received 'reload_toolbox' task, executing now.
galaxy.queue_worker DEBUG 2026-09-17 16:22:11,740 [pN:main.1,p:70319,tN:Thread-2] Executing toolbox reload on 'main.1'
galaxy.util WARNING 2026-09-17 16:22:11,742 [pN:main.1,p:70319,tN:Thread-2] directory not found: /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/galaxy-dev/config/plugins/activities
galaxy.tools WARNING 2026-09-17 16:22:11,743 [pN:main.1,p:70319,tN:Thread-2] The default shed tool config file (/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file
galaxy.tool_util.toolbox.base INFO 2026-09-17 16:22:11,744 [pN:main.1,p:70319,tN:Thread-2] Parsing the tool configuration /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/tool_conf.xml
galaxy.tool_util.toolbox.base DEBUG 2026-09-17 16:22:11,745 [pN:main.1,p:70319,tN:Thread-2] Tool path for tool configuration /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/tool_conf.xml is None
galaxy.tool_util.parser.factory INFO 2026-09-17 16:22:11,746 [pN:main.1,p:70319,tN:Thread-2] Loading tool from YAML - this is experimental - tool will not function in future.
galaxy.tool_util.toolbox.base ERROR 2026-09-17 16:22:11,755 [pN:main.1,p:70319,tN:Thread-2] Error reading tool from path: /Users/mvandenb/src/worktrees/foundry/brc-c-auris/.foundry-runs/auris-scf1/galaxy-workflow.gxwf.yml
Traceback (most recent call last):
  File "/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/galaxy-dev/lib/galaxy/tool_util/toolbox/base.py", line 967, in _load_tool_tag_set
    tool = self.load_tool(concrete_path, use_cached=False)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/galaxy-dev/lib/galaxy/tool_util/toolbox/base.py", line 1222, in load_tool
    tool = self.create_tool(
           ^^^^^^^^^^^^^^^^^
  File "/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/galaxy-dev/lib/galaxy/tools/__init__.py", line 619, in create_tool
    return self._create_tool_from_source(tool_source, config_file=config_file, **kwds)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/galaxy-dev/lib/galaxy/tools/__init__.py", line 634, in _create_tool_from_source
    return create_tool_from_source(self.app, tool_source, **kwds)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/galaxy-dev/lib/galaxy/tools/__init__.py", line 448, in create_tool_from_source
    tool = ToolClass(config_file, tool_source, app, **kwds)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/galaxy-dev/lib/galaxy/tools/__init__.py", line 1099, in __init__
    raise e
  File "/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/galaxy-dev/lib/galaxy/tools/__init__.py", line 1096, in __init__
    self.parse(tool_source, guid=guid, dynamic=dynamic)
  File "/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/galaxy-dev/lib/galaxy/tools/__init__.py", line 1329, in parse
    raise Exception(f"Missing tool 'id' for tool at '{tool_source}'")
Exception: Missing tool 'id' for tool at 'YamlToolSource[/Users/mvandenb/src/worktrees/foundry/brc-c-auris/.foundry-runs/auris-scf1/galaxy-workflow.gxwf.yml]'
galaxy.tools WARNING 2026-09-17 16:22:11,757 [pN:main.1,p:70319,tN:Thread-2] The default shed tool config file (/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file
galaxy.tool_util.toolbox.base INFO 2026-09-17 16:22:11,757 [pN:main.1,p:70319,tN:Thread-2] Parsing the tool configuration /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/shed_tools_conf.xml
galaxy.tool_util.toolbox.base DEBUG 2026-09-17 16:22:11,758 [pN:main.1,p:70319,tN:Thread-2] Tool path for shed tool configuration /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/shed_tools_conf.xml is /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/shed_tools
galaxy.tool_util.toolbox.base ERROR 2026-09-17 16:22:11,759 [pN:main.1,p:70319,tN:Thread-2] Error reading tool configuration file from path 'toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/d8d32326fbfb/rgrnastar/rg_rnaStar.xml': [Errno 2] No such file or directory
galaxy.tools WARNING 2026-09-17 16:22:11,759 [pN:main.1,p:70319,tN:Thread-2] The default shed tool config file (/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file
galaxy.tool_util.toolbox.base INFO 2026-09-17 16:22:11,760 [pN:main.1,p:70319,tN:Thread-2] Parsing the tool configuration /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/empty_tool_conf.xml
galaxy.tool_util.toolbox.base DEBUG 2026-09-17 16:22:11,761 [pN:main.1,p:70319,tN:Thread-2] Tool path for tool configuration /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/empty_tool_conf.xml is None
galaxy.tool_util.toolbox.base DEBUG 2026-09-17 16:22:11,761 [pN:main.1,p:70319,tN:Thread-2] Reading tools from config files finished (17.640 ms)
galaxy.tool_util.toolbox.base DEBUG 2026-09-17 16:22:11,761 [pN:main.1,p:70319,tN:Thread-2] Loading section: Built-in Converters
galaxy.tool_util.toolbox.base DEBUG 2026-09-17 16:22:11,762 [pN:main.1,p:70319,tN:Thread-2] Loading section: Tools from workflows
galaxy.tool_util.toolbox.base DEBUG 2026-09-17 16:22:11,762 [pN:main.1,p:70319,tN:Thread-2] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.8+galaxy4, version: 2.11.40.8+galaxy4 into tool panel....
galaxy.tool_util.toolbox.base DEBUG 2026-09-17 16:22:11,762 [pN:main.1,p:70319,tN:Thread-2] Loading tool panel finished (1.019 ms)
galaxy.tool_util.toolbox.base DEBUG 2026-09-17 16:22:11,764 [pN:main.1,p:70319,tN:Thread-2] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.8+galaxy4, version: 2.11.40.8+galaxy4 into tool panel....
galaxy.tool_util.toolbox.views.edam DEBUG 2026-09-17 16:22:11,764 [pN:main.1,p:70319,tN:Thread-2] Loading EDAM tool panel finished (1.311 ms)
galaxy.tool_util.toolbox.base DEBUG 2026-09-17 16:22:11,765 [pN:main.1,p:70319,tN:Thread-2] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.8+galaxy4, version: 2.11.40.8+galaxy4 into tool panel....
galaxy.tool_util.toolbox.views.edam DEBUG 2026-09-17 16:22:11,765 [pN:main.1,p:70319,tN:Thread-2] Loading EDAM tool panel finished (1.053 ms)
galaxy.tool_util.toolbox.integrated_panel DEBUG 2026-09-17 16:22:11,765 [pN:main.1,p:70319,tN:Thread-2] Writing integrated tool panel config file to '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/integrated_tool_panel_conf.xml'
galaxy.tool_util.toolbox.base DEBUG 2026-09-17 16:22:11,767 [pN:main.1,p:70319,tN:Thread-2] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.8+galaxy4, version: 2.11.40.8+galaxy4 into tool panel....
galaxy.tool_util.toolbox.views.edam DEBUG 2026-09-17 16:22:11,767 [pN:main.1,p:70319,tN:Thread-2] Loading EDAM tool panel finished (1.045 ms)
galaxy.tool_util.toolbox.base DEBUG 2026-09-17 16:22:11,768 [pN:main.1,p:70319,tN:Thread-2] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.8+galaxy4, version: 2.11.40.8+galaxy4 into tool panel....
galaxy.tool_util.toolbox.views.edam DEBUG 2026-09-17 16:22:11,769 [pN:main.1,p:70319,tN:Thread-2] Loading EDAM tool panel finished (1.021 ms)
galaxy.datatypes.registry DEBUG 2026-09-17 16:22:11,772 [pN:main.1,p:70319,tN:Thread-2] Loaded external metadata tool: __SET_METADATA__
galaxy.tools.special_tools DEBUG 2026-09-17 16:22:11,773 [pN:main.1,p:70319,tN:Thread-2] Loaded history export tool: __EXPORT_HISTORY__
galaxy.tools.special_tools DEBUG 2026-09-17 16:22:11,774 [pN:main.1,p:70319,tN:Thread-2] Loaded history export to uri tool: __EXPORT_HISTORY_TO_URI__
galaxy.tools.special_tools DEBUG 2026-09-17 16:22:11,775 [pN:main.1,p:70319,tN:Thread-2] Loaded history import tool: __IMPORT_HISTORY__
galaxy.tools DEBUG 2026-09-17 16:22:11,775 [pN:main.1,p:70319,tN:Thread-2] No parameter model for tool '__DATA_FETCH__': Cannot generate a tool parameter model for upload_dataset inputs
galaxy.tools.special_tools DEBUG 2026-09-17 16:22:11,776 [pN:main.1,p:70319,tN:Thread-2] Loaded data fetch tool: __DATA_FETCH__
galaxy.queue_worker INFO 2026-09-17 16:22:11,776 [pN:main.1,p:70319,tN:Thread-2] Queuing async task rebuild_toolbox_search_index for main.1.
galaxy.queue_worker DEBUG 2026-09-17 16:22:11,778 [pN:main.1,p:70319,tN:Thread-2] Toolbox reload (38.462 ms)
galaxy.queue_worker INFO 2026-09-17 16:22:11,781 [pN:main.1,p:70319,tN:Thread-2] Instance 'main.1' received 'rebuild_toolbox_search_index' task, executing now.
galaxy.tools.search DEBUG 2026-09-17 16:22:11,782 [pN:main.1,p:70319,tN:Thread-2] Starting to build toolbox index of panel default.
galaxy.app DEBUG 2026-09-17 16:22:11,810 [pN:main.1,p:70319,tN:WSGI_0] Finished waiting for toolbox reload (963.622 ms)
galaxy.tool_util.deps.conda_util DEBUG 2026-09-17 16:22:11,812 [pN:main.1,p:70319,tN:WSGI_0] Executing command: /Users/mvandenb/src/worktrees/.planemo-home/conda/bin/conda create -y --quiet --strict-channel-priority --solver libmamba --override-channels --channel conda-forge --channel bioconda --name mulled-v1-8d4693d910782170c2aba3414da311da10ab7b89dd02e0bdd97408dcaf39d0fe bioconductor-deseq2=1.40.2 bioconductor-apeglm=1.22.1 bioconductor-rhdf5=2.44.0 bioconductor-tximport=1.28.0 bioconductor-genomicfeatures=1.52.1 r-ashr=2.2_63 r-getopt=1.20.3 r-ggrepel=0.9.3 r-gplots=3.1.3 r-pheatmap=1.0.12 r-rjson=0.2.21 r-base64enc=0.1_3
galaxy.tools.search DEBUG 2026-09-17 16:22:11,856 [pN:main.1,p:70319,tN:Thread-2] Toolbox index of panel default finished (74.263 ms)
galaxy.tools.search DEBUG 2026-09-17 16:22:11,856 [pN:main.1,p:70319,tN:Thread-2] Starting to build toolbox index of panel my_panel.
galaxy.tools.search DEBUG 2026-09-17 16:22:11,858 [pN:main.1,p:70319,tN:Thread-2] Toolbox index of panel my_panel finished (1.718 ms)
galaxy.tools.search DEBUG 2026-09-17 16:22:11,858 [pN:main.1,p:70319,tN:Thread-2] Starting to build toolbox index of panel ontology:edam_operations.
galaxy.tools.search DEBUG 2026-09-17 16:22:11,884 [pN:main.1,p:70319,tN:Thread-2] Toolbox index of panel ontology:edam_operations finished (25.370 ms)
galaxy.tools.search DEBUG 2026-09-17 16:22:11,884 [pN:main.1,p:70319,tN:Thread-2] Starting to build toolbox index of panel ontology:edam_topics.
galaxy.tools.search DEBUG 2026-09-17 16:22:11,909 [pN:main.1,p:70319,tN:Thread-2] Toolbox index of panel ontology:edam_topics finished (24.907 ms)
galaxy.queue_worker INFO 2026-09-17 16:22:12,462 [pN:main.1,p:70319,tN:Thread-4 (check)] Sending reload_toolbox control task.
galaxy.tool_util.deps.conda_util DEBUG 2026-09-17 16:22:17,856 [pN:main.1,p:70319,tN:WSGI_0] Executing command: /Users/mvandenb/src/worktrees/.planemo-home/conda/bin/conda create -y --quiet --solver libmamba --override-channels --channel conda-forge --channel bioconda --name mulled-v1-8d4693d910782170c2aba3414da311da10ab7b89dd02e0bdd97408dcaf39d0fe bioconductor-deseq2=1.40.2 bioconductor-apeglm=1.22.1 bioconductor-rhdf5=2.44.0 bioconductor-tximport=1.28.0 bioconductor-genomicfeatures=1.52.1 r-ashr=2.2_63 r-getopt=1.20.3 r-ggrepel=0.9.3 r-gplots=3.1.3 r-pheatmap=1.0.12 r-rjson=0.2.21 r-base64enc=0.1_3
galaxy.tool_util.deps.resolvers.conda DEBUG 2026-09-17 16:22:21,740 [pN:main.1,p:70319,tN:WSGI_0] Removing failed conda install of [CondaTarget[package=bioconductor-deseq2,version=1.40.2], CondaTarget[package=bioconductor-apeglm,version=1.22.1], CondaTarget[package=bioconductor-rhdf5,version=2.44.0], CondaTarget[package=bioconductor-tximport,version=1.28.0], CondaTarget[package=bioconductor-genomicfeatures,version=1.52.1], CondaTarget[package=r-ashr,version=2.2_63], CondaTarget[package=r-getopt,version=1.20.3], CondaTarget[package=r-ggrepel,version=0.9.3], CondaTarget[package=r-gplots,version=3.1.3], CondaTarget[package=r-pheatmap,version=1.0.12], CondaTarget[package=r-rjson,version=0.2.21], CondaTarget[package=r-base64enc,version=0.1_3]]
galaxy.tool_util.deps.conda_util DEBUG 2026-09-17 16:22:21,741 [pN:main.1,p:70319,tN:WSGI_0] Executing command: /Users/mvandenb/src/worktrees/.planemo-home/conda/bin/conda create -y --quiet --strict-channel-priority --solver libmamba --override-channels --channel conda-forge --channel bioconda --name __bioconductor-deseq2@1.40.2 bioconductor-deseq2=1.40.2
galaxy.tool_util.deps.conda_util DEBUG 2026-09-17 16:22:23,003 [pN:main.1,p:70319,tN:WSGI_0] Executing command: /Users/mvandenb/src/worktrees/.planemo-home/conda/bin/conda create -y --quiet --solver libmamba --override-channels --channel conda-forge --channel bioconda --name __bioconductor-deseq2@1.40.2 bioconductor-deseq2=1.40.2
galaxy.tool_util.deps.resolvers.conda DEBUG 2026-09-17 16:22:24,262 [pN:main.1,p:70319,tN:WSGI_0] Removing failed conda install of bioconductor-deseq2, version '1.40.2'
galaxy.tool_util.deps.conda_util DEBUG 2026-09-17 16:22:24,262 [pN:main.1,p:70319,tN:WSGI_0] Executing command: /Users/mvandenb/src/worktrees/.planemo-home/conda/bin/conda create -y --quiet --strict-channel-priority --solver libmamba --override-channels --channel conda-forge --channel bioconda --name __bioconductor-apeglm@1.22.1 bioconductor-apeglm=1.22.1
galaxy.tool_util.deps.conda_util DEBUG 2026-09-17 16:22:25,077 [pN:main.1,p:70319,tN:WSGI_0] Executing command: /Users/mvandenb/src/worktrees/.planemo-home/conda/bin/conda create -y --quiet --solver libmamba --override-channels --channel conda-forge --channel bioconda --name __bioconductor-apeglm@1.22.1 bioconductor-apeglm=1.22.1
galaxy.tool_util.deps.resolvers.conda DEBUG 2026-09-17 16:22:25,920 [pN:main.1,p:70319,tN:WSGI_0] Removing failed conda install of bioconductor-apeglm, version '1.22.1'
galaxy.tool_util.deps.conda_util DEBUG 2026-09-17 16:22:25,921 [pN:main.1,p:70319,tN:WSGI_0] Executing command: /Users/mvandenb/src/worktrees/.planemo-home/conda/bin/conda create -y --quiet --strict-channel-priority --solver libmamba --override-channels --channel conda-forge --channel bioconda --name __bioconductor-rhdf5@2.44.0 bioconductor-rhdf5=2.44.0
galaxy.tool_util.deps.conda_util DEBUG 2026-09-17 16:22:26,704 [pN:main.1,p:70319,tN:WSGI_0] Executing command: /Users/mvandenb/src/worktrees/.planemo-home/conda/bin/conda create -y --quiet --solver libmamba --override-channels --channel conda-forge --channel bioconda --name __bioconductor-rhdf5@2.44.0 bioconductor-rhdf5=2.44.0
galaxy.tool_util.deps.resolvers.conda DEBUG 2026-09-17 16:22:27,468 [pN:main.1,p:70319,tN:WSGI_0] Removing failed conda install of bioconductor-rhdf5, version '2.44.0'
galaxy.tool_util.deps.conda_util DEBUG 2026-09-17 16:22:27,468 [pN:main.1,p:70319,tN:WSGI_0] Executing command: /Users/mvandenb/src/worktrees/.planemo-home/conda/bin/conda create -y --quiet --strict-channel-priority --solver libmamba --override-channels --channel conda-forge --channel bioconda --name __bioconductor-tximport@1.28.0 bioconductor-tximport=1.28.0
galaxy.tool_util.deps DEBUG 2026-09-17 16:22:35,140 [pN:main.1,p:70319,tN:WSGI_0] Using dependency bioconductor-tximport version 1.28.0 of type conda
galaxy.tool_util.deps.conda_util DEBUG 2026-09-17 16:22:35,143 [pN:main.1,p:70319,tN:WSGI_0] Executing command: /Users/mvandenb/src/worktrees/.planemo-home/conda/bin/conda create -y --quiet --strict-channel-priority --solver libmamba --override-channels --channel conda-forge --channel bioconda --name __bioconductor-genomicfeatures@1.52.1 bioconductor-genomicfeatures=1.52.1
galaxy.tool_util.deps.conda_util DEBUG 2026-09-17 16:22:36,715 [pN:main.1,p:70319,tN:WSGI_0] Executing command: /Users/mvandenb/src/worktrees/.planemo-home/conda/bin/conda create -y --quiet --solver libmamba --override-channels --channel conda-forge --channel bioconda --name __bioconductor-genomicfeatures@1.52.1 bioconductor-genomicfeatures=1.52.1
galaxy.tool_util.deps.resolvers.conda DEBUG 2026-09-17 16:22:37,881 [pN:main.1,p:70319,tN:WSGI_0] Removing failed conda install of bioconductor-genomicfeatures, version '1.52.1'
galaxy.tool_util.deps.conda_util DEBUG 2026-09-17 16:22:37,882 [pN:main.1,p:70319,tN:WSGI_0] Executing command: /Users/mvandenb/src/worktrees/.planemo-home/conda/bin/conda create -y --quiet --strict-channel-priority --solver libmamba --override-channels --channel conda-forge --channel bioconda --name __r-ashr@2.2_63 r-ashr=2.2_63
galaxy.tool_util.deps DEBUG 2026-09-17 16:22:45,707 [pN:main.1,p:70319,tN:WSGI_0] Using dependency r-ashr version 2.2_63 of type conda
galaxy.tool_util.deps.conda_util DEBUG 2026-09-17 16:22:45,707 [pN:main.1,p:70319,tN:WSGI_0] Executing command: /Users/mvandenb/src/worktrees/.planemo-home/conda/bin/conda create -y --quiet --strict-channel-priority --solver libmamba --override-channels --channel conda-forge --channel bioconda --name __r-getopt@1.20.3 r-getopt=1.20.3
galaxy.tool_util.deps DEBUG 2026-09-17 16:22:51,464 [pN:main.1,p:70319,tN:WSGI_0] Using dependency r-getopt version 1.20.3 of type conda
galaxy.tool_util.deps.conda_util DEBUG 2026-09-17 16:22:51,464 [pN:main.1,p:70319,tN:WSGI_0] Executing command: /Users/mvandenb/src/worktrees/.planemo-home/conda/bin/conda create -y --quiet --strict-channel-priority --solver libmamba --override-channels --channel conda-forge --channel bioconda --name __r-ggrepel@0.9.3 r-ggrepel=0.9.3
galaxy.tool_util.deps DEBUG 2026-09-17 16:22:59,373 [pN:main.1,p:70319,tN:WSGI_0] Using dependency r-ggrepel version 0.9.3 of type conda
galaxy.tool_util.deps.conda_util DEBUG 2026-09-17 16:22:59,374 [pN:main.1,p:70319,tN:WSGI_0] Executing command: /Users/mvandenb/src/worktrees/.planemo-home/conda/bin/conda create -y --quiet --strict-channel-priority --solver libmamba --override-channels --channel conda-forge --channel bioconda --name __r-gplots@3.1.3 r-gplots=3.1.3
galaxy.tool_util.deps DEBUG 2026-09-17 16:23:05,783 [pN:main.1,p:70319,tN:WSGI_0] Using dependency r-gplots version 3.1.3 of type conda
galaxy.tool_util.deps.conda_util DEBUG 2026-09-17 16:23:05,783 [pN:main.1,p:70319,tN:WSGI_0] Executing command: /Users/mvandenb/src/worktrees/.planemo-home/conda/bin/conda create -y --quiet --strict-channel-priority --solver libmamba --override-channels --channel conda-forge --channel bioconda --name __r-pheatmap@1.0.12 r-pheatmap=1.0.12
galaxy.tool_util.deps DEBUG 2026-09-17 16:23:11,905 [pN:main.1,p:70319,tN:WSGI_0] Using dependency r-pheatmap version 1.0.12 of type conda
galaxy.tool_util.deps.conda_util DEBUG 2026-09-17 16:23:11,905 [pN:main.1,p:70319,tN:WSGI_0] Executing command: /Users/mvandenb/src/worktrees/.planemo-home/conda/bin/conda create -y --quiet --strict-channel-priority --solver libmamba --override-channels --channel conda-forge --channel bioconda --name __r-rjson@0.2.21 r-rjson=0.2.21
galaxy.tool_util.deps DEBUG 2026-09-17 16:23:18,651 [pN:main.1,p:70319,tN:WSGI_0] Using dependency r-rjson version 0.2.21 of type conda
galaxy.tool_util.deps.conda_util DEBUG 2026-09-17 16:23:18,652 [pN:main.1,p:70319,tN:WSGI_0] Executing command: /Users/mvandenb/src/worktrees/.planemo-home/conda/bin/conda create -y --quiet --strict-channel-priority --solver libmamba --override-channels --channel conda-forge --channel bioconda --name __r-base64enc@0.1_3 r-base64enc=0.1_3
galaxy.tool_util.deps DEBUG 2026-09-17 16:23:24,977 [pN:main.1,p:70319,tN:WSGI_0] Using dependency r-base64enc version 0.1_3 of type conda
galaxy.tool_util.deps.conda_util DEBUG 2026-09-17 16:23:24,977 [pN:main.1,p:70319,tN:WSGI_0] Executing command: /Users/mvandenb/src/worktrees/.planemo-home/conda/bin/conda create -y --quiet --strict-channel-priority --solver libmamba --override-channels --channel conda-forge --channel bioconda --name __bioconductor-deseq2@_uv_ 'bioconductor-deseq2=*'
galaxy.tool_util.deps DEBUG 2026-09-17 16:23:43,493 [pN:main.1,p:70319,tN:WSGI_0] Using dependency bioconductor-deseq2 version None of type conda
galaxy.tool_util.deps.conda_util DEBUG 2026-09-17 16:23:43,495 [pN:main.1,p:70319,tN:WSGI_0] Executing command: /Users/mvandenb/src/worktrees/.planemo-home/conda/bin/conda create -y --quiet --strict-channel-priority --solver libmamba --override-channels --channel conda-forge --channel bioconda --name __bioconductor-apeglm@_uv_ 'bioconductor-apeglm=*'
galaxy.tool_util.deps DEBUG 2026-09-17 16:23:54,496 [pN:main.1,p:70319,tN:WSGI_0] Using dependency bioconductor-apeglm version None of type conda
galaxy.tool_util.deps.conda_util DEBUG 2026-09-17 16:23:54,498 [pN:main.1,p:70319,tN:WSGI_0] Executing command: /Users/mvandenb/src/worktrees/.planemo-home/conda/bin/conda create -y --quiet --strict-channel-priority --solver libmamba --override-channels --channel conda-forge --channel bioconda --name __bioconductor-rhdf5@_uv_ 'bioconductor-rhdf5=*'
galaxy.tool_util.deps DEBUG 2026-09-17 16:24:03,056 [pN:main.1,p:70319,tN:WSGI_0] Using dependency bioconductor-rhdf5 version None of type conda
galaxy.tool_util.deps.conda_util DEBUG 2026-09-17 16:24:03,057 [pN:main.1,p:70319,tN:WSGI_0] Executing command: /Users/mvandenb/src/worktrees/.planemo-home/conda/bin/conda create -y --quiet --strict-channel-priority --solver libmamba --override-channels --channel conda-forge --channel bioconda --name __bioconductor-genomicfeatures@_uv_ 'bioconductor-genomicfeatures=*'
galaxy.tool_util.deps DEBUG 2026-09-17 16:24:15,908 [pN:main.1,p:70319,tN:WSGI_0] Using dependency bioconductor-genomicfeatures version None of type conda
galaxy.tool_util.deps.conda_util DEBUG 2026-09-17 16:24:15,908 [pN:main.1,p:70319,tN:WSGI_0] Executing command: /Users/mvandenb/src/worktrees/.planemo-home/conda/bin/conda create -y --quiet --strict-channel-priority --solver libmamba --override-channels --channel conda-forge --channel bioconda --name mulled-v1-8d4693d910782170c2aba3414da311da10ab7b89dd02e0bdd97408dcaf39d0fe bioconductor-deseq2=1.40.2 bioconductor-apeglm=1.22.1 bioconductor-rhdf5=2.44.0 bioconductor-tximport=1.28.0 bioconductor-genomicfeatures=1.52.1 r-ashr=2.2_63 r-getopt=1.20.3 r-ggrepel=0.9.3 r-gplots=3.1.3 r-pheatmap=1.0.12 r-rjson=0.2.21 r-base64enc=0.1_3
galaxy.tool_util.deps.conda_util DEBUG 2026-09-17 16:24:20,128 [pN:main.1,p:70319,tN:WSGI_0] Executing command: /Users/mvandenb/src/worktrees/.planemo-home/conda/bin/conda create -y --quiet --solver libmamba --override-channels --channel conda-forge --channel bioconda --name mulled-v1-8d4693d910782170c2aba3414da311da10ab7b89dd02e0bdd97408dcaf39d0fe bioconductor-deseq2=1.40.2 bioconductor-apeglm=1.22.1 bioconductor-rhdf5=2.44.0 bioconductor-tximport=1.28.0 bioconductor-genomicfeatures=1.52.1 r-ashr=2.2_63 r-getopt=1.20.3 r-ggrepel=0.9.3 r-gplots=3.1.3 r-pheatmap=1.0.12 r-rjson=0.2.21 r-base64enc=0.1_3
galaxy.tool_util.deps.resolvers.conda DEBUG 2026-09-17 16:24:23,830 [pN:main.1,p:70319,tN:WSGI_0] Removing failed conda install of [CondaTarget[package=bioconductor-deseq2,version=1.40.2], CondaTarget[package=bioconductor-apeglm,version=1.22.1], CondaTarget[package=bioconductor-rhdf5,version=2.44.0], CondaTarget[package=bioconductor-tximport,version=1.28.0], CondaTarget[package=bioconductor-genomicfeatures,version=1.52.1], CondaTarget[package=r-ashr,version=2.2_63], CondaTarget[package=r-getopt,version=1.20.3], CondaTarget[package=r-ggrepel,version=0.9.3], CondaTarget[package=r-gplots,version=3.1.3], CondaTarget[package=r-pheatmap,version=1.0.12], CondaTarget[package=r-rjson,version=0.2.21], CondaTarget[package=r-base64enc,version=0.1_3]]
galaxy.tool_util.deps.conda_util DEBUG 2026-09-17 16:24:23,831 [pN:main.1,p:70319,tN:WSGI_0] Executing command: /Users/mvandenb/src/worktrees/.planemo-home/conda/bin/conda create -y --quiet --strict-channel-priority --solver libmamba --override-channels --channel conda-forge --channel bioconda --name __bioconductor-deseq2@1.40.2 bioconductor-deseq2=1.40.2
galaxy.tool_util.deps.conda_util DEBUG 2026-09-17 16:24:25,150 [pN:main.1,p:70319,tN:WSGI_0] Executing command: /Users/mvandenb/src/worktrees/.planemo-home/conda/bin/conda create -y --quiet --solver libmamba --override-channels --channel conda-forge --channel bioconda --name __bioconductor-deseq2@1.40.2 bioconductor-deseq2=1.40.2
galaxy.tool_util.deps.resolvers.conda DEBUG 2026-09-17 16:24:26,414 [pN:main.1,p:70319,tN:WSGI_0] Removing failed conda install of bioconductor-deseq2, version '1.40.2'
galaxy.tool_util.deps.conda_util DEBUG 2026-09-17 16:24:26,415 [pN:main.1,p:70319,tN:WSGI_0] Executing command: /Users/mvandenb/src/worktrees/.planemo-home/conda/bin/conda create -y --quiet --strict-channel-priority --solver libmamba --override-channels --channel conda-forge --channel bioconda --name __bioconductor-apeglm@1.22.1 bioconductor-apeglm=1.22.1
galaxy.tool_util.deps.conda_util DEBUG 2026-09-17 16:24:27,233 [pN:main.1,p:70319,tN:WSGI_0] Executing command: /Users/mvandenb/src/worktrees/.planemo-home/conda/bin/conda create -y --quiet --solver libmamba --override-channels --channel conda-forge --channel bioconda --name __bioconductor-apeglm@1.22.1 bioconductor-apeglm=1.22.1
galaxy.tool_util.deps.resolvers.conda DEBUG 2026-09-17 16:24:28,086 [pN:main.1,p:70319,tN:WSGI_0] Removing failed conda install of bioconductor-apeglm, version '1.22.1'
galaxy.tool_util.deps.conda_util DEBUG 2026-09-17 16:24:28,087 [pN:main.1,p:70319,tN:WSGI_0] Executing command: /Users/mvandenb/src/worktrees/.planemo-home/conda/bin/conda create -y --quiet --strict-channel-priority --solver libmamba --override-channels --channel conda-forge --channel bioconda --name __bioconductor-rhdf5@2.44.0 bioconductor-rhdf5=2.44.0
galaxy.tool_util.deps.conda_util DEBUG 2026-09-17 16:24:28,904 [pN:main.1,p:70319,tN:WSGI_0] Executing command: /Users/mvandenb/src/worktrees/.planemo-home/conda/bin/conda create -y --quiet --solver libmamba --override-channels --channel conda-forge --channel bioconda --name __bioconductor-rhdf5@2.44.0 bioconductor-rhdf5=2.44.0
galaxy.tool_util.deps.resolvers.conda DEBUG 2026-09-17 16:24:29,693 [pN:main.1,p:70319,tN:WSGI_0] Removing failed conda install of bioconductor-rhdf5, version '2.44.0'
galaxy.tool_util.deps DEBUG 2026-09-17 16:24:29,694 [pN:main.1,p:70319,tN:WSGI_0] Using dependency bioconductor-tximport version 1.28.0 of type conda
galaxy.tool_util.deps.conda_util DEBUG 2026-09-17 16:24:29,694 [pN:main.1,p:70319,tN:WSGI_0] Executing command: /Users/mvandenb/src/worktrees/.planemo-home/conda/bin/conda create -y --quiet --strict-channel-priority --solver libmamba --override-channels --channel conda-forge --channel bioconda --name __bioconductor-genomicfeatures@1.52.1 bioconductor-genomicfeatures=1.52.1
galaxy.tool_util.deps.conda_util DEBUG 2026-09-17 16:24:30,823 [pN:main.1,p:70319,tN:WSGI_0] Executing command: /Users/mvandenb/src/worktrees/.planemo-home/conda/bin/conda create -y --quiet --solver libmamba --override-channels --channel conda-forge --channel bioconda --name __bioconductor-genomicfeatures@1.52.1 bioconductor-genomicfeatures=1.52.1
galaxy.tool_util.deps.resolvers.conda DEBUG 2026-09-17 16:24:32,014 [pN:main.1,p:70319,tN:WSGI_0] Removing failed conda install of bioconductor-genomicfeatures, version '1.52.1'
galaxy.tool_util.deps DEBUG 2026-09-17 16:24:32,014 [pN:main.1,p:70319,tN:WSGI_0] Using dependency r-ashr version 2.2_63 of type conda
galaxy.tool_util.deps DEBUG 2026-09-17 16:24:32,015 [pN:main.1,p:70319,tN:WSGI_0] Using dependency r-getopt version 1.20.3 of type conda
galaxy.tool_util.deps DEBUG 2026-09-17 16:24:32,015 [pN:main.1,p:70319,tN:WSGI_0] Using dependency r-ggrepel version 0.9.3 of type conda
galaxy.tool_util.deps DEBUG 2026-09-17 16:24:32,015 [pN:main.1,p:70319,tN:WSGI_0] Using dependency r-gplots version 3.1.3 of type conda
galaxy.tool_util.deps DEBUG 2026-09-17 16:24:32,015 [pN:main.1,p:70319,tN:WSGI_0] Using dependency r-pheatmap version 1.0.12 of type conda
galaxy.tool_util.deps DEBUG 2026-09-17 16:24:32,015 [pN:main.1,p:70319,tN:WSGI_0] Using dependency r-rjson version 0.2.21 of type conda
galaxy.tool_util.deps DEBUG 2026-09-17 16:24:32,016 [pN:main.1,p:70319,tN:WSGI_0] Using dependency r-base64enc version 0.1_3 of type conda
galaxy.tool_util.deps DEBUG 2026-09-17 16:24:32,016 [pN:main.1,p:70319,tN:WSGI_0] Using dependency bioconductor-deseq2 version None of type conda
galaxy.tool_util.deps DEBUG 2026-09-17 16:24:32,016 [pN:main.1,p:70319,tN:WSGI_0] Using dependency bioconductor-apeglm version None of type conda
galaxy.tool_util.deps DEBUG 2026-09-17 16:24:32,016 [pN:main.1,p:70319,tN:WSGI_0] Using dependency bioconductor-rhdf5 version None of type conda
galaxy.tool_util.deps DEBUG 2026-09-17 16:24:32,016 [pN:main.1,p:70319,tN:WSGI_0] Using dependency bioconductor-genomicfeatures version None of type conda
galaxy.tool_util.deps.conda_util DEBUG 2026-09-17 16:24:32,018 [pN:main.1,p:70319,tN:WSGI_0] Executing command: /Users/mvandenb/src/worktrees/.planemo-home/conda/bin/conda list --name __bioconductor-tximport@1.28.0 --export > '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/tmp/jobdepsfhc2o2caf22b5da87bcf5ad55916c136de1777f9d2202816a6d69053e228b778a3a6e017/__bioconductor-tximport@1.28.0'
galaxy.tool_util.deps.conda_util DEBUG 2026-09-17 16:24:32,507 [pN:main.1,p:70319,tN:WSGI_0] Executing command: /Users/mvandenb/src/worktrees/.planemo-home/conda/bin/conda create -y --quiet --strict-channel-priority --solver libmamba --override-channels --channel conda-forge --channel bioconda --unknown --offline --prefix /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/deps/_cache/fab2ffb9 --file /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/tmp/jobdepsfhc2o2caf22b5da87bcf5ad55916c136de1777f9d2202816a6d69053e228b778a3a6e017/__bioconductor-tximport@1.28.0
galaxy.tool_util.deps.conda_util DEBUG 2026-09-17 16:24:38,417 [pN:main.1,p:70319,tN:WSGI_0] Executing command: /Users/mvandenb/src/worktrees/.planemo-home/conda/bin/conda clean --tarballs -y
galaxy.tool_util.deps.conda_util DEBUG 2026-09-17 16:24:39,311 [pN:main.1,p:70319,tN:WSGI_0] Executing command: /Users/mvandenb/src/worktrees/.planemo-home/conda/bin/conda list --name __r-ashr@2.2_63 --export > '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/tmp/jobdeps1rkn4tuja9f8341684b8f48cdcc067519cc12b108eb76cf49410dbf5903af8ac3cac7c2e/__r-ashr@2.2_63'
galaxy.tool_util.deps.conda_util DEBUG 2026-09-17 16:24:39,814 [pN:main.1,p:70319,tN:WSGI_0] Executing command: /Users/mvandenb/src/worktrees/.planemo-home/conda/bin/conda install -y --strict-channel-priority --solver libmamba --override-channels --channel conda-forge --channel bioconda --unknown --offline --prefix /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/deps/_cache/fab2ffb9 --file /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/tmp/jobdeps1rkn4tuja9f8341684b8f48cdcc067519cc12b108eb76cf49410dbf5903af8ac3cac7c2e/__r-ashr@2.2_63
galaxy.tool_util.deps.conda_util DEBUG 2026-09-17 16:24:41,144 [pN:main.1,p:70319,tN:WSGI_0] Executing command: /Users/mvandenb/src/worktrees/.planemo-home/conda/bin/conda install -y --solver libmamba --override-channels --channel conda-forge --channel bioconda --unknown --offline --prefix /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/deps/_cache/fab2ffb9 --file /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/tmp/jobdeps1rkn4tuja9f8341684b8f48cdcc067519cc12b108eb76cf49410dbf5903af8ac3cac7c2e/__r-ashr@2.2_63
galaxy.tool_util.deps.conda_util DEBUG 2026-09-17 16:24:42,486 [pN:main.1,p:70319,tN:WSGI_0] Executing command: /Users/mvandenb/src/worktrees/.planemo-home/conda/bin/conda clean --tarballs -y
galaxy.tool_shed.galaxy_install.install_manager ERROR 2026-09-17 16:24:42,887 [pN:main.1,p:70319,tN:WSGI_0] Error installing repository 'deseq2'
Traceback (most recent call last):
  File "/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/galaxy-dev/lib/galaxy/tool_shed/galaxy_install/install_manager.py", line 520, in install_repositories
    self.install_tool_shed_repository(
  File "/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/galaxy-dev/lib/galaxy/tool_shed/galaxy_install/install_manager.py", line 652, in install_tool_shed_repository
    [dependency_manager.build_cache(r) for r in new_requirements]
     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/galaxy-dev/lib/galaxy/tool_util/deps/__init__.py", line 418, in build_cache
    [dep.build_cache(hashed_dependencies_dir) for dep in cacheable_dependencies]
     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/galaxy-dev/lib/galaxy/tool_util/deps/resolvers/conda.py", line 495, in build_cache
    self.build_environment()
  File "/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/galaxy-dev/lib/galaxy/tool_util/deps/resolvers/conda.py", line 511, in build_environment
    raise DependencyException(
galaxy.tool_util.deps.resolvers.DependencyException: Conda dependency failed to build job environment. This is most likely a limitation in conda. You can try to shorten the path to the job_working_directory.
galaxy.tool_shed.util.repository_util DEBUG 2026-09-17 16:24:42,907 [pN:main.1,p:70319,tN:WSGI_0] Removed repository installation directory: /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/shed_tools/toolshed.g2.bx.psu.edu/repos/iuc/deseq2/05f9e54d7e81
galaxy.tools.cache DEBUG 2026-09-17 16:24:43,585 [pN:main.1,p:70319,tN:Thread-4 (check)] Removed the following tools from cache: ['toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.8+galaxy4', 'toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2', 'deseq2']
galaxy.queue_worker INFO 2026-09-17 16:24:43,586 [pN:main.1,p:70319,tN:Thread-4 (check)] Queuing sync task reload_toolbox for main.1.
galaxy.tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager DEBUG 2026-09-17 16:24:43,869 [pN:main.1,p:70319,tN:WSGI_0] Creating repository dependency objects...
galaxy.queue_worker INFO 2026-09-17 16:24:44,289 [pN:main.1,p:70319,tN:Thread-2] Instance 'main.1' received 'reload_toolbox' task, executing now.
galaxy.queue_worker DEBUG 2026-09-17 16:24:44,290 [pN:main.1,p:70319,tN:Thread-2] Executing toolbox reload on 'main.1'
galaxy.util WARNING 2026-09-17 16:24:44,295 [pN:main.1,p:70319,tN:Thread-2] directory not found: /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/galaxy-dev/config/plugins/activities
galaxy.tools WARNING 2026-09-17 16:24:44,297 [pN:main.1,p:70319,tN:Thread-2] The default shed tool config file (/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file
galaxy.tool_util.toolbox.base INFO 2026-09-17 16:24:44,298 [pN:main.1,p:70319,tN:Thread-2] Parsing the tool configuration /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/tool_conf.xml
galaxy.tool_util.toolbox.base DEBUG 2026-09-17 16:24:44,300 [pN:main.1,p:70319,tN:Thread-2] Tool path for tool configuration /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/tool_conf.xml is None
galaxy.tool_util.parser.factory INFO 2026-09-17 16:24:44,302 [pN:main.1,p:70319,tN:Thread-2] Loading tool from YAML - this is experimental - tool will not function in future.
galaxy.tool_util.toolbox.base ERROR 2026-09-17 16:24:44,313 [pN:main.1,p:70319,tN:Thread-2] Error reading tool from path: /Users/mvandenb/src/worktrees/foundry/brc-c-auris/.foundry-runs/auris-scf1/galaxy-workflow.gxwf.yml
Traceback (most recent call last):
  File "/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/galaxy-dev/lib/galaxy/tool_util/toolbox/base.py", line 967, in _load_tool_tag_set
    tool = self.load_tool(concrete_path, use_cached=False)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/galaxy-dev/lib/galaxy/tool_util/toolbox/base.py", line 1222, in load_tool
    tool = self.create_tool(
           ^^^^^^^^^^^^^^^^^
  File "/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/galaxy-dev/lib/galaxy/tools/__init__.py", line 619, in create_tool
    return self._create_tool_from_source(tool_source, config_file=config_file, **kwds)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/galaxy-dev/lib/galaxy/tools/__init__.py", line 634, in _create_tool_from_source
    return create_tool_from_source(self.app, tool_source, **kwds)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/galaxy-dev/lib/galaxy/tools/__init__.py", line 448, in create_tool_from_source
    tool = ToolClass(config_file, tool_source, app, **kwds)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/galaxy-dev/lib/galaxy/tools/__init__.py", line 1099, in __init__
    raise e
  File "/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/galaxy-dev/lib/galaxy/tools/__init__.py", line 1096, in __init__
    self.parse(tool_source, guid=guid, dynamic=dynamic)
  File "/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/galaxy-dev/lib/galaxy/tools/__init__.py", line 1329, in parse
    raise Exception(f"Missing tool 'id' for tool at '{tool_source}'")
Exception: Missing tool 'id' for tool at 'YamlToolSource[/Users/mvandenb/src/worktrees/foundry/brc-c-auris/.foundry-runs/auris-scf1/galaxy-workflow.gxwf.yml]'
galaxy.tools WARNING 2026-09-17 16:24:44,316 [pN:main.1,p:70319,tN:Thread-2] The default shed tool config file (/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file
galaxy.tool_util.toolbox.base INFO 2026-09-17 16:24:44,316 [pN:main.1,p:70319,tN:Thread-2] Parsing the tool configuration /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/shed_tools_conf.xml
galaxy.tool_util.toolbox.base DEBUG 2026-09-17 16:24:44,317 [pN:main.1,p:70319,tN:Thread-2] Tool path for shed tool configuration /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/shed_tools_conf.xml is /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/shed_tools
galaxy.tool_util.toolbox.base ERROR 2026-09-17 16:24:44,318 [pN:main.1,p:70319,tN:Thread-2] Error reading tool configuration file from path 'toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/d8d32326fbfb/rgrnastar/rg_rnaStar.xml': [Errno 2] No such file or directory
galaxy.tool_util.toolbox.base ERROR 2026-09-17 16:24:44,319 [pN:main.1,p:70319,tN:Thread-2] Error reading tool configuration file from path 'toolshed.g2.bx.psu.edu/repos/iuc/deseq2/05f9e54d7e81/deseq2/deseq2.xml': [Errno 2] No such file or directory
galaxy.tools WARNING 2026-09-17 16:24:44,319 [pN:main.1,p:70319,tN:Thread-2] The default shed tool config file (/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file
galaxy.tool_util.toolbox.base INFO 2026-09-17 16:24:44,320 [pN:main.1,p:70319,tN:Thread-2] Parsing the tool configuration /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/empty_tool_conf.xml
galaxy.tool_util.toolbox.base DEBUG 2026-09-17 16:24:44,321 [pN:main.1,p:70319,tN:Thread-2] Tool path for tool configuration /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/empty_tool_conf.xml is None
galaxy.tool_util.toolbox.base DEBUG 2026-09-17 16:24:44,321 [pN:main.1,p:70319,tN:Thread-2] Reading tools from config files finished (23.935 ms)
galaxy.tool_util.toolbox.base DEBUG 2026-09-17 16:24:44,321 [pN:main.1,p:70319,tN:Thread-2] Loading section: Built-in Converters
galaxy.tool_util.toolbox.base DEBUG 2026-09-17 16:24:44,322 [pN:main.1,p:70319,tN:Thread-2] Loading section: Tools from workflows
galaxy.tool_util.toolbox.base DEBUG 2026-09-17 16:24:44,322 [pN:main.1,p:70319,tN:Thread-2] Loading tool panel finished (0.818 ms)
galaxy.tool_util.toolbox.views.edam DEBUG 2026-09-17 16:24:44,324 [pN:main.1,p:70319,tN:Thread-2] Loading EDAM tool panel finished (1.033 ms)
galaxy.tool_util.toolbox.views.edam DEBUG 2026-09-17 16:24:44,324 [pN:main.1,p:70319,tN:Thread-2] Loading EDAM tool panel finished (0.686 ms)
galaxy.tool_util.toolbox.integrated_panel DEBUG 2026-09-17 16:24:44,325 [pN:main.1,p:70319,tN:Thread-2] Writing integrated tool panel config file to '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/integrated_tool_panel_conf.xml'
galaxy.tool_util.toolbox.views.edam DEBUG 2026-09-17 16:24:44,327 [pN:main.1,p:70319,tN:Thread-2] Loading EDAM tool panel finished (0.779 ms)
galaxy.tool_util.toolbox.views.edam DEBUG 2026-09-17 16:24:44,328 [pN:main.1,p:70319,tN:Thread-2] Loading EDAM tool panel finished (0.713 ms)
galaxy.datatypes.registry DEBUG 2026-09-17 16:24:44,331 [pN:main.1,p:70319,tN:Thread-2] Loaded external metadata tool: __SET_METADATA__
galaxy.tools.special_tools DEBUG 2026-09-17 16:24:44,333 [pN:main.1,p:70319,tN:Thread-2] Loaded history export tool: __EXPORT_HISTORY__
galaxy.tools.special_tools DEBUG 2026-09-17 16:24:44,334 [pN:main.1,p:70319,tN:Thread-2] Loaded history export to uri tool: __EXPORT_HISTORY_TO_URI__
galaxy.tools.special_tools DEBUG 2026-09-17 16:24:44,335 [pN:main.1,p:70319,tN:Thread-2] Loaded history import tool: __IMPORT_HISTORY__
galaxy.tools DEBUG 2026-09-17 16:24:44,336 [pN:main.1,p:70319,tN:Thread-2] No parameter model for tool '__DATA_FETCH__': Cannot generate a tool parameter model for upload_dataset inputs
galaxy.tools.special_tools DEBUG 2026-09-17 16:24:44,337 [pN:main.1,p:70319,tN:Thread-2] Loaded data fetch tool: __DATA_FETCH__
galaxy.queue_worker INFO 2026-09-17 16:24:44,337 [pN:main.1,p:70319,tN:Thread-2] Queuing async task rebuild_toolbox_search_index for main.1.
galaxy.queue_worker DEBUG 2026-09-17 16:24:44,339 [pN:main.1,p:70319,tN:Thread-2] Toolbox reload (48.523 ms)
galaxy.queue_worker INFO 2026-09-17 16:24:44,341 [pN:main.1,p:70319,tN:Thread-2] Instance 'main.1' received 'rebuild_toolbox_search_index' task, executing now.
galaxy.tools.search DEBUG 2026-09-17 16:24:44,342 [pN:main.1,p:70319,tN:Thread-2] Starting to build toolbox index of panel default.
galaxy.tools.search DEBUG 2026-09-17 16:24:44,389 [pN:main.1,p:70319,tN:Thread-2] Toolbox index of panel default finished (46.831 ms)
galaxy.tools.search DEBUG 2026-09-17 16:24:44,389 [pN:main.1,p:70319,tN:Thread-2] Starting to build toolbox index of panel my_panel.
galaxy.tools.search DEBUG 2026-09-17 16:24:44,392 [pN:main.1,p:70319,tN:Thread-2] Toolbox index of panel my_panel finished (2.325 ms)
galaxy.tools.search DEBUG 2026-09-17 16:24:44,392 [pN:main.1,p:70319,tN:Thread-2] Starting to build toolbox index of panel ontology:edam_operations.
galaxy.tools.search DEBUG 2026-09-17 16:24:44,429 [pN:main.1,p:70319,tN:Thread-2] Toolbox index of panel ontology:edam_operations finished (36.864 ms)
galaxy.tools.search DEBUG 2026-09-17 16:24:44,430 [pN:main.1,p:70319,tN:Thread-2] Starting to build toolbox index of panel ontology:edam_topics.
galaxy.tools.search DEBUG 2026-09-17 16:24:44,445 [pN:main.1,p:70319,tN:Thread-2] Toolbox index of panel ontology:edam_topics finished (15.650 ms)
galaxy.queue_worker INFO 2026-09-17 16:24:44,619 [pN:main.1,p:70319,tN:Thread-4 (check)] Sending reload_toolbox control task.
galaxy.tool_util.toolbox.base DEBUG 2026-09-17 16:24:44,913 [pN:main.1,p:70319,tN:WSGI_0] Appending to tool panel section: Tools from workflows
galaxy.tool_shed.util.repository_util DEBUG 2026-09-17 16:24:44,915 [pN:main.1,p:70319,tN:WSGI_0] Updating an existing row for repository 'deseq2' in the tool_shed_repository table, status set to 'installation_status.NEW'.
galaxy.tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager DEBUG 2026-09-17 16:24:44,922 [pN:main.1,p:70319,tN:WSGI_0] Building repository dependency relationships...
galaxy.tool_util.toolbox.base DEBUG 2026-09-17 16:24:44,923 [pN:main.1,p:70319,tN:WSGI_0] Appending to tool panel section: Tools from workflows
galaxy.tool_util.toolbox.base DEBUG 2026-09-17 16:24:44,931 [pN:main.1,p:70319,tN:WSGI_0] Appending to tool panel section: Tools from workflows
galaxy.tool_shed.galaxy_install.install_manager INFO 2026-09-17 16:24:44,941 [pN:main.1,p:70319,tN:WSGI_0] Cloning repository 'https://toolshed.g2.bx.psu.edu/repos/iuc/deseq2' at 35:05f9e54d7e81
charset_normalizer DEBUG 2026-09-17 16:24:48,344 [pN:main.1,p:70319,tN:WSGI_0] Encoding detection: ascii is most likely the one.
galaxy.tool_util.toolbox.base DEBUG 2026-09-17 16:24:48,452 [pN:main.1,p:70319,tN:WSGI_0] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.8+galaxy4, version: 2.11.40.8+galaxy4 into tool panel....
galaxy.tool_util.toolbox.integrated_panel DEBUG 2026-09-17 16:24:48,452 [pN:main.1,p:70319,tN:WSGI_0] Writing integrated tool panel config file to '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/integrated_tool_panel_conf.xml'
galaxy.app DEBUG 2026-09-17 16:24:48,454 [pN:main.1,p:70319,tN:WSGI_0] Waiting for toolbox reload
galaxy.tool_util.toolbox.watcher DEBUG 2026-09-17 16:24:48,666 [pN:main.1,p:70319,tN:Thread-4 (check)] The file '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/shed_tools_conf.xml' has changes.
galaxy.queue_worker INFO 2026-09-17 16:24:48,668 [pN:main.1,p:70319,tN:Thread-4 (check)] Queuing sync task reload_toolbox for main.1.
galaxy.queue_worker INFO 2026-09-17 16:24:49,525 [pN:main.1,p:70319,tN:Thread-2] Instance 'main.1' received 'reload_toolbox' task, executing now.
galaxy.queue_worker DEBUG 2026-09-17 16:24:49,527 [pN:main.1,p:70319,tN:Thread-2] Executing toolbox reload on 'main.1'
galaxy.util WARNING 2026-09-17 16:24:49,530 [pN:main.1,p:70319,tN:Thread-2] directory not found: /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/galaxy-dev/config/plugins/activities
galaxy.tools WARNING 2026-09-17 16:24:49,533 [pN:main.1,p:70319,tN:Thread-2] The default shed tool config file (/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file
galaxy.tool_util.toolbox.base INFO 2026-09-17 16:24:49,534 [pN:main.1,p:70319,tN:Thread-2] Parsing the tool configuration /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/tool_conf.xml
galaxy.tool_util.toolbox.base DEBUG 2026-09-17 16:24:49,536 [pN:main.1,p:70319,tN:Thread-2] Tool path for tool configuration /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/tool_conf.xml is None
galaxy.tool_util.parser.factory INFO 2026-09-17 16:24:49,537 [pN:main.1,p:70319,tN:Thread-2] Loading tool from YAML - this is experimental - tool will not function in future.
galaxy.tool_util.toolbox.base ERROR 2026-09-17 16:24:50,478 [pN:main.1,p:70319,tN:Thread-2] Error reading tool from path: /Users/mvandenb/src/worktrees/foundry/brc-c-auris/.foundry-runs/auris-scf1/galaxy-workflow.gxwf.yml
Traceback (most recent call last):
  File "/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/galaxy-dev/lib/galaxy/tool_util/toolbox/base.py", line 967, in _load_tool_tag_set
    tool = self.load_tool(concrete_path, use_cached=False)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/galaxy-dev/lib/galaxy/tool_util/toolbox/base.py", line 1222, in load_tool
    tool = self.create_tool(
           ^^^^^^^^^^^^^^^^^
  File "/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/galaxy-dev/lib/galaxy/tools/__init__.py", line 619, in create_tool
    return self._create_tool_from_source(tool_source, config_file=config_file, **kwds)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/galaxy-dev/lib/galaxy/tools/__init__.py", line 634, in _create_tool_from_source
    return create_tool_from_source(self.app, tool_source, **kwds)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/galaxy-dev/lib/galaxy/tools/__init__.py", line 448, in create_tool_from_source
    tool = ToolClass(config_file, tool_source, app, **kwds)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/galaxy-dev/lib/galaxy/tools/__init__.py", line 1099, in __init__
    raise e
  File "/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/galaxy-dev/lib/galaxy/tools/__init__.py", line 1096, in __init__
    self.parse(tool_source, guid=guid, dynamic=dynamic)
  File "/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/galaxy-dev/lib/galaxy/tools/__init__.py", line 1329, in parse
    raise Exception(f"Missing tool 'id' for tool at '{tool_source}'")
Exception: Missing tool 'id' for tool at 'YamlToolSource[/Users/mvandenb/src/worktrees/foundry/brc-c-auris/.foundry-runs/auris-scf1/galaxy-workflow.gxwf.yml]'
galaxy.tools WARNING 2026-09-17 16:24:50,479 [pN:main.1,p:70319,tN:Thread-2] The default shed tool config file (/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file
galaxy.tool_util.toolbox.base INFO 2026-09-17 16:24:50,480 [pN:main.1,p:70319,tN:Thread-2] Parsing the tool configuration /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/shed_tools_conf.xml
galaxy.tool_util.toolbox.base DEBUG 2026-09-17 16:24:50,480 [pN:main.1,p:70319,tN:Thread-2] Tool path for shed tool configuration /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/shed_tools_conf.xml is /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/shed_tools
galaxy.tool_util.toolbox.base ERROR 2026-09-17 16:24:50,480 [pN:main.1,p:70319,tN:Thread-2] Error reading tool configuration file from path 'toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/d8d32326fbfb/rgrnastar/rg_rnaStar.xml': [Errno 2] No such file or directory
galaxy.tools WARNING 2026-09-17 16:24:50,481 [pN:main.1,p:70319,tN:Thread-2] The default shed tool config file (/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file
galaxy.tool_util.toolbox.base INFO 2026-09-17 16:24:50,481 [pN:main.1,p:70319,tN:Thread-2] Parsing the tool configuration /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/empty_tool_conf.xml
galaxy.tool_util.toolbox.base DEBUG 2026-09-17 16:24:50,482 [pN:main.1,p:70319,tN:Thread-2] Tool path for tool configuration /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/empty_tool_conf.xml is None
galaxy.tool_util.toolbox.base DEBUG 2026-09-17 16:24:50,482 [pN:main.1,p:70319,tN:Thread-2] Reading tools from config files finished (949.113 ms)
galaxy.tool_util.toolbox.base DEBUG 2026-09-17 16:24:50,482 [pN:main.1,p:70319,tN:Thread-2] Loading section: Built-in Converters
galaxy.tool_util.toolbox.base DEBUG 2026-09-17 16:24:50,482 [pN:main.1,p:70319,tN:Thread-2] Loading section: Tools from workflows
galaxy.tool_util.toolbox.base DEBUG 2026-09-17 16:24:50,483 [pN:main.1,p:70319,tN:Thread-2] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.8+galaxy4, version: 2.11.40.8+galaxy4 into tool panel....
galaxy.tool_util.toolbox.base DEBUG 2026-09-17 16:24:50,483 [pN:main.1,p:70319,tN:Thread-2] Loading tool panel finished (0.679 ms)
galaxy.tool_util.toolbox.base DEBUG 2026-09-17 16:24:50,484 [pN:main.1,p:70319,tN:Thread-2] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.8+galaxy4, version: 2.11.40.8+galaxy4 into tool panel....
galaxy.tool_util.toolbox.views.edam DEBUG 2026-09-17 16:24:50,484 [pN:main.1,p:70319,tN:Thread-2] Loading EDAM tool panel finished (0.811 ms)
galaxy.tool_util.toolbox.base DEBUG 2026-09-17 16:24:50,485 [pN:main.1,p:70319,tN:Thread-2] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.8+galaxy4, version: 2.11.40.8+galaxy4 into tool panel....
galaxy.tool_util.toolbox.views.edam DEBUG 2026-09-17 16:24:50,485 [pN:main.1,p:70319,tN:Thread-2] Loading EDAM tool panel finished (0.757 ms)
galaxy.tool_util.toolbox.integrated_panel DEBUG 2026-09-17 16:24:50,485 [pN:main.1,p:70319,tN:Thread-2] Writing integrated tool panel config file to '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/integrated_tool_panel_conf.xml'
galaxy.tool_util.toolbox.base DEBUG 2026-09-17 16:24:50,486 [pN:main.1,p:70319,tN:Thread-2] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.8+galaxy4, version: 2.11.40.8+galaxy4 into tool panel....
galaxy.tool_util.toolbox.views.edam DEBUG 2026-09-17 16:24:50,487 [pN:main.1,p:70319,tN:Thread-2] Loading EDAM tool panel finished (0.800 ms)
galaxy.tool_util.toolbox.base DEBUG 2026-09-17 16:24:50,487 [pN:main.1,p:70319,tN:Thread-2] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.8+galaxy4, version: 2.11.40.8+galaxy4 into tool panel....
galaxy.tool_util.toolbox.views.edam DEBUG 2026-09-17 16:24:50,488 [pN:main.1,p:70319,tN:Thread-2] Loading EDAM tool panel finished (0.741 ms)
galaxy.datatypes.registry DEBUG 2026-09-17 16:24:50,490 [pN:main.1,p:70319,tN:Thread-2] Loaded external metadata tool: __SET_METADATA__
galaxy.tools.special_tools DEBUG 2026-09-17 16:24:50,491 [pN:main.1,p:70319,tN:Thread-2] Loaded history export tool: __EXPORT_HISTORY__
galaxy.tools.special_tools DEBUG 2026-09-17 16:24:50,492 [pN:main.1,p:70319,tN:Thread-2] Loaded history export to uri tool: __EXPORT_HISTORY_TO_URI__
galaxy.tools.special_tools DEBUG 2026-09-17 16:24:50,492 [pN:main.1,p:70319,tN:Thread-2] Loaded history import tool: __IMPORT_HISTORY__
galaxy.tools DEBUG 2026-09-17 16:24:50,493 [pN:main.1,p:70319,tN:Thread-2] No parameter model for tool '__DATA_FETCH__': Cannot generate a tool parameter model for upload_dataset inputs
galaxy.tools.special_tools DEBUG 2026-09-17 16:24:50,493 [pN:main.1,p:70319,tN:Thread-2] Loaded data fetch tool: __DATA_FETCH__
galaxy.queue_worker INFO 2026-09-17 16:24:50,494 [pN:main.1,p:70319,tN:Thread-2] Queuing async task rebuild_toolbox_search_index for main.1.
galaxy.queue_worker DEBUG 2026-09-17 16:24:50,495 [pN:main.1,p:70319,tN:Thread-2] Toolbox reload (968.450 ms)
galaxy.queue_worker INFO 2026-09-17 16:24:50,499 [pN:main.1,p:70319,tN:Thread-2] Instance 'main.1' received 'rebuild_toolbox_search_index' task, executing now.
galaxy.tools.search DEBUG 2026-09-17 16:24:50,499 [pN:main.1,p:70319,tN:Thread-2] Starting to build toolbox index of panel default.
galaxy.tools.search DEBUG 2026-09-17 16:24:50,531 [pN:main.1,p:70319,tN:Thread-2] Toolbox index of panel default finished (31.485 ms)
galaxy.tools.search DEBUG 2026-09-17 16:24:50,531 [pN:main.1,p:70319,tN:Thread-2] Starting to build toolbox index of panel my_panel.
galaxy.tools.search DEBUG 2026-09-17 16:24:50,533 [pN:main.1,p:70319,tN:Thread-2] Toolbox index of panel my_panel finished (1.279 ms)
galaxy.tools.search DEBUG 2026-09-17 16:24:50,533 [pN:main.1,p:70319,tN:Thread-2] Starting to build toolbox index of panel ontology:edam_operations.
galaxy.tools.search DEBUG 2026-09-17 16:24:50,563 [pN:main.1,p:70319,tN:Thread-2] Toolbox index of panel ontology:edam_operations finished (30.488 ms)
galaxy.tools.search DEBUG 2026-09-17 16:24:50,564 [pN:main.1,p:70319,tN:Thread-2] Starting to build toolbox index of panel ontology:edam_topics.
galaxy.app DEBUG 2026-09-17 16:24:50,584 [pN:main.1,p:70319,tN:WSGI_0] Finished waiting for toolbox reload (2130.127 ms)
galaxy.tool_util.deps.conda_util DEBUG 2026-09-17 16:24:50,586 [pN:main.1,p:70319,tN:WSGI_0] Executing command: /Users/mvandenb/src/worktrees/.planemo-home/conda/bin/conda create -y --quiet --strict-channel-priority --solver libmamba --override-channels --channel conda-forge --channel bioconda --name mulled-v1-8d4693d910782170c2aba3414da311da10ab7b89dd02e0bdd97408dcaf39d0fe bioconductor-deseq2=1.40.2 bioconductor-apeglm=1.22.1 bioconductor-rhdf5=2.44.0 bioconductor-tximport=1.28.0 bioconductor-genomicfeatures=1.52.1 r-ashr=2.2_63 r-getopt=1.20.3 r-ggrepel=0.9.3 r-gplots=3.1.3 r-pheatmap=1.0.12 r-rjson=0.2.21 r-base64enc=0.1_3
galaxy.tools.search DEBUG 2026-09-17 16:24:50,616 [pN:main.1,p:70319,tN:Thread-2] Toolbox index of panel ontology:edam_topics finished (51.954 ms)
galaxy.queue_worker INFO 2026-09-17 16:24:51,490 [pN:main.1,p:70319,tN:Thread-4 (check)] Sending reload_toolbox control task.
galaxy.tool_util.deps.conda_util DEBUG 2026-09-17 16:24:54,508 [pN:main.1,p:70319,tN:WSGI_0] Executing command: /Users/mvandenb/src/worktrees/.planemo-home/conda/bin/conda create -y --quiet --solver libmamba --override-channels --channel conda-forge --channel bioconda --name mulled-v1-8d4693d910782170c2aba3414da311da10ab7b89dd02e0bdd97408dcaf39d0fe bioconductor-deseq2=1.40.2 bioconductor-apeglm=1.22.1 bioconductor-rhdf5=2.44.0 bioconductor-tximport=1.28.0 bioconductor-genomicfeatures=1.52.1 r-ashr=2.2_63 r-getopt=1.20.3 r-ggrepel=0.9.3 r-gplots=3.1.3 r-pheatmap=1.0.12 r-rjson=0.2.21 r-base64enc=0.1_3
galaxy.tool_util.deps.resolvers.conda DEBUG 2026-09-17 16:24:58,482 [pN:main.1,p:70319,tN:WSGI_0] Removing failed conda install of [CondaTarget[package=bioconductor-deseq2,version=1.40.2], CondaTarget[package=bioconductor-apeglm,version=1.22.1], CondaTarget[package=bioconductor-rhdf5,version=2.44.0], CondaTarget[package=bioconductor-tximport,version=1.28.0], CondaTarget[package=bioconductor-genomicfeatures,version=1.52.1], CondaTarget[package=r-ashr,version=2.2_63], CondaTarget[package=r-getopt,version=1.20.3], CondaTarget[package=r-ggrepel,version=0.9.3], CondaTarget[package=r-gplots,version=3.1.3], CondaTarget[package=r-pheatmap,version=1.0.12], CondaTarget[package=r-rjson,version=0.2.21], CondaTarget[package=r-base64enc,version=0.1_3]]
galaxy.tool_util.deps.conda_util DEBUG 2026-09-17 16:24:58,482 [pN:main.1,p:70319,tN:WSGI_0] Executing command: /Users/mvandenb/src/worktrees/.planemo-home/conda/bin/conda create -y --quiet --strict-channel-priority --solver libmamba --override-channels --channel conda-forge --channel bioconda --name __bioconductor-deseq2@1.40.2 bioconductor-deseq2=1.40.2
galaxy.tool_util.deps.conda_util DEBUG 2026-09-17 16:24:59,803 [pN:main.1,p:70319,tN:WSGI_0] Executing command: /Users/mvandenb/src/worktrees/.planemo-home/conda/bin/conda create -y --quiet --solver libmamba --override-channels --channel conda-forge --channel bioconda --name __bioconductor-deseq2@1.40.2 bioconductor-deseq2=1.40.2
galaxy.tool_util.deps.resolvers.conda DEBUG 2026-09-17 16:25:01,172 [pN:main.1,p:70319,tN:WSGI_0] Removing failed conda install of bioconductor-deseq2, version '1.40.2'
galaxy.tool_util.deps.conda_util DEBUG 2026-09-17 16:25:01,173 [pN:main.1,p:70319,tN:WSGI_0] Executing command: /Users/mvandenb/src/worktrees/.planemo-home/conda/bin/conda create -y --quiet --strict-channel-priority --solver libmamba --override-channels --channel conda-forge --channel bioconda --name __bioconductor-apeglm@1.22.1 bioconductor-apeglm=1.22.1
galaxy.tool_util.deps.conda_util DEBUG 2026-09-17 16:25:02,103 [pN:main.1,p:70319,tN:WSGI_0] Executing command: /Users/mvandenb/src/worktrees/.planemo-home/conda/bin/conda create -y --quiet --solver libmamba --override-channels --channel conda-forge --channel bioconda --name __bioconductor-apeglm@1.22.1 bioconductor-apeglm=1.22.1
galaxy.tool_util.deps.resolvers.conda DEBUG 2026-09-17 16:25:03,044 [pN:main.1,p:70319,tN:WSGI_0] Removing failed conda install of bioconductor-apeglm, version '1.22.1'
galaxy.tool_util.deps.conda_util DEBUG 2026-09-17 16:25:03,045 [pN:main.1,p:70319,tN:WSGI_0] Executing command: /Users/mvandenb/src/worktrees/.planemo-home/conda/bin/conda create -y --quiet --strict-channel-priority --solver libmamba --override-channels --channel conda-forge --channel bioconda --name __bioconductor-rhdf5@2.44.0 bioconductor-rhdf5=2.44.0
galaxy.tool_util.deps.conda_util DEBUG 2026-09-17 16:25:03,839 [pN:main.1,p:70319,tN:WSGI_0] Executing command: /Users/mvandenb/src/worktrees/.planemo-home/conda/bin/conda create -y --quiet --solver libmamba --override-channels --channel conda-forge --channel bioconda --name __bioconductor-rhdf5@2.44.0 bioconductor-rhdf5=2.44.0
galaxy.tool_util.deps.resolvers.conda DEBUG 2026-09-17 16:25:04,636 [pN:main.1,p:70319,tN:WSGI_0] Removing failed conda install of bioconductor-rhdf5, version '2.44.0'
galaxy.tool_util.deps DEBUG 2026-09-17 16:25:04,636 [pN:main.1,p:70319,tN:WSGI_0] Using dependency bioconductor-tximport version 1.28.0 of type conda
galaxy.tool_util.deps.conda_util DEBUG 2026-09-17 16:25:04,637 [pN:main.1,p:70319,tN:WSGI_0] Executing command: /Users/mvandenb/src/worktrees/.planemo-home/conda/bin/conda create -y --quiet --strict-channel-priority --solver libmamba --override-channels --channel conda-forge --channel bioconda --name __bioconductor-genomicfeatures@1.52.1 bioconductor-genomicfeatures=1.52.1
galaxy.tool_util.deps.conda_util DEBUG 2026-09-17 16:25:05,757 [pN:main.1,p:70319,tN:WSGI_0] Executing command: /Users/mvandenb/src/worktrees/.planemo-home/conda/bin/conda create -y --quiet --solver libmamba --override-channels --channel conda-forge --channel bioconda --name __bioconductor-genomicfeatures@1.52.1 bioconductor-genomicfeatures=1.52.1
galaxy.tool_util.deps.resolvers.conda DEBUG 2026-09-17 16:25:06,900 [pN:main.1,p:70319,tN:WSGI_0] Removing failed conda install of bioconductor-genomicfeatures, version '1.52.1'
galaxy.tool_util.deps DEBUG 2026-09-17 16:25:06,901 [pN:main.1,p:70319,tN:WSGI_0] Using dependency r-ashr version 2.2_63 of type conda
galaxy.tool_util.deps DEBUG 2026-09-17 16:25:06,901 [pN:main.1,p:70319,tN:WSGI_0] Using dependency r-getopt version 1.20.3 of type conda
galaxy.tool_util.deps DEBUG 2026-09-17 16:25:06,901 [pN:main.1,p:70319,tN:WSGI_0] Using dependency r-ggrepel version 0.9.3 of type conda
galaxy.tool_util.deps DEBUG 2026-09-17 16:25:06,902 [pN:main.1,p:70319,tN:WSGI_0] Using dependency r-gplots version 3.1.3 of type conda
galaxy.tool_util.deps DEBUG 2026-09-17 16:25:06,902 [pN:main.1,p:70319,tN:WSGI_0] Using dependency r-pheatmap version 1.0.12 of type conda
galaxy.tool_util.deps DEBUG 2026-09-17 16:25:06,902 [pN:main.1,p:70319,tN:WSGI_0] Using dependency r-rjson version 0.2.21 of type conda
galaxy.tool_util.deps DEBUG 2026-09-17 16:25:06,902 [pN:main.1,p:70319,tN:WSGI_0] Using dependency r-base64enc version 0.1_3 of type conda
galaxy.tool_util.deps DEBUG 2026-09-17 16:25:06,902 [pN:main.1,p:70319,tN:WSGI_0] Using dependency bioconductor-deseq2 version None of type conda
galaxy.tool_util.deps DEBUG 2026-09-17 16:25:06,902 [pN:main.1,p:70319,tN:WSGI_0] Using dependency bioconductor-apeglm version None of type conda
galaxy.tool_util.deps DEBUG 2026-09-17 16:25:06,903 [pN:main.1,p:70319,tN:WSGI_0] Using dependency bioconductor-rhdf5 version None of type conda
galaxy.tool_util.deps DEBUG 2026-09-17 16:25:06,903 [pN:main.1,p:70319,tN:WSGI_0] Using dependency bioconductor-genomicfeatures version None of type conda
galaxy.tool_util.deps.conda_util DEBUG 2026-09-17 16:25:06,903 [pN:main.1,p:70319,tN:WSGI_0] Executing command: /Users/mvandenb/src/worktrees/.planemo-home/conda/bin/conda create -y --quiet --strict-channel-priority --solver libmamba --override-channels --channel conda-forge --channel bioconda --name mulled-v1-8d4693d910782170c2aba3414da311da10ab7b89dd02e0bdd97408dcaf39d0fe bioconductor-deseq2=1.40.2 bioconductor-apeglm=1.22.1 bioconductor-rhdf5=2.44.0 bioconductor-tximport=1.28.0 bioconductor-genomicfeatures=1.52.1 r-ashr=2.2_63 r-getopt=1.20.3 r-ggrepel=0.9.3 r-gplots=3.1.3 r-pheatmap=1.0.12 r-rjson=0.2.21 r-base64enc=0.1_3
galaxy.tool_util.deps.conda_util DEBUG 2026-09-17 16:25:10,681 [pN:main.1,p:70319,tN:WSGI_0] Executing command: /Users/mvandenb/src/worktrees/.planemo-home/conda/bin/conda create -y --quiet --solver libmamba --override-channels --channel conda-forge --channel bioconda --name mulled-v1-8d4693d910782170c2aba3414da311da10ab7b89dd02e0bdd97408dcaf39d0fe bioconductor-deseq2=1.40.2 bioconductor-apeglm=1.22.1 bioconductor-rhdf5=2.44.0 bioconductor-tximport=1.28.0 bioconductor-genomicfeatures=1.52.1 r-ashr=2.2_63 r-getopt=1.20.3 r-ggrepel=0.9.3 r-gplots=3.1.3 r-pheatmap=1.0.12 r-rjson=0.2.21 r-base64enc=0.1_3
galaxy.tool_util.deps.resolvers.conda DEBUG 2026-09-17 16:25:14,511 [pN:main.1,p:70319,tN:WSGI_0] Removing failed conda install of [CondaTarget[package=bioconductor-deseq2,version=1.40.2], CondaTarget[package=bioconductor-apeglm,version=1.22.1], CondaTarget[package=bioconductor-rhdf5,version=2.44.0], CondaTarget[package=bioconductor-tximport,version=1.28.0], CondaTarget[package=bioconductor-genomicfeatures,version=1.52.1], CondaTarget[package=r-ashr,version=2.2_63], CondaTarget[package=r-getopt,version=1.20.3], CondaTarget[package=r-ggrepel,version=0.9.3], CondaTarget[package=r-gplots,version=3.1.3], CondaTarget[package=r-pheatmap,version=1.0.12], CondaTarget[package=r-rjson,version=0.2.21], CondaTarget[package=r-base64enc,version=0.1_3]]
galaxy.tool_util.deps.conda_util DEBUG 2026-09-17 16:25:14,512 [pN:main.1,p:70319,tN:WSGI_0] Executing command: /Users/mvandenb/src/worktrees/.planemo-home/conda/bin/conda create -y --quiet --strict-channel-priority --solver libmamba --override-channels --channel conda-forge --channel bioconda --name __bioconductor-deseq2@1.40.2 bioconductor-deseq2=1.40.2
galaxy.tool_util.deps.conda_util DEBUG 2026-09-17 16:25:15,782 [pN:main.1,p:70319,tN:WSGI_0] Executing command: /Users/mvandenb/src/worktrees/.planemo-home/conda/bin/conda create -y --quiet --solver libmamba --override-channels --channel conda-forge --channel bioconda --name __bioconductor-deseq2@1.40.2 bioconductor-deseq2=1.40.2
galaxy.tool_util.deps.resolvers.conda DEBUG 2026-09-17 16:25:17,109 [pN:main.1,p:70319,tN:WSGI_0] Removing failed conda install of bioconductor-deseq2, version '1.40.2'
galaxy.tool_util.deps.conda_util DEBUG 2026-09-17 16:25:17,110 [pN:main.1,p:70319,tN:WSGI_0] Executing command: /Users/mvandenb/src/worktrees/.planemo-home/conda/bin/conda create -y --quiet --strict-channel-priority --solver libmamba --override-channels --channel conda-forge --channel bioconda --name __bioconductor-apeglm@1.22.1 bioconductor-apeglm=1.22.1
galaxy.tool_util.deps.conda_util DEBUG 2026-09-17 16:25:17,961 [pN:main.1,p:70319,tN:WSGI_0] Executing command: /Users/mvandenb/src/worktrees/.planemo-home/conda/bin/conda create -y --quiet --solver libmamba --override-channels --channel conda-forge --channel bioconda --name __bioconductor-apeglm@1.22.1 bioconductor-apeglm=1.22.1
galaxy.tool_util.deps.resolvers.conda DEBUG 2026-09-17 16:25:18,783 [pN:main.1,p:70319,tN:WSGI_0] Removing failed conda install of bioconductor-apeglm, version '1.22.1'
galaxy.tool_util.deps.conda_util DEBUG 2026-09-17 16:25:18,784 [pN:main.1,p:70319,tN:WSGI_0] Executing command: /Users/mvandenb/src/worktrees/.planemo-home/conda/bin/conda create -y --quiet --strict-channel-priority --solver libmamba --override-channels --channel conda-forge --channel bioconda --name __bioconductor-rhdf5@2.44.0 bioconductor-rhdf5=2.44.0
galaxy.tool_util.deps.conda_util DEBUG 2026-09-17 16:25:19,609 [pN:main.1,p:70319,tN:WSGI_0] Executing command: /Users/mvandenb/src/worktrees/.planemo-home/conda/bin/conda create -y --quiet --solver libmamba --override-channels --channel conda-forge --channel bioconda --name __bioconductor-rhdf5@2.44.0 bioconductor-rhdf5=2.44.0
galaxy.tool_util.deps.resolvers.conda DEBUG 2026-09-17 16:25:20,395 [pN:main.1,p:70319,tN:WSGI_0] Removing failed conda install of bioconductor-rhdf5, version '2.44.0'
galaxy.tool_util.deps DEBUG 2026-09-17 16:25:20,395 [pN:main.1,p:70319,tN:WSGI_0] Using dependency bioconductor-tximport version 1.28.0 of type conda
galaxy.tool_util.deps.conda_util DEBUG 2026-09-17 16:25:20,395 [pN:main.1,p:70319,tN:WSGI_0] Executing command: /Users/mvandenb/src/worktrees/.planemo-home/conda/bin/conda create -y --quiet --strict-channel-priority --solver libmamba --override-channels --channel conda-forge --channel bioconda --name __bioconductor-genomicfeatures@1.52.1 bioconductor-genomicfeatures=1.52.1
galaxy.tool_util.deps.conda_util DEBUG 2026-09-17 16:25:21,499 [pN:main.1,p:70319,tN:WSGI_0] Executing command: /Users/mvandenb/src/worktrees/.planemo-home/conda/bin/conda create -y --quiet --solver libmamba --override-channels --channel conda-forge --channel bioconda --name __bioconductor-genomicfeatures@1.52.1 bioconductor-genomicfeatures=1.52.1
galaxy.tool_util.deps.resolvers.conda DEBUG 2026-09-17 16:25:22,607 [pN:main.1,p:70319,tN:WSGI_0] Removing failed conda install of bioconductor-genomicfeatures, version '1.52.1'
galaxy.tool_util.deps DEBUG 2026-09-17 16:25:22,608 [pN:main.1,p:70319,tN:WSGI_0] Using dependency r-ashr version 2.2_63 of type conda
galaxy.tool_util.deps DEBUG 2026-09-17 16:25:22,608 [pN:main.1,p:70319,tN:WSGI_0] Using dependency r-getopt version 1.20.3 of type conda
galaxy.tool_util.deps DEBUG 2026-09-17 16:25:22,608 [pN:main.1,p:70319,tN:WSGI_0] Using dependency r-ggrepel version 0.9.3 of type conda
galaxy.tool_util.deps DEBUG 2026-09-17 16:25:22,608 [pN:main.1,p:70319,tN:WSGI_0] Using dependency r-gplots version 3.1.3 of type conda
galaxy.tool_util.deps DEBUG 2026-09-17 16:25:22,608 [pN:main.1,p:70319,tN:WSGI_0] Using dependency r-pheatmap version 1.0.12 of type conda
galaxy.tool_util.deps DEBUG 2026-09-17 16:25:22,609 [pN:main.1,p:70319,tN:WSGI_0] Using dependency r-rjson version 0.2.21 of type conda
galaxy.tool_util.deps DEBUG 2026-09-17 16:25:22,609 [pN:main.1,p:70319,tN:WSGI_0] Using dependency r-base64enc version 0.1_3 of type conda
galaxy.tool_util.deps DEBUG 2026-09-17 16:25:22,609 [pN:main.1,p:70319,tN:WSGI_0] Using dependency bioconductor-deseq2 version None of type conda
galaxy.tool_util.deps DEBUG 2026-09-17 16:25:22,609 [pN:main.1,p:70319,tN:WSGI_0] Using dependency bioconductor-apeglm version None of type conda
galaxy.tool_util.deps DEBUG 2026-09-17 16:25:22,609 [pN:main.1,p:70319,tN:WSGI_0] Using dependency bioconductor-rhdf5 version None of type conda
galaxy.tool_util.deps DEBUG 2026-09-17 16:25:22,610 [pN:main.1,p:70319,tN:WSGI_0] Using dependency bioconductor-genomicfeatures version None of type conda
galaxy.tool_util.deps DEBUG 2026-09-17 16:25:22,610 [pN:main.1,p:70319,tN:WSGI_0] Cached dependencies directory '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpzx1whhuh/deps/_cache/fab2ffb9' already exists, skipping build
galaxy.tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager DEBUG 2026-09-17 16:25:23,307 [pN:main.1,p:70319,tN:WSGI_0] Creating repository dependency objects...
galaxy.tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager INFO 2026-09-17 16:25:24,337 [pN:main.1,p:70319,tN:WSGI_0] Skipping installation of revision e188c9826e0f of repository 'compose_text_param' because it was installed with the (possibly updated) revision e188c9826e0f and its current installation status is 'Installed'.
galaxy.tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager DEBUG 2026-09-17 16:25:24,337 [pN:main.1,p:70319,tN:WSGI_0] Building repository dependency relationships...
galaxy.tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager DEBUG 2026-09-17 16:25:25,037 [pN:main.1,p:70319,tN:WSGI_0] Creating repository dependency objects...
galaxy.tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager INFO 2026-09-17 16:25:26,170 [pN:main.1,p:70319,tN:WSGI_0] Skipping installation of revision e188c9826e0f of repository 'compose_text_param' because it was installed with the (possibly updated) revision e188c9826e0f and its current installation status is 'Installed'.
galaxy.tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager DEBUG 2026-09-17 16:25:26,172 [pN:main.1,p:70319,tN:WSGI_0] Building repository dependency relationships...
galaxy.tools INFO 2026-09-17 16:25:26,407 [pN:main.1,p:70319,tN:AnyIO worker thread] Validated and populated state for tool request (0.242 ms)
galaxy.tools.actions.upload DEBUG 2026-09-17 16:25:26,410 [pN:main.1,p:70319,tN:AnyIO worker thread] Persisted uploads (0.005 ms)
galaxy.tools.actions.upload DEBUG 2026-09-17 16:25:26,426 [pN:main.1,p:70319,tN:AnyIO worker thread] Created upload job (0.697 ms)
galaxy.tools.execute DEBUG 2026-09-17 16:25:26,426 [pN:main.1,p:70319,tN:AnyIO worker thread] Tool __DATA_FETCH__ created job None (15.941 ms)
galaxy.tools.execute DEBUG 2026-09-17 16:25:26,500 [pN:main.1,p:70319,tN:AnyIO worker thread] Created 1 job(s) for tool __DATA_FETCH__ request (91.869 ms)
galaxy.tools INFO 2026-09-17 16:25:36,850 [pN:main.1,p:70319,tN:AnyIO worker thread] Validated and populated state for tool request (0.473 ms)
galaxy.tools.actions.upload DEBUG 2026-09-17 16:25:36,852 [pN:main.1,p:70319,tN:AnyIO worker thread] Persisted uploads (0.006 ms)
galaxy.tools.actions.upload DEBUG 2026-09-17 16:25:36,869 [pN:main.1,p:70319,tN:AnyIO worker thread] Created upload job (1.045 ms)
galaxy.tools.execute DEBUG 2026-09-17 16:25:36,869 [pN:main.1,p:70319,tN:AnyIO worker thread] Tool __DATA_FETCH__ created job None (16.863 ms)
galaxy.tools.execute DEBUG 2026-09-17 16:25:36,879 [pN:main.1,p:70319,tN:AnyIO worker thread] Created 1 job(s) for tool __DATA_FETCH__ request (28.281 ms)
galaxy.tools INFO 2026-09-17 16:25:40,801 [pN:main.1,p:70319,tN:AnyIO worker thread] Validated and populated state for tool request (0.371 ms)
galaxy.tools.actions.upload DEBUG 2026-09-17 16:25:40,803 [pN:main.1,p:70319,tN:AnyIO worker thread] Persisted uploads (0.002 ms)
galaxy.tools.actions.upload DEBUG 2026-09-17 16:25:40,816 [pN:main.1,p:70319,tN:AnyIO worker thread] Created upload job (0.759 ms)
galaxy.tools.execute DEBUG 2026-09-17 16:25:40,816 [pN:main.1,p:70319,tN:AnyIO worker thread] Tool __DATA_FETCH__ created job None (13.484 ms)
galaxy.tools.execute DEBUG 2026-09-17 16:25:40,824 [pN:main.1,p:70319,tN:AnyIO worker thread] Created 1 job(s) for tool __DATA_FETCH__ request (22.222 ms)
galaxy.tools INFO 2026-09-17 16:25:45,865 [pN:main.1,p:70319,tN:AnyIO worker thread] Validated and populated state for tool request (0.253 ms)
galaxy.tools.actions.upload DEBUG 2026-09-17 16:25:45,866 [pN:main.1,p:70319,tN:AnyIO worker thread] Persisted uploads (0.002 ms)
galaxy.tools.actions.upload DEBUG 2026-09-17 16:25:45,876 [pN:main.1,p:70319,tN:AnyIO worker thread] Created upload job (0.624 ms)
galaxy.tools.execute DEBUG 2026-09-17 16:25:45,877 [pN:main.1,p:70319,tN:AnyIO worker thread] Tool __DATA_FETCH__ created job None (10.256 ms)
galaxy.tools.execute DEBUG 2026-09-17 16:25:45,883 [pN:main.1,p:70319,tN:AnyIO worker thread] Created 1 job(s) for tool __DATA_FETCH__ request (17.482 ms)
galaxy.tools INFO 2026-09-17 16:25:50,075 [pN:main.1,p:70319,tN:AnyIO worker thread] Validated and populated state for tool request (0.271 ms)
galaxy.tools.actions.upload DEBUG 2026-09-17 16:25:50,076 [pN:main.1,p:70319,tN:AnyIO worker thread] Persisted uploads (0.002 ms)
galaxy.tools.actions.upload DEBUG 2026-09-17 16:25:50,086 [pN:main.1,p:70319,tN:AnyIO worker thread] Created upload job (0.733 ms)
galaxy.tools.execute DEBUG 2026-09-17 16:25:50,087 [pN:main.1,p:70319,tN:AnyIO worker thread] Tool __DATA_FETCH__ created job None (10.555 ms)
galaxy.tools.execute DEBUG 2026-09-17 16:25:50,094 [pN:main.1,p:70319,tN:AnyIO worker thread] Created 1 job(s) for tool __DATA_FETCH__ request (18.737 ms)
galaxy.tools INFO 2026-09-17 16:25:54,019 [pN:main.1,p:70319,tN:AnyIO worker thread] Validated and populated state for tool request (0.247 ms)
galaxy.tools.actions.upload DEBUG 2026-09-17 16:25:54,020 [pN:main.1,p:70319,tN:AnyIO worker thread] Persisted uploads (0.002 ms)
galaxy.tools.actions.upload DEBUG 2026-09-17 16:25:54,029 [pN:main.1,p:70319,tN:AnyIO worker thread] Created upload job (0.586 ms)
galaxy.tools.execute DEBUG 2026-09-17 16:25:54,030 [pN:main.1,p:70319,tN:AnyIO worker thread] Tool __DATA_FETCH__ created job None (9.490 ms)
galaxy.tools.execute DEBUG 2026-09-17 16:25:54,036 [pN:main.1,p:70319,tN:AnyIO worker thread] Created 1 job(s) for tool __DATA_FETCH__ request (16.748 ms)
galaxy.tools INFO 2026-09-17 16:25:58,266 [pN:main.1,p:70319,tN:AnyIO worker thread] Validated and populated state for tool request (0.425 ms)
galaxy.tools.actions.upload DEBUG 2026-09-17 16:25:58,267 [pN:main.1,p:70319,tN:AnyIO worker thread] Persisted uploads (0.004 ms)
galaxy.tools.actions.upload DEBUG 2026-09-17 16:25:58,283 [pN:main.1,p:70319,tN:AnyIO worker thread] Created upload job (0.817 ms)
galaxy.tools.execute DEBUG 2026-09-17 16:25:58,283 [pN:main.1,p:70319,tN:AnyIO worker thread] Tool __DATA_FETCH__ created job None (15.955 ms)
galaxy.tools.execute DEBUG 2026-09-17 16:25:58,292 [pN:main.1,p:70319,tN:AnyIO worker thread] Created 1 job(s) for tool __DATA_FETCH__ request (25.282 ms)
galaxy.tools INFO 2026-09-17 16:26:02,251 [pN:main.1,p:70319,tN:AnyIO worker thread] Validated and populated state for tool request (0.286 ms)
galaxy.tools.actions.upload DEBUG 2026-09-17 16:26:02,252 [pN:main.1,p:70319,tN:AnyIO worker thread] Persisted uploads (0.003 ms)
galaxy.tools.actions.upload DEBUG 2026-09-17 16:26:02,263 [pN:main.1,p:70319,tN:AnyIO worker thread] Created upload job (0.643 ms)
galaxy.tools.execute DEBUG 2026-09-17 16:26:02,263 [pN:main.1,p:70319,tN:AnyIO worker thread] Tool __DATA_FETCH__ created job None (10.976 ms)
galaxy.tools.execute DEBUG 2026-09-17 16:26:02,270 [pN:main.1,p:70319,tN:AnyIO worker thread] Created 1 job(s) for tool __DATA_FETCH__ request (18.443 ms)
galaxy.tools INFO 2026-09-17 16:26:06,268 [pN:main.1,p:70319,tN:AnyIO worker thread] Validated and populated state for tool request (0.238 ms)
galaxy.tools.actions.upload DEBUG 2026-09-17 16:26:06,269 [pN:main.1,p:70319,tN:AnyIO worker thread] Persisted uploads (0.002 ms)
galaxy.tools.actions.upload DEBUG 2026-09-17 16:26:06,278 [pN:main.1,p:70319,tN:AnyIO worker thread] Created upload job (0.588 ms)
galaxy.tools.execute DEBUG 2026-09-17 16:26:06,278 [pN:main.1,p:70319,tN:AnyIO worker thread] Tool __DATA_FETCH__ created job None (9.223 ms)
galaxy.tools.execute DEBUG 2026-09-17 16:26:06,285 [pN:main.1,p:70319,tN:AnyIO worker thread] Created 1 job(s) for tool __DATA_FETCH__ request (16.262 ms)
galaxy.tools INFO 2026-09-17 16:26:10,560 [pN:main.1,p:70319,tN:AnyIO worker thread] Validated and populated state for tool request (0.487 ms)
galaxy.tools.actions.upload DEBUG 2026-09-17 16:26:10,562 [pN:main.1,p:70319,tN:AnyIO worker thread] Persisted uploads (0.004 ms)
galaxy.tools.actions.upload DEBUG 2026-09-17 16:26:10,579 [pN:main.1,p:70319,tN:AnyIO worker thread] Created upload job (0.839 ms)
galaxy.tools.execute DEBUG 2026-09-17 16:26:10,579 [pN:main.1,p:70319,tN:AnyIO worker thread] Tool __DATA_FETCH__ created job None (17.400 ms)
galaxy.tools.execute DEBUG 2026-09-17 16:26:10,588 [pN:main.1,p:70319,tN:AnyIO worker thread] Created 1 job(s) for tool __DATA_FETCH__ request (27.278 ms)
galaxy.tools INFO 2026-09-17 16:26:14,665 [pN:main.1,p:70319,tN:AnyIO worker thread] Validated and populated state for tool request (0.475 ms)
galaxy.tools.actions.upload DEBUG 2026-09-17 16:26:14,666 [pN:main.1,p:70319,tN:AnyIO worker thread] Persisted uploads (0.005 ms)
galaxy.tools.actions.upload DEBUG 2026-09-17 16:26:14,682 [pN:main.1,p:70319,tN:AnyIO worker thread] Created upload job (0.836 ms)
galaxy.tools.execute DEBUG 2026-09-17 16:26:14,682 [pN:main.1,p:70319,tN:AnyIO worker thread] Tool __DATA_FETCH__ created job None (15.589 ms)
galaxy.tools.execute DEBUG 2026-09-17 16:26:14,691 [pN:main.1,p:70319,tN:AnyIO worker thread] Created 1 job(s) for tool __DATA_FETCH__ request (25.273 ms)
galaxy.tools INFO 2026-09-17 16:26:18,682 [pN:main.1,p:70319,tN:AnyIO worker thread] Validated and populated state for tool request (0.312 ms)
galaxy.tools.actions.upload DEBUG 2026-09-17 16:26:18,684 [pN:main.1,p:70319,tN:AnyIO worker thread] Persisted uploads (0.002 ms)
galaxy.tools.actions.upload DEBUG 2026-09-17 16:26:18,696 [pN:main.1,p:70319,tN:AnyIO worker thread] Created upload job (0.707 ms)
galaxy.tools.execute DEBUG 2026-09-17 16:26:18,696 [pN:main.1,p:70319,tN:AnyIO worker thread] Tool __DATA_FETCH__ created job None (12.061 ms)
galaxy.tools.execute DEBUG 2026-09-17 16:26:18,703 [pN:main.1,p:70319,tN:AnyIO worker thread] Created 1 job(s) for tool __DATA_FETCH__ request (21.037 ms)
galaxy.managers.collections_util DEBUG 2026-09-17 16:26:22,704 [pN:main.1,p:70319,tN:AnyIO worker thread] Validating 6 element identifiers for collection creation.
galaxy.managers.collections_util DEBUG 2026-09-17 16:26:22,704 [pN:main.1,p:70319,tN:AnyIO worker thread] Validating 2 element identifiers for collection creation.
galaxy.managers.collections_util DEBUG 2026-09-17 16:26:22,705 [pN:main.1,p:70319,tN:AnyIO worker thread] Validating 2 element identifiers for collection creation.
galaxy.managers.collections_util DEBUG 2026-09-17 16:26:22,705 [pN:main.1,p:70319,tN:AnyIO worker thread] Validating 2 element identifiers for collection creation.
galaxy.managers.collections_util DEBUG 2026-09-17 16:26:22,705 [pN:main.1,p:70319,tN:AnyIO worker thread] Validating 2 element identifiers for collection creation.
galaxy.managers.collections_util DEBUG 2026-09-17 16:26:22,705 [pN:main.1,p:70319,tN:AnyIO worker thread] Validating 2 element identifiers for collection creation.
galaxy.managers.collections_util DEBUG 2026-09-17 16:26:22,705 [pN:main.1,p:70319,tN:AnyIO worker thread] Validating 2 element identifiers for collection creation.
galaxy.managers.collections DEBUG 2026-09-17 16:26:22,710 [pN:main.1,p:70319,tN:AnyIO worker thread] Created collection with 6 elements
galaxy.files.uris DEBUG 2026-09-17 16:26:22,746 [pN:main.1,p:70319,tN:AnyIO worker thread] parsed url ftp.ncbi.nlm.nih.gov, port:  None
galaxy.tools INFO 2026-09-17 16:26:23,020 [pN:main.1,p:70319,tN:AnyIO worker thread] Validated and populated state for tool request (1.963 ms)
galaxy.tools.actions.upload DEBUG 2026-09-17 16:26:23,027 [pN:main.1,p:70319,tN:AnyIO worker thread] Persisted uploads (0.012 ms)
galaxy.tools.actions.upload DEBUG 2026-09-17 16:26:23,058 [pN:main.1,p:70319,tN:AnyIO worker thread] Created upload job (1.336 ms)
galaxy.tools.execute DEBUG 2026-09-17 16:26:23,058 [pN:main.1,p:70319,tN:AnyIO worker thread] Tool __DATA_FETCH__ created job None (31.490 ms)
galaxy.tools.execute DEBUG 2026-09-17 16:26:23,071 [pN:main.1,p:70319,tN:AnyIO worker thread] Created 1 job(s) for tool __DATA_FETCH__ request (47.454 ms)
galaxy.files.uris DEBUG 2026-09-17 16:26:27,883 [pN:main.1,p:70319,tN:AnyIO worker thread] parsed url ftp.ncbi.nlm.nih.gov, port:  None
galaxy.tools INFO 2026-09-17 16:26:27,888 [pN:main.1,p:70319,tN:AnyIO worker thread] Validated and populated state for tool request (0.367 ms)
galaxy.tools.actions.upload DEBUG 2026-09-17 16:26:27,889 [pN:main.1,p:70319,tN:AnyIO worker thread] Persisted uploads (0.004 ms)
galaxy.tools.actions.upload DEBUG 2026-09-17 16:26:27,903 [pN:main.1,p:70319,tN:AnyIO worker thread] Created upload job (0.820 ms)
galaxy.tools.execute DEBUG 2026-09-17 16:26:27,904 [pN:main.1,p:70319,tN:AnyIO worker thread] Tool __DATA_FETCH__ created job None (14.359 ms)
galaxy.tools.execute DEBUG 2026-09-17 16:26:27,912 [pN:main.1,p:70319,tN:AnyIO worker thread] Created 1 job(s) for tool __DATA_FETCH__ request (23.575 ms)
Failed to execute Galaxy activity, throwing ErrorRunResponse
Shut down
supervisord has terminated
There were problems with 1 test(s) - out of 1 test(s) executed. See /Users/mvandenb/src/worktrees/foundry/brc-c-auris/.foundry-runs/auris-scf1/planemo-smoke.html for detailed breakdown.
Traceback (most recent call last):
  File "/Users/mvandenb/.local/share/uv/tools/planemo/lib/python3.13/site-packages/planemo/galaxy/activity.py", line 89, in execute
    return _execute(ctx, config, runnable, job_path, fail_fast=fail_fast, **kwds)
  File "/Users/mvandenb/.local/share/uv/tools/planemo/lib/python3.13/site-packages/planemo/galaxy/activity.py", line 313, in _execute
    invocation = user_gi.workflows.invoke_workflow(
        workflow_id,
    ...<3 lines>...
        inputs_by="name",
    )
  File "/Users/mvandenb/.local/share/uv/tools/planemo/lib/python3.13/site-packages/bioblend/galaxy/workflows/__init__.py", line 593, in invoke_workflow
    return self._post(payload, url=url)
           ~~~~~~~~~~^^^^^^^^^^^^^^^^^^
  File "/Users/mvandenb/.local/share/uv/tools/planemo/lib/python3.13/site-packages/bioblend/galaxy/client.py", line 196, in _post
    return self.gi.make_post_request(url, payload=payload, files_attached=files_attached)
           ~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mvandenb/.local/share/uv/tools/planemo/lib/python3.13/site-packages/bioblend/galaxyclient.py", line 206, in make_post_request
    raise ConnectionError(
    ...<3 lines>...
    )
bioblend.ConnectionError: Unexpected HTTP status code: 400: {"err_msg":"Workflow was not invoked; the following required tools are not installed: toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (version 5.2+galaxy2), toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param (version 0.1.1), toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value (version 0.2.0), toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc (version 0.74+galaxy1), toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star (version 2.7.11b+galaxy1), toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts (version 2.1.1+galaxy1), toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2 (version 2.11.40.8+galaxy4)","err_code":0}
galaxy-workflow.gxwf.yml_1: failed
=== PLANEMO_EXIT=1 2026-09-17T14:26:43Z ===