Updating workflows/bacterial_genomics/amr_gene_detection from 1.1.5 to 1.1.6

[clsiguret]

Hello,

This code (close #642):

• Changes the StarAMR wrapper version: toolshed.g2.bx.psu.edu/repos/nml/staramr/staramr_search/0.10.0+galaxy1 to toolshed.g2.bx.psu.edu/repos/iuc/staramr/staramr_search/0.11.0+galaxy2
• Changes the ToolDistillator wrapper version:
  • toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator/tooldistillator/0.9.1+galaxy1 to toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator/tooldistillator/0.9.2+galaxy0
  • toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator_summarize/tooldistillator_summarize/0.9.1+galaxy1 to toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator_summarize/tooldistillator_summarize/0.9.2+galaxy0
• Adds 2 more input parameters
• Changes the output name/tag of Tooldistillator to tooldistillator_[results|summarize]_amr
• Fixes syntax and parameter errors

This workflow uses 1 more database (StarAMR) which must be available on http://datacache.galaxyproject.org/: staramr_downloaded_07042025_resfinder_d1e607b_pointfinder_694919f_plasmidfinder_3e77502 (Issue galaxyproject/idc#66)
--> available here : http://datacache.galaxyproject.org/indexes/staramr/

Thanks 😃

[github-actions]

Test Results (powered by Planemo)

Test Summary

Test State	Count
Total	1
Passed	0
Error	1
Failure	0
Skipped	0

Errored Tests

• ❌ amr_gene_detection.ga_0

  Execution Problem:

  • Unexpected HTTP status code: 400: {"err_msg":"Workflow was not invoked; the following required tools are not installed: toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator/tooldistillator/0.9.2+galaxy0 (version 0.9.2+galaxy0), toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator_summarize/tooldistillator_summarize/0.9.2+galaxy0 (version 0.9.2+galaxy0)","err_code":0}
    

[clsiguret]

Error in test Combine chunked test results:
Unexpected HTTP status code: 400: {"err_msg":"Workflow was not invoked; the following required tools are not installed: toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator/tooldistillator/0.9.2+galaxy0 (version 0.9.2+galaxy0), toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator_summarize/tooldistillator_summarize/0.9.2+galaxy0 (version 0.9.2+galaxy0)","err_code":0}

Do I need to do something ?

I updated ToolDistillator wrapper last week, so today I changed the version in the .ga file

[clsiguret]

I think the tests are too long with a tool, I don't know which ...

[github-actions]

Test Results (powered by Planemo)

Test Summary

Test State	Count
Total	1
Passed	0
Error	1
Failure	0
Skipped	0

Errored Tests

• ❌ amr_gene_detection.ga_0

  Execution Problem:

  • Failed to upload data, upload state is [error].
    

[mvdbeek]

❌ Failed job 7b670abbc603e830:
   Tool ID: 
toolshed.g2.bx.psu.edu/repos/iuc/staramr/staramr_search/0.11.0+galaxy2
   Exit code: 1
   Command line: ln -s 
'/tmp/tmpuj1m12ec/files/9/2/0/dataset_920db1e3-d89a-4436-921f-c770e5d0d717.dat' 
shovill_contigs_fasta_contig00089.fasta.fasta &&    staramr search  -d 
'/cvmfs/data.galaxyproject.org/byhand/staramr/resfinder_d1e607b_pointfinder_6949
19f_plasmidfinder_3e77502' --nprocs "${GALAXY_SLOTS:-1}"  
--genome-size-lower-bound 4000000 --genome-size-upper-bound 6000000 
--minimum-N50-value 10000 --minimum-contig-length 300 
--unacceptable-number-contigs 1000  --pid-threshold 90.0 
--percent-length-overlap-resfinder 60.0 --percent-length-overlap-plasmidfinder 
60.0 --percent-length-overlap-pointfinder 95.0          --output-summary 
'/tmp/tmpuj1m12ec/job_working_directory/000/2/outputs/dataset_d7218930-38e2-4c19
-b085-dfb29a6c00ab.dat' --output-detailed-summary 
'/tmp/tmpuj1m12ec/job_working_directory/000/2/outputs/dataset_40443a57-dfbe-4898
-b9d6-7020b7bd0a59.dat' --output-resfinder 
'/tmp/tmpuj1m12ec/job_working_directory/000/2/outputs/dataset_e2c7823a-e270-4912
-b851-e0739c75aa42.dat' --output-plasmidfinder 
'/tmp/tmpuj1m12ec/job_working_directory/000/2/outputs/dataset_07394792-761c-4243
-a5e8-5fac5d6ec42b.dat' --output-settings 
'/tmp/tmpuj1m12ec/job_working_directory/000/2/outputs/dataset_f8bef2fa-96af-4649
-b4b1-9b1c17e87cdf.dat' --output-excel results.xlsx --output-mlst 
'/tmp/tmpuj1m12ec/job_working_directory/000/2/outputs/dataset_dcf5a734-343a-4c57
-bfb3-b2a5bb0628ec.dat'  --output-hits-dir staramr_hits  --output-pointfinder 
'/tmp/tmpuj1m12ec/job_working_directory/000/2/outputs/dataset_33a89720-118e-4fd2
-8624-acb0e510272b.dat' --pointfinder-organism 'enterococcus_faecalis'  
shovill_contigs_fasta_contig00089.fasta.fasta
   Stderr:
     /usr/local/lib/python3.9/site-packages/Bio/Application/__init__.py:39: 
BiopythonDeprecationWarning: The Bio.Application modules and modules relying on 
it have been deprecated.
     Due to the on going maintenance burden of keeping command line application
     wrappers up to date, we have decided to deprecate and eventually remove 
these
     modules.
     We instead now recommend building your command line and invoking it 
directly
     with the subprocess module.
       warnings.warn(
     2025-08-22 16:23:05 ERROR: SHA is empty, possible dubious ownership in the 
repository at 
/cvmfs/data.galaxyproject.org/byhand/staramr/resfinder_d1e607b_pointfinder_69491
9f_plasmidfinder_3e77502/update/resfinder.
                 If this is unintended run:
                           "git config --global --add safe.directory 
/cvmfs/data.galaxyproject.org/byhand/staramr/resfinder_d1e607b_pointfinder_69491
9f_plasmidfinder_3e77502/update/resfinder" 
     Traceback (most recent call last):
       File "/usr/local/bin/staramr", line 68, in <module>
         args.run_command(args)
       File 
"/usr/local/lib/python3.9/site-packages/staramr/subcommand/Search.py", line 372,
in run
         if not 
AMRDatabasesManager.is_database_repos_default_commits(database_repos):
       File 
"/usr/local/lib/python3.9/site-packages/staramr/databases/AMRDatabasesManager.py
", line 89, in is_database_repos_default_commits
         return database_repos.is_at_commits(self.DEFAULT_COMMITS)
       File 
"/usr/local/lib/python3.9/site-packages/staramr/databases/BlastDatabaseRepositor
ies.py", line 118, in is_at_commits
         if name in commits and not repo.is_at_commit(commits):
       File 
"/usr/local/lib/python3.9/site-packages/staramr/databases/BlastDatabaseRepositor
y.py", line 91, in is_at_commit
         return self.info() == commit
       File 
"/usr/local/lib/python3.9/site-packages/staramr/databases/BlastDatabaseRepositor
y.py", line 102, in info
         repo_head = repo.commit('HEAD')
       File "/usr/local/lib/python3.9/site-packages/git/repo/base.py", line 726,
in commit
         return self.rev_parse(str(rev) + "^0")
       File "/usr/local/lib/python3.9/site-packages/git/repo/fun.py", line 284, 
in rev_parse
         obj = name_to_object(repo, rev[:start])
       File "/usr/local/lib/python3.9/site-packages/git/repo/fun.py", line 205, 
in name_to_object
         return Object.new_from_sha(repo, hex_to_bin(hexsha))
       File "/usr/local/lib/python3.9/site-packages/git/objects/base.py", line 
149, in new_from_sha
         oinfo = repo.odb.info(sha1)
       File "/usr/local/lib/python3.9/site-packages/git/db.py", line 41, in info
         hexsha, typename, size = 
self._git.get_object_header(bin_to_hex(binsha))
       File "/usr/local/lib/python3.9/site-packages/git/cmd.py", line 1679, in 
get_object_header
         return self.__get_object_header(cmd, ref)
       File "/usr/local/lib/python3.9/site-packages/git/cmd.py", line 1663, in 
__get_object_header
         return self._parse_object_header(cmd.stdout.readline())
       File "/usr/local/lib/python3.9/site-packages/git/cmd.py", line 1622, in 
_parse_object_header
         raise ValueError(err_msg)
     ValueError: SHA is empty, possible dubious ownership in the repository at 
/cvmfs/data.galaxyproject.org/byhand/staramr/resfinder_d1e607b_pointfinder_69491
9f_plasmidfinder_3e77502/update/resfinder.
                 If this is unintended run:
                           "git config --global --add safe.directory 
/cvmfs/data.galaxyproject.org/byhand/staramr/resfinder_d1e607b_pointfinder_69491
9f_plasmidfinder_3e77502/update/resfinder"
galaxy.jobs.runners.util.process_groups DEBUG 2025-08-22 16:23:10,403 [pN:main.1,p:22293,tN:LocalRunner.work_thread-3] check_pg(): No process found in process group 22812
galaxy.jobs.runners.local DEBUG 2025-08-22 16:23:10,404 [pN:main.1,p:22293,tN:LocalRunner.work_thread-3] execution finished: /tmp/tmpuj1m12ec/job_working_directory/000/2/galaxy_2.sh
galaxy.tool_util.output_checker INFO 2025-08-22 16:23:10,405 [pN:main.1,p:22293,tN:LocalRunner.work_thread-3] Job error detected, failing job. Reasons are [{'type': 'exit_code', 'desc': 'Fatal error: Exit code 1 ()', 'exit_code': 1, 'code_desc': '', 'error_level': 3}]

[mvdbeek]

For https://github.com/phac-nml/staramr/releases/tag/0.11.0 it says:

The Resfinder and Pointfinder databases now use FASTA record IDs with accession numbers (ex: pmrA -> pmrA_1_CP055130.1). StarAMR has been updated to support this, but database backwards compatibility is unlikely.

[hugolefeuvre]

I think the error comes from the cvmfs datacache. I tried the starAMR tool on galaxy FR and galaxy EU, which use databases that are not on cvmfs, and it works fine. Then I tried it on galaxy.org, which uses a database stored in cvmfs, and I got the same error as here.
There is already an issue on the idc repo about this issue : galaxyproject/idc#71

[hugolefeuvre]

I opened a new PR so I could make the final changes. The issue encountered during the latest tests concerning the starAMR database has been resolved here: galaxyproject/usegalaxy-playbook@5447308