`rpcompletion`, `rpextractsink` permission issued

[guillaume-gricourt]

Execution for galaxy wrappers raises the error attached
brsynth/galaxytools#265

[tduigou]

@breakthewall may you have a look?

[breakthewall]

Hi, this is when rrCache downloads the material to generate the cache. It downloads it in the conda package folder that could be the problem but this part mechanism works for a long time in rrCache...

@guillaume-gricourt what is the context of your execution (OS, platform, planemo...)?

[guillaume-gricourt]

The package is running in a docker container managed by planemo.
Can we change the default destination of the rrcache download to a directory belonging to the user, such as XDG_CACHE_HOME?

[guillaume-gricourt]

the error persists in the 6.6.5 release

[breakthewall]

@guillaume-gricourt I ran the following command in the Terminal on my Mac:

planemo test galaxytools/tools/rptools/rpcompletion.xml

after to have changed 6.5.0 into 6.6.5 in macros.xml and --cache-dir into --chemical-space in rpcompletion.xml, both on my local copy of galaxytools. And I am not able to reproduce the PermissionError you have...

[breakthewall]

I have created the branch test-joan on galaxytools repo.

@guillaume-gricourt Can you test the planemo command and tell me if you have the same result?

[guillaume-gricourt]

The command is:

planemo test \
  --galaxy_source https://github.com/galaxyproject/galaxy \
  --galaxy_branch master \
  --galaxy_python_version 3.11 \
  --test_timeout 86400 \
  --biocontainers \
  --no_dependency_resolution \
  --no_conda_auto_init \
  --docker_extra_volume . \
  --test_output_json output.json \
  --test_output output.html \
  /opt/brsynth/galaxytools/tools/rptools/rpcompletion.xml

You can work on this PR: brsynth/galaxytools#229

[breakthewall]

Ok I merged locally the PR and ran the command you gave, I have this error:

Job in error state.. tool_id: rptools_rpcompletion, exit_code: 1, stderr: /Users/jherisson/.planemo/gx_venv_3.11/bin/python: Error while finding module specification for 'rptools.rpcompletion' (ModuleNotFoundError: No module named 'rptools')

Ran again planemo test galaxytools/tools/rptools/rpcompletion.xml on the PR as well, ends well...