Adapt DRMAA job runner to push env vars to jobs

[meso-uca]

What : adapt DRMAA job runner to push environment variables to jobs. Change sample config files accordingly.
Why : on our galaxy instance which submits jobs onto an hpc slurm cluster, when the jobs need to get data from internet, it needs an http proxy to be set via environment variables. As slurm munge does not load variables defined in the user profile, and as galaxy uses libdrmaa to submit the jobs which accepts in the job template a parameter listing the env vars to add, the fix was quite obvious.

• Instructions for manual testing are as follows:
  1. Adapt your config file following the example from job_conf.xml.sample_advanced to add environment variables
  2. Use galaxy to submit a job on the cluster ; the job should dump its environment.
  3. Check in the job output that the additional environment variables are present.

License

• I agree to license these and all my past contributions to the core galaxy codebase under the MIT license.

[bernt-matthias]

@meso-uca is the existing mechanism insufficient:

galaxy/lib/galaxy/config/sample/job_conf.sample.yml

Line 669 in bad3f8a

env:

?

See also #16666 in case you use containers.

[meso-uca]

Oh yes, you're absolutely right, the existing mechanism is enough. However, our production galaxy instance is currently running version 22.05, which does not offer this possibility. My bad, I should have checked next versions before submitting this pull request.
Is there any interest in merging this PR into the 22.05 version ? If not, just ignore this PR and we'll switch to the existing possibility when we upgrade our instance.

Thanks !

[mvdbeek]

This has been possible for many years, so it should also work on 22.05.

[bernt-matthias]

I'm going to close this. Check with the admin channel if you have trouble setting this up.