Add support for running IRIDA

[pvanheus]

This adds the ability to run IRIDA and Galaxy simultaneously. IRIDA is available on port 80 with Galaxy on port 90. Current status is that this works, but it needs cleaning up.

TODO

1. Ensure minimum disruption of existing Galaxy-oriented code
2. Add support for installing all tools and running all DMs needed by IRIDA automatically.
3. Extract tool descriptions from IRIDA workflows
4. Provide a framework for specifying workflows and DMs, running them and testing the outputs.
5. Add irida-galaxy-importer on the Galaxy side
6. Add SSL support and framework for maintaining it

[bgruening]

@pvanheus can we remove all those changes in this file? I think the Galaxy upgrade should happen in a different PR.

[pvanheus]

That's true. Also there's stuff in there that needs to be made conditional - i.e. the ability of the Galaxy and IRIDA containers to talk to each other (share users).

[bgruening]

@pvanheus please let me know if you think this is ready. I do not expect that you fix the failing test - that are largely other problems. Of course, I appreciate any help, but just to let you know that it's not required.

[bgruening]

Note to self:

galaxy-bioblend-test_1 | FAILED bioblend/_tests/TestGalaxyRoles.py::TestGalaxyRoles::test_create_role
galaxy-bioblend-test_1 | FAILED bioblend/_tests/TestGalaxyRoles.py::TestGalaxyRoles::test_get_roles - ...
galaxy-bioblend-test_1 | = 2 failed, 137 passed, 15 skipped, 17 deselected, 5 warnings in 381.68s (0:06:21) =

I guess we need to update to the latest bioblend and check what is wrong in Galaxy or bioblend.

#5 230.7 ERROR: Command errored out with exit status 1:
#5 230.7 command: /usr/bin/python3.8 -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-9102p5xv/pysam_c65e4e1e10804b339b411026b325c02f/setup.py'"'"'; file='"'"'/tmp/pip-install-9102p5xv/pysam_c65e4e1e10804b339b411026b325c02f/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(file) if os.path.exists(file) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, file, '"'"'exec'"'"'))' install --record /tmp/pip-record-q8qx4dvd/install-record.txt --single-version-externally-managed --compile --install-headers /usr/include/python3.8/pysam

Seems that Galaxy is building pysam for some containers under python 3.8. Not sure why, should not happen, we should use a wheel.

[bgruening]

Thanks to @jyotipm29 we are back on track 😄
The new 24.1 image contains a lot of changes and reflects the latest developments in Galaxy. I'm not sure if I will maintain the compose version in the future as well.

Please give it a try:

docker run -p 8080:80 -p 8021:21 -p 4002:4002 --privileged=true -e "GALAXY_DESTINATIONS_DEFAULT=slurm_cluster_docker"   -v /tmp/galaxy-data/:/export/ quay.io/bgruening/galaxy:24.1

... or any other combination. The readme has been updated. Please add any useful tip to it.

For a list of changes, see the Changelog.