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bgruening / docker-galaxy-stable

:whale::bar_chart::books: Docker Images tracking the stable Galaxy releases.
http://bgruening.github.io/docker-galaxy-stable
MIT License
225 stars 133 forks source link

Add support for running IRIDA #589

Open pvanheus opened 2 years ago

pvanheus commented 2 years ago

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.
    1. Extract tool descriptions from IRIDA workflows
    2. Provide a framework for specifying workflows and DMs, running them and testing the outputs.
  3. Add irida-galaxy-importer on the Galaxy side
  4. Add SSL support and framework for maintaining it
bgruening commented 2 years ago

@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 commented 2 years ago

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.