[galaxy-commits] [galaxyproject/galaxy] cad400: Allow more rich container description in job_conf....

GitHub noreply at github.com
Tue Sep 27 12:32:15 EDT 2016


  Branch: refs/heads/dev
  Home:   https://github.com/galaxyproject/galaxy
  Commit: cad4002efed5547ccc1f89a3a45d2d4b9b12f76d
      https://github.com/galaxyproject/galaxy/commit/cad4002efed5547ccc1f89a3a45d2d4b9b12f76d
  Author: John Chilton <jmchilton at gmail.com>
  Date:   2016-08-15 (Mon, 15 Aug 2016)

  Changed paths:
    M lib/galaxy/jobs/__init__.py
    M lib/galaxy/tools/deps/containers.py
    M lib/galaxy/tools/deps/requirements.py

  Log Message:
  -----------
  Allow more rich container description in job_conf.xml.


  Commit: 6466ffe31e250575cc4ca278b0730ba7f1207e0d
      https://github.com/galaxyproject/galaxy/commit/6466ffe31e250575cc4ca278b0730ba7f1207e0d
  Author: John Chilton <jmchilton at gmail.com>
  Date:   2016-08-15 (Mon, 15 Aug 2016)

  Changed paths:
    M lib/galaxy/jobs/command_factory.py
    M lib/galaxy/tools/deps/containers.py
    M lib/galaxy/tools/deps/requirements.py

  Log Message:
  -----------
  Allow more configurability in container descriptions.

<container> descriptions (in job_conf.xml or in tool files) can now specify a few more options - including if Galaxy should perform tool dependency resolution (using the resolve_dependencies attribute - defaults to false) and job script shell (defaults to /bin/sh - but for containers with bash this should be overridden and set to /bin/bash).

This should enable use cases such as that outlined in #2764.


  Commit: 002d974f8adae4cfc52c434c46c4966ac90918bd
      https://github.com/galaxyproject/galaxy/commit/002d974f8adae4cfc52c434c46c4966ac90918bd
  Author: Dannon Baker <dannon.baker at gmail.com>
  Date:   2016-09-27 (Tue, 27 Sep 2016)

  Changed paths:
    M lib/galaxy/jobs/__init__.py
    M lib/galaxy/jobs/command_factory.py
    M lib/galaxy/tools/deps/containers.py
    M lib/galaxy/tools/deps/requirements.py

  Log Message:
  -----------
  Merge pull request #2790 from jmchilton/docker_container_xml

More configurability for containerized jobs


Compare: https://github.com/galaxyproject/galaxy/compare/0df6ff9f2d7d...002d974f8ada


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