Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 5a72449246be6f0f2fe3955bebf6f42ae89966bc https://github.com/galaxyproject/galaxy/commit/5a72449246be6f0f2fe3955bebf6f... Author: John Chilton jmchilton@gmail.com Date: 2016-10-08 (Sat, 08 Oct 2016)

Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/tools/deps/__init__.py A lib/galaxy/tools/deps/conda_compat.py M lib/galaxy/tools/deps/conda_util.py A lib/galaxy/tools/deps/container_resolvers/__init__.py A lib/galaxy/tools/deps/container_resolvers/explicit.py A lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/tools/deps/containers.py A lib/galaxy/tools/deps/installable.py A lib/galaxy/tools/deps/mulled/__init__.py A lib/galaxy/tools/deps/mulled/_cli.py A lib/galaxy/tools/deps/mulled/invfile.lua A lib/galaxy/tools/deps/mulled/mulled_build.py A lib/galaxy/tools/deps/mulled/mulled_build_channel.py A lib/galaxy/tools/deps/mulled/mulled_build_files.py A lib/galaxy/tools/deps/mulled/mulled_build_tool.py A lib/galaxy/tools/deps/mulled/mulled_search.py A lib/galaxy/tools/deps/mulled/util.py M lib/galaxy/tools/deps/resolvers/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py A test/functional/tools/mulled_example_multi_1.xml M test/functional/tools/samples_tool_conf.xml

Log Message: ----------- Implement beta support for dynamically discovering mulled containers for dependencies.

Contains all mulled fixes and enhancements through 16.10.7 including several bug fixes from @bgruening.

Commit: e389e1939160dfef7c364785a17869f5de30198b https://github.com/galaxyproject/galaxy/commit/e389e1939160dfef7c364785a1786... Author: John Chilton jmchilton@gmail.com Date: 2016-10-08 (Sat, 08 Oct 2016)

Changed paths: M config/job_conf.xml.sample_advanced M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/runners/__init__.py M test/unit/jobs/test_runner_local.py

Log Message: ----------- Implement option to require containerization of jobs.

This is great for security in production. For my own greedy concerns, I'm adding it for development however. I don't want someone to be testing mulled containers and accidently run the job locally.

Commit: 654b5e9322f5c54332c8d8861bc8ed34c6e71a8e https://github.com/galaxyproject/galaxy/commit/654b5e9322f5c54332c8d8861bc8e... Author: Björn Grüning bjoern@gruenings.eu Date: 2016-10-09 (Sun, 09 Oct 2016)

Changed paths: A doc/source/admin/mulled_containers.rst

Log Message: ----------- Add initial documentation about the new mulled features.

Commit: 4b5114bed1c09c655654972b084274e74310ebe8 https://github.com/galaxyproject/galaxy/commit/4b5114bed1c09c655654972b08427... Author: John Chilton jmchilton@gmail.com Date: 2016-10-10 (Mon, 10 Oct 2016)

Changed paths: A doc/source/admin/mulled_containers.rst

Log Message: ----------- Merge pull request #50 from jmchilton/mulled_docs

Add initial documentation about the new mulled features.

Commit: f0b988da78f081bf6845ce2d280d153e221f3633 https://github.com/galaxyproject/galaxy/commit/f0b988da78f081bf6845ce2d280d1... Author: John Chilton jmchilton@gmail.com Date: 2016-10-10 (Mon, 10 Oct 2016)

Changed paths: M lib/galaxy/tools/deps/mulled/mulled_build.py M lib/galaxy/tools/deps/mulled/util.py

Log Message: ----------- Bring in latest galaxy-lib fixes.

Commit: 20dcc4d693ae8fa7e846eb32e65292c3c4a38863 https://github.com/galaxyproject/galaxy/commit/20dcc4d693ae8fa7e846eb32e6529... Author: Martin Cech cech.marten@gmail.com Date: 2016-10-10 (Mon, 10 Oct 2016)

Changed paths: M config/galaxy.ini.sample

Log Message: ----------- remove duplicated option from config sample

Commit: bcabbd8707e0064e041e730e5abd1d8dfc0a692c https://github.com/galaxyproject/galaxy/commit/bcabbd8707e0064e041e730e5abd1... Author: Martin Cech cech.marten@gmail.com Date: 2016-10-10 (Mon, 10 Oct 2016)

Changed paths: M doc/source/admin/mulled_containers.rst

Log Message: ----------- minor changes to mulled admin docs

Commit: 7db241faa6d505427108c5ddeae8dbc77c384613 https://github.com/galaxyproject/galaxy/commit/7db241faa6d505427108c5ddeae8d... Author: Martin Cech cech.marten@gmail.com Date: 2016-10-10 (Mon, 10 Oct 2016)

Changed paths: M config/galaxy.ini.sample M config/job_conf.xml.sample_advanced A doc/source/admin/mulled_containers.rst M lib/galaxy/config.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/tools/deps/__init__.py A lib/galaxy/tools/deps/conda_compat.py M lib/galaxy/tools/deps/conda_util.py A lib/galaxy/tools/deps/container_resolvers/__init__.py A lib/galaxy/tools/deps/container_resolvers/explicit.py A lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/tools/deps/containers.py A lib/galaxy/tools/deps/installable.py A lib/galaxy/tools/deps/mulled/__init__.py A lib/galaxy/tools/deps/mulled/_cli.py A lib/galaxy/tools/deps/mulled/invfile.lua A lib/galaxy/tools/deps/mulled/mulled_build.py A lib/galaxy/tools/deps/mulled/mulled_build_channel.py A lib/galaxy/tools/deps/mulled/mulled_build_files.py A lib/galaxy/tools/deps/mulled/mulled_build_tool.py A lib/galaxy/tools/deps/mulled/mulled_search.py A lib/galaxy/tools/deps/mulled/util.py M lib/galaxy/tools/deps/resolvers/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py A test/functional/tools/mulled_example_multi_1.xml M test/functional/tools/samples_tool_conf.xml M test/unit/jobs/test_runner_local.py

Log Message: ----------- Merge pull request #2986 from jmchilton/mulled

Implement beta support for discovering mulled containers for dependencies.

Compare: https://github.com/galaxyproject/galaxy/compare/217854827ac7...7db241faa6d5