Branch: refs/heads/release_17.09 Home: https://github.com/galaxyproject/galaxy Commit: 2eed478545857ab2c3b4c958bc3e2c360656af42 https://github.com/galaxyproject/galaxy/commit/2eed478545857ab2c3b4c958bc3e2... Author: Nicola Soranzo nicola.soranzo@earlham.ac.uk Date: 2017-10-02 (Mon, 02 Oct 2017)

Changed paths: M config/galaxy.ini.sample M doc/source/admin/dependency_resolvers.rst M lib/galaxy/tools/deps/resolvers/conda.py

Log Message: ----------- Update conda channel order to sync with Bioconda

Commit: a5b7dce09fb690f09d25f1b806d3339bdf2171c9 https://github.com/galaxyproject/galaxy/commit/a5b7dce09fb690f09d25f1b806d33... Author: Nicola Soranzo nicola.soranzo@earlham.ac.uk Date: 2017-10-02 (Mon, 02 Oct 2017)

Changed paths: M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/resolvers/conda.py

Log Message: ----------- Remove _ensure_conda_context() function

and make conda_context argument mandatory in functions/methods. This should help making sure the correct context (e.g. channels) is used for all Conda operations.

Also remove unused is_target_available() function.

Conflicts: lib/galaxy/tools/deps/conda_util.py

Commit: 3551386a1ac667e0d2f7c6e82256d180aa5100f7 https://github.com/galaxyproject/galaxy/commit/3551386a1ac667e0d2f7c6e82256d... Author: Nicola Soranzo nicola.soranzo@earlham.ac.uk Date: 2017-10-02 (Mon, 02 Oct 2017)

Changed paths: M lib/galaxy/tools/deps/conda_util.py

Log Message: ----------- Override channel list on the command line instead of modifying condarc

The way we were modifying condarc in the ensure_channels_configured() method was broken because we were appending the missing channels at the end, so the final order may not be the one specified in conda_ensure_channels .

Also: - not modifying the user condarc is a much better approach - overriding the channel list on the command line will make debugging easier

Commit: 81ece2551cea27cbd0e718ef5b7a2fe8d4abd071 https://github.com/galaxyproject/galaxy/commit/81ece2551cea27cbd0e718ef5b7a2... Author: John Chilton jmchilton@gmail.com Date: 2017-10-02 (Mon, 02 Oct 2017)

Changed paths: M config/galaxy.ini.sample M doc/source/admin/dependency_resolvers.rst M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/resolvers/conda.py

Log Message: ----------- Merge pull request #4731 from nsoranzo/release_17.05_backport_4409

[17.05] Backport #4409

Commit: 280dc48c386f41c850ae3bbf9971979296b5abbc https://github.com/galaxyproject/galaxy/commit/280dc48c386f41c850ae3bbf99719... Author: Nate Coraor nate@bx.psu.edu Date: 2017-10-02 (Mon, 02 Oct 2017)

Log Message: ----------- Merge branch 'release_17.05' into release_17.09

Compare: https://github.com/galaxyproject/galaxy/compare/04a572e509e8...280dc48c386f