Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 18977d4132556a0c2bd0348db510cf765d434e6a https://github.com/galaxyproject/galaxy/commit/18977d4132556a0c2bd0348db510c... Author: Nate Coraor <nate@bx.psu.edu> Date: 2017-09-29 (Fri, 29 Sep 2017) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Don't load hidden tools into the tool panel at all. 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: 04a572e509e875414b07e73c295f1c4bb37c1e0c https://github.com/galaxyproject/galaxy/commit/04a572e509e875414b07e73c295f1... Author: John Chilton <jmchilton@gmail.com> Date: 2017-10-02 (Mon, 02 Oct 2017) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Merge pull request #4726 from natefoo/panel-hidden-fix [17.09] If the newest version of a tool is hidden, load the newest older version, if any, into the tool panel 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 Commit: 3d87afbb4174be1068aa701ca4d36d3b3f89591c https://github.com/galaxyproject/galaxy/commit/3d87afbb4174be1068aa701ca4d36... Author: Nate Coraor <nate@bx.psu.edu> Date: 2017-10-02 (Mon, 02 Oct 2017) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Merge branch 'release_17.09' into dev Compare: https://github.com/galaxyproject/galaxy/compare/068c61a310e6...3d87afbb4174