Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4dd503046f59b13e925a76f88862882747dc6ad7 https://github.com/galaxyproject/galaxy/commit/4dd503046f59b13e925a76f888628... Author: Nicola Soranzo nicola.soranzo@earlham.ac.uk Date: 2017-08-14 (Mon, 14 Aug 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: 420e7a4f3408ec064403a4283ba22a134b65ece5 https://github.com/galaxyproject/galaxy/commit/420e7a4f3408ec064403a4283ba22... Author: Nicola Soranzo nicola.soranzo@earlham.ac.uk Date: 2017-08-14 (Mon, 14 Aug 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.
Commit: cdbac056cb664e4c51f84c41c2519993d0412d74 https://github.com/galaxyproject/galaxy/commit/cdbac056cb664e4c51f84c41c2519... Author: Nicola Soranzo nicola.soranzo@earlham.ac.uk Date: 2017-08-14 (Mon, 14 Aug 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: 44548f8f2fe258051ad2df45b153642586b85e00 https://github.com/galaxyproject/galaxy/commit/44548f8f2fe258051ad2df45b1536... Author: John Chilton jmchilton@gmail.com Date: 2017-08-15 (Tue, 15 Aug 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 #4409 from nsoranzo/fix_conda_channel_order
Update conda channel order to sync with Bioconda
Compare: https://github.com/galaxyproject/galaxy/compare/8721da8ca2e1...44548f8f2fe2
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