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fix: Use mamba in mulled-build #810

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merged 1 commit into from
Oct 11, 2022
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@mbargull mbargull commented Oct 9, 2022

With this little shell injection we can force mulled-build to invoke mamba install in place of conda install.
(It abuses the fact that --conda-version invokes a conda install conda={conda_version} in which we interject a conda->mamba aliasing right before the actual conda install for the target packages.)
This should only be taken as a possible temporary workaround that works with our current galaxy-lib dependency.

This now uses the existing involucro wrapper to inject a conda->mamba alias so mamba install is used in the container builds.

@dpryan79 suggested we could also add galaxyproject/galaxy#14770 (via https://github.com/johanneskoester/galaxy-lib/tree/feat/use-mamba ) as a patch to https://github.com/bioconda/bioconda-recipes/blob/master/recipes/galaxy-lib/meta.yaml . That would certainly be less hacky than this PR by changing

-    # We also inject a PREINSTALL to alias conda to mamba so `mamba install` is
-    # used instead of `conda install` in the container builds.
+    cmd += ['--use-mamba']

. To be able to use that proposed --use-mamba flag with such patch, we should also increase the version of galaxy-lib to 19.5.2.post1 or the like and then have galaxy-lib>=19.5.2.post1 in bioconda_utils-requirements.txt.
Or we just use this PR until galaxyproject/galaxy#14770 gets into a release and we update to use galaxy-tool-util instead of galaxy-lib.

@mbargull mbargull force-pushed the hack-mamba-in-mulled-build branch 2 times, most recently from dee156d to 5a07406 Compare October 9, 2022 14:34
@mbargull mbargull marked this pull request as ready for review October 9, 2022 20:05
bioconda_utils/pkg_test.py Outdated Show resolved Hide resolved
@mbargull mbargull force-pushed the hack-mamba-in-mulled-build branch from 5a07406 to 066187f Compare October 9, 2022 21:36
@mbargull mbargull changed the title fix: Hack mamba in mulled build fix: Use mamba in mulled-build Oct 9, 2022
@mbargull mbargull force-pushed the hack-mamba-in-mulled-build branch 2 times, most recently from aa5b4e7 to 912f8cc Compare October 9, 2022 22:27
@dpryan79
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Since we'll want to update to galaxy-tool-util anyway then we might as well do that now.

@mbargull
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Since we'll want to update to galaxy-tool-util anyway then we might as well do that now.

Yes, we could (we'd just have to test if everything still works correctly -- IDK if everything is covered by our tests; if yes, then great and we should be all set).
But that wouldn't change anything regarding the mulled-build/mamba-issue without galaxyproject/galaxy#14770 being merged/released.

N.B.: The current PREINSTALL override of this PR should work with galaxy-lib as well as galaxy-tool-util, i.e., merging this PR would resolve the current issue and would not pose any issue even if we'd update to galaxy-tool-util (with or without galaxyproject/galaxy#14770 ).

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Trying out galaxy-tool-util in gh-813. (We could merge this PR before or after that one.)

@dpryan79 dpryan79 merged commit 554e15b into master Oct 11, 2022
@dpryan79 dpryan79 deleted the hack-mamba-in-mulled-build branch October 11, 2022 11:01
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2 participants