fix: Use mamba in mulled-build #810
Merged
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With this little shell injection we can forcemulled-buildto invokemamba installin place ofconda install.(It abuses the fact that
--conda-versioninvokes aconda install conda={conda_version}in which we interject aconda->mambaaliasing right before the actualconda installfor the target packages.)This should only be taken as a possible temporary workaround that works with our current
galaxy-libdependency.This now uses the existing
involucrowrapper to inject aconda->mambaalias somamba installis 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
. To be able to use that proposed
--use-mambaflag with such patch, we should also increase the version ofgalaxy-libto19.5.2.post1or the like and then havegalaxy-lib>=19.5.2.post1inbioconda_utils-requirements.txt.Or we just use this PR until galaxyproject/galaxy#14770 gets into a release and we update to use
galaxy-tool-utilinstead ofgalaxy-lib.