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With this little shell injection we can forcemulled-build
to invokemamba install
in place ofconda install
.(It abuses the fact that
--conda-version
invokes aconda install conda={conda_version}
in which we interject aconda
->mamba
aliasing right before the actualconda 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 aconda
->mamba
alias somamba 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
. To be able to use that proposed
--use-mamba
flag with such patch, we should also increase the version ofgalaxy-lib
to19.5.2.post1
or the like and then havegalaxy-lib>=19.5.2.post1
inbioconda_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 ofgalaxy-lib
.