Unverified Commit d10506a5 authored by M Bernt's avatar M Bernt Committed by GitHub
Browse files

Merge pull request #19714 from bernt-matthias/revert-19545 

[24.0] Fix container building
parents 6c281d2c 083981fa

lib/galaxy/tool_util/deps/mulled/invfile.lua

+2 −3
Original line number Diff line number Diff line
@@ -88,14 +88,13 @@ inv.task('build') 
    .using(conda_image)

        .withHostConfig({binds = bind_args})

        .run('/bin/sh', '-c', preinstall

            .. conda_bin .. ' create --quiet --yes -p /usr/local/env --copy  && '

            .. conda_bin .. ' install '

            .. channel_args .. ' '

            .. target_args

            .. ' --strict-channel-priority -p /usr/local/env --copy --yes '

            .. ' --strict-channel-priority -p /usr/local --copy --yes '

            .. verbose

            .. postinstall)

    .wrap('build/dist/env')

    .wrap('build/dist')

        .at('/usr/local')

        .inImage(destination_base_image)

        .as(repo)

lib/galaxy/tool_util/deps/mulled/mulled_build.py

+1 −1
Original line number Diff line number Diff line
@@ -313,11 +313,11 @@ def mull_targets( 
        if conda_version is not None:

            specs.append(f"conda={conda_version}")

        if mamba_version is not None:

            specs.append(f"mamba={mamba_version}")

            if mamba_version == "" and not specs:

                # If nothing but mamba without a specific version is requested,

                # then only run conda install if mamba is not already installed.

                mamba_test = "[ '[]' = \"$( conda list --json --full-name mamba )\" ]"

            specs.append(f"mamba={mamba_version}")

        conda_install = f"""conda install {verbose} --yes {" ".join(f"'{spec}'" for spec in specs)}"""

        involucro_args.extend(["-set", f"PREINSTALL=if {mamba_test} ; then {conda_install} ; fi"])