Galaxy workflow and Dockerfile #707
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ebolyen
reviewed
Apr 30, 2025
Dockerfile.galaxy
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| ENV \ | ||
| GALAXY_CONFIG_TOOL_CONFIG_FILE=/qiime2_tools/qiime2_tool_conf.xml \ | ||
| GALAXY_CONFIG_CONDA_AUTO_INSTALL=true \ | ||
| GALAXY_CONFIG_CONDA_ENSURE_CHANNELS=https://packages.qiime2.org/qiime2/${EPOCH}/${DISTRO}/released,iuc,conda-forge,bioconda,defaults |
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oh we should drop defaults from this list
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Should --channel defaults be dropped from the command as well?
ebolyen
reviewed
May 1, 2025
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| RUN /export/tool_deps/_conda/bin/conda create -y --quiet --solver libmamba --override-channels \ | ||
| --channel https://packages.qiime2.org/qiime2/${EPOCH}/${DISTRO}/released --channel iuc --channel \ | ||
| conda-forge --channel bioconda --name __qiime2-${DISTRO}@${EPOCH} qiime2-${DISTRO}=${EPOCH} |
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something that will be a little annoying, the version of the metapackage isn't actually the epoch, it's whatever timestamp we had when we ended up building it
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for example:
qiime2-amplicon=2025.04.20.04.09.37
qiime2-amplicon=2025.04.28.17.25.53
qiime2-amplicon=2025.05.01.03.29.07
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Adds a build for galaxy docker containers, I opened this off my remote for now to make sure we don't run it and potentially do something stupid to quay before we're sure it's correct enough.