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Update to Snakemake version 8 #231

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🚧 Install Snakemake 8.1.2
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victorlin committed Aug 23, 2024
commit 67ef9ac1ec638eb75ecdb40bc14d923671a335d5
7 changes: 4 additions & 3 deletions Dockerfile
Original file line number Diff line number Diff line change
@@ -258,9 +258,10 @@ RUN python3 -m venv /usr/local/libexec/awscli \
&& ln -sv /usr/local/libexec/awscli/bin/aws /usr/local/bin/aws

# Install Snakemake and related optional dependencies.
# Pinned to 7.32.3 for stability (2023-09-09)
# Pulp>=2.8.0 breaks snakemake <=8.1.1, see https://github.com/snakemake/snakemake/issues/2607
RUN pip3 install snakemake[reports]==7.32.3 "pulp<2.8"
# FIXME: Pin a later version? I chose 8.1.2 to remove the pulp pin.
# Consider skimming the changelog.
# https://snakemake.readthedocs.io/en/stable/project_info/history.html
RUN pip3 install snakemake[reports]==8.1.2
# Google Cloud Storage package is required for Snakemake to fetch remote files
# from Google Storage URIs.
RUN pip3 install google-cloud-storage==2.7.0