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perf: upgrade to latest conda, conda-build, and boa versions #872

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merged 6 commits into from
May 2, 2023
Merged

perf: upgrade to latest conda, conda-build, and boa versions #872

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0ae2c7c
perf: upgrade to latest conda, conda-build, and boa versions
johanneskoester Apr 28, 2023
298fc18
perf: remove superfluous conda reinstall in the base image
johanneskoester Apr 28, 2023
cd3474d
update boltons
johanneskoester Apr 28, 2023
c0aebab
Use mamba to install requirements
johanneskoester Apr 29, 2023
e28cf35
dbg
johanneskoester Apr 29, 2023
18cfb70
fix: remove superfluous test case (the build setup ensures that we al…
johanneskoester May 1, 2023
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28 changes: 14 additions & 14 deletions Dockerfile
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Original file line number Diff line number Diff line change
Expand Up @@ -21,9 +21,9 @@ RUN yum install -y mesa-libGL-devel \
# This changes root's .condarc which ENTRYPOINT copies to /home/conda/.condarc later.
RUN . /opt/conda/etc/profile.d/conda.sh && \
conda config \
--prepend channels defaults \
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Can we use install-and-set-up-conda.sh to install in this dockerfile? Otherwise this risks getting out-of-sync with how it's being installed everywhere else.

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Yes, we should do that. But let us do that in a separate PR. There are some steps in this dockerfile that I do not fully understand, such that it would need more time. For now, I just want to upgrade the conda and mamba versions as quickly as possible.

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Sounds good. The base linux-anvil image used here has a lot of moving parts as well; I have a local branch that completely rewrites the dockerfile for simplicity but that can be for later.

--prepend channels bioconda \
--prepend channels conda-forge \
--prepend channels defaults \
--prepend channels bioconda \
--prepend channels conda-forge \
&& \
{ conda config --remove repodata_fns current_repodata.json 2> /dev/null || true ; } && \
conda config --prepend repodata_fns repodata.json && \
Expand All @@ -38,8 +38,8 @@ RUN . /opt/conda/etc/profile.d/conda.sh && conda activate base && \
pip wheel . && \
mkdir - /opt/bioconda-utils && \
cp ./bioconda_utils-*.whl \
./bioconda_utils/bioconda_utils-requirements.txt \
/opt/bioconda-utils/ \
./bioconda_utils/bioconda_utils-requirements.txt \
/opt/bioconda-utils/ \
&& \
chgrp -R lucky /opt/bioconda-utils && \
chmod -R g=u /opt/bioconda-utils
Expand All @@ -49,15 +49,15 @@ COPY --from=build /opt/bioconda-utils /opt/bioconda-utils
RUN . /opt/conda/etc/profile.d/conda.sh && conda activate base && \
# Make sure we get the (working) conda we want before installing the rest.
sed -nE \
'/^conda([><!=~ ].+)?$/p' \
/opt/bioconda-utils/bioconda_utils-requirements.txt \
| xargs -r conda install --yes && \
conda install --yes --file /opt/bioconda-utils/bioconda_utils-requirements.txt && \
'/^conda([><!=~ ].+)?$/p' \
/opt/bioconda-utils/bioconda_utils-requirements.txt \
| xargs -r mamba install --yes && \
mamba install --yes --file /opt/bioconda-utils/bioconda_utils-requirements.txt && \
pip install --no-deps --find-links /opt/bioconda-utils bioconda_utils && \
conda clean --yes --index --tarballs && \
mamba clean --yes --index --tarballs && \
# Find files that are not already in group "lucky" and change their group and mode.
find /opt/conda \
\! -group lucky \
-exec chgrp --no-dereference lucky {} + \
\! -type l \
-exec chmod g=u {} +
\! -group lucky \
-exec chgrp --no-dereference lucky {} + \
\! -type l \
-exec chmod g=u {} +