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Snakemake docker (#317)

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* Copied from https://github.com/maurerv/alphaabriss

* CI/CD

* Restructured snakemake workflow topology. Updated Dockerfile to compatible jax cuda versions. Included analysis container in CI/CD

* Run container build in parallel

* Free container space for analysis image

* Updated container paths in Snakefile

* Moved snakemake pipeline to kosinskilab/AlphaPulldownSnakemake

* Added tag for container from the release. Add test_feats_with_templates

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Co-authored-by: maurerv <valentin.maurer@embl-hamburg.de>
This commit is contained in:
Dima
2024-04-25 11:18:14 +02:00
committed by GitHub
parent 4d118b6033
commit 67b89f94f9
3 changed files with 154 additions and 53 deletions
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15
docker/analysis.dockerfile Normal file
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FROM geoffreyyu/alpha_analysis_basis_jax0.4:latest
RUN mkdir -p /app/alpha-analysis/
COPY alphapulldown/analysis_pipeline/*sh /app
COPY alphapulldown/analysis_pipeline/*py /app/alpha-analysis/
RUN chmod +x /app/run_get_good_pae.sh \
&& chmod +x /app/run_execute_notebook.sh \
&& chmod +x /app/run_pi_score.sh \
&& chmod +x /app/alpha-analysis/get_good_inter_pae.py
ENV PATH="/app/alpha-analysis:$PATH" \
PYTHONPATH="/app:$PYTHONPATH"
ENTRYPOINT [ "bash" ]