Add skipper-clipper-compare 1.0.0 image

CHANGELOG.md

@@ -20,6 +20,10 @@
 
 ### Added
 
+- skipper-clipper-compare 1.0.0 (`images/skipper-clipper-compare/1.0.0`): the
+  pinned Python/bedtools environment for skipper-clipper-snakemake's
+  Skipper-vs-CLIPper comparison, published as
+  `ghcr.io/yeolab/skipper-clipper-compare:1.0.0`.
 - Singularity-first DRUID deployment and tutorial instructions for Dockerless
   clusters, including the tested `sha-7941ba6aebf0fd4beb48643ec373374b50b02bbc`
   image pull command.

images/skipper-clipper-compare/1.0.0/Dockerfile

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+# Environment for skipper-clipper-snakemake's compare_skipper_clipper.py:
+# Skipper enriched windows vs CLIPper peaks (pandas, pybedtools/bedtools,
+# scipy, matplotlib, seaborn, matplotlib-venn). The script itself lives in the
+# workflow repository and is run inside this image by the workflow.
+
+FROM mambaorg/micromamba:2.9.0-debian12-slim@sha256:edce84d758b6c3029cebdf2777d9cdfdd6e44f9eee0a31c6a09a7df14be17fd2
+
+LABEL software="skipper-clipper-compare"
+LABEL software.version="1.0.0"
+LABEL about.summary="Python environment comparing Skipper enriched windows with CLIPper peaks"
+LABEL about.url="https://github.com/byee4/skipper-clipper-snakemake"
+LABEL about.tags="Genomics,eCLIP"
+
+COPY --chown=$MAMBA_USER:$MAMBA_USER environment.yml /tmp/environment.yml
+RUN micromamba install -y -n base -f /tmp/environment.yml \
+    && micromamba clean --all --yes
+
+# Tools resolve on PATH without micromamba's activating entrypoint, as they
+# must when Snakemake runs this image through Singularity/Apptainer.
+ENV PATH=/opt/conda/bin:$PATH \
+    MPLBACKEND=Agg
+
+# Fail the build, not a pipeline job, if the environment is incomplete.
+RUN python -c "import pandas, numpy, scipy, matplotlib, seaborn, matplotlib_venn, pybedtools; \
+from pybedtools import BedTool; \
+assert len(BedTool('chr1 1 9 a 0 +', from_string=True).sort()) == 1" \
+    && bedtools --version

images/skipper-clipper-compare/1.0.0/README.md

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+# skipper-clipper-compare 1.0.0
+
+Python environment for `workflow/scripts/compare_skipper_clipper.py` in
+[skipper-clipper-snakemake](https://github.com/byee4/skipper-clipper-snakemake),
+which compares Skipper enriched windows with CLIPper peaks. The image holds the
+environment only; the workflow supplies the script.
+
+Pinned in `environment.yml`: Python 3.12, bedtools 2.31.1, pybedtools 0.12.0,
+pandas 2.2.3, numpy 2.2.6, scipy 1.15.2, matplotlib 3.10.3, seaborn 0.13.2, and
+matplotlib-venn 1.1.2. Everything is on `PATH` without activation, so the image
+works under Singularity/Apptainer:
+
+```bash
+apptainer exec docker://ghcr.io/yeolab/skipper-clipper-compare:1.0.0 \
+    python compare_skipper_clipper.py --help
+```

images/skipper-clipper-compare/1.0.0/environment.yml

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+name: skipper-clipper-compare
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - python=3.12
+  - bedtools=2.31.1
+  - pybedtools=0.12.0
+  - pandas=2.2.3
+  - numpy=2.2.6
+  - scipy=1.15.2
+  - matplotlib-base=3.10.3
+  - seaborn-base=0.13.2
+  - matplotlib-venn=1.1.2