Add HOMER 5.1 image

CHANGELOG.md

@@ -20,6 +20,8 @@
 
 ### Added
 
+- HOMER 5.1 (`images/homer/5.1`) with bedtools 2.31.1 and Python 3.12 for
+  FASTA-mode motif discovery, published as `ghcr.io/yeolab/homer:5.1`.
 - 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

images/homer/5.1/Dockerfile

@@ -0,0 +1,29 @@
+# HOMER 5.1 with bedtools and Python 3 for de novo motif discovery in CLIP
+# peaks against region-matched random backgrounds (FASTA mode, -rna). Used by
+# skipper-clipper-snakemake's homer_motifs rule, which follows
+# yeolab/clip_analysis_legacy's analyze_motifs.
+
+FROM mambaorg/micromamba:2.9.0-debian12-slim@sha256:edce84d758b6c3029cebdf2777d9cdfdd6e44f9eee0a31c6a09a7df14be17fd2
+
+LABEL software="homer"
+LABEL software.version="5.1"
+LABEL about.summary="HOMER motif discovery with bedtools and Python 3"
+LABEL about.url="http://homer.ucsd.edu/homer/"
+LABEL about.tags="Genomics,motifs,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
+
+# Fail the build if HOMER cannot find motifs in FASTA mode.
+RUN printf '>a\nACGTACGTTTTTACGT\n>b\nACGTACGTTTTTACGT\n' > /tmp/fg.fa \
+    && printf '>c\nGGCCGGCCAAAAGGCC\n>d\nGGCCGGCCAAAAGGCC\n' > /tmp/bg.fa \
+    && findMotifs.pl /tmp/fg.fa fasta /tmp/homer-check -rna -len 6 -S 2 -p 1 \
+        -nofacts -noconvert -nogo -fasta /tmp/bg.fa > /dev/null 2>&1 \
+    && test -s /tmp/homer-check/homerMotifs.all.motifs \
+    && rm -rf /tmp/fg.fa /tmp/bg.fa /tmp/homer-check \
+    && bedtools --version && python3 --version

images/homer/5.1/README.md

@@ -0,0 +1,13 @@
+# HOMER 5.1
+
+[HOMER](http://homer.ucsd.edu/homer/) 5.1 with bedtools 2.31.1 and Python 3.12,
+pinned in `environment.yml`. No genome packages are installed: it is meant for
+FASTA-mode motif finding (`findMotifs.pl <fg.fa> fasta <out> -fasta <bg.fa>`),
+as used by
+[skipper-clipper-snakemake](https://github.com/byee4/skipper-clipper-snakemake)'s
+`homer_motifs` rule. Everything is on `PATH` without activation, so it runs under
+Singularity/Apptainer:
+
+```bash
+apptainer exec docker://ghcr.io/yeolab/homer:5.1 findMotifs.pl
+```

images/homer/5.1/environment.yml

@@ -0,0 +1,8 @@
+name: homer
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - python=3.12
+  - homer=5.1
+  - bedtools=2.31.1