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feat: add hlahd-tools 1.0.0 container #85

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19b6e35
feat: add hlahd-tools 1.0.0 container
johnoooh Aug 26, 2026
4acd68a
feat: install mskcc/hla-annotate in hlahd-tools instead of bare deps
johnoooh Aug 26, 2026
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54 changes: 54 additions & 0 deletions containers/hlahd-tools/1.0.0/Dockerfile
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# hlahd-tools — Python/bioinformatics runtime for the msk annotate_hlahd module
# (and future HLA-HD post-processing modules), with the mskcc/hla-annotate
# package (https://github.com/mskcc/hla-annotate) installed on top.
FROM condaforge/miniforge3:25.3.1-0

# Labels
LABEL org.opencontainers.image.vendor="MSKCC-OMICS-WORKFLOWS" \
org.opencontainers.image.authors="John Orgera (orgeraj@mskcc.org)" \
org.opencontainers.image.created="2026-08-26T00:00:00Z" \
org.opencontainers.image.licenses="MIT" \
org.opencontainers.image.version="1.0.0" \
imageprivacy="False" \
org.opencontainers.image.source="https://github.com/mskcc-omics-workflows/containers/containers/hlahd-tools/" \
org.opencontainers.image.url="https://github.com/mskcc-omics-workflows/modules" \
org.opencontainers.image.title="hlahd-tools" \
org.opencontainers.image.description="Python + bowtie2/samtools runtime for HLA-HD post-processing modules (e.g. annotate_hlahd), with mskcc/hla-annotate installed."

ENV HLA_ANNOTATE_TAG=v1.0.0

SHELL ["/bin/bash", "-o", "pipefail", "-c"]

# bowtie2/samtools are on PATH for modules that shell out to them (e.g. a future
# pileup-evidence module); weasyprint comes from conda-forge (not pip) so its
# pango/cairo/harfbuzz system libraries install alongside it.
RUN mamba install -y -c conda-forge -c bioconda \
python=3.11 \
bowtie2=2.5.5 \
samtools=1.21 \
pysam \
matplotlib \
requests \
weasyprint \
git \
pip \
&& mamba clean -afy

# hla-annotate is private, so cloning it needs a token (fine-grained PAT, read-only,
# scoped to just this repo) passed as a BuildKit secret — never baked into the image.
# Tests run at build time so a broken release fails the image build, not a pipeline run.
RUN --mount=type=secret,id=MSK_GH_TOKEN \
git clone --depth 1 --branch ${HLA_ANNOTATE_TAG} \
"https://x-access-token:$(cat /run/secrets/MSK_GH_TOKEN)@github.com/mskcc/hla-annotate.git" \
/tmp/hla-annotate \
&& pip install --no-cache-dir -e '/tmp/hla-annotate[dev]' \
&& pytest /tmp/hla-annotate \
&& pip install --no-cache-dir --no-deps --force-reinstall /tmp/hla-annotate \
&& rm -rf /tmp/hla-annotate

# matplotlib/fontconfig write caches on first use; $HOME is not writable under
# Nextflow's container user mapping.
ENV MPLCONFIGDIR=/tmp/mplconfig \
XDG_CACHE_HOME=/tmp/cache

WORKDIR /data
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