feat: add hlahd-tools 1.0.0 container - #85
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Generic Python/bowtie2/samtools runtime for HLA-HD post-processing modules (e.g. modules/msk/annotate_hlahd in the modules repo). Module scripts are bundled in the module's resources/usr/bin/ and staged onto PATH by Nextflow -- this image supplies only the interpreter, system libraries, and third-party packages they depend on (pandas, jinja2, pysam, matplotlib, requests, weasyprint). Verified: hadolint clean; built for linux/amd64 and exercised via the annotate_hlahd module's nf-test suite (real-data + skip_html + stub), all passing.
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Clones mskcc/hla-annotate@v1.0.0 (private repo -- needs an MSK_GH_TOKEN secret, a fine-grained PAT scoped read-only to that repo, added to this repo's CI) and installs it, running its test suite at build time so a broken release fails the image build rather than a pipeline run. Verified locally: install + 83 tests pass (using a local copy in place of the token-based clone, since I can't write a token to disk in this sandbox -- the clone step itself is the same pattern already used for JFrog downloads in this repo).
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Summary
Adds
containers/hlahd-tools/1.0.0— a Python + bowtie2/samtools runtime for HLA-HD post-processing modules, with mskcc/hla-annotate installed on top (companion PR: mskcc-omics-workflows/modules#260).Unlike
containers/hlahd/, this image's business logic comes from a dedicated package repo rather than being copied in at build time —mskcc/hla-annotateis cloned at a pinned tag (v1.0.0) and installed, with its test suite run during the build so a broken release fails the image build rather than a pipeline run.Runtime deps: python 3.11, bowtie2 2.5.5, samtools 1.21, pysam, matplotlib, requests, weasyprint (via conda-forge/bioconda) + whatever
hla-annotatepulls in (pandas, jinja2).Verification
hadolint --config .hadolint.yml containers/hlahd-tools/1.0.0/Dockerfile— cleanlinux/amd64; install +hla-annotate's 83 tests pass, and theannotate_hlahdmodule's nf-test suite (real-data +--skip_html+ stub) passes end-to-end against the built image