Hotfix neoantigen-utils-base:1.6.1 -- add missing unzip - #75
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NEOANTIGENUTILS_NEOANTIGENINPUT (modules/msk/neoantigenutils/neoantigeninput) shells out to `unzip` to extract the phyloWGS tree archive, but the final runtime stage of neoantigen-utils-base:1.6.1 only installs `unzip` in the build stage -- it never makes it into the final image, so the process fails with "unzip: not found" (exit 127) on real input. `gzip` (also used by the same process, via `gzip -d`) was already present; no change needed there. Hotfixing 1.6.1 in place rather than cutting a new version, following the precedent set by PR #71 (feature/hotfix_neoantigen_utils, which added `procps` to this same file/stage without a version bump) -- modules PR mskcc-omics-workflows/modules#258 already pins this module to 1.6.1, so this needs no follow-up version bump there. Audited every other module sharing this container (neosv, generatemutfasta, convertannotjson, formatnetmhcpan, generatehlastring, mutalyzer/normalizer, mutalyzer/retriever) for other binaries they shell out to (tar, bgzip, gunzip, bunzip2, awk, sed, tr, od, head, coreutils) -- all already present, no other gaps. Verified: rebuilt the image and confirmed both `unzip` and `gzip -d` now resolve and correctly extract a test phyloWGS zip archive and gzipped JSON files using the exact shell sequence from the neoantigeninput module's script block.
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NEOANTIGENUTILS_NEOANTIGENINPUT (modules/msk/neoantigenutils/neoantigeninput) shells out to
unzipto extract the phyloWGS tree archive, but the final runtime stage of neoantigen-utils-base:1.6.1 only installsunzipin the build stage -- it never makes it into the final image, so the process fails with "unzip: not found" (exit 127) on real input.gzip(also used by the same process, viagzip -d) was already present; no change needed there.Hotfixing 1.6.1 in place rather than cutting a new version, following the precedent set by PR #71 (feature/hotfix_neoantigen_utils, which added
procpsto this same file/stage without a version bump) -- modules PR mskcc-omics-workflows/modules#258 already pins this module to 1.6.1, so this needs no follow-up version bump there.Audited every other module sharing this container (neosv, generatemutfasta, convertannotjson, formatnetmhcpan, generatehlastring, mutalyzer/normalizer, mutalyzer/retriever) for other binaries they shell out to (tar, bgzip, gunzip, bunzip2, awk, sed, tr, od, head, coreutils) -- all already present, no other gaps.
Verified: rebuilt the image and confirmed both
unzipandgzip -dnow resolve and correctly extract a test phyloWGS zip archive and gzipped JSON files using the exact shell sequence from the neoantigeninput module's script block.