Hotfix neoantigen-editing:1.1 -- fix PATH/exec bit for bundled scripts - #77
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NEOANTIGENEDITING_ALIGNTOIEDB and NEOANTIGENEDITING_COMPUTEFITNESS invoke align_neoantigens_to_IEDB.py / compute_fitness.py as bare commands, relying on PATH: .command.sh: line 3: compute_fitness.py: command not found .command.sh: line 3: align_neoantigens_to_IEDB.py: command not found Root cause: `cp -r /tmp/NeoantigenEditing/ /usr/bin` copies the whole git checkout in as a subdirectory, /usr/bin/NeoantigenEditing/, rather than flattening its contents onto /usr/bin -- so the scripts never actually land on PATH (which is just /usr/bin, /usr/local/bin, etc.). Separately, the checked-out files also aren't executable (-rw-r--r--), so even a full-path invocation fails with "Permission denied". (This previously worked because these two modules carried their own executable copies of these scripts as local nf-core module resources under resources/usr/bin/, which Nextflow stages onto PATH regardless of what's in the container. mskcc-omics-workflows/modules#258 removed those local copies in favor of the ones baked into this image.) Fix: add /usr/bin/NeoantigenEditing to PATH via ENV, and chmod +x the checkout's *.py scripts, instead of relying on flattening everything into /usr/bin (which would also dump the checkout's README, Dockerfile, ACRRI_TERMS_OF_USE, .git/, data/, and Results/ directly into /usr/bin). The scripts take all their inputs as explicit CLI args (verified no hardcoded relative-path defaults), so relocating them onto PATH this way doesn't change their behavior. Hotfixing 1.1 in place rather than cutting a new version, following the precedent set by PR #71 and the neoantigen-utils-base:1.6.1 unzip hotfix -- modules#258 already pins both modules to neoantigen-editing:1.1. Verified: rebuilt the image and confirmed both scripts now resolve on PATH, are executable, and run successfully via bare invocation (`compute_fitness.py --help`, `align_neoantigens_to_IEDB.py --help`), matching exactly how the modules' .command.sh scripts call them.
Updated Dockerfile to modify PATH for NeoantigenEditing scripts.
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NEOANTIGENEDITING_ALIGNTOIEDB and NEOANTIGENEDITING_COMPUTEFITNESS invoke align_neoantigens_to_IEDB.py / compute_fitness.py as bare commands, relying on PATH:
.command.sh: line 3: compute_fitness.py: command not found
.command.sh: line 3: align_neoantigens_to_IEDB.py: command not found
Root cause:
cp -r /tmp/NeoantigenEditing/ /usr/bincopies the whole git checkout in as a subdirectory, /usr/bin/NeoantigenEditing/, rather than flattening its contents onto /usr/bin -- so the scripts never actually land on PATH (which is just /usr/bin, /usr/local/bin, etc.). Separately, the checked-out files also aren't executable (-rw-r--r--), so even a full-path invocation fails with "Permission denied".(This previously worked because these two modules carried their own executable copies of these scripts as local nf-core module resources under resources/usr/bin/, which Nextflow stages onto PATH regardless of what's in the container. mskcc-omics-workflows/modules#258 removed those local copies in favor of the ones baked into this image.)
Fix: add /usr/bin/NeoantigenEditing to PATH via ENV, and chmod +x the checkout's *.py scripts, instead of relying on flattening everything into /usr/bin (which would also dump the checkout's README, Dockerfile, ACRRI_TERMS_OF_USE, .git/, data/, and Results/ directly into /usr/bin). The scripts take all their inputs as explicit CLI args (verified no hardcoded relative-path defaults), so relocating them onto PATH this way doesn't change their behavior.
Hotfixing 1.1 in place rather than cutting a new version, following the precedent set by PR #71 and the neoantigen-utils-base:1.6.1 unzip hotfix -- modules#258 already pins both modules to neoantigen-editing:1.1.
Verified: rebuilt the image and confirmed both scripts now resolve on PATH, are executable, and run successfully via bare invocation (
compute_fitness.py --help,align_neoantigens_to_IEDB.py --help), matching exactly how the modules' .command.sh scripts call them.