CADD scripts with bundled required environments #546
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One question may be: Why not "fix" the bioconda package upstream instead, and let the container images be generated from the bioconda package? My reason is that the existing Edit to add: I'm not affiliated with CADD in any way, just a user. |
cadd-scripts/1.6/Dockerfile
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| ARG CADD_VERSION=1.6 | ||
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| MAINTAINER "biocontainers" <biodocker@gmail.com> |
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You can probably set your own email here, since it's a custom image.
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Seems ok, to me, but there should be a name difference between the official 'cadd-script' and this image, to avoid confusion I think. (This means changing the LABEL software=, and the directory name to match) |
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Thanks for the review! I have another question: Is there a place I can add some usage documenation for the image itself? The user has to mount their CADD reference data into /opt/conda/share/cadd-scripts-1.6-1/data/annotations to use it (and that's not really obvious). |
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Hmm, you should be able to add a README.md in the 'cadd-scripts-with-envs' folder, but I'm not sure if this will be enough visibility-wise? |
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about.license field is not in spdx list: https://spdx.org/licenses/, if it is a typo error, please fix it. If this is not a standard license, please specify Custom License and use about.license_file label to specify license location (in container or url). |
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No biotools label defined, please check if tool is not already defined in biotools (https://bio.tools) and add extra.identifiers.biotools label if it exists. If it is not defined, you can ignore this comment. |
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No test-cmds.txt (test file) present, skipping tests |
| about.summary="CADD is a tool for scoring the deleteriousness of single nucleotide variants as well as insertion/deletions variants in the human genome" \ | ||
| about.home="https://cadd.gs.washington.edu/" \ | ||
| about.documentation="https://github.com/kircherlab/CADD-scripts" \ | ||
| about.license="SPDX:Custom" \ |
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| about.license="SPDX:Custom" \ | |
| about.license="Custom License" \ |
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Thanks for the suggestions about README and micromamba clean! I've now fixed the issues, but it doesn't build on ARM64 arch. I'm troubleshooting, so it can wait a bit. |
I could get tabix installed, but mamba is unable to solve CADD's environment in the arm64 arch - so I think this container will only be supported on x86_64. |
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It should be fine to only build x86_64. I believe as a whole, biocontainers does not support arm64 build anyway (for now) |
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No biotools label defined, please check if tool is not already defined in biotools (https://bio.tools) and add extra.identifiers.biotools label if it exists. If it is not defined, you can ignore this comment. |
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No test-cmds.txt (test file) present, skipping tests |
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Should be fine to merge on my end. |
Submitting a Container
Attempt to address #528.
Warning: I'm creating a container with the same name as the existing
cadd-scriptsfrom bioconda (https://biocontainers.pro/tools/cadd-scripts). The hope that I can replace it with an improved container image. I hope this is fine, or we could maybe rename this tocadd-scripts-bundleor some other name. See the issue and first checklist item for the rationale.Check BioContainers' Dockerfile specifications
Checklist
quay.io/biocontainers/cadd-scripts:1.6--hdfd78af_1. (2) It requires write-access to the container filesystem when executed.