Update to SAMtools v1.14 #3
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tyamaguchi-ucla
approved these changes
Feb 14, 2022
metadata.yaml
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| @@ -2,10 +2,9 @@ | |||
| Category: 'docker' | |||
| Description: 'Docker repository for SAMtools' | |||
| Maintainers: ['rhughwhite@mednet.ucla.edu'] | |||
| Contributors: ['Rupert Hugh-White', 'Helena Winata'] | |||
| Contributors: ['Rupert Hugh-White', 'Helena Winata', 'Arpi Beshlikyan'] | |||
| Languages: ['Docker', 'bash'] | |||
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I think we replaced this with Dockerfile by following GitHub. (see template)
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I just changed it to Languages: ['Dockerfile', 'bash']
Should it be just Languages: ['Dockerfile'] without "bash"?
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Right, I don't think we need bash here based on the languages section (100% Dockerfile)
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Checklist
Formatting
I have read the code review guidelines and the code review best practice on GitHub check-list.
The name of the branch is meaningful and well formatted following the standards, using [AD_username (or 5 letters of AD if AD is too long)-[brief_description_of_branch].
I have set up or verified the branch protection rule following the github standards before opening this pull request.
File Updates
I have ensured that the version number update follows the versioning standards.
I have updated the version number/dependencies and added my name to the maintainer list in the
Dockerfile.I have updated the version number/feature changes in the
README.md.I have updated the version number and added my name to the contributors list in the
metadata.yaml.I have added the changes included in this pull request to the
CHANGELOG.mdunder the next release version or unreleased, and updated the date.CHANGELOG.mdin the release.Docker Hub Auto Build Rules
blcdsdockerregistryon Docker Hub.Docker Image Testing
docker runcommand as described below.Test the Docker image with at least one sample. Verify the new Docker image works using:
docker run -u $(id -u):$(id -g) –w <working-directory> -v <directory-you-want-to-mount>:<how-you-want-to-mount-it-within-the-docker> --rm <docker-image-name> <command-to-the-docker-with-all-parameters>My command:
docker build -t test-samtools .docker run -it --rm test-samtools whoamidocker run -it --rm test-samtools groupsdocker run -it --rm test-samtools samtools --versionDescription
Updates to SAMtools 1.14 and installs using Mamba instead of Conda.
Adds 'blocker' user/group to the container.
Adds PR template to repository.