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Update to use bl-base for builder and samtools images as base image #5
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A couple of comments:
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Looks good to me!
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Very minor comment but otherwise looks good!
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Looks good!
Imperative tense Co-authored-by: Yash Patel <[email protected]>
Change SAMTools to SAMtools
Description
Closes #4 - Updates Dockerfile to use samtools:1.17 as the base image to prevent needing to re-install samtools here
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.md
under the next release version or unreleased, and updated the date.CHANGELOG.md
in the release.Docker Hub Auto Build Rules
blcdsdockerregistry
on Docker Hub.Docker Image Testing
docker run
command 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:
Case 1:
docker run --rm -u $(id -u):$(id -g) bwa-mem2_samtools-1.17:latest bwa-mem2 version
Case 2:
docker run --rm -u $(id -u):$(id -g) bwa-mem2_samtools-1.17:latest samtools version
Testing Results
Case 1:
Launching executable "/usr/local/bin/bwa-mem2.avx512bw"
2.2.1
Case 2:
samtools 1.17
Using htslib 1.17
Copyright (C) 2023 Genome Research Ltd.