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Update to v2.2.1_samtools-1.17 #3
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A couple of comments:
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Minor comment on the README but otherwise looks good! Anything else to add @tyamaguchi-ucla ?
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Added a few minor suggestions although we can't implement them together at the same time.. Otherwise, looks good to me.
Dockerfile
Outdated
@@ -1,12 +1,12 @@ | |||
FROM blcdsdockerregistry/bl-base:1.0.0 AS builder | |||
ARG MINIFORGE_VERSION=22.9.0-2 |
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Any reason not to use the latest version? https://github.com/conda-forge/miniforge/releases
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Updated to version 23.1.0-3
|
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LABEL maintainer="Yash Patel <[email protected]>" | ||
FROM condaforge/mambaforge:${MINIFORGE_VERSION} AS builder |
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Minor point but I think we can take advantage of the existing samtools image that we recently updated, which should reduce the build time.
https://github.com/uclahs-cds/docker-SAMtools/blob/main/Dockerfile
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We probably can't use that image directly since that image shouldn't contain conda/mamba since the SAMtools build gets deployed into the base Ubuntu image, which doesn't contain those. We could potentially install just BWA-MEM2 through mamba and then deploy into the SAMtools image rather than Ubuntu for some build speedup
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Good point! We can implement the both suggestions then!
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I am not sure how to readily complete this, so plan to merge the current pull request and created a new issue to address this on a separate branch.
Co-authored-by: Yash Patel <[email protected]>
…docker-BWA-MEM2 into bneilsen-UpdateSAMToolsv1.17
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.
Description
Closes NA - Updates SAMTools to the latest version 1.17, added auto build Docker functionality, updated to use mamba to build
Partially addresses issue #258 within pipeline-align-DNA