Update to v2.2.1_samtools-1.17

[bethneilsen]

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.

• I have drafted the new version release with any additions/changes and have linked the CHANGELOG.md in the release.

Docker Hub Auto Build Rules

• I have created automated build rules following this page and I have not manually pushed this Docker image to the blcdsdockerregistry on Docker Hub.

Docker Image Testing

• I have tested the Docker image with the 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

[yashpatel6]

A couple of comments:

[yashpatel6]

Minor comment on the README but otherwise looks good! Anything else to add @tyamaguchi-ucla ?

[tyamaguchi-ucla]

Added a few minor suggestions although we can't implement them together at the same time.. Otherwise, looks good to me.

[tyamaguchi-ucla]

Any reason not to use the latest version? https://github.com/conda-forge/miniforge/releases

[bethneilsen]

Updated to version 23.1.0-3

[tyamaguchi-ucla]

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

[yashpatel6]

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

[tyamaguchi-ucla]

Good point! We can implement the both suggestions then!

[bethneilsen]

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.