add gnuplot for plot-bamstats

[sorelfitzgibbon]

Description

• gnuplot is needed for plot-bamstats which can be used to generate QC plots from SAMtools stats output as proposed for pipeline-generate-SQC-BAM.

• samtools image size went from 285MB to 318MB

• I'm not sure how the version will be handled since the release number is tied to the SAMtools version.

Testing Results

Docker Image Testing

• I have tested the Docker image with the docker run command as described below.

docker run --workdir $(pwd) --rm --user $(id -u):$(id -g) --volume $(pwd):$(pwd) \
     --volume /hot/ref/mitochondria_ref/mt_test_bams/:/hot/ref/mitochondria_ref/mt_test_bams/ \
    ghcr.io/uclahs-cds/samtools:branch-sfitz-add-gnu \
    samtools stats tcga_test_file_normal.bam > tcga_test_file_normal_stats.txt

docker run --workdir $(pwd) --rm --user $(id -u):$(id -g) --volume $(pwd):$(pwd) \
     --volume /hot/ref/mitochondria_ref/mt_test_bams/:/hot/ref/mitochondria_ref/mt_test_bams/ \
    ghcr.io/uclahs-cds/samtools:branch-sfitz-add-gnu \
    plot-bamstats -p tcga_test tcga_test_file_normal_stats.txt

This test yields a few Fontconfig error: No writable cache directories errors and "tcga_test-quals2.gp" line 626: warning: y2 axis range undefined or overflow, resetting to [0:0]. But the plots are created and look fine. The same errors were seen for the PCAWG test run linked above proposed for....

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 in the Dockerfile, README.md and metadata.yaml files.

• I have updated the dependencies and added my name to the maintainer list in the Dockerfile.

• I have updated the feature changes in the README.md (optional).

• 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.

GitHub Packages Auto Build Rules

• I have not manually pushed this Docker image to the uclahs-cds container registry (ghcr.io/uclahs-cds) on GitHub.

• I have updated the image_name in the metadata.yaml which is required by GitHub action to automatically build and push the image.

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[yashpatel6]

For the release, we can essentially re-tag the SAMtools version since I don't think we're pinning a specific version of gnuplot in the Docker