Use pkgdepends

[Faizal-Eeman]

Description

This PR adds pkgdepends to install Battenberg and other dependencies.

Closes #...

Testing Results

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:

docker run --rm -u $(id -u):$(id -g) battenberg:2.2.9 Rscript /usr/local/bin/battenberg_wgs.R -h

[mmootor@ip-0A125937 docker-Battenberg]$ docker run --rm -u $(id -u):$(id -g) bb:2.2.9 Rs
cript /usr/local/bin/battenberg_wgs.R -h
Usage: /usr/local/bin/battenberg_wgs.R [options]


Options:
        -t CHARACTER, --tumourname=CHARACTER
                Samplename of the tumour

        -n CHARACTER, --normalname=CHARACTER
                Samplename of the normal

        --tb=CHARACTER
                Tumour BAM file

        --nb=CHARACTER
                Normal BAM file

        --sex=CHARACTER
                Sex of the sample

        -o CHARACTER, --output=CHARACTER
                Directory where output will be written

        --skip_allelecount
                Provide when alleles don't have to be counted. This expects allelecount files on disk

        --skip_preprocessing
                Provide when pre-processing has previously completed. This expects the files on disk

        --skip_phasing
                Provide when phasing has previously completed. This expects the files on disk

        --cpu=CHARACTER
                The number of CPU cores to be used by the pipeline (Default: 8)

        --bp=CHARACTER
                Optional two column file (chromosome and position) specifying prior breakpoints to be used during segmentation

        -h, --help
                Show this help message and exit

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.

[wiz-inc-8da00b022c]

Wiz Scan Summary

IaC Misconfigurations
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[yashpatel6]

Generally looks good!