update version

[sorelfitzgibbon]

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.

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

Docker Image Testing

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

My command:

docker build -t test-bedtools .
docker run -it --rm test-bedtools whoami
docker run -it --rm test-bedtools bedtools

Output:

bldocker

bedtools is a powerful toolset for genome arithmetic.

Version:   v2.31.0
About:     developed in the quinlanlab.org and by many contributors worldwide.
Docs:      http://bedtools.readthedocs.io/
...

[tyamaguchi-ucla]

Is this the latest version?

[sorelfitzgibbon]

Nope. Updated to latest mambaforge: v23.1.0-1.

[tyamaguchi-ucla]

Do you want to update the maintainer as well since the yaml was updated?

[sorelfitzgibbon]

updated and retested. Ready to merge?

[tyamaguchi-ucla]

@sorelfitzgibbon It looks like we're missing the auto-build github action? Can you check the template and add any missing files?

[tyamaguchi-ucla]

Looks good to me. I'll leave the final approval to @yashpatel6.

[yashpatel6]

We'll want to add image_name in metadata.yaml for the auto-building action to name the image

[sorelfitzgibbon]

@yashpatel6, done.

[yashpatel6]

Looks good!

[tyamaguchi-ucla]

@sorelfitzgibbon can you also put the image here /hot/software/image/docker-BEDtools?

.
└── Docker
    └── release
        └── bedtools_2.29.2.tar.gz

[sorelfitzgibbon]

@tyamaguchi-ucla, boutrosuser/group doesn't have write permission:

drwxr-sr-x. 2 yashpatel boutrosuser 16384 Sep 26 2022 /hot/software/image/docker-BEDtools/Docker/release

[yashpatel6]

I've updated the permissions now.

Also, on a side note, since this isn't automated for packages, we'll want to add a function to the BL util similar to getPipeline to get a package and save it to the cluster