Update Picard to 3.10

[j2salmingo]

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 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:

docker run -u $(id -u):$(id -g) -it --rm picard310 picard SortSam --version
/usr/local/bin/picard: line 5: warning: setlocale: LC_ALL: cannot change locale (en_US.UTF-8): No such file or directory
Version:3.1.0

docker run -u $(id -u):$(id -g) -v $(pwd):/home -it --rm picard310 picard ValidateSamFile -I /home/HG002.N-n2.bam
/usr/local/bin/picard: line 5: warning: setlocale: LC_ALL: cannot change locale (en_US.UTF-8): No such file or directory
Sep 12, 2023 6:54:04 PM com.intel.gkl.NativeLibraryLoader load
INFO: Loading libgkl_compression.so from jar:file:/usr/local/share/picard-slim-3.1.0-0/picard.jar!/com/intel/gkl/native/libgkl_compression.so
[Tue Sep 12 18:54:04 GMT 2023] ValidateSamFile --INPUT /home/HG002.N-n2.bam --MODE VERBOSE --MAX_OUTPUT 100 --IGNORE_WARNINGS false --VALIDATE_INDEX true --INDEX_VALIDATION_STRINGENCY EXHAUSTIVE --IS_BISULFITE_SEQUENCED false --MAX_OPEN_TEMP_FILES 8000 --SKIP_MATE_VALIDATION false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Tue Sep 12 18:54:04 GMT 2023] Executing as ?@38819569ea4e on Linux 5.15.90.1-microsoft-standard-WSL2 amd64; OpenJDK 64-Bit Server VM 20.0.2-internal-adhoc..src; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:3.1.0
WARNING 2023-09-12 18:54:04 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur.
No errors found
[Tue Sep 12 18:54:05 GMT 2023] picard.sam.ValidateSamFile done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=538968064

Description

Updates Picard version and builds from miniforge.

Closes #29

[tyamaguchi-ucla]

I've added a few minor comments. Otherwise, looks good. Anything else to add @Faizal-Eeman ?

[Faizal-Eeman]

Looks good to me!