Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
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
blcdsdockerregistry
on Docker Hub.Docker Image Testing
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 picard311 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:3.1.1
docker run -u $(id -u):$(id -g) -v $(pwd):/home -it --rm picard311 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
Nov 15, 2023 8:53:41 PM com.intel.gkl.NativeLibraryLoader load
INFO: Loading libgkl_compression.so from jar:file:/usr/local/share/picard-slim-3.1.1-0/picard.jar!/com/intel/gkl/native/libgkl_compression.so
[Wed Nov 15 20:53:42 GMT 2023] ValidateSamFile --INPUT /home/HG002.N-n2-adjust.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
[Wed Nov 15 20:53:42 GMT 2023] Executing as ?@ac26099c947a on Linux 3.10.0-1160.92.1.el7.x86_64 amd64; OpenJDK 64-Bit Server VM 21.0.1-internal-adhoc.conda.src; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:3.1.1
WARNING 2023-11-15 20:53:42 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur.
No errors found
[Wed Nov 15 20:53:44 GMT 2023] picard.sam.ValidateSamFile done. Elapsed time: 0.04 minutes.
Runtime.totalMemory()=538968064
Description
Updates Picard to v3.1.1
Closes #33