Update Picard to 2.26.8 to address Log4j critical vulnerability

[tyamaguchi-ucla]

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• 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:

(base) [tyamaguchi@ip-0A12520A docker-Picard]$ docker run -u $(id -u):$(id -g) -it --rm blcdsdockerregistry/picard:2.26.3 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:2.26.3

(base) [tyamaguchi@ip-0A12520A docker-Picard]$ docker run -u $(id -u):$(id -g) -it --rm blcdsdockerregistry/picard:branch-dev 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:2.26.8

(base) [tyamaguchi@ip-0A12520A output]$ docker run -u $(id -u):$(id -g) -v $(pwd):$(pwd) -it --rm blcdsdockerregistry/picard:branch-dev picard ValidateSamFile -I /hot/resources/SMC-HET/normal/bams/A-mini/n2/output/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
21:17:39.125 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/usr/local/share/picard-slim-2.26.8-0/picard.jar!/com/intel/gkl/native/libgkl_compression.so
[Thu Dec 16 21:17:39 GMT 2021] ValidateSamFile --INPUT /hot/resources/SMC-HET/normal/bams/A-mini/n2/output/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 --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Dec 16 21:17:39 GMT 2021] Executing as ?@0d05ea95c9ea on Linux 3.10.0-1127.19.1.el7.x86_64 amd64; OpenJDK 64-Bit Server VM 1.8.0_152-release-1056-b12; Deflater: Intel; Inflater: Intel; Provider GCS is not available; Picard version: Version:2.26.8
WARNING 2021-12-16 21:17:39     ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur.
No errors found
[Thu Dec 16 21:17:42 GMT 2021] picard.sam.ValidateSamFile done. Elapsed time: 0.06 minutes.
Runtime.totalMemory()=693633024

Update Picard to 2.26.8 to address Log4j critical vulnerability

[tyamaguchi-ucla]

Both 2.26.3 and 2.26.8 showed a warning statement - created an issue #14

[yashpatel6]

Both 2.26.3 and 2.26.8 showed a warning statement - created an issue #14

The problem seems to be with one of the commands in the wrapper script picard. It seems specific to the OS/system rather than Picard itself (the same line causes the same warning with the SAMtools docker image for example). Running the JAR directly doesn't produce the warning.

[tyamaguchi-ucla]

Both 2.26.3 and 2.26.8 showed a warning statement - created an issue #14

The problem seems to be with one of the commands in the wrapper script picard. It seems specific to the OS/system rather than Picard itself (the same line causes the same warning with the SAMtools docker image for example). Running the JAR directly doesn't produce the warning.

Yup, the warning shouldn't affect picard performance itself.

[yashpatel6]

Looks good!