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usegalaxy-no / galaxyadmin

A repository for managing the work of the usegalaxy.no GalaxyAdmin team
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Merge BAM Files fails: problems finding .jar file #36

Closed ehj000 closed 3 years ago

ehj000 commented 3 years ago

A user reports that the tools fails with the following error: Error: Unable to access jarfile /MergeSamFiles.jar

I see from an old post in Biostar from Bjoern Gruening that "we are not allowed to ship the JAR file, because of licensing issues. You need to download it by yourself and specify the location in the env.sh file in you GATK Tool Shed installation directory."

Although a different tool, could this be whats causing the problem?

torfinnnome commented 3 years ago

Can the "Samtools merge" tool be used?

(And if so; remove this non-functional tool.)

ehj000 commented 3 years ago

Do you know if they give the same output? I have forwarded this suggestion to the user. Thanks

kjetilkl commented 3 years ago

The Picard requirement is installed from BioConda, and it includes the file "MergeSamFiles.jar". But the command-line in the wrapper specifies the path to this JAR file as "$JAVA_JAR_PATH/MergeSamFiles.jar" and the environment variable "$JAVA_JAR_PATH" is not set anywhere.

torfinnnome commented 3 years ago

Should we put these jar files on our CVMFS somewhere?

torfinnnome commented 3 years ago

Fixed: https://github.com/usegalaxy-no/infrastructure-playbook/commit/0d4e5fe3e17fbe7a31e8b35d86591bd5d4ec15ca