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picard_CollectWgsMetrics fails to find CollectWgsMetrics.jar due to undefined $JAVA_JAR_PATH #1

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unode opened this issue Nov 13, 2014 · 0 comments · May be fixed by #3
Open

picard_CollectWgsMetrics fails to find CollectWgsMetrics.jar due to undefined $JAVA_JAR_PATH #1

unode opened this issue Nov 13, 2014 · 0 comments · May be fixed by #3

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@unode
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unode commented Nov 13, 2014

Hi Anton,

We installed picard_plus from the main galaxy toolshed. So far all of the tools we tried work but CollectWgsMetrics is failing with the error:

Fatal error: Exit code 1 ()
Error: Unable to access jarfile /CollectWgsMetrics.jar

Looking at the script created by galaxy it seems that the env.sh file that exports JAVA_JAR_PATH is not loaded.
The source of the problem seems to be that the requirement tag of this tool refers to picard 1.121.0 instead of 1.122.0.
bgruening added a commit to bgruening/picard that referenced this issue Dec 3, 2014
@bgruening
Fix requirement tag.
d66c343 
Should fix: nekrut#1
Anton can we move this to tools-devteam and update the "old" wrappers?
@bgruening bgruening linked a pull request Dec 3, 2014 that will close this issue
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Fix requirement tag. bgruening/picard
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@unode