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nmdp-bioinformatics / pipeline

Consensus assembly and allele interpretation pipeline.
GNU Lesser General Public License v3.0
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Update picard dependency to htsjdk version 1.118 #22

Closed ghost closed 9 years ago

ghost commented 9 years ago

Picard/HTSJDK/samtools changed its package structure and library name after version 1.102.

There still isn't a proper htsjdk release to Maven Central but they are working towards it. Meanwhile, version 1.118 is available here

http://search.maven.org/#artifactdetails|org.seqdoop|htsjdk|1.118|jar

$ wget http://repo1.maven.org/maven2/org/seqdoop/htsjdk/1.118/htsjdk-1.118.jar

If this pull request is merged, the tutorial (and wrapper script, if any) classpath will have to be changed (remove picard-1.102.0.jar and add htsjdk-1.118.jar).

ghost commented 9 years ago

Just for the record, Travis CI is not yet configured for this project, so the build failure doesn't have anything to do with this pull request.