Re: libbarclay-java needs update, libpicard-java runtime tests by pigx-scrnaseq
On Fri, Sep 11, 2020 at 03:27:55PM +0200, Steffen Möller wrote:
> ~/git/med-team/pigx/pigx-scrnaseq$ cat
> /home/moeller/git/med-team/pigx/pigx-scrnaseq/tests/out/Log/WT_HEK_0h_br1.0.merge_fastq_to_bam.
> log
> Error: Unable to initialize main class picard.cmdline.PicardCommandLine
> Caused by: java.lang.NoClassDefFoundError:
> org/broadinstitute/barclay/argparser/CommandLineProgramProperties
>
> But the classes do exist
>
> ~/git/med-team/pigx/pigx-scrnaseq$ jar tf
> /usr/share/java/barclay.jar|grep CommandLineProgram
> org/broadinstitute/barclay/argparser/CommandLineProgramGroup.class
> org/broadinstitute/barclay/argparser/CommandLineProgramProperties.class
>
> and the error prevails when minimizing the invocation as to
>
>
> ~/git/med-team/pigx/pigx-scrnaseq$ /usr/bin/java -XX:ParallelGCThreads=1
> -Xmx4G -Xss16M -Djava.io.tmpdir=/tmp -cp $PICARD_CLASSPATH -j
> ar /usr/share/java/picard.jar FastqToSam
> Error: Unable to initialize main class picard.cmdline.PicardCommandLine
>
> while the following (without the -jar) is working (borrowed from the
> picard-tools script):
>
>
> export
> PICARD_CLASSPATH=/usr/share/java/picard.jar:/usr/share/java/htsjdk.jar:/usr/share/java/guava
> .jar:/usr/lib/jvm/default-java/lib/tools.jar:/usr/share/java/commons-lang3.jar:/usr/share/java/gkl.jar:/usr/share/java/gatk-native-bindings.jar:/usr/share/java/barc
> lay.jar
>
> ~/git/med-team/pigx/pigx-scrnaseq$ /usr/bin/java -XX:ParallelGCThreads=1
> -Xmx4G -Xss16M -Djava.io.tmpdir=/tmp -cp $PICARD_CLASSPATH p
> icard.cmdline.PicardCommandLine FastqToSam
>
> With a quick confirmation from
> https://stackoverflow.com/questions/15930782/call-java-jar-myfile-jar-with-additional-classpath-option
> it seems like some work is needed on the Manifest that accompanies our
> libpicard-java package.
>
> I'll read up how to do that properly in Debian, so our .jar is
> compatible with what the community apparently expects. @Andreas, if this
> is something close to your routine, please jump in.
All this Java stuff is extremely far from my routine and I'm so happy we
have Pierre on board who was always a great help in cases like these.
Kind regards
Andreas.
--
http://fam-tille.de
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