Hi Steffen, Le 11/09/2020 à 15:27, Steffen Möller a écrit : > Hello again, > > [...] > > 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. >
I have just looked at picard-tools and I saw that, yesterday, you modified libpicard-java.manifest. I suspect this fixed the test-case you submitted above. Can you confirm? Let me know if the classpath of libpicard-java needs further investigation. > > Best, > > Steffen > > Best, Pierre
