Hi Pierre, On 13.09.20 11:25, Pierre Gruet wrote: > 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.
Sorry, yes, I forgot to forward this to the list. It works now and I also added a smallish test invoking that picard.jar in d/rules Thank you for chasing this up, Pierre, much appreciated. I somehow thought that this classpath-fruit hangs low enough for me reach if I just stretch myself a bit. Best, Steffen
