Re: libbarclay-java needs update, libpicard-java runtime tests by pigx-scrnaseq

[Pierre Gruet <pgtdebian@free.fr>]

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