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