Re: libbarclay-java needs update, libpicard-java runtime tests by pigx-scrnaseq
Hello again,
On 11.09.20 02:23, Steffen Möller wrote:
> libpicard-java just finished building and testing (and it tested
> intensively), but pigx-scrnaseq will need to wait for another day.
So, libpicard-java and libbarclay-java are both updated
~/git/med-team/pigx/pigx-scrnaseq$ /usr/bin/java -XX:ParallelGCThreads=1
-Xmx4G -Xss16M -Djava.io.tmpdir=/tmp -jar /usr/share/java/pic
ard.jar FastqToSam
O=/home/moeller/git/med-team/pigx/pigx-scrnaseq/tests/out/Mapped/WT_HEK_0h_br1/Fastq_0.bam
F1=/home/moeller/git/med-team/pigx/pigx-scrnaseq/tests/sample_data/reads/HEK_0h_br1_R1_1.fastq.gz
F2=/home/moeller/git/med-team/pigx/pigx-scrnaseq/tests/sample_data/reads/HEK_0h_br1_R2_1.fastq.gz
QUALITY_FORMAT=Standard SAMPLE_NAME=WT_HEK_0h_br1_0 SORT_ORDER=unsorted
2>/home/moeller/git/med-team/pigx/pigx-scrnaseq/tests/out/Log/WT_HEK_0h_br1.0.merge_fastq_to_bam.log
moeller@steffen-laptop-debian:~/git/med-team/pigx/pigx-scrnaseq$ less
/home/moeller/git/med-team/pigx/pigx-scrnaseq/tests/out/Log/WT_HEK_0h_br1.0.merge_fastq_to_bam
.log
~/git/med-team/pigx/pigx-scrnaseq$ dpkg -S /usr/share/java/picard.jar
libpicard-java: /usr/share/java/picard.jar
moeller@steffen-laptop-debian:~/git/med-team/pigx/pigx-scrnaseq$ dpkg -l
libpicard-java libbarclay-java
Desired=Unknown/Install/Remove/Purge/Hold
|
Status=Not/Inst/Conf-files/Unpacked/halF-conf/Half-inst/trig-aWait/Trig-pend
|/ Err?=(none)/Reinst-required (Status,Err: uppercase=bad)
||/ Name Version Architecture Description
+++-===============-=============-============-============================================
ii libbarclay-java 4.0.0-1 all Java library to parse
command line
ii libpicard-java 2.23.4+dfsg-1 amd64 Java library to
manipulate SAM and BAM files
~/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.
Best,
Steffen
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