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
