Picard_tools_missing_jars_on_Biolinux_6_Galaxy

[Simon Wagstaff]

The galaxy-server-all package does not pull down the jars for picard tools although they appear in the LH pane of the galaxy server.
I can confirm that the tools work when the jars are manually installed into /usr/lib/galaxy-server/tool-data/shared/jars/picard

Note that there is some cross-fertilisation with SamTools here - e.g. NGS: Sam Tools calls the picard merge jar causing the same issues with some Sam Tools scripts

[Tim Booth (tbooth)]

The way picard-tools provides one .jar per tool is very unusual, and as Debian doesn't like unusual stuff it opts to package the tools into a single .jar, so instead of:

java -jar /path/to/picard-tools/PicardCommand.jar OPTION1=value1 OPTION2=value2

you say just:

picard-tools PicardCommand OPTION1=value1 OPTION2=value2

This means that the Galaxy Picard wrappers are completely incompatible. Modifying the wrappers may be more trouble than it's worth, but nevertheless I'll give it a try.

TIM

[Tim Booth (tbooth)]

An update on this bug...

Simon has reported further problems, but it looks like the issue is with an invalid option being passed to Picard Tools:

"
I've been running SamToFastq Galaxy picard tools as part of a Galaxy
workglow on BL-7 and getting less than useful errors when it fails:

ERROR: Unrecognized option: INCLUDE_NON_PRIMARY_ALIGNMENTS
"

This error is not misleading - Galaxy needs a newer version of Picard tools to do its thing. We only have 1.46 but the latest is 1.84. Downloading the updated .jar files manually would have fixed the problem, as it did last time, except I modified the tools/samtools/sam_merge.xml file to see the packaged version of Samtools so it ignores the .jar files.

I'd like to update the source build of picard-tools but this requires libjbzip2-java and libsnappy-java and in turn libsnappy-java needs an updated maven-debian-helper. I've sorted all those updates and got it building but there are still problems. Need to debug runtime dependencies on the command line, test on Galaxy and push all the updates through. I'm hoping I can finish all this tomorrow. Failing that I can at least direct Simon to a fix.

TIM