Picard_tools_missing_jars_on_Biolinux_6_Galaxy
Bug #1070736 reported by
Simon Wagstaff
This bug affects 1 person
Affects | Status | Importance | Assigned to | Milestone | |
---|---|---|---|---|---|
Bio-Linux |
In Progress
|
Medium
|
Unassigned |
Bug Description
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/
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
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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/PicardCom mand.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