We recently updated to the latest galaxy-dist, and learned that the 
sam_merge.xml tool now uses picard MergeSamFiles.jar to merge the files instead 
of the samtools merge wrapper sam_merge.py.

this is a problem for us because MergeSamFiles.jar does not honor $TMPDIR when 
creating temporary file names (the jvm developers inexplicably hard code the 
value of java.io.tmpdir to /tmp in Unix/Linux rather than doing the Right 
Thing) .  On our cluster, TMPDIR is set to something like 
/scratch/batch_job_id/.  This location has plenty of free space, however /tmp 
does not and now we can't successfully merge largeish bam files. 

In case anyone else is bit by this, I think there are two options

the Picard tools take an optional TMP_DIR= argument that lets us specify the 
location we want to use for a temporary directory.  Initially we ended up 
modifying the .xml to add TMP_DIR=\$TMPDIR to the arguments to 
MergeSamFiles.jar. This works, but we could potentially need to do this with 
multiple Picard tools and not just MergeSamFiles.   Now I am probably going to 
go with the following solution:

add something like "export _JAVA_OPTIONS=-Djava.io.tmpdir=$TMPDIR" to the 
.bashrc file for my Galaxy user.


--
Glen L. Beane
Senior Software Engineer
The Jackson Laboratory
(207) 288-6153


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