Glen Beane wrote:
> 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.

This is what I've just done on our local cluster as well.  I was also
confounded by the lack of a proper environment variable to do this.

--nate

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