On Sep 27, 2011, at 1:14 PM, Nate Coraor wrote: > 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. >
It looks like the export _JAVA_OPTIONS=-Djava.io.tmpdir=$TMPDIR solution breaks some tools (like snpEFF, which is a 3rd party tool we use). The Jvm prints a diagnostic message to stderr that looks something like this: Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/scratch/32095.scyld.localdomain so in this case the tool fails, since it does not have a wrapper. The sam_merge.xml tool redirects stderr, so it doesn't have this problem. I am thinking about putting a wrapper script for java in my galaxy user's path that adds -Djava.io.tmpdir=$TMPDIR to the arguments. -- Glen L. Beane Senior Software Engineer The Jackson Laboratory (207) 288-6153 ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
