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.
Glen L. Beane
Senior Software Engineer
The Jackson Laboratory
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: