Lance Parsons wrote:
> For what it's worth, I ran into an issue with the use of /tmp as
> well. When merging a lot of BAM files, /tmp filled up and the merge
> failed. To make matters worse, since STDERR is redirected and the
> exit status of java is not checked, the item in the Galaxy history
> appeared OK. Though examination of the .log file revealed the
> issue, users weren't aware of the problem right away, causing
> further confusion. To get around this, I implemented two fixes:
> 1 - Wrapper for sam_merge2 very similar to hide_stderr.py used by
> the ncbi_blast_plus tools. I did have to "hack" it a bit, however,
> since when I output the captured stderr, galaxy would hang if it was
> too large. My "fix" was to output the first and last 7500
> characters of stderr (truncating the middle). Now when the merge
> fails, users see a failure in Galaxy (red history item).
> 2 - Looking at other Picard tools, it seems that at least some of
> them explicitly set TMP_DIR to $__new_files_directory__, which in
> this case seemed appropriate, at least for my use case. So I added
> that simple change to the sam_merge.xml command line.
> I'm open to better solutions if people see issues with these, but I
> would suggest that Galaxy be updated to include fixes for these
> issues since it seems others are likely to run into these problems.
> If people generally agree I'd be happy to provide create tickets
> and/or provide changesets or whatever the Galaxy maintainers would
Could you put these patches in an issue (or create a pull request)?
> Glen Beane wrote:
> >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
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> > http://lists.bx.psu.edu/
> Lance Parsons - Scientific Programmer
> 134 Carl C. Icahn Laboratory
> Lewis-Sigler Institute for Integrative Genomics
> Princeton University
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