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
> prefer.

Hi Lance,

Could you put these patches in an issue (or create a pull request)?

Thanks,
--nate

> 
> Lance
> 
> 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"
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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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