On Oct 3, 2011, at 5:08 PM, Lance Parsons wrote:

> The patches have been put into a pull request.

Hi Lance,

I finally had a chance to go through pull requests, and this is now in 


> Lance
> Nate Coraor wrote:
>> 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 Parsons - Scientific Programmer
> 134 Carl C. Icahn Laboratory
> Lewis-Sigler Institute for Integrative Genomics
> Princeton University

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