On Oct 3, 2011, at 5:08 PM, Lance Parsons wrote:
The patches have been put into a pull request.
I finally had a chance to go through pull requests, and this is now in galaxy-central.
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
> Hi Lance,
> Could you put these patches in an issue (or create a pull request)?
Lance Parsons - Scientific Programmer
134 Carl C. Icahn Laboratory
Lewis-Sigler Institute for Integrative Genomics