To clear things up, I am using my own tool which uses samtools internally. I think I have tried the SAM-to-BAM tool when I was exploring Galaxy and I think it worked fine. By the way, I am using Perl.
Thanks for the tips! I'll get back here if something goes awry again. CL On Wed, Apr 25, 2012 at 12:54 AM, Jim Johnson <johns...@umn.edu> wrote: > * > I put a samtools_filter tool in the toolshed that uses samtools view command. > I called the samtools view command from the command section of the > tool_config and redirected stderr to stdout to avoid having galaxy interpret > it as an error. > > Jim Johnson > Minnesota Supercomputing Institute > University of Minnesota > > > On Tue, Apr 24, 2012 at 10:03 AM, Ciara Ledero <lede...@gmail.com> > <lede...@gmail.com> wrote: > * > > *Hi there, > > I know? Galaxy already has a SAM-to-BAM converter, but part of my > exercise/task is to incorporate a script that uses samtools' view command. I > get this error: > > [samopen] SAM header is present: 66338 sequences. > > according to Galaxy. But this might not be an error at all. Is? there any > way that I could tell Galaxy to ignore this and just continue with the > script? > > Thanks in advance! Any help would be greatly appreciated. > > CL* > > > >
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