Hi all, This is what I did:
$output = `/home/applications/samtools-0.1.7a/samtools view -bS $ARGV[0] * 2>&1*`; The STDOUT was captured and redirected after I added the 2>&1. Now, the result of the operation isn't in red. On Wed, Apr 25, 2012 at 8:44 AM, Ciara Ledero <lede...@gmail.com> wrote: > 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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