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 <johns198@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 <lederoc@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