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