Re: [galaxy-dev] About an additional tool
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
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> <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*
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 <lederoc@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 <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> <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*
participants (2)
-
Ciara Ledero -
Jim Johnson