Hi all,
This is what I did:
$output = `/home/applications/samtools-0.1.7a/samtools view -bS $ARGV[0] *
21*`;
The STDOUT was captured and redirected after I added the 21. 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
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
On Tue, Apr 24, 2012 at 10:03 AM, Ciara Ledero 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.
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
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
