Re: [galaxy-dev] About an additional tool
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 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* ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-dev] About an additional tool
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 ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] About an additional tool
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. 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 As you have probably guessed, that is not an error. Rather it is a progress/diagnostic message from samtools printed to stderr. There is a long standing bug with Galaxy assuming that any output on stderr indicates a failure, despite typical usage on Unix/Linux for progress, diagnostics or warning messages: https://bitbucket.org/galaxy/galaxy-central/issue/325/ In this situation Galaxy tools use a wrapper script to cope with these non-error messages. That should be happening already with sam_to_bam.py - but I am unclear if you are having a problem with the provided SAM to BAM tool, or your own tool which uses samtools internally. Peter ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
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 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 ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] About an additional tool
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* ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
