Hey Ryan, Thanks for the tip, redirecting to /dev/null works but then I lose the script output that used to be visible in the history (dataset generation still works fine). Trying to redirect stderr to stdout, using 2>&1, seems to cause a parse error in my .xml configuration file. The line:
<command> soap -a $singleEndedReads -D $referenceGenome -o $output -r $multipleMatchMode 2>&1 </command>
Causes my tool not to show up under the tools section at all.
Cheers
-Branden
On 8/19/2010 9:48 AM, Ry4an Brase wrote:
On Thu, Aug 19, 2010 at 09:34:40AM -0500, Branden Timm wrote:
Hi All, I have been working to integrate SOAPaligner/soap2 into my Galaxy instance, and now have it mostly working thanks to some good advice from this list. However when I execute my tool, the history item for the resulting dataset turns red and says an error occured while running the job. When I look at the error message, it is simply the output of the soap2 tool, as follows: Begin Program SOAPaligner/soap2
[snip]
So why is Galaxy thinking there was an error generating the dataset? Do I have to suppress output from soap2 using a wrapper?
Galaxy will consider the job to have errored out if any text was output to the STDERR file handle. Output to STDOUT file handle is okay and is saved.
See this one for more details:
http://bitbucket.org/galaxy/galaxy-central/issue/325/allow-tool-authors-to-decide-whether-to-use-return-codes-or-stderr-for-detecting-jobIf your output is correct using
jobcommand ARGS 2>&1or
jobcommand ARGS 2>/dev/nullshould get you there.
On Thu, Aug 19, 2010 at 10:24:19AM -0500, Branden Timm wrote:
Hey Ryan, Thanks for the tip, redirecting to /dev/null works but then I lose the script output that used to be visible in the history (dataset generation still works fine).
Yeah the redirect to stderr is definitely the better way to go.
Trying to redirect stderr to stdout, using 2>&1, seems to cause a parse error in my .xml configuration file. The line:
<command> soap -a $singleEndedReads -D $referenceGenome -o $output -r $multipleMatchMode 2>&1 </command>
Causes my tool not to show up under the tools section at all.
I think that > and & both need to be escaped in XML using > and & respectively. Though I don't know if galaxy does some pre-parsing magic to make that unnecessary in its tools files since I would have expected your > /dev/null to fail in the same way.
I'm a big fan of 'xmllint' from the command line when checking for valid XML docs.
Thanks Ryan, I figured out the > and & right as you messaged me. Indeed, it is strange that redirecting to /dev/null worked however...
Cheers Branden
On 8/19/2010 10:33 AM, Ry4an Brase wrote:
On Thu, Aug 19, 2010 at 10:24:19AM -0500, Branden Timm wrote:
Hey Ryan, Thanks for the tip, redirecting to /dev/null works but then I lose the script output that used to be visible in the history (dataset generation still works fine).
Yeah the redirect to stderr is definitely the better way to go.
Trying to redirect stderr to stdout, using 2>&1, seems to cause a parse error in my .xml configuration file. The line:
<command> soap -a $singleEndedReads -D $referenceGenome -o $output -r $multipleMatchMode 2>&1</command>
Causes my tool not to show up under the tools section at all.
I think that> and& both need to be escaped in XML using> and& respectively. Though I don't know if galaxy does some pre-parsing magic to make that unnecessary in its tools files since I would have expected your> /dev/null to fail in the same way.
I'm a big fan of 'xmllint' from the command line when checking for valid XML docs.
Hi Branden,
Try xml escaping the > and & to > and & respectively:
<command> soap -a $singleEndedReads -D $referenceGenome -o $output -r $multipleMatchMode 2>&1 </command>
Let us know if this doesn't help.
Thanks for using Galaxy,
Dan
On Aug 19, 2010, at 11:24 AM, Branden Timm wrote:
Hey Ryan, Thanks for the tip, redirecting to /dev/null works but then I lose the script output that used to be visible in the history (dataset generation still works fine). Trying to redirect stderr to stdout, using 2>&1, seems to cause a parse error in my .xml configuration file. The line:
<command> soap -a $singleEndedReads -D $referenceGenome -o $output -r $multipleMatchMode 2>&1 </command>
Causes my tool not to show up under the tools section at all.
Cheers
-Branden
On 8/19/2010 9:48 AM, Ry4an Brase wrote:
On Thu, Aug 19, 2010 at 09:34:40AM -0500, Branden Timm wrote:
Hi All, I have been working to integrate SOAPaligner/soap2 into my Galaxy instance, and now have it mostly working thanks to some good advice from this list. However when I execute my tool, the history item for the resulting dataset turns red and says an error occured while running the job. When I look at the error message, it is simply the output of the soap2 tool, as follows: Begin Program SOAPaligner/soap2
[snip]
So why is Galaxy thinking there was an error generating the dataset? Do I have to suppress output from soap2 using a wrapper?
Galaxy will consider the job to have errored out if any text was output to the STDERR file handle. Output to STDOUT file handle is okay and is saved.
See this one for more details:
http://bitbucket.org/galaxy/galaxy-central/issue/325/allow-tool-authors-to-decide-whether-to-use-return-codes-or-stderr-for-detecting-jobIf your output is correct using
jobcommand ARGS 2>&1or
jobcommand ARGS 2>/dev/nullshould get you there.
galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
galaxy-dev@lists.galaxyproject.org
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Branden Timm -
Daniel Blankenberg -
Ry4an Brase