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-d...
If your output is correct using
jobcommand ARGS 2>&1
or
jobcommand ARGS 2>/dev/null
should get you there.