On Thu, Aug 19, 2010 at 09:34:40AM -0500, Branden Timm wrote:
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
So why is Galaxy thinking there was an error generating the dataset?
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
See this one for more details:
If your output is correct using
jobcommand ARGS 2>&1
jobcommand ARGS 2>/dev/null
should get you there.
Ry4an Brase 612-626-6575
University of Minnesota Supercomputing Institute
for Advanced Computational Research http://www.msi.umn.edu