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.