21 Apr
2010
21 Apr
'10
12:58 p.m.
Ry4an Brase wrote:
If you're employing a shell script wrapper around your tool in the tool runner, as many seem to do, you can just add "2>&1" to the end of your command. For example in the /galaxy-dist/tools/plotting/r_wrapper.sh file the line that looks like:
R --vanilla --slave $* < $infile
would change to
R --vanilla --slave $* < $infile 2>&1
Hi Ry4an, While this would indeed fix the problem of the job failing, it'd prevent any failures from ever being detected. What we've done for tools that don't set a return code is attempt to parse the output for errors. --nate