Hi Brian,
A couple of days ago, smcmanus https://bitbucket.org/smcmanus pushed the
following change to the repo:
Tools can now specify their own handling of stderr and stdout regular
expressions as well as exit code ranges.
Hi,
I wrote a pipeline (xml attached) that, from what I can gather,
succeeds, but galaxy shows it as an error and doesn't make the output
file accessible as a new data set.
From the server log, I can see that the command line is being
constructed correctly, and it even indicates that it's
Brian;
I wrote a pipeline (xml attached) that, from what I can gather,
succeeds, but galaxy shows it as an error and doesn't make the output
file accessible as a new data set.
Is it possible the software is writing to standard error? Galaxy doesn't
check status codes, but rather check for
Thanks Brad and Nicole! This definitely explains it. The stderr
(which almost all my tools generate for monitoring purposes) was
resulting in galaxy thinking the process failed.
All is well and good now. HUGE THANKS!
-brian
On Fri, Jul 20, 2012 at 1:53 PM, Nicole Rockweiler
