On Thu, Jan 17, 2013 at 11:14 PM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
On Thursday, January 17, 2013, Carlos Borroto wrote:
On Wed, Jan 16, 2013 at 7:28 AM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
Renaming the file to replace the colon with (say) an underscore allows a manual qsub to work fine with UGE. I've edited Galaxy to avoid the colons (patch below) but the submission still fails.
Hi Peter,
After seeing your email I now wonder if the problem I described here[1] and didn't get any answer about it is related to your findings while trying UGE.
[1]http://dev.list.galaxyproject.org/Issue-when-enabling-use-tasked-jobs-with-t...
I noticed the only mayor different I can notice between jobs submission with and without tasked option enabled is a colon in the name.
Some overlap yes, and I do normally have BLAST running with task splitting. That does probably explain the source of the colon. I now suspect the colon is only a problem in SGE / UGE at the command line using qsub - it may work via the Python API.
Confirmed - on our system using UGE (and likely our old system with SGE), when task split jobs are assigned job shell scripts with a colon in the filename it does work. However, the presence of the colon prevents manual submission of the same script, which I have found extremely useful in debugging. e.g. $ qsub sleep:colon.sh Unable to run job: Colon (':') not allowed in objectname. Exiting. Escaping the colon did not help: $ qsub sleep\:colon.sh Unable to run job: Colon (':') not allowed in objectname. Exiting. (Sadly the Univa Grid Engine UGE version of qsub does not appear to have a version switch so I'm not sure which version this is) For this reason alone, I would prefer Galaxy avoided colons in its job filenames - and I suspect there could be other corner cases with other cluster systems and shared file-systems (as found by Carlos). Regards, Peter