On Thu, Jan 17, 2013 at 11:14 PM, Peter Cock <p.j.a.c...@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.c...@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-torque-and-nfs-td4657294.html
>> 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.

Escaping the colon did not help:

$ qsub sleep\:colon.sh
Unable to run job: Colon (':') not allowed in objectname.

(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).


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