Hey Peter, Carlos,

Thanks for tracking this down, I've updated the composite job/task id tag to 
use an underscore instead in changeset 8658:c901bbb4eca8.

-Dannon


On Jan 23, 2013, at 12:00 PM, Peter Cock <p.j.a.c...@googlemail.com> wrote:

> 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.
> 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
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