On Jul 30, 2011, at 4:58 AM, Peter Cock wrote:
On Saturday, July 30, 2011, Shantanu Pavgi <pavgi(a)uab.edu> wrote:
> The -V option is not for verbose mode but for exporting your
> shell environment. Refer to qsub manual for details:
> "Specifies that all environment variables active within the
> qsub utility be exported to the context of the job."
> We are already using it in our configuration as needed.
That is such a common need it would be great to have
it in the Galaxy documentation as an example of using
native SGE options with drmaa:// in universe_wsgi.ini
Plus the http://linux.die.net/man/5/sge_complex
> I think we are having problem with the galaxy (or drmaa
> Python lib) parsing correct drmaa/SGE messages and
> not with the drmaa URL configuration. Thoughts?
I'd try adding a few debug log/print statements to the
code to try and diagnose it.
The option is the same for Torque/PBS as well. We'll have the chance (or misfortune
depending on how you look at it) of testing both SGE and Torque locally.