On Saturday, July 30, 2011, Shantanu Pavgi <pavgi@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 link. Thanks!
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. Peter