Ok, so I figured out how to get the username in drama.py and pass it along to SGE(in our case) using the Gordon patch. Now I am getting an error that "Job output not returned from cluster" which comes from the finish job sub routine in drama.py . I am assuming this is because the .dat file are owned by the galaxy user and do not have write permission by other users. Where are these files created? I am hoping to add a system call to chmod to see if this fixes the problem.
Thanks, Ilya -----Original Message----- From: Nate Coraor [mailto:n...@bx.psu.edu] Sent: Thursday, June 09, 2011 9:47 AM To: Chorny, Ilya Cc: firstname.lastname@example.org Subject: Re: [galaxy-dev] Passing username to drmaa.py Chorny, Ilya wrote: > I am trying to figure out how to pass the current user name to drama.py. I > have had little success so far. None of the environmental variables contain > any current user information. Any thoughts? > > Thanks, > > Ilya Hi Ilya, You can use $__user_email__ in the command template in the tool's configuration, if you need it there. In the drmaa.py code itself, you can use the '.user' property on the job wrapper to get the email address. --nate > > > Ilya Chorny Ph.D. > Bioinformatics - Intern > icho...@illumina.com<mailto:icho...@illumina.com> > 858-202-4582 > > ___________________________________________________________ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this and other > Galaxy lists, please use the interface at: > > http://lists.bx.psu.edu/ ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/