[galaxy-dev] Traceback on original execution

2012-04-10 Thread Daniel Patrick Sullivan
Hi, Galaxy, Developers, My name is Dan Sullivan and I work at the University of Chicago in the newly-formed Center for Research Informatics. This is my first post to this list, and I am a very new Galaxy user, so please be patient with me :-) I have a question regarding an error I am

[galaxy-dev] Submitting Jobs as User

2012-05-10 Thread Daniel Patrick Sullivan
Hi, Galaxy Developers, I have a hopefully quick question regarding configuring Galaxy cluster integration; I've configured our universe_wsgi.ini to include the options specified in this document: http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Cluster#Submitting_Jobs_as_the_Real_User

[galaxy-dev] Follow Up

2012-05-14 Thread Daniel Patrick Sullivan
Hi, Galaxy Developers, I sent an email to this list earlier this week regarding an issue I was having with the 'schedule jobs as user' functionality of Galaxy. I am taking a closer look at the documentation on this configuration option, and based on my reading, this feature is only supported with

[galaxy-dev] PBS Server Throwing Errors

2012-07-30 Thread Daniel Patrick Sullivan
Hi, Galaxy Community, Greetings from The University of Chicago; I hope all who attended the Galaxy conference enjoyed it as much as I did. I have searched the mailing list archives as well as Google to a resolve problem I am seeing, however I am somewhat at a loss as to the next course of action

Re: [galaxy-dev] missing slash when installing from toolshed?

2012-08-29 Thread Daniel Patrick Sullivan
Hi, Greg, Thank-you so much for taking the time to answer my question. You appear to be correct; I removed the virtual hosting configuration from apache (I had some redirection configured to automatically forward from port 80 to port 443), and this problem went away. I think I should be able to

[galaxy-dev] Question regarding frequency of pbs_mom authentications

2013-01-30 Thread Daniel Patrick Sullivan
Hi, Galaxy Developers, I have a couple of hopefully quick questions regarding PBS integration with Galaxy; I noticed (based on taking a look at the PBS log data) that Galaxy authenticates rather frequently to the pbs_mom server (please see the log data at the end of this email). Is the

Re: [galaxy-dev] Galaxy Server Processes Dying?

2013-07-10 Thread Daniel Patrick Sullivan
Hi, Ross, I appreciate you taking the time to answer my inquiry. I did know about the options that technically should not be set on a production server (i.e. debug), although I have to admit I did not fully understand the implications of this (i.e. your Galaxy process may run out of memory if

Re: [galaxy-dev] Question regarding walltime exceeded not being correctly reported via the WebUI

2013-11-06 Thread Daniel Patrick Sullivan
issues. Respectfully yours, Dan Sullivan On Tue, Nov 5, 2013 at 8:52 PM, John Chilton chil...@msi.umn.edu wrote: On Tue, Nov 5, 2013 at 11:53 AM, Daniel Patrick Sullivan dansulli...@gmail.com wrote: Hi, John, Thank you for taking the time to help me look into this issue. I have applied

[galaxy-dev] Per-tool overrides for environment variables (non-tool shed)?

2013-12-05 Thread Daniel Patrick Sullivan
Hi, Galaxy-Developers, I apologize if this question has been answered before; I'm trying to override a couple of environment variables on a per-tool level, for a tool that is not installed in the toolshed. I've read a post on the mailing list that suggests this is possible for tools installed

[galaxy-dev] Question about custom styling

2014-01-02 Thread Daniel Patrick Sullivan
Hi, Galaxy Developers, I have searched the wiki and the mailing list and I can't seem to find an answer to this question (if there is a wiki page or a post that I missed, I apologize). Presumably there is a preferred way to do what I'm trying to do. I basically want to make some small cosmetic

Re: [galaxy-dev] Question about custom styling

2014-01-02 Thread Daniel Patrick Sullivan
further assistance. Thank you so much for taking the time to read my post. Dan Sullivan On Thu, Jan 2, 2014 at 3:09 PM, Daniel Patrick Sullivan dansulli...@gmail.com wrote: Hi, Galaxy Developers, I have searched the wiki and the mailing list and I can't seem to find an answer