Re: [galaxy-user] Teaching GALAXY

2012-11-12 Thread Reiter, Larry T
I'm out of town till Tuesday. Lawrence T Reiter, PhD UTHSC, Memphis, TN On Nov 9, 2012, at 4:40 PM, Lei Yan leiyan2...@gmail.commailto:leiyan2...@gmail.com wrote: Dear Dannon, We appreciate your helps. It looks like jobs can run now. But I found a strange thing here, and I don’t know it is an

Re: [galaxy-user] Teaching GALAXY

2012-11-09 Thread Larry Reiter
Dannon, Maybe you can, but not through me. I'm just a lowly user and biologist. You would have to contact the guy who did the installation and runs the server: Lei Yan (leiyan2...@gmail.com) I would think he would be receptive to some help, so you should mail him. LTR On 11/7/12 4:05 PM,

Re: [galaxy-user] Teaching GALAXY

2012-11-09 Thread Larry Reiter
It looks like both the main server and our local install are frozen. Nothing has run since we started yesterday at about 11:30am. Anybody know why? LTR On 11/7/12 4:05 PM, Dannon Baker wrote: Main will complete the jobs eventually, though obviously that's not particularly useful in the

Re: [galaxy-user] Teaching GALAXY

2012-11-09 Thread Dannon Baker
Lei - It looks like you have two worker nodes, but both are currently listed as non-idle, yet have low load. My guess is that something has gone wrong with the SGE configuration causing jobs to simply wait in the queue. If you look at the contents of qconf and qstat on the admin page, does

Re: [galaxy-user] Teaching GALAXY

2012-11-08 Thread Dannon Baker
NGS jobs are experiencing significant delays at this time due to load -- we're looking into it. Regarding the local install I'd have to recommend pinging the administrator on site there -- they should be able to help out. -Dannon On Nov 8, 2012, at 10:44 AM, Larry Reiter lrei...@uthsc.edu

Re: [galaxy-user] Teaching GALAXY

2012-11-07 Thread Dannon Baker
Can you describe more about what is broken with your cloud install? Regarding main - the server has been under heavy load today and, while it shouldn't remain frozen, might be slow to dispatch and, depending on the type, execute) jobs. -Dannon On Nov 7, 2012, at 1:12 PM, Larry Reiter

Re: [galaxy-user] Teaching GALAXY

2012-11-07 Thread Larry Reiter
Dannon, Thanks for getting back to me. Both the local cloud install and the main server are frozen. Well, not exactly frozen. I can still rename or delete jobs, etc. I can even switch histories and such, but I can't get it to run even simple jobs - like taking a demo file and running

Re: [galaxy-user] Teaching GALAXY

2012-11-07 Thread Tilahun Abebe
I also had a similar issue. I thought it has to do with the hurricane in the east coat and never bothered to ask. Even small analyses (such as running the RNA-seq analysis exercise by Jeremy Goecks) were stalled; in a couple of instances for a day or more. Thanks. Tilahun

Re: [galaxy-user] Teaching GALAXY

2012-11-07 Thread Dannon Baker
Main will complete the jobs eventually, though obviously that's not particularly useful in the context of your class today. How is your cloud instance set up? Cloud or local instances should be the best and most reliable option for teaching with and I'd definitely like to figure out why yours