Re: [galaxy-user] cufflinks eference annotation

2012-07-23 Thread Jennifer Jackson
Hello Irene, Please see below: On 7/23/12 2:17 AM, i b wrote: Thanks Jen. One thing I still don't get: what if I want to discover novel tanscripts? Does this have anythign to do with selecting or not a reference annotation Best I On Mon, Jul 23, 2012 at 5:58 AM, Jennifer Jackson wrote: Hel

Re: [galaxy-user] flaking regions across TSS

2012-07-23 Thread shamsher jagat
I want to have list of genes from UCSC browser or known genes. Thanks Kanwar On Fri, Jul 20, 2012 at 8:00 PM, Jennifer Jackson wrote: > Hello Kanwar, > > > On 7/20/12 3:31 PM, shamsher jagat wrote: > >> I am interested in getting regions flanking TSS, I am using Glaxaxy and >> have downloaded

[galaxy-user] CloudMan - Can't start nodes

2012-07-23 Thread mailing list
Hi guys, I created a new Galaxy instance (probably around early July) with the web launcher (https://biocloudcentral.herokuapp.com/launch). I've been coming back and re-using it since then. However for the past week at least I haven't been able to launch new nodes. They show up as red on the in

Re: [galaxy-user] "Jobs is waiting to run" all day on Main

2012-07-23 Thread Jennifer Jackson
Hello Mengmeng, Please try your upload process again and let us know if you continue to have problems. Thank you! Jen Galaxy team On 7/22/12 12:46 PM, Lu, Mengmeng wrote: Same problem here. I want to add a custom build, but it has been processing for more than 5 hours. Is it normal? PS:

Re: [galaxy-user] "Jobs is waiting to run" all day on Main

2012-07-23 Thread Jennifer Jackson
Hello Lee, When Galaxy is busy, the grey 'waiting to run' states means that the job is in the queue. You want to be sure to not delete/restart queued jobs or they move back to the end. Queue wait times can vary. It appears that your jobs have completed (there are none in the largest queue at

Re: [galaxy-user] CloudMan - Can't start nodes

2012-07-23 Thread Brad Chapman
Greg; > I created a new Galaxy instance (probably around early July) with the > web launcher (https://biocloudcentral.herokuapp.com/launch). > > I've been coming back and re-using it since then. However for the > past week at least I haven't been able to launch new nodes. They show > up as red

[galaxy-user] Uploading files into local instance! Please help!

2012-07-23 Thread Di Nguyen
Dear all, I am having a problem uploading my RNA-seq files into my local instance. What would be the easiest way to set this up? I already setup libraries under Admin but cannot upload file directly, perhaps due to the size limit of the browser. 1.FTP? Please give me a step by step instructi

Re: [galaxy-user] Uploading files into local instance! Please help!

2012-07-23 Thread Jennifer Jackson
Hello Di, The good way to load data in a local instance is through the Data Library function: http://wiki.g2.bx.psu.edu/Admin/Data%20Libraries http://wiki.g2.bx.psu.edu/Admin/Data%20Libraries/Uploading%20Library%20Files If you run into trouble, you will probably want to switch over to the gal