[galaxy-dev] Trackster - not showing data.

2012-05-10 Thread Mohammad Heydarian
Hi, I have been trying to use trackster on the main Galaxy server for a couple of days now. It was working fine for me early yesterday, I was looking at (larger) BAM files, then it just stopped and would not display the data of the loaded tracks (but did display the track title). I have tried to

[galaxy-dev] problems with running jobs on Galaxy

2012-05-10 Thread Philipp Kapranov
Hello, I keep on getting this error today: Error executing tool: [Errno 13] Permission denied: '/galaxy/main_pool/pool4/files/004' . What is wrong? Thank you! Phil ___ Please keep all replies on the list by using reply all in your mail

[galaxy-dev] Server Error when downloading files from history

2012-05-10 Thread Rathi D. Thiagarajan
Hi there, I received the following error when trying to download/save my tabular files with 5k lines: Server Error An error occurred. See the error logs for more information. (Turn debug on to display exception reports here) Please help! Thanks in advance. Cheers, Rathi -- Rathi

Re: [galaxy-dev] Trackster - not showing data.

2012-05-10 Thread Jeremy Goecks
Mo, This was a temporary problem and has been fixed. However, the datasets you tried to visualize are now in an error state, so you'll have to copy them (History Menu -- Copy Datasets) to create new ones, which you can then visualize. You can copy datasets to the same history without

Re: [galaxy-dev] Error when exporting history to file

2012-05-10 Thread Sarah Diehl
Hi Jeremy, I was able to reproduce the error on the public Galaxy server. I shared the history with you (jeremy.goe...@emory.edu). It's named export history to file bug. Thanks. Sarah - Original Message - From: Sarah Diehl di...@immunbio.mpg.de To: Jeremy Goecks

Re: [galaxy-dev] [galaxy-user] Help on installing cutadapt

2012-05-10 Thread Nate Coraor
On May 9, 2012, at 10:37 AM, Tilahun Abebe wrote: Hi Jen, Thank you for the suggestions. I did try to log in to Galaxy under User --Login. The password is the one I use for the Galaxy Main. However, it gives me the error message No such user (please note that login is case sensitive). I

Re: [galaxy-dev] Running Galaxy on PBS/Torque cluster

2012-05-10 Thread Nate Coraor
On May 3, 2012, at 3:42 PM, Dorset, Daniel C wrote: I have had Galaxy running on a local BAS, and after success with that we’re ready to create an instance on our local cluster computing service. The local cluster uses PBS/Torque. I’m familiar with the basics of configuration, but our

Re: [galaxy-dev] Running Galaxy on PBS/Torque cluster

2012-05-10 Thread Fields, Christopher J
On May 10, 2012, at 11:02 AM, Nate Coraor wrote: On May 3, 2012, at 3:42 PM, Dorset, Daniel C wrote: I have had Galaxy running on a local BAS, and after success with that we’re ready to create an instance on our local cluster computing service. The local cluster uses PBS/Torque. I’m

Re: [galaxy-dev] Running Galaxy on PBS/Torque cluster

2012-05-10 Thread Dorset, Daniel C
Thanks Nate! I'm looking forward to it! -Original Message- From: Nate Coraor [mailto:n...@bx.psu.edu] Sent: Thursday, May 10, 2012 11:02 AM To: Dorset, Daniel C Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Running Galaxy on PBS/Torque cluster On May 3, 2012, at 3:42 PM,

Re: [galaxy-dev] Error when exporting history to file

2012-05-10 Thread Jeremy Goecks
Fixed in galaxy-central changeset cc70c3dcd6f7 Sarah, thanks for taking the time to reproduce on the public server. Best, J. On May 10, 2012, at 10:17 AM, Sarah Diehl wrote: Hi Jeremy, I was able to reproduce the error on the public Galaxy server. I shared the history with you

Re: [galaxy-dev] Loc file configuration question

2012-05-10 Thread Raja Kelkar
Hi Fred, Thanks for the tip on the alignseq file. It did work (I do now have sequence that came back from the tool, will have to check if it correct). Anyone have a logical explanation? Perhaps these myriad loc files can be streamlined down to something simple in future. Thanks. Dan: The

Re: [galaxy-dev] Loc file configuration question

2012-05-10 Thread Federico De Masi
Hi, I agree that *.loc files should be consolidated or, at least, we should have proper documentation about which loc file is required for each tool... Took me quite some time to find that solution. I would suggest can we have a open wiki where these things are annotated. ie: if I find a

Re: [galaxy-dev] Interested in speaking with other institutions deploying Galaxy locally?

2012-05-10 Thread Edward Hills
RE: The chat about NZ/AUS communication us here at Otago University (Dunedin, NZ) are very very keen for this. Please email us at edward.hi...@otago.ac.nz if this does decide to take off :) Cheers, Ed ___ Please keep all replies on the list

Re: [galaxy-dev] Interested in speaking with other institutions deploying Galaxy locally?

2012-05-10 Thread Greg Edwards
Clare, I'm running an AWS Cloudman instance (on US East region) from Sydney for a developing suite of proteomics PTM tools in Perl, for use mainly by http://sydney.edu.au/science/molecular_bioscience/ and http://www.sdu.dk/en/om_sdu/institutter_centre/bmb_biokemi_og_molekylaer_biologi Hard to

[galaxy-dev] About the creation of a new folder

2012-05-10 Thread Ciara Ledero
Hi all, I would just like to ask if it's possible to create a new folder (via script) in the galaxy-dist folder. Cheers, CL ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to