[galaxy-dev] problems with display at UCSC

2012-03-05 Thread Hans-Rudolf Hotz
Hi everybody This is kind of an embarrassing question, but I am struggling to get the display at UCSC to work. Finally after several years, our sysadmin agreed to change the Apache configuration (which handles the authentication via LDAP) according to the configuration provided in the

Re: [galaxy-dev] Problem with python ./scripts/make_egg_packager.py

2012-03-05 Thread Nate Coraor
On Feb 14, 2012, at 11:07 PM, Jose William Valero Velasquez wrote: Hi, I'm writing you because i'm trying to install galaxy in a server running suse behind a proxy, so i have to build the eggs like if the server were offline, in the guide says that i should execute the command

[galaxy-dev] functional test issue - PDF output file comparison

2012-03-05 Thread Anne Pajon
Dear All, I have noticed that some output files of functional tests are of type PDF. When comparing the one produced by the tool and the one stored in test-data/, they obviously differ even if they visually look identical. Is there a better way to compare PDF files within Galaxy than using

Re: [galaxy-dev] uploads stuck in history

2012-03-05 Thread Nate Coraor
By any chance, do you all happen to be using the nginx upload module? I am guessing not. --nate On Feb 23, 2012, at 3:16 AM, Bossers, Alex wrote: I confirm the same strange behaviour since some of the last updates on the central version. We are at the latest now. It is also with medium

Re: [galaxy-dev] Defining Job Runners Dynamically

2012-03-05 Thread Tony Raymond
Hi Nate, Has there been any progress on this? This enhancement would actually be very useful for our local Galaxy instance. Cheers, Tony -Original Message- From: galaxy-dev-boun...@lists.bx.psu.edu [mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Nate Coraor Sent: Wednesday,

Re: [galaxy-dev] uploads stuck in history

2012-03-05 Thread Luciano Cosme
I had same issue recently. I tried to upload files locally and give same error (from 50Mb or 17Gb as admin). The files never finish uploading. A few days ago I tried to upload around 20 files (up to 200Mb), most of them uploaded normally, but some wouldn't. I will try a different browser them

Re: [galaxy-dev] uploads stuck in history

2012-03-05 Thread Luciano Cosme
Hi, I was trying to upload data again and here is the error message that I get: Can't create peek [Errno 2] No such file or directory: '/home/koala2/galaxy-dist/database/files/000/dataset_24.dat' Exception happened during processing of request from

[galaxy-dev] BOSC 2012 Call for Abstracts

2012-03-05 Thread Brad Chapman
Call for Abstracts for the 13th Annual Bioinformatics Open Source Conference (BOSC 2012) A Special Interest Group (SIG) of ISMB 2012 Dates: July 13-14, 2012 Location: Long Beach, California Web site: http://www.open-bio.org/wiki/BOSC_2012 Email: b...@open-bio.org BOSC announcements mailing

Re: [galaxy-dev] HMMER wrappers

2012-03-05 Thread Edward Kirton
i created a new toolshed repo, hmmer since i couldn't rename it. as suggested, it has the hmmscan/hmmsearch as one tool, plus hmmpress. will add hmmbuild, hmmalign asap; others upon request. dave, is there a way to delete an old tool? (hmmscan) On Wed, Feb 29, 2012 at 10:12 AM, Edward Kirton