[galaxy-dev] A job is stuck in queue

2012-04-27 Thread cwardman.umass
Hello, I am working with galaxy for a bioinfomatics class at Umass Amherst. I have tried doing the http://manuals.bioinformatics.ucr.edu/home/gui-ngs-analysis tutorial. I am currently on the quality control section trying to use the illumina human data set and the NGS mapping bowtie for

[galaxy-dev] MarkupSafe cannot be fetched

2012-04-27 Thread Sarah Maman
Hello, After pulling latest changes (March 2012 - r 40f1816d6857), jobs launched run properly (output files OK) but I get the following warning: /WARNING:galaxy.eggs:Warning: MarkupSafe (a dependent egg of Mako) cannot be fetched/ In addition, Galaxy GUI is not exactly GUI seen in the

[galaxy-dev] ERROR MESSAGE: Running with the -et NO_ET or -et STDOUT option requires a GATK Key file

2012-04-27 Thread Carlos Borroto
It seems like GATK authors at Broad really really want you to phone home every time you use their software. I'm getting this error while running the lastest version: ERROR MESSAGE: Running with the -et NO_ET or -et STDOUT option requires a GATK Key file. Please see

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

2012-04-27 Thread Ann Black-Ziegelbein
Hi everyone - Here at the University of Iowa we are working on deploying Galaxy locally for campus wide access. I am interested in forming a community of other institutions trying to deploy Galaxy locally and mange/operate it on a broad level. Is anyone else? If there is enough interest,

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

2012-04-27 Thread Ryan Golhar
This is a great idea. On Fri, Apr 27, 2012 at 2:45 PM, Ann Black-Ziegelbein annbl...@eng.uiowa.edu wrote: Hi everyone - Here at the University of Iowa we are working on deploying Galaxy locally for campus wide access. I am interested in forming a community of other institutions trying to

Re: [galaxy-dev] MarkupSafe cannot be fetched

2012-04-27 Thread Nate Coraor
On Apr 27, 2012, at 6:00 AM, Sarah Maman wrote: Hello, After pulling latest changes (March 2012 - r 40f1816d6857), jobs launched run properly (output files OK) but I get the following warning: /WARNING:galaxy.eggs:Warning: MarkupSafe (a dependent egg of Mako) cannot be fetched/ Hi

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

2012-04-27 Thread Nate Coraor
On Apr 27, 2012, at 3:14 PM, Ryan Golhar wrote: This is a great idea. +1 On Fri, Apr 27, 2012 at 2:45 PM, Ann Black-Ziegelbein annbl...@eng.uiowa.edu wrote: Hi everyone - Here at the University of Iowa we are working on deploying Galaxy locally for campus wide access. I am interested

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

2012-04-27 Thread Langhorst, Brad
I'm interested On Apr 27, 2012, at 3:14 PM, Ryan Golhar wrote: This is a great idea. On Fri, Apr 27, 2012 at 2:45 PM, Ann Black-Ziegelbein annbl...@eng.uiowa.edumailto:annbl...@eng.uiowa.edu wrote: Hi everyone - Here at the University of Iowa we are working on deploying Galaxy locally for

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

2012-04-27 Thread David Hoover
Not a bad idea. Most of the conversations on this list are very limited and detailed in scope, dealing with the minutia of tools and variables. There isn't much on the bird's eye view. I'm in. On Apr 27, 2012, at 2:45 PM, Ann Black-Ziegelbein wrote: Hi everyone - Here at the University

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

2012-04-27 Thread Mohammad Heydarian
Great idea. In! Cheers, Mo Heydarian PhD candidate The Johns Hopkins School of Medicine Department of Biological Chemistry 725 Wolfe Street 414 Hunterian Baltimore, MD 21205 On Fri, Apr 27, 2012 at 2:45 PM, Ann Black-Ziegelbein annbl...@eng.uiowa.edu wrote: Hi everyone - Here at the

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

2012-04-27 Thread JIE CHEN
Cool idea. I am very interested in it. One question: how could we attend the conference since we all at different place? Cheers, Tyler On Fri, Apr 27, 2012 at 12:33 PM, Mohammad Heydarian mheyd...@jhmi.eduwrote: Great idea. In! Cheers, Mo Heydarian PhD candidate The Johns Hopkins School

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

2012-04-27 Thread Dave Walton
JAX would be interested in this. Dave From: Ryan Golhar ngsbioinformat...@gmail.commailto:ngsbioinformat...@gmail.com Date: Friday, April 27, 2012 3:14 PM To: Ann Black-Ziegelbein annbl...@eng.uiowa.edumailto:annbl...@eng.uiowa.edu Cc:

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

2012-04-27 Thread Ann Black-Ziegelbein
Thanks everyone! Glad to find some common interest. I will see if I can arrange an initial call. Hi Tyler - I was hoping we could just do a voice conference call. It would be great to meet those face to face at the Galaxy Conference in Chicago if some are attending. Thanks! Ann On

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

2012-04-27 Thread Anne Pajon
I'm interested too. On 27 Apr 2012, at 21:13, Ann Black-Ziegelbein wrote: Thanks everyone! Glad to find some common interest. I will see if I can arrange an initial call. Hi Tyler - I was hoping we could just do a voice conference call. It would be great to meet those face to face at

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

2012-04-27 Thread Cittaro Davide
Here's another interested! On Apr 27, 2012, at 8:45 PM, Ann Black-Ziegelbein wrote: Hi everyone - Here at the University of Iowa we are working on deploying Galaxy locally for campus wide access. I am interested in forming a community of other institutions trying to deploy Galaxy locally and

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

2012-04-27 Thread Shantanu Pavgi
We are interested too. Thanks Ann for taking the initiative. -- Shantanu On Apr 27, 2012, at 3:38 PM, Anne Pajon wrote: I'm interested too. On 27 Apr 2012, at 21:13, Ann Black-Ziegelbein wrote: Thanks everyone! Glad to find some common interest. I will see if I can arrange an