Re: [galaxy-dev] Display BAM with IGV

2011-09-01 Thread Dave Walton
Minor correction. It wasn't commented out... # Force everyone to log in (disable anonymous access). require_login = True But yes, changing to Require_login = False Fixed the problem. Thanks Iry. Dave On 9/1/11 8:42 AM, "Iry Witham" wrote: > Hi Nate, > > We have found the solution to

Re: [galaxy-dev] Display BAM with IGV

2011-09-01 Thread Iry Witham
Hi Nate, We have found the solution to our/this issue. The way we have our Galaxy instance configured is to have users required to log on. So in the universe.wsgi.webapp.ini file we had set the User and Security settings to: # Force everyone to log in (disable anonymous access). #require_lo

Re: [galaxy-dev] Display BAM with IGV

2011-08-29 Thread Nate Coraor
Iry Witham wrote: > Hi Nate, > > I have been able to get this to work on a Mac and Windows XP within > limited guide lines. The following are what I had to do to make it work: > > My Mac is now running Java 1.6.0_26, Firefox 3.6.20, Google Crome > ver.13.0.782.215 and Safari 5.1 (6534.50).

Re: [galaxy-dev] Display BAM with IGV

2011-08-24 Thread Iry Witham
Hi Nate, I have been able to get this to work on a Mac and Windows XP within limited guide lines. The following are what I had to do to make it work: My Mac is now running Java 1.6.0_26, Firefox 3.6.20, Google Crome ver.13.0.782.215 and Safari 5.1 (6534.50). In addition I have installed Max

Re: [galaxy-dev] Display BAM with IGV

2011-08-15 Thread Iry Witham
On 8/15/11 2:46 PM, "Nate Coraor" wrote: > Iry Witham wrote: >> Hi Nate, >> >> I have checked the nginx.conf file and they comply to the documentation: >> >> # added to allow nginx to handle file downloads >> location /_x_accel_redirect/ { >> internal; >>

Re: [galaxy-dev] Display BAM with IGV

2011-08-15 Thread Nate Coraor
Iry Witham wrote: > Hi Nate, > > I have checked the nginx.conf file and they comply to the documentation: > > # added to allow nginx to handle file downloads > location /_x_accel_redirect/ { > internal; > alias /; > > I have also confirmed that the unive

Re: [galaxy-dev] Display BAM with IGV

2011-08-15 Thread Iry Witham
Hi Nate, I have checked the nginx.conf file and they comply to the documentation: # added to allow nginx to handle file downloads location /_x_accel_redirect/ { internal; alias /; I have also confirmed that the universe_wsgi.ini file contains the followi

Re: [galaxy-dev] Display BAM with IGV

2011-08-15 Thread Nate Coraor
Iry Witham wrote: > Hi Everyone, > > I have been tasked with getting the IGV working within our Galaxy > instance. I have modified our Nginx configuration based on the more advanced > configuration under "Sending files using nginx" on the nginxProxy page in the > wiki. The IGV viewer comp

Re: [galaxy-dev] Display BAM with IGV

2011-08-10 Thread Iry Witham
Hi Everyone, I have been tasked with getting the IGV working within our Galaxy instance. I have modified our Nginx configuration based on the more advanced configuration under "Sending files using nginx" on the nginxProxy page in the wiki. The IGV viewer component in Galaxy does not displ

Re: [galaxy-dev] Display BAM with IGV

2011-05-10 Thread Nate Coraor
Alexander Graf wrote: > Yesterday I just managed to run Galaxy behind an Apache2 proxy. I followed > the steps described in > https://bitbucket.org/galaxy/galaxy-central/wiki/Config/ApacheProxy. And > still I encounter the same problem, that the content-length is NULL. I > thought that I could be s

Re: [galaxy-dev] Display BAM with IGV

2011-05-09 Thread Nate Coraor
Dave Walton wrote: > Could someone who has successfully gotten the IGV tool to work using NGINX as > your proxy, tell me if there was anything specific they needed to do with > their NGINX or galaxy config to get it working? Hi Dave, It's necessary to set up the more advanced configuration unde

Re: [galaxy-dev] Display BAM with IGV

2011-05-04 Thread Dave Walton
Could someone who has successfully gotten the IGV tool to work using NGINX as your proxy, tell me if there was anything specific they needed to do with their NGINX or galaxy config to get it working? Thanks, Dave On 4/27/11 9:07 PM, "Dave Walton" wrote: I’m getting this same error and I’m r

Re: [galaxy-dev] Display BAM with IGV

2011-04-27 Thread Dave Walton
I’m getting this same error and I’m running nginx as a proxy server. Is there a specfic parameter we should be aware of to allow partial gets? I don’t see anything in the wiki page for setting up the ProductionServer. Thanks, Dave On 4/27/11 12:33 PM, "Daniel Blankenberg" wrote: Hi Alex,

Re: [galaxy-dev] Display BAM with IGV

2011-04-27 Thread Daniel Blankenberg
Hi Alex, Displaying BAM files at external applications usually requires an http server that supports partial gets. Unfortunately, the current lightweight http server that is built into Galaxy does not support these advanced http options. However, this limitation can be overcome by using a prox

[galaxy-dev] Display BAM with IGV

2011-04-27 Thread Alexander Graf
Hello all, I just updated our local copy of Galaxy and just wanted to try the new IGV display application. When I try to display a BAM file with the local IGV or the web IGV I encounter following error complaining about the Null content-length. Has any of you encountered the same problem? Do I miss