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
following:

And the following to the [app:main] section of universe_wsgi.ini:
nginx_x_accel_redirect_base = /_x_accel_redirect

Iry

On 8/15/11 10:46 AM, "Nate Coraor" <n...@bx.psu.edu> wrote:

> 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 component in Galaxy does not display the results from a
>> BAM file in either the web or local instance of IGV.  I have tested with
>> IGV1.5 and with version 2.03.  Neither produce a visual representation of the
>> sequence. When attempting to use the web option we get the same error
>> provided in the original post as noted below.  Has anyone gotten this to work
>> with Nginx-0.8.53 or any of the newer versions?
> 
> Hi Iry,
> 
> Have you checked to make sure that your nginx server is serving the file
> for download, as opposed to the internal Galaxy web server?  In the
> original email, it looked like nginx was being bypassed entirely (due to
> serving on port 8080 - Galaxy's intenal server's default port).  But
> even once nginx is in use, it's necessary to set up X-Accel-Redirect to
> serve datasets.  See the instructions here:
> 
>     http://usegalaxy.org/production
> 
> --nate
> 
>> 
>> Thanks,
>> 
>> Iry Witham
>> Applications Administrator
>> Scientific Computing Group
>> Computational Sciences Dept.
>> The Jackson Laboratory
>> 600 Main Street
>> Bar Harbor, ME  04609
>> Phone: 207-288-6744
>> email: iry.wit...@jax.org
>> 
>> 
>> 
>> 
>> 
>> On Apr 27, 2011; 10:06am
>> ³Hello 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 something?
>> Thanks in advance
>> 
>> Alex
>> 
>> 
>> INFO [2011-04-27 16:00:14,440]  [TrackManager.java:225] [Thread-6]  Loading1
>> resources.
>> ERROR [2011-04-27 16:00:14,589]  [SeekableHTTPStream.java:59] [Thread-6]
>> Null content-length for:
>> http://localhost:8080/display_application/a1f8a55a946ee078/igv_bam/local/454e
>> df2520b73a7e/data/galaxy_a1f8a55a946ee078.bam
>> ERROR [2011-04-27 16:00:14,590]  [TrackLoader.java:821] [Thread-6]  Error
>> loading sam track
>> java.lang.RuntimeException: Error loading file:
>> http://localhost:8080/display_application/a1f8a55a946ee078/igv_bam/local/454e
>> df2520b73a7e/data/galaxy_a1f8a55a946ee078.bam NULL content-length
>>     at 
>> org.broad.igv.util.SeekableHTTPStream.<init>(SeekableHTTPStream.java:60)
>>     at 
>> org.broad.igv.util.SeekableStreamFactory.getStreamFor(SeekableStreamFactory.j
>> ava:42)
>>     at 
>> org.broad.igv.sam.reader.BAMHttpQueryReader.loadHeader(BAMHttpQueryReader.jav
>> a:129)
>>     at 
>> org.broad.igv.sam.reader.BAMHttpQueryReader.getHeader(BAMHttpQueryReader.java
>> :70)
>>     at 
>> org.broad.igv.sam.reader.BAMHttpQueryReader.getSequenceNames(BAMHttpQueryRead
>> er.java:80)
>>     at 
>> org.broad.igv.sam.reader.CachingQueryReader.getSequenceNames(CachingQueryRead
>> er.java:97)
>>     at 
>> org.broad.igv.sam.AlignmentDataManager.initChrMap(AlignmentDataManager.java:7
>> 5)
>>     at 
>> org.broad.igv.sam.AlignmentDataManager.<init>(AlignmentDataManager.java:69)
>>     at 
>> org.broad.igv.sam.AlignmentDataManager.getDataManager(AlignmentDataManager.ja
>> va:54)
>>     at 
>> org.broad.igv.track.TrackLoader.loadAlignmentsTrack(TrackLoader.java:761)
>>     at org.broad.igv.track.TrackLoader.load(TrackLoader.java:143)
>>     at org.broad.igv.track.TrackManager.load(TrackManager.java:271)
>>     at org.broad.igv.track.TrackManager.loadResources(TrackManager.java:241)
>>     at org.broad.igv.main.CommandExecutor.loadFiles(CommandExecutor.java:282)
>>     at org.broad.igv.main.CommandExecutor.hget(CommandExecutor.java:148)
>>     at org.broad.igv.main.CommandExecutor.execute(CommandExecutor.java:88)
>>     at 
>> org.broad.igv.main.CommandListener.processGet(CommandListener.java:193)
>>     at org.broad.igv.main.CommandListener.run(CommandListener.java:93)
>>     at java.lang.Thread.run(Thread.java:636)
>> ERROR [2011-04-27 16:00:14,592]  [TrackLoader.java:211] [Thread-6]
>> java.lang.RuntimeException: java.lang.RuntimeException: Error loading file:
>> http://localhost:8080/display_application/a1f8a55a946ee078/igv_bam/local/454e
>> df2520b73a7e/data/galaxy_a1f8a55a946ee078.bam NULL content-length²
>> 
>> 
>> On Apr 27, 2011; 12:33pm
>> ³Hi 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 proxy server
>> that is able to handle http1.1 requests. Please see "Using a Proxy server" at
>> https://bitbucket.org/galaxy/galaxy-central/wiki/Config/ProductionServer for
>> help on setting this up.
>> 
>> Thanks for using Galaxy,
>> 
>> Dan²
>> 
>> On Apr 27, 2011; 9:07pm
>> ³I¹m getting this same error and I¹m running nginx as a proxy server.  Is
>> there a specfic parameter we should be aware of to allow partial gets?  I
>> don¹t see anything in the wiki page for setting up the ProductionServer.
>> 
>> Thanks,
>> 
>> Dave²
>> 
>> On May 04, 2011; 7:47am
>> ³Could 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,
>> 
>> Dave²
>> 
>> On May 09, 2011; 2:52pm
>> ³It's necessary to set up the more advanced configuration under "Sending
>> files using nginx" on the nginxProxy page in the wiki.  Could you let us
>> know whether you're using that configuration or just a basic
>> pass-through proxy?
>> 
>> Thanks,
>> --nate²
> 
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