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?

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
“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 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/454edf2520b73a7e/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/454edf2520b73a7e/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.java:42)
    at 
org.broad.igv.sam.reader.BAMHttpQueryReader.loadHeader(BAMHttpQueryReader.java:129)
    at 
org.broad.igv.sam.reader.BAMHttpQueryReader.getHeader(BAMHttpQueryReader.java:70)
    at 
org.broad.igv.sam.reader.BAMHttpQueryReader.getSequenceNames(BAMHttpQueryReader.java:80)
    at 
org.broad.igv.sam.reader.CachingQueryReader.getSequenceNames(CachingQueryReader.java:97)
    at 
org.broad.igv.sam.AlignmentDataManager.initChrMap(AlignmentDataManager.java:75)
    at 
org.broad.igv.sam.AlignmentDataManager.<init>(AlignmentDataManager.java:69)
    at 
org.broad.igv.sam.AlignmentDataManager.getDataManager(AlignmentDataManager.java: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/454edf2520b73a7e/data/galaxy_a1f8a55a946ee078.bam
 NULL content-length”


On Apr 27, 2011; 12:33pm
“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 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,

Dan”

On Apr 27, 2011; 9:07pm
“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 May 04, 2011; 7:47am
“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 May 09, 2011; 2:52pm
“It'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,
--nate”
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