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" <dave.wal...@jax.org> wrote:

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" <d...@bx.psu.edu> wrote:

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, at 10:06 AM, Alexander Graf wrote:

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



___________________________________________________________

                  Alexander Graf

    Laboratory of Functional Genome Analysis
    Gene Center, University of Munich (LMU)
    Feodor-Lynen-Strasse 25; 81377 Munich; Germany
    email: g...@lmb.uni-muenchen.de
    Internet: www.lafuga.de/genomics.htm <http://www.lafuga.de/genomics.htm>
 ___________________________________________________________

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