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: graf@lmb.uni-muenchen.de
    Internet: www.lafuga.de/genomics.htm <http://www.lafuga.de/genomics.htm>
 ___________________________________________________________

___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:

  http://lists.bx.psu.edu/