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 > ___________________________________________________________ > > ___________________________________________________________ > 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/
___________________________________________________________ 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/
