From Iry.Witham@jax.org Wed Aug 24 09:43:47 2011 From: Iry Witham To: galaxy-dev@lists.galaxyproject.org Subject: Re: [galaxy-dev] Display BAM with IGV Date: Wed, 24 Aug 2011 13:43:37 +0000 Message-ID: In-Reply-To: <20110815184631.GU19359@bx.psu.edu> MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="===============5578666602077198260==" --===============5578666602077198260== Content-Type: text/plain; charset="utf-8" Content-Transfer-Encoding: quoted-printable Hi Nate, I have been able to get this to work on a Mac and Windows XP within limited guide lines. The following are what I had to do to make it work: My Mac is now running Java 1.6.0_26, Firefox 3.6.20, Google Crome ver.13.0.782.215 and Safari 5.1 (6534.50). In addition I have installed Max OS 10.6.8 Supplemental Update 1.0. My PC is running Windows XP SP3 with Java 1.6.0_26, Firefox 3.6.20 and IE8. Windows updates are at current levels. I have not tested this on Windows 7. I am currently able to run the IGV-web tool from Galaxy via Firefox, Crome and Safari on the Mac and IE8 only on Windows. When I use either Firefox or Crome on Windows I get the following error. ERROR [2011-08-24 09:22:40,169] [TrackLoader.java:211] [SwingWorker-pool-20352093-thread-1] java.lang.RuntimeException: java.lang.RuntimeException: Error loading file: http://galaxy/display_application/afa21414c9c9e7eb/igv_bam/web/8e5efb082c908 0aa/data/galaxy_afa21414c9c9e7eb.bam NULL content-length ERROR [2011-08-24 09:22:40,169] [TrackManager.java:245] [SwingWorker-pool-20352093-thread-1] Error loading tracks org.broad.igv.exceptions.DataLoadException: An error occurred while loading: =20 http://galaxy/display_application/afa21414c9c9e7eb/igv_bam/web/8e5efb082c908 0aa/data/galaxy_afa21414c9c9e7eb.bam
java.lang.RuntimeException: Error loading file:=20 http://galaxy/display_application/afa21414c9c9e7eb/igv_bam/web/8e5efb082c908 0aa/data/galaxy_afa21414c9c9e7eb.bam NULL content-length at org.broad.igv.track.TrackLoader.load(TrackLoader.java:212) at org.broad.igv.track.TrackManager.load(TrackManager.java:271) at org.broad.igv.track.TrackManager.loadResources(TrackManager.java:241) at=20 org.broad.igv.ui.IGVMainFrame$StartupWorker.doInBackground(IGVMainFrame.java :2775) at com.jidesoft.utils.SwingWorker$1.call(Unknown Source) at java.util.concurrent.FutureTask$Sync.innerRun(Unknown Source) at java.util.concurrent.FutureTask.run(Unknown Source) at com.jidesoft.utils.SwingWorker.run(Unknown Source) at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(Unknown Source) at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source) at java.lang.Thread.run(Unknown Source) This error appears to be different from the original, at least in details though the results are the same. I am also going to post this with IGV support. Thanks, Iry On 8/15/11 2:46 PM, "Nate Coraor" wrote: > Iry Witham wrote: >> Hi Nate, >>=20 >> I have checked the nginx.conf file and they comply to the documentatio= n: >>=20 >> # added to allow nginx to handle file downloads >> location /_x_accel_redirect/ { >> internal; >> alias /; >>=20 >> I have also confirmed that the universe_wsgi.ini file contains the >> following: >>=20 >> And the following to the [app:main] section of universe_wsgi.ini: >> nginx_x_accel_redirect_base =3D /_x_accel_redirect >>=20 >> Iry >=20 > This will need some in-depth debugging, then. >=20 > If you access Galaxy directly via the port of its built-in web server > (by default, 8080), and request to display a dataset, does it set the > X-Accel-Redirect header in the response? >=20 > If you access the same dataset via the nginx address but rename the > underlying disk file, do you get an error message from nginx or from > Galaxy? >=20 > --nate >=20 >>=20 >> On 8/15/11 10:46 AM, "Nate Coraor" wrote: >>=20 >>> Iry Witham wrote: >>>> Hi Everyone, >>>>=20 >>>> 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 f= rom >>>> 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? >>>=20 >>> Hi Iry, >>>=20 >>> 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: >>>=20 >>> http://usegalaxy.org/production >>>=20 >>> --nate >>>=20 >>>>=20 >>>> Thanks, >>>>=20 >>>> 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.witham(a)jax.org >>>>=20 >>>>=20 >>>>=20 >>>>=20 >>>>=20 >>>> On Apr 27, 2011; 10:06am >>>> =C2=B3Hello all, >>>> I just updated our local copy of Galaxy and just wanted to try the new I= GV >>>> 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 >>>>=20 >>>> Alex >>>>=20 >>>>=20 >>>> 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= /45 >>>> 4e >>>> 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= /45 >>>> 4e >>>> df2520b73a7e/data/galaxy_a1f8a55a946ee078.bam NULL content-length >>>> at=20 >>>> org.broad.igv.util.SeekableHTTPStream.(SeekableHTTPStream.java:60) >>>> at=20 >>>> org.broad.igv.util.SeekableStreamFactory.getStreamFor(SeekableStreamFact= ory >>>> .j >>>> ava:42) >>>> at=20 >>>> org.broad.igv.sam.reader.BAMHttpQueryReader.loadHeader(BAMHttpQueryReade= r.j >>>> av >>>> a:129) >>>> at=20 >>>> org.broad.igv.sam.reader.BAMHttpQueryReader.getHeader(BAMHttpQueryReader= .ja >>>> va >>>> :70) >>>> at=20 >>>> org.broad.igv.sam.reader.BAMHttpQueryReader.getSequenceNames(BAMHttpQuer= yRe >>>> ad >>>> er.java:80) >>>> at=20 >>>> org.broad.igv.sam.reader.CachingQueryReader.getSequenceNames(CachingQuer= yRe >>>> ad >>>> er.java:97) >>>> at=20 >>>> org.broad.igv.sam.AlignmentDataManager.initChrMap(AlignmentDataManager.j= ava >>>> :7 >>>> 5) >>>> at=20 >>>> org.broad.igv.sam.AlignmentDataManager.(AlignmentDataManager.java:= 69) >>>> at=20 >>>> org.broad.igv.sam.AlignmentDataManager.getDataManager(AlignmentDataManag= er. >>>> ja >>>> va:54) >>>> at=20 >>>> 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=20 >>>> org.broad.igv.track.TrackManager.loadResources(TrackManager.java:241) >>>> at=20 >>>> 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:8= 8) >>>> at=20 >>>> 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 fi= le: >>>> http://localhost:8080/display_application/a1f8a55a946ee078/igv_bam/local= /45 >>>> 4e >>>> df2520b73a7e/data/galaxy_a1f8a55a946ee078.bam NULL content-length=C2=B2 >>>>=20 >>>>=20 >>>> On Apr 27, 2011; 12:33pm >>>> =C2=B3Hi Alex, >>>>=20 >>>> 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 serv= er >>>> that is able to handle http1.1 requests. Please see "Using a Proxy serve= r" >>>> at >>>> https://bitbucket.org/galaxy/galaxy-central/wiki/Config/ProductionServer >>>> for >>>> help on setting this up. >>>>=20 >>>> Thanks for using Galaxy, >>>>=20 >>>> Dan=C2=B2 >>>>=20 >>>> On Apr 27, 2011; 9:07pm >>>> =C2=B3I=C2=B9m getting this same error and I=C2=B9m running nginx as a p= roxy server. Is >>>> there a specfic parameter we should be aware of to allow partial gets? I >>>> don=C2=B9t see anything in the wiki page for setting up the ProductionSe= rver. >>>>=20 >>>> Thanks, >>>>=20 >>>> Dave=C2=B2 >>>>=20 >>>> On May 04, 2011; 7:47am >>>> =C2=B3Could someone who has successfully gotten the IGV tool to work usi= ng 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? >>>>=20 >>>> Thanks, >>>>=20 >>>> Dave=C2=B2 >>>>=20 >>>> On May 09, 2011; 2:52pm >>>> =C2=B3It's necessary to set up the more advanced configuration under "Se= nding >>>> 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? >>>>=20 >>>> Thanks, >>>> --nate=C2=B2 >>>=20 >>>> ___________________________________________________________ >>>> 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: >>>>=20 >>>> http://lists.bx.psu.edu/ >>>=20 >>=20 >>=20 --===============5578666602077198260==--