From nate@bx.psu.edu Mon Aug 29 14:50:15 2011 From: Nate Coraor To: galaxy-dev@lists.galaxyproject.org Subject: Re: [galaxy-dev] Display BAM with IGV Date: Mon, 29 Aug 2011 14:50:14 -0400 Message-ID: <20110829185014.GG21849@bx.psu.edu> In-Reply-To: MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="===============4170086469556410408==" --===============4170086469556410408== Content-Type: text/plain; charset="utf-8" Content-Transfer-Encoding: quoted-printable Iry Witham wrote: > Hi Nate, >=20 > 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: >=20 > 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. >=20 > 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. >=20 >=20 > 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 >=20 > ERROR [2011-08-24 09:22:40,169] [TrackManager.java:245] > [SwingWorker-pool-20352093-thread-1] Error loading tracks >=20 > 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 >=20 > at org.broad.igv.track.TrackLoader.load(TrackLoader.java:212) >=20 > at org.broad.igv.track.TrackManager.load(TrackManager.java:271) >=20 > at org.broad.igv.track.TrackManager.loadResources(TrackManager.java:241) >=20 > at=20 > org.broad.igv.ui.IGVMainFrame$StartupWorker.doInBackground(IGVMainFrame.java > :2775) >=20 > at com.jidesoft.utils.SwingWorker$1.call(Unknown Source) >=20 > at java.util.concurrent.FutureTask$Sync.innerRun(Unknown Source) >=20 > at java.util.concurrent.FutureTask.run(Unknown Source) >=20 > at com.jidesoft.utils.SwingWorker.run(Unknown Source) >=20 > at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(Unknown > Source) >=20 > at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source) >=20 > at java.lang.Thread.run(Unknown Source) >=20 > 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. Hi Iry, If you get anything back from the IGV folks please post a followup. Since IGV runs in the local JVM, that it works with one browser and not another on the same system doesn't make a lot of sense. --nate >=20 > Thanks, > Iry >=20 >=20 > On 8/15/11 2:46 PM, "Nate Coraor" wrote: >=20 > > Iry Witham wrote: > >> Hi Nate, > >>=20 > >> I have checked the nginx.conf file and they comply to the documentat= ion: > >>=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= from > >>>> a > >>>> BAM file in either the web or local instance of IGV. I have tested wi= th > >>>> 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= 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 > >>>>=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/loc= al/45 > >>>> 4e > >>>> df2520b73a7e/data/galaxy_a1f8a55a946ee078.bam > >>>> ERROR [2011-04-27 16:00:14,590] [TrackLoader.java:821] [Thread-6] Er= ror > >>>> loading sam track > >>>> java.lang.RuntimeException: Error loading file: > >>>> http://localhost:8080/display_application/a1f8a55a946ee078/igv_bam/loc= al/45 > >>>> 4e > >>>> df2520b73a7e/data/galaxy_a1f8a55a946ee078.bam NULL content-length > >>>> at=20 > >>>> org.broad.igv.util.SeekableHTTPStream.(SeekableHTTPStream.java:6= 0) > >>>> at=20 > >>>> org.broad.igv.util.SeekableStreamFactory.getStreamFor(SeekableStreamFa= ctory > >>>> .j > >>>> ava:42) > >>>> at=20 > >>>> org.broad.igv.sam.reader.BAMHttpQueryReader.loadHeader(BAMHttpQueryRea= der.j > >>>> av > >>>> a:129) > >>>> at=20 > >>>> org.broad.igv.sam.reader.BAMHttpQueryReader.getHeader(BAMHttpQueryRead= er.ja > >>>> va > >>>> :70) > >>>> at=20 > >>>> org.broad.igv.sam.reader.BAMHttpQueryReader.getSequenceNames(BAMHttpQu= eryRe > >>>> ad > >>>> er.java:80) > >>>> at=20 > >>>> org.broad.igv.sam.reader.CachingQueryReader.getSequenceNames(CachingQu= eryRe > >>>> ad > >>>> er.java:97) > >>>> at=20 > >>>> org.broad.igv.sam.AlignmentDataManager.initChrMap(AlignmentDataManager= .java > >>>> :7 > >>>> 5) > >>>> at=20 > >>>> org.broad.igv.sam.AlignmentDataManager.(AlignmentDataManager.jav= a:69) > >>>> at=20 > >>>> org.broad.igv.sam.AlignmentDataManager.getDataManager(AlignmentDataMan= ager. > >>>> ja > >>>> va:54) > >>>> at=20 > >>>> org.broad.igv.track.TrackLoader.loadAlignmentsTrack(TrackLoader.java:7= 61) > >>>> 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:14= 8) > >>>> at org.broad.igv.main.CommandExecutor.execute(CommandExecutor.java= :88) > >>>> 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 = file: > >>>> http://localhost:8080/display_application/a1f8a55a946ee078/igv_bam/loc= al/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 se= rver > >>>> that is able to handle http1.1 requests. Please see "Using a Proxy ser= ver" > >>>> at > >>>> https://bitbucket.org/galaxy/galaxy-central/wiki/Config/ProductionServ= er > >>>> 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= proxy 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 Production= Server. > >>>>=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 u= sing 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 "= 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? > >>>>=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 >=20 >=20 --===============4170086469556410408==--