From Dave.Walton@jax.org Thu Sep 1 09:06:52 2011 From: Dave Walton To: galaxy-dev@lists.galaxyproject.org Subject: Re: [galaxy-dev] Display BAM with IGV Date: Thu, 01 Sep 2011 13:06:42 +0000 Message-ID: In-Reply-To: MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="===============7060880188995119994==" --===============7060880188995119994== Content-Type: text/plain; charset="utf-8" Content-Transfer-Encoding: quoted-printable Minor correction. It wasn't commented out... # Force everyone to log in (disable anonymous access). require_login =3D True But yes, changing to Require_login =3D False Fixed the problem. Thanks Iry. Dave On 9/1/11 8:42 AM, "Iry Witham" wrote: > Hi Nate, >=20 > We have found the solution to our/this issue. The way we have our > Galaxy instance configured is to have users required to log on. So in the > universe.wsgi.webapp.ini file we had set the User and Security settings to: >=20 > # Force everyone to log in (disable anonymous access). > #require_login =3D True >=20 > This was where we found the issue. We have changed the settings as > follows and we can now view BAM files through IGV: >=20 > # Force everyone to log in (disable anonymous access). > require_login =3D False > #require_login =3D True >=20 > Thanks for all of you assistance. >=20 > Iry >=20 >=20 > On 8/29/11 2:50 PM, "Nate Coraor" wrote: >=20 >> 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/8e5efb082c= 908 >>> 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/8e5efb082c= 908 >>> 0aa/data/galaxy_afa21414c9c9e7eb.bam
java.lang.RuntimeException: Error >>> loading file:=20 >>> http://galaxy/display_application/afa21414c9c9e7eb/igv_bam/web/8e5efb082c= 908 >>> 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:2= 41) >>>=20 >>> at=20 >>> org.broad.igv.ui.IGVMainFrame$StartupWorker.doInBackground(IGVMainFrame.j= ava >>> :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 wi= th >>> IGV support. >>=20 >> Hi Iry, >>=20 >> 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. >>=20 >> --nate >>=20 >>>=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 >>>>> documentation: >>>>>=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 w= ith >>>>>>> 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 fi= le >>>>>> 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: >>>>>>>=20 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: >>>>>>>=20 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 >>>>>>>=20 org.broad.igv.util.SeekableStreamFactory.getStreamFor(SeekableStreamFact>>>>>= >> o >>>>>>> ry >>>>>>> .j >>>>>>> ava:42) >>>>>>> at=20 >>>>>>>=20 org.broad.igv.sam.reader.BAMHttpQueryReader.loadHeader(BAMHttpQueryReade>>>>>= >> r >>>>>>> .j >>>>>>> av >>>>>>> a:129) >>>>>>> at=20 >>>>>>>=20 org.broad.igv.sam.reader.BAMHttpQueryReader.getHeader(BAMHttpQueryReader>>>>>= >> . >>>>>>> ja >>>>>>> va >>>>>>> :70) >>>>>>> at=20 >>>>>>>=20 org.broad.igv.sam.reader.BAMHttpQueryReader.getSequenceNames(BAMHttpQuer>>>>>= >> y >>>>>>> Re >>>>>>> ad >>>>>>> er.java:80) >>>>>>> at=20 >>>>>>>=20 org.broad.igv.sam.reader.CachingQueryReader.getSequenceNames(CachingQuer>>>>>= >> y >>>>>>> Re >>>>>>> ad >>>>>>> er.java:97) >>>>>>> at=20 >>>>>>>=20 org.broad.igv.sam.AlignmentDataManager.initChrMap(AlignmentDataManager.j>>>>>= >> a >>>>>>> va >>>>>>> :7 >>>>>>> 5) >>>>>>> at=20 >>>>>>>=20 org.broad.igv.sam.AlignmentDataManager.(AlignmentDataManager.java:>>>>>= >> 6 >>>>>>> 9) >>>>>>> at=20 >>>>>>>=20 org.broad.igv.sam.AlignmentDataManager.getDataManager(AlignmentDataManag>>>>>= >> e >>>>>>> r. >>>>>>> ja >>>>>>> va:54) >>>>>>> at=20 >>>>>>>=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:1= 48) >>>>>>> at=20 >>>>>>> org.broad.igv.main.CommandExecutor.execute(CommandExecutor.java:88) >>>>>>> at=20 >>>>>>> org.broad.igv.main.CommandListener.processGet(CommandListener.java:19= 3) >>>>>>> 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: >>>>>>>=20 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 ht= tp >>>>>>> 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/ProductionSer= ver >>>>>>> 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 Productio= nServer. >>>>>>>=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 = 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? >>>>>>>=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 >=20 >=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/ --===============7060880188995119994==--