Minor correction. It wasn't commented out... # Force everyone to log in (disable anonymous access). require_login = True
But yes, changing to Require_login = False Fixed the problem. Thanks Iry. Dave On 9/1/11 8:42 AM, "Iry Witham" <iry.wit...@jax.org> wrote: > Hi Nate, > > 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: > > # Force everyone to log in (disable anonymous access). > #require_login = True > > This was where we found the issue. We have changed the settings as > follows and we can now view BAM files through IGV: > > # Force everyone to log in (disable anonymous access). > require_login = False > #require_login = True > > Thanks for all of you assistance. > > Iry > > > On 8/29/11 2:50 PM, "Nate Coraor" <n...@bx.psu.edu> wrote: > >> Iry Witham wrote: >>> 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: <html>An error occurred while >>> loading: >>> http://galaxy/display_application/afa21414c9c9e7eb/igv_bam/web/8e5efb082c908 >>> 0aa/data/galaxy_afa21414c9c9e7eb.bam<br>java.lang.RuntimeException: Error >>> loading file: >>> 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 >>> 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. >> >> 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 >> >>> >>> Thanks, >>> Iry >>> >>> >>> On 8/15/11 2:46 PM, "Nate Coraor" <n...@bx.psu.edu> wrote: >>> >>>> Iry Witham wrote: >>>>> Hi Nate, >>>>> >>>>> I have checked the nginx.conf file and they comply to the >>>>> documentation: >>>>> >>>>> # added to allow nginx to handle file downloads >>>>> location /_x_accel_redirect/ { >>>>> internal; >>>>> alias /; >>>>> >>>>> I have also confirmed that the universe_wsgi.ini file contains the >>>>> following: >>>>> >>>>> And the following to the [app:main] section of universe_wsgi.ini: >>>>> nginx_x_accel_redirect_base = /_x_accel_redirect >>>>> >>>>> Iry >>>> >>>> This will need some in-depth debugging, then. >>>> >>>> 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? >>>> >>>> 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? >>>> >>>> --nate >>>> >>>>> >>>>> On 8/15/11 10:46 AM, "Nate Coraor" <n...@bx.psu.edu> wrote: >>>>> >>>>>> Iry Witham wrote: >>>>>>> Hi Everyone, >>>>>>> >>>>>>> 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 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? >>>>>> >>>>>> Hi Iry, >>>>>> >>>>>> 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: >>>>>> >>>>>> http://usegalaxy.org/production >>>>>> >>>>>> --nate >>>>>> >>>>>>> >>>>>>> Thanks, >>>>>>> >>>>>>> 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.wit...@jax.org >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> On Apr 27, 2011; 10:06am >>>>>>> ³Hello 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>>>>>>> / >>>>>>> 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 >>>>>>> org.broad.igv.util.SeekableHTTPStream.<init>(SeekableHTTPStream.java:60) >>>>>>> at >>>>>>> org.broad.igv.util.SeekableStreamFactory.getStreamFor(SeekableStreamFact>>>>>>> o >>>>>>> ry >>>>>>> .j >>>>>>> ava:42) >>>>>>> at >>>>>>> org.broad.igv.sam.reader.BAMHttpQueryReader.loadHeader(BAMHttpQueryReade>>>>>>> r >>>>>>> .j >>>>>>> av >>>>>>> a:129) >>>>>>> at >>>>>>> org.broad.igv.sam.reader.BAMHttpQueryReader.getHeader(BAMHttpQueryReader>>>>>>> . >>>>>>> ja >>>>>>> va >>>>>>> :70) >>>>>>> at >>>>>>> org.broad.igv.sam.reader.BAMHttpQueryReader.getSequenceNames(BAMHttpQuer>>>>>>> y >>>>>>> Re >>>>>>> ad >>>>>>> er.java:80) >>>>>>> at >>>>>>> org.broad.igv.sam.reader.CachingQueryReader.getSequenceNames(CachingQuer>>>>>>> y >>>>>>> Re >>>>>>> ad >>>>>>> er.java:97) >>>>>>> at >>>>>>> org.broad.igv.sam.AlignmentDataManager.initChrMap(AlignmentDataManager.j>>>>>>> a >>>>>>> va >>>>>>> :7 >>>>>>> 5) >>>>>>> at >>>>>>> org.broad.igv.sam.AlignmentDataManager.<init>(AlignmentDataManager.java:>>>>>>> 6 >>>>>>> 9) >>>>>>> at >>>>>>> org.broad.igv.sam.AlignmentDataManager.getDataManager(AlignmentDataManag>>>>>>> e >>>>>>> r. >>>>>>> ja >>>>>>> va: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>>>>>>> / >>>>>>> 45 >>>>>>> 4e >>>>>>> df2520b73a7e/data/galaxy_a1f8a55a946ee078.bam NULL content-length² >>>>>>> >>>>>>> >>>>>>> On Apr 27, 2011; 12:33pm >>>>>>> ³Hi 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, >>>>>>> >>>>>>> Dan² >>>>>>> >>>>>>> On Apr 27, 2011; 9:07pm >>>>>>> ³I¹m getting this same error and I¹m running nginx as a proxy server. >>>>>>> Is >>>>>>> there a specfic parameter we should be aware of to allow partial gets? >>>>>>> I >>>>>>> don¹t see anything in the wiki page for setting up the ProductionServer. >>>>>>> >>>>>>> Thanks, >>>>>>> >>>>>>> Dave² >>>>>>> >>>>>>> On May 04, 2011; 7:47am >>>>>>> ³Could 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? >>>>>>> >>>>>>> Thanks, >>>>>>> >>>>>>> Dave² >>>>>>> >>>>>>> On May 09, 2011; 2:52pm >>>>>>> ³It'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? >>>>>>> >>>>>>> Thanks, >>>>>>> --nate² >>>>>> >>>>>>> ___________________________________________________________ >>>>>>> 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/ ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. 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