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(SeekableStreamFactory
> >>>> .j
> >>>> ava:42)
> >>>>     at 
> >>>> org.broad.igv.sam.reader.BAMHttpQueryReader.loadHeader(BAMHttpQueryReader.j
> >>>> av
> >>>> a:129)
> >>>>     at 
> >>>> org.broad.igv.sam.reader.BAMHttpQueryReader.getHeader(BAMHttpQueryReader.ja
> >>>> va
> >>>> :70)
> >>>>     at 
> >>>> org.broad.igv.sam.reader.BAMHttpQueryReader.getSequenceNames(BAMHttpQueryRe
> >>>> ad
> >>>> er.java:80)
> >>>>     at 
> >>>> org.broad.igv.sam.reader.CachingQueryReader.getSequenceNames(CachingQueryRe
> >>>> ad
> >>>> er.java:97)
> >>>>     at 
> >>>> org.broad.igv.sam.AlignmentDataManager.initChrMap(AlignmentDataManager.java
> >>>> :7
> >>>> 5)
> >>>>     at 
> >>>> org.broad.igv.sam.AlignmentDataManager.<init>(AlignmentDataManager.java:69)
> >>>>     at 
> >>>> org.broad.igv.sam.AlignmentDataManager.getDataManager(AlignmentDataManager.
> >>>> 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/

Reply via email to