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.

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/
>>> 
>> 
>> 


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