Alexander Graf wrote:
> Yesterday I just managed to run Galaxy behind an Apache2 proxy. I followed
> the steps described in
> https://bitbucket.org/galaxy/galaxy-central/wiki/Config/ApacheProxy. And
> still I encounter the same problem, that the content-length is NULL. I
> thought that I could be something with the compression of sending files
> (mod_deflate)?
> I hope somebody can help me?

Hi Alex,

I've never used the XSendFile setup myself, perhaps someone with
experience with it will comment.  Could you ensure that the following is
set in your Galaxy config file (universe_wsgi.ini)?:

    apache_xsendfile = True

Also, since you are serving Galaxy from '/galaxy', you may need to
change your Location blocks:

    <Location "/galaxy">
        XSendFile on
        XSendFilePath /
        # Compress all uncompressed content.
        SetOutputFilter DEFLATE
        SetEnvIfNoCase Request_URI \.(?:gif|jpe?g|png)$ no-gzip dont-vary
        SetEnvIfNoCase Request_URI \.(?:t?gz|zip|bz2)$ no-gzip dont-vary
    </Location>
    <Location "/galaxy/static">
        # Allow browsers to cache everything from /static for 6 hours
        ExpiresActive On
        ExpiresDefault "access plus 6 hours"
    </Location>

It'd be simpler to serve directly from / if your VirutalHost is
dedicated to Galaxy (your DocumentRoot suggests that it is).

--nate

> 
> Thanks,
> Alex
> 
> My http.conf is:
> 
> <VirtualHost *:80>
> DocumentRoot /opt/galaxy
> RewriteEngine on
> RewriteRule ^/galaxy$ /galaxy/ [R]
> RewriteRule ^/galaxy/static/style/(.*)
> /opt/galaxy/static/june_2007_style/blue/$1 [L]
> RewriteRule ^/galaxy/static/scripts/(.*)
> /opt/galaxy/static/scripts/packed/$1 [L]
> RewriteRule ^/galaxy/static/(.*) /opt/galaxy/static/$1 [L]
> RewriteRule ^/galaxy/favicon.ico /opt/galaxy/static/favicon.ico [L]
> RewriteRule ^/galaxy/robots.txt /opt/galaxy/static/robots.txt [L]
> RewriteRule ^/galaxy(.*) http://localhost:8081$1 [P]
> 
> <Proxy http://localhost:8080>
>     Order deny,allow
>     Allow from all
> </Proxy>
> 
> <Location "/">
>      XSendFile on
>      XSendFilePath /
>     # Compress all uncompressed content.
>     SetOutputFilter DEFLATE
>     SetEnvIfNoCase Request_URI \.(?:gif|jpe?g|png)$ no-gzip dont-vary
>     SetEnvIfNoCase Request_URI \.(?:t?gz|zip|bz2)$ no-gzip dont-vary
> </Location>
> <Location "/static">
>     # Allow browsers to cache everything from /static for 6 hours
>     ExpiresActive On
>     ExpiresDefault "access plus 6 hours"
> </Location>
> </VirtualHost>
> 
> 2011/5/9 Nate Coraor <n...@bx.psu.edu>
> 
> > Dave Walton wrote:
> > > Could 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?
> > Hi Dave,
> >
> >
> > It'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,
> > --nate
> >
> > >
> > > Thanks,
> > >
> > > Dave
> > >
> > >
> > > On 4/27/11 9:07 PM, "Dave Walton" <dave.wal...@jax.org> wrote:
> > >
> > > I’m getting this same error and I’m running nginx as a proxy server.  Is
> > there a specfic parameter we should be aware of to allow partial gets?  I
> > don’t see anything in the wiki page for setting up the ProductionServer.
> > >
> > > Thanks,
> > >
> > > Dave
> > >
> > >
> > > On 4/27/11 12:33 PM, "Daniel Blankenberg" <d...@bx.psu.edu> wrote:
> > >
> > > Hi 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/ProductionServerfor 
> > help on setting this up.
> > >
> > > Thanks for using Galaxy,
> > >
> > > Dan
> > >
> > >
> > > On Apr 27, 2011, at 10:06 AM, Alexander Graf wrote:
> > >
> > > Hello 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/454edf2520b73a7e/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/454edf2520b73a7e/data/galaxy_a1f8a55a946ee078.bamNULL
> >  content-length
> > >     at
> > org.broad.igv.util.SeekableHTTPStream.<init>(SeekableHTTPStream.java:60)
> > >     at
> > org.broad.igv.util.SeekableStreamFactory.getStreamFor(SeekableStreamFactory.java:42)
> > >     at
> > org.broad.igv.sam.reader.BAMHttpQueryReader.loadHeader(BAMHttpQueryReader.java:129)
> > >     at
> > org.broad.igv.sam.reader.BAMHttpQueryReader.getHeader(BAMHttpQueryReader.java:70)
> > >     at
> > org.broad.igv.sam.reader.BAMHttpQueryReader.getSequenceNames(BAMHttpQueryReader.java:80)
> > >     at
> > org.broad.igv.sam.reader.CachingQueryReader.getSequenceNames(CachingQueryReader.java:97)
> > >     at
> > org.broad.igv.sam.AlignmentDataManager.initChrMap(AlignmentDataManager.java:75)
> > >     at
> > org.broad.igv.sam.AlignmentDataManager.<init>(AlignmentDataManager.java:69)
> > >     at
> > org.broad.igv.sam.AlignmentDataManager.getDataManager(AlignmentDataManager.java: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/454edf2520b73a7e/data/galaxy_a1f8a55a946ee078.bamNULL
> >  content-length
> > >
> > >
> > >
> > > ___________________________________________________________
> > >
> > >                   Alexander Graf
> > >
> > >     Laboratory of Functional Genome Analysis
> > >     Gene Center, University of Munich (LMU)
> > >     Feodor-Lynen-Strasse 25; 81377 Munich; Germany
> > >     email: g...@lmb.uni-muenchen.de
> > >     Internet: www.lafuga.de/genomics.htm <
> > http://www.lafuga.de/genomics.htm>
> > >  ___________________________________________________________
> > >
> > > ___________________________________________________________
> > > Please keep all replies on the list by using "reply all"
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> > >
> > >
> > >
> >
> > > ___________________________________________________________
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> > >
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> >
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