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 <nate@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.walton@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" <dan@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/454... 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/454... 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/454... content-length
___________________________________________________________
Alexander Graf
Laboratory of Functional Genome Analysis Gene Center, University of Munich (LMU) Feodor-Lynen-Strasse 25; 81377 Munich; Germany email: graf@lmb.uni-muenchen.de Internet: www.lafuga.de/genomics.htm <
http://www.lafuga.de/genomics.htm>
___________________________________________________________
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Nate Coraor