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
