On Feb 1, 2012, at 10:05 AM, Jim Johnson wrote:
Nate,
John Chilton got that fixed for us. As you suggest, it involved a fix in our proxy configuration.
JJ
Great, thanks! --nate
On 2/1/12 9:01 AM, Nate Coraor wrote:
On Dec 19, 2011, at 12:24 PM, Jim Johnson wrote:
Hi,
I'm seeing the same behavior. Galaxy is returning a web page rather than the requested .bai index file for the BAM file. In class WebApplication ( lib/galaxy/web/framework/base.py ) in __call__( self, environ, start_response ) line 133 # Setup the transaction trans = self.transaction_factory( environ ) Gets routed to the root controller and returns the galaxy server main page html.
JJ Hi JJ,
What URL is causing this? I figured this was a proxy prefix problem, but I tried setting it up here and the URL to the bai is still correct:
--nate
On Dec 14, 2011, at 4:22 PM, Alexander Graf wrote:
Hi nate, I have tried it with several BAM files, resulting in the same error. If I download the BAM and bai files from Galaxy and load it into IGV manually, everything works like charm. Up to now I could not figure out why it is not working. Could I have better success switching to the nginx-server?
Hi Alex,
It should work with Apache as well. I don't have an environment set up here to test, but could you take a look at the Apache access and error logs to determine whether the file is being found and read properly? It's possible that the request is returning something other than a 200 code and the file data.
--nate
Alex
Am 12.12.2011 um 16:11 schrieb Nate Coraor:
On Dec 9, 2011, at 6:45 AM, Alexander Graf wrote:
> Hello, > I have recently updated our Galaxy dist and I'm running into problems viewing BAM files in IGV (v2.0.22), saying: Invalid GZIP header. > Hi Alex,
Your config below looks okay at first glance. Can you verify that the file in question is a valid BAM? Or is this happening with all BAMs?
--nate
> I have configured the Apache as explained in the Wiki using this http.conf: > > > ------------------------------------------------------------------------------------------------------------------------------------ > <VirtualHost *:80> > ServerName 127.0.0.1 > 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$1 [P] > > <Proxy > http://localhost:8081 > Order deny,allow > Allow from all > </Proxy> > > <Location "/galaxy"> > # Define the authentication method > XSendFile on > XSendFilePath / > # Compress all uncompressed content.http.conf > SetOutputFilter DEFLATE > SetEnvIfNoCase Request_URI \.(?:gif|jpe?g|png)$ no-gzip dont-vary > SetEnvIfNoCase Request_URI \.(?:t?gz|zip|bz2)$ no-gzip dont-vary > </Location> > <Directory "/galaxy/static"> > ExpiresActive On > ExpiresDefault "access plus 6 hours" > </Directory> > </VirtualHost> > ---------------------------------------------------------------------------------------------------------------------------------------- > > > By having this parts changed in universe_wsgi.ini: > ---------------------------------------------------------------------------------------------------------------------------------------- > [server:main] > use = egg:Paste#http > port = 8081 > host = 0.0.0.0 > use_threadpool = True > > [filter:gzip] > use = egg:Paste#gzip > > [filter:proxy-prefix] > use = egg:PasteDeploy#prefix > prefix = /galaxy > > [app:main] > paste.app_factory = galaxy.web.buildapp:app_factory > filter-with = proxy-prefix > cookie_path = /galaxy > apache_xsendfile = True > upstream_gzip = False > ---------------------------------------------------------------------------------------------------------------------------------------- > > The resulting Galaxy error log is: > ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- > galaxy.web.framework DEBUG 2011-12-09 12:32:08,825 Error: this request returned None from get_history(): > http://10.153.182.203/galaxy/root > > 10.163.241.110 - - [09/Dec/2011:12:32:08 +0200] "GET /galaxy/root?app_action=data&user_id=c9a3f3a19e75965d&app_name=igv_bam&link_name=local_default&action_param=galaxy_9b0f702d0207cd78.bam.bai&dataset_id=9b0f702d0207cd78 HTTP/1.1" 200 - "-" "IGV Version 2.0.22 (1360)11/29/2011 02:24 PM Java/1.6.0_22" > 10.163.241.110 - - [09/Dec/2011:12:32:08 +0200] "HEAD /galaxy/display_application/9b0f702d0207cd78/igv_bam/local_default/c9a3f3a19e75965d/data/galaxy_9b0f702d0207cd78.bam HTTP/1.1" 302 - "-" "IGV Version 2.0.22 (1360)11/29/2011 02:24 PM Java/1.6.0_22" > galaxy.web.framework DEBUG 2011-12-09 12:32:08,915 Error: this request returned None from get_history(): > http://10.153.182.203/galaxy/root > > 10.163.241.110 - - [09/Dec/2011:12:32:08 +0200] "HEAD /galaxy/root?app_action=data&user_id=c9a3f3a19e75965d&app_name=igv_bam&link_name=local_default&action_param=galaxy_9b0f702d0207cd78.bam&dataset_id=9b0f702d0207cd78 HTTP/1.1" 200 - "-" "IGV Version 2.0.22 (1360)11/29/2011 02:24 PM Java/1.6.0_22" > ---------------------------------------- > Exception happened during processing of request from ('127.0.0.1', 52683) > Traceback (most recent call last): > File "/opt/galaxy/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py", line 1053, in process_request_in_thread > self.finish_request(request, client_address) > File "/usr/lib/python2.6/SocketServer.py", line 322, in finish_request > self.RequestHandlerClass(request, client_address, self) > File "/usr/lib/python2.6/SocketServer.py", line 618, in __init__ > self.finish() > File "/usr/lib/python2.6/SocketServer.py", line 661, in finish > self.wfile.flush() > File "/usr/lib/python2.6/socket.py", line 297, in flush > self._sock.sendall(buffer(data, write_offset, buffer_size)) > error: [Errno 32] Broken pipe > ---------------------------------------- > > --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- > > > Thanks in advance for your help > > Alex > > ___________________________________________________________ > 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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