Nate,

John Chilton got that fixed for us.   As you suggest, it involved a fix in our 
proxy configuration.

JJ

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:

     
http://example.org/<proxy_prefix>/display_application/<encoded_dataset_id>/igv_bam/local_default/None/data/galaxy_<encoded_dataset_id>.bam.bai

--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

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