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_d...
>
> --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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>>>>>>
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