solution + request -> RE: Error viewing BAM files in IGV

11 Apr 2012

      I had similar error stack trace and discovered that it does not occur in IE. It seems to be some problem in the combination Chrome + the simple web-server that comes by default with Galaxy.

See for example the link http://stackoverflow.com/questions/8088941/broken-pipe-error-in-django-nonre...
for similar error in another platform.

@Galaxy developers: can you please figure this out?

Thanks and regards,

Pieter Lukasse
Wageningen UR, Plant Research International
Departments of Bioscience and Bioinformatics
Wageningen Campus, Building 107, Droevendaalsesteeg 1, 6708 PB, 
Wageningen, the Netherlands
+31-317480891; skype: pieter.lukasse.wur
http://www.pri.wur.nl

-----Original Message-----
From: galaxy-dev-bounces@lists.bx.psu.edu [mailto:galaxy-dev-bounces@lists.bx.psu.edu] On Behalf Of Nate Coraor
Sent: woensdag 1 februari 2012 16:07
To: jj@umn.edu
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] Error viewing BAM files in IGV

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:
http://example.org/<proxy_prefix>/display_application/<encoded_datase
t_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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___________________________________________________________
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Lukasse, Pieter

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