Error viewing BAM files in IGV
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. 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
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. 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
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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participants (2)
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Alexander Graf -
Nate Coraor