On Jan 17, 2012, at 10:50 AM, Alexander Graf wrote: > Hi Nate, > sorry for my late reply, but I was on holiday last weeks. > I have looked in my apache error.log and access.log resulting into no new > insights - no output is given there. > So I gave nginx a try, getting the same error as before. > I think it is not a configuration issue of apache or nginx, but I don't have > any clue any more what's going on. > Hope you or somebody else can help me figure out the problem.
Hi Alex, I thought this might be a problem with the way Galaxy was handling proxy prefixes (/galaxy) but I don't believe that's the problem. It looks like your XSendFile config is not working, as evidenced by the 'HEAD' HTTP commands in the Galaxy log (these should be interrupted by the Apache/nginx server and not passed through to Galaxy). Check your proxy server logs. --nate > > Alex > > Below are the newly generated error logs: > > > If I try to view the BAM file locally, I get: > > XX.XXX.XXX.XXX - - [17/Jan/2012:16:34:25 +0200] "GET > /galaxy/display_application/8b4e4b7bbaf9bc68/igv_bam/local_default HTTP/1.0" > 302 - "http://10.153.182.203/galaxy/history"; "Mozilla/5.0 (Ubuntu; X11; Linux > x86_64; rv:9.0.1) Gecko/20100101 Firefox/9.0.1" > XX.XXX.XXX.XXX - - [17/Jan/2012:16:34:25 +0200] "GET > /galaxy/display_application/8b4e4b7bbaf9bc68/igv_bam/local_default/5ce1ba9f488a6ce5/data/galaxy_8b4e4b7bbaf9bc68.bam.bai > HTTP/1.0" 302 - "-" "IGV Version 2.0.34 (1623)01/14/2012 12:45 AM > Java/1.6.0_22" > galaxy.web.framework DEBUG 2012-01-17 16:34:25,389 Error: this request > returned None from get_history(): http://10.153.182.203/galaxy/root > XX.XXX.XXX.XXX - - [17/Jan/2012:16:34:25 +0200] "GET > /galaxy/root?app_action=data&user_id=5ce1ba9f488a6ce5&app_name=igv_bam&link_name=local_default&action_param=galaxy_8b4e4b7bbaf9bc68.bam.bai&dataset_id=8b4e4b7bbaf9bc68 > HTTP/1.0" 200 - "-" "IGV Version 2.0.34 (1623)01/14/2012 12:45 AM > Java/1.6.0_22" > XX.XXX.XXX.XXX - - [17/Jan/2012:16:34:25 +0200] "HEAD > /galaxy/display_application/8b4e4b7bbaf9bc68/igv_bam/local_default/5ce1ba9f488a6ce5/data/galaxy_8b4e4b7bbaf9bc68.bam > HTTP/1.0" 302 - "-" "IGV Version 2.0.34 (1623)01/14/2012 12:45 AM > Java/1.6.0_22" > galaxy.web.framework DEBUG 2012-01-17 16:34:25,470 Error: this request > returned None from get_history(): http://10.153.182.203/galaxy/root > XX.XXX.XXX.XXX - - [17/Jan/2012:16:34:25 +0200] "HEAD > /galaxy/root?app_action=data&user_id=5ce1ba9f488a6ce5&app_name=igv_bam&link_name=local_default&action_param=galaxy_8b4e4b7bbaf9bc68.bam&dataset_id=8b4e4b7bbaf9bc68 > HTTP/1.0" 200 - "-" "IGV Version 2.0.34 (1623)01/14/2012 12:45 AM > Java/1.6.0_22" > XX.XXX.XXX.XXX - - [17/Jan/2012:16:34:25 +0200] "GET > /galaxy/display_application/8b4e4b7bbaf9bc68/igv_bam/local_default/5ce1ba9f488a6ce5/data/galaxy_8b4e4b7bbaf9bc68.bam > HTTP/1.0" 302 - "-" "IGV Version 2.0.34 (1623)01/14/2012 12:45 AM > Java/1.6.0_22" > galaxy.web.framework DEBUG 2012-01-17 16:34:25,639 Error: this request > returned None from get_history(): http://10.153.182.203/galaxy/root > XX.XXX.XXX.XXX - - [17/Jan/2012:16:34:25 +0200] "GET > /galaxy/root?app_action=data&user_id=5ce1ba9f488a6ce5&app_name=igv_bam&link_name=local_default&action_param=galaxy_8b4e4b7bbaf9bc68.bam&dataset_id=8b4e4b7bbaf9bc68 > HTTP/1.0" 200 - "-" "IGV Version 2.0.34 (1623)01/14/2012 12:45 AM > Java/1.6.0_22" > > > and if I run it with the web current, I still get: > > galaxy.web.framework DEBUG 2012-01-17 16:35:26,820 Error: this request > returned None from get_history(): http://10.153.182.203/galaxy/root > XX.XXX.XXX.XXX - - [17/Jan/2012:16:35:26 +0200] "HEAD > /galaxy/root?app_action=data&user_id=5ce1ba9f488a6ce5&app_name=igv_bam&link_name=web_link_main&action_param=galaxy_8b4e4b7bbaf9bc68.bam&dataset_id=8b4e4b7bbaf9bc68 > HTTP/1.0" 200 - "-" "Java/1.6.0_22" > ---------------------------------------- > Exception happened during processing of request from ('127.0.0.1', 33901) > 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 > ---------------------------------------- > XX.XXX.XXX.XXX - - [17/Jan/2012:16:35:26 +0200] "GET > /galaxy/display_application/8b4e4b7bbaf9bc68/igv_bam/web_link_main/5ce1ba9f488a6ce5/data/galaxy_8b4e4b7bbaf9bc68.bam > HTTP/1.0" 302 - "-" "Java/1.6.0_22" > galaxy.web.framework DEBUG 2012-01-17 16:35:26,910 Error: this request > returned None from get_history(): http://10.153.182.203/galaxy/root > > > > > 2011/12/19 Nate Coraor <n...@bx.psu.edu> > 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/ > > > > > > > > -- > ___________________________________________________________ > > Alexander Graf > > Laboratory of Functional Genome Analysis > Gene Center, University of Munich (LMU) > Feodor-Lynen-Strasse 25; 81377 Munich; Germany > email: g...@lmb.uni-muenchen.de > Internet: www.lafuga.de/genomics.htm > ___________________________________________________________ > ___________________________________________________________ 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/
