On Apr 30, 2013, at 5:15 PM, Jeffrey Long wrote: > 1) Any idea which proxy settings in the universe_wsgi file need to be set other than the ones on the website? Those are the only ones I changed. I scrolled down to the 'Advanced Proxy' settings but didn't see anything that looked relevant to me. > > Probably I should have sent this earlier, but this is the traceback I get; it looks like there's a url somewhere that's not getting passed along or re-assembled properly. > > Exception happened during processing of request from ('127.0.0.1', 47424) > Traceback (most recent call last): > File "/mnt2/birl/MAVEN/bin/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/httpserver.py", line 1053, in process_request_in_thread > self.finish_request(request, client_address) > File "/usr/lib/python2.7/SocketServer.py", line 323, in finish_request > self.RequestHandlerClass(request, client_address, self) > File "/usr/lib/python2.7/SocketServer.py", line 638, in __init__ > self.handle() > File "/mnt2/birl/MAVEN/bin/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/httpserver.py", line 432, in handle > BaseHTTPRequestHandler.handle(self) > File "/usr/lib/python2.7/BaseHTTPServer.py", line 340, in handle > self.handle_one_request() > File "/mnt2/birl/MAVEN/bin/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/httpserver.py", line 427, in handle_one_request > self.wsgi_execute() > File "/mnt2/birl/MAVEN/bin/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/httpserver.py", line 287, in wsgi_execute > self.wsgi_start_response) > File "/mnt2/birl/MAVEN/bin/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/config.py", line 285, in __call__ > return self.app(environ, start_response) > File "/mnt2/birl/MAVEN/bin/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/urlmap.py", line 193, in __call__ > path_info = self.normalize_url(path_info, False)[1] > File "/mnt2/birl/MAVEN/bin/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/urlmap.py", line 117, in normalize_url > or self.domain_url_re.search(url)), "URL fragments must start with / or http:// (you gave %r)" % url > AssertionError: URL fragments must start with / or http:// (you gave '.') Hi Jeff, Does the Apache log give any indication of what path is being accessed? You may also want to enable mod_rewrite's debug logging to make sure it's behaving correctly. > 2) Are the static subdirectories strictly necessary, or can I worry about one problem at a time? I've tried both commenting out the proxy lines (in apache2.conf) and leaving them in, and I get the same behaviour. You can exclude the static page rewrites for the purposes of getting it working. Galaxy's internal HTTP server will serve the static pages itself. --nate > > Thanks, I'll try to remember to 'reply-all' here! > > -Jeff > > > On Mon, Apr 29, 2013 at 1:23 PM, Adam Brenner <aebrenne(a)uci.edu&gt; wrote: > Hia Jeff, > > I think this is related to the proxy settings in Galaxy (universe_wsgi.ini) > > What is happening is that if you look at the source code for your > galaxy website, it is trying to load css/images from: > http://trove.usask.ca/galaxy/static/style/base.css?v=1367254127 But if > you visit that link it offers you a 404 not found. Make sure the proxy > settings in your universe_wsgi.ini is set correctly. > > If it is, it could be that you need to setup proxies for the > subdirectories as well. If you look at the nginx guide here: > http://wiki.galaxyproject.org/Admin/Config/Performance/nginx%20Proxy > you will notice that we provide alias for /static/*. > > In terms of doing this in Apache, you may need to add more proxy pass > lines that correspond to the subdirectories in question. > > > Be sure to post back to the Galaxy listsrv so that future people may > benefit from this! > -Adam > > -- > Adam Brenner > Computer Science, Undergraduate Student > Donald Bren School of Information and Computer Sciences > > Research Computing Support > Office of Information Technology > http://www.oit.uci.edu/rcs/ > > University of California, Irvine > www.ics.uci.edu/~aebrenne/ > aebrenne(a)uci.edu > > > On Mon, Apr 29, 2013 at 9:51 AM, Jeffrey Long <jlong1(a)ualberta.ca&gt; wrote: > > Hi Adam thanks for the response, > > I'm not using VirtualHosts. I just copied the lines shown into > > /etc/apache2/apache.conf (this is on Ubuntu Linux). > > > > I copied the lines you list (with appropriate modification) into this same > > apache.conf. That seems to work - as far as Apache goes! However, when I > > load galaxy in a browser now, I get a bunch of gobbledigook (it looks like > > the frames aren't being built properly or something). You can take a look; > > I've temporarily enabled the site to be world-viewable. > > > > http://trove.usask.ca/galaxy > > > > Thanks for your help! > > > > -Jeff > > > > > > On Fri, Apr 26, 2013 at 10:11 PM, Adam Brenner <aebrenne(a)uci.edu&gt; wrote: > >> > >> Jeff, > >> > >> How / Where did you add the apache changes? Are you using VirutalHosts > >> or ... ? Quick glance, everything appears correct. Its been a while > >> since I used Apache (switched everything to nginx) however I believe > >> if you want to setup a Reverse Proxy, you need to add / use the proxy > >> pass lines which does not appear in the Galaxy Wiki. > >> > >> Something like this should work: (untested...) > >> > >> <IfModule mod_proxy.c> > >> ProxyRequests Off > >> <Proxy *> > >> AddDefaultCharset off > >> Order Deny,Allow > >> Deny from all > >> Allow from *.ualberta.ca # Change / Remove as needed > >> </Proxy> > >> > >> ProxyPass /galaxy http://localhost:8080/ > >> ProxyPassReverse /galaxy http://localhost:8080/ > >> # Line below is optional > >> Redirect permanent /galaxy http://mymachine.com/galaxy > >> > >> ProxyVia On > >> </IfModule> > >> > >> > >> Let us know, > >> -Adam > >> > >> -- > >> Adam Brenner > >> Computer Science, Undergraduate Student > >> Donald Bren School of Information and Computer Sciences > >> > >> Research Computing Support > >> Office of Information Technology > >> http://www.oit.uci.edu/rcs/ > >> > >> University of California, Irvine > >> www.ics.uci.edu/~aebrenne/ > >> aebrenne(a)uci.edu > >> > >> > >> On Fri, Apr 26, 2013 at 2:56 PM, Jeffrey Long <jlong1(a)ualberta.ca&gt; wrote: > >> > Hi folks, > >> > I am wanting to run a galaxy instance and serve it at a location other > >> > than > >> > the webserver root, i.e. at http://mymachine.com/galaxy rather than > >> > just at > >> > http://mymachine. > >> > > >> > To do this, I've followed the instructions about proxying Galaxy through > >> > Apache at http://wiki.galaxyproject.org/Admin/Config/Apache%20Proxy . > >> > I'm > >> > pretty sure I've followed the instructions exactly. I enabled the > >> > necessary > >> > apache proxy modules and then I added these lines to my apache.conf > >> > file: > >> > > >> > > >> > RewriteEngine on RewriteRule ^/galaxy$ /galaxy/ [R] RewriteRule > >> > ^/galaxy/static/style/(.*) > >> > /myplace/galaxy-dist/static/june_2007_style/blue/$1 [L] RewriteRule > >> > ^/galaxy/static/scripts/(.*) > >> > /myplace/galaxy-dist/static/scripts/packed/$1 > >> > [L] RewriteRule ^/galaxy/static/(.*) /myplace/galaxy-dist/static/$1 [L] > >> > RewriteRule ^/galaxy/favicon.ico /myplace/galaxy-dist/static/favicon.ico > >> > [L] > >> > RewriteRule ^/galaxy/robots.txt /myplace/galaxy-dist/static/robots.txt > >> > [L] > >> > RewriteRule ^/galaxy(.*) http://localhost:8080$1 [P] > >> > > >> > ...and re-started the apache server without a problem (note: I also > >> > tried it > >> > commenting out everything but the first, second and last line in case > >> > there > >> > was an issue with the static stuff). > >> > > >> > I then made sure the following lines were present and uncommented in my > >> > universe_wsgi.ini file > >> > > >> > [filter:proxy-prefix] > >> > use = egg:PasteDeploy#prefix > >> > prefix = /galaxy > >> > > >> > [app:main] > >> > > >> > filter-with = proxy-prefix > >> > cookie_path = /galaxy > >> > > >> > > >> > I start up Galaxy. And still, I can only reach it on > >> > http://mymachine:8080, > >> > not at http://mymachine/galaxy as I intend. > >> > > >> > Any help would be appreciated! Thanks! > >> > > >> > -Jeff > >> > > >> > > >> > ___________________________________________________________ > >> > 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/ > >> > > >> > To search Galaxy mailing lists use the unified search at: > >> > http://galaxyproject.org/search/mailinglists/ > >> > > > > > ___________________________________________________________ > 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/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/

Jeff, Did you ever get this to work? -Adam -- Adam Brenner Computer Science, Undergraduate Student Donald Bren School of Information and Computer Sciences Research Computing Support Office of Information Technology http://www.oit.uci.edu/rcs/ University of California, Irvine www.ics.uci.edu/~aebrenne/ aebrenne(a)uci.edu On Wed, May 1, 2013 at 1:52 PM, Jeffrey Long <jlong1(a)ualberta.ca&gt; wrote: > In the Apache access.log, a single access link results in a great many > output lines; the first two look like this: > > 128.233.109.35 - - [01/May/2013:14:31:29 -0600] "GET /galaxy HTTP/1.1" > 200 5058 "-" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_5) > AppleWebKit/536.29.13 (KHTML, like Gecko) Version/6.0.4 Safari/536.29.13" > 128.233.109.35 - - [01/May/2013:14:31:29 -0600] "GET > /galaxy/static/style/base.css?v=1367440234 HTTP/1.1" 404 495 " > http://trove.usask.ca/galaxy" "Mozilla/5.0 (Macintosh; Intel Mac OS X > 10_7_5) AppleWebKit/536.29.13 (KHTML, like Gecko) Version/6.0.4 > Safari/536.29.13" > > If I'm reading this right, the second one involves a 404 error. Indeed, > I don't see any static/style directory in my galaxy location...should there > be one? > > I don't get anything new in apache's error.log as a result of a single > access attempt. > > -Jeff > > > > On Wed, May 1, 2013 at 6:16 AM, Nate Coraor <nate(a)bx.psu.edu&gt; wrote: > >> On Apr 30, 2013, at 5:15 PM, Jeffrey Long wrote: >> >> > 1) Any idea which proxy settings in the universe_wsgi file need to be >> set other than the ones on the website? Those are the only ones I changed. >> I scrolled down to the 'Advanced Proxy' settings but didn't see anything >> that looked relevant to me. >> > >> > Probably I should have sent this earlier, but this is the traceback I >> get; it looks like there's a url somewhere that's not getting passed along >> or re-assembled properly. >> > >> > Exception happened during processing of request from ('127.0.0.1', >> 47424) >> > Traceback (most recent call last): >> > File >> "/mnt2/birl/MAVEN/bin/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/httpserver.py", >> line 1053, in process_request_in_thread >> > self.finish_request(request, client_address) >> > File "/usr/lib/python2.7/SocketServer.py", line 323, in >> finish_request >> > self.RequestHandlerClass(request, client_address, self) >> > File "/usr/lib/python2.7/SocketServer.py", line 638, in __init__ >> > self.handle() >> > File >> "/mnt2/birl/MAVEN/bin/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/httpserver.py", >> line 432, in handle >> > BaseHTTPRequestHandler.handle(self) >> > File "/usr/lib/python2.7/BaseHTTPServer.py", line 340, in handle >> > self.handle_one_request() >> > File >> "/mnt2/birl/MAVEN/bin/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/httpserver.py", >> line 427, in handle_one_request >> > self.wsgi_execute() >> > File >> "/mnt2/birl/MAVEN/bin/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/httpserver.py", >> line 287, in wsgi_execute >> > self.wsgi_start_response) >> > File >> "/mnt2/birl/MAVEN/bin/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/config.py", >> line 285, in __call__ >> > return self.app(environ, start_response) >> > File >> "/mnt2/birl/MAVEN/bin/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/urlmap.py", >> line 193, in __call__ >> > path_info = self.normalize_url(path_info, False)[1] >> > File >> "/mnt2/birl/MAVEN/bin/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/urlmap.py", >> line 117, in normalize_url >> > or self.domain_url_re.search(url)), "URL fragments must start with >> / or http:// (you gave %r)" % url >> > AssertionError: URL fragments must start with / or http:// (you gave >> '.') >> >> Hi Jeff, >> >> Does the Apache log give any indication of what path is being accessed? >> You may also want to enable mod_rewrite's debug logging to make sure it's >> behaving correctly. >> >> > 2) Are the static subdirectories strictly necessary, or can I worry >> about one problem at a time? I've tried both commenting out the proxy >> lines (in apache2.conf) and leaving them in, and I get the same behaviour. >> >> You can exclude the static page rewrites for the purposes of getting it >> working. Galaxy's internal HTTP server will serve the static pages itself. >> >> --nate >> >> > >> > Thanks, I'll try to remember to 'reply-all' here! >> > >> > -Jeff >> > >> > >> > On Mon, Apr 29, 2013 at 1:23 PM, Adam Brenner <aebrenne(a)uci.edu&gt; >> wrote: >> > Hia Jeff, >> > >> > I think this is related to the proxy settings in Galaxy >> (universe_wsgi.ini) >> > >> > What is happening is that if you look at the source code for your >> > galaxy website, it is trying to load css/images from: >> > http://trove.usask.ca/galaxy/static/style/base.css?v=1367254127 But if >> > you visit that link it offers you a 404 not found. Make sure the proxy >> > settings in your universe_wsgi.ini is set correctly. >> > >> > If it is, it could be that you need to setup proxies for the >> > subdirectories as well. If you look at the nginx guide here: >> > http://wiki.galaxyproject.org/Admin/Config/Performance/nginx%20Proxy >> > you will notice that we provide alias for /static/*. >> > >> > In terms of doing this in Apache, you may need to add more proxy pass >> > lines that correspond to the subdirectories in question. >> > >> > >> > Be sure to post back to the Galaxy listsrv so that future people may >> > benefit from this! >> > -Adam >> > >> > -- >> > Adam Brenner >> > Computer Science, Undergraduate Student >> > Donald Bren School of Information and Computer Sciences >> > >> > Research Computing Support >> > Office of Information Technology >> > http://www.oit.uci.edu/rcs/ >> > >> > University of California, Irvine >> > www.ics.uci.edu/~aebrenne/ >> > aebrenne(a)uci.edu >> > >> > >> > On Mon, Apr 29, 2013 at 9:51 AM, Jeffrey Long <jlong1(a)ualberta.ca&gt; >> wrote: >> > > Hi Adam thanks for the response, >> > > I'm not using VirtualHosts. I just copied the lines shown into >> > > /etc/apache2/apache.conf (this is on Ubuntu Linux). >> > > >> > > I copied the lines you list (with appropriate modification) into >> this same >> > > apache.conf. That seems to work - as far as Apache goes! However, >> when I >> > > load galaxy in a browser now, I get a bunch of gobbledigook (it >> looks like >> > > the frames aren't being built properly or something). You can take >> a look; >> > > I've temporarily enabled the site to be world-viewable. >> > > >> > > http://trove.usask.ca/galaxy >> > > >> > > Thanks for your help! >> > > >> > > -Jeff >> > > >> > > >> > > On Fri, Apr 26, 2013 at 10:11 PM, Adam Brenner <aebrenne(a)uci.edu&gt; >> wrote: >> > >> >> > >> Jeff, >> > >> >> > >> How / Where did you add the apache changes? Are you using >> VirutalHosts >> > >> or ... ? Quick glance, everything appears correct. Its been a while >> > >> since I used Apache (switched everything to nginx) however I believe >> > >> if you want to setup a Reverse Proxy, you need to add / use the >> proxy >> > >> pass lines which does not appear in the Galaxy Wiki. >> > >> >> > >> Something like this should work: (untested...) >> > >> >> > >> <IfModule mod_proxy.c> >> > >> ProxyRequests Off >> > >> <Proxy *> >> > >> AddDefaultCharset off >> > >> Order Deny,Allow >> > >> Deny from all >> > >> Allow from *.ualberta.ca # Change / Remove as needed >> > >> </Proxy> >> > >> >> > >> ProxyPass /galaxy http://localhost:8080/ >> > >> ProxyPassReverse /galaxy http://localhost:8080/ >> > >> # Line below is optional >> > >> Redirect permanent /galaxy http://mymachine.com/galaxy >> > >> >> > >> ProxyVia On >> > >> </IfModule> >> > >> >> > >> >> > >> Let us know, >> > >> -Adam >> > >> >> > >> -- >> > >> Adam Brenner >> > >> Computer Science, Undergraduate Student >> > >> Donald Bren School of Information and Computer Sciences >> > >> >> > >> Research Computing Support >> > >> Office of Information Technology >> > >> http://www.oit.uci.edu/rcs/ >> > >> >> > >> University of California, Irvine >> > >> www.ics.uci.edu/~aebrenne/ >> > >> aebrenne(a)uci.edu >> > >> >> > >> >> > >> On Fri, Apr 26, 2013 at 2:56 PM, Jeffrey Long <jlong1(a)ualberta.ca&gt; >> wrote: >> > >> > Hi folks, >> > >> > I am wanting to run a galaxy instance and serve it at a location >> other >> > >> > than >> > >> > the webserver root, i.e. at http://mymachine.com/galaxy rather >> than >> > >> > just at >> > >> > http://mymachine. >> > >> > >> > >> > To do this, I've followed the instructions about proxying Galaxy >> through >> > >> > Apache at >> http://wiki.galaxyproject.org/Admin/Config/Apache%20Proxy. >> > >> > I'm >> > >> > pretty sure I've followed the instructions exactly. I enabled the >> > >> > necessary >> > >> > apache proxy modules and then I added these lines to my >> apache.conf >> > >> > file: >> > >> > >> > >> > >> > >> > RewriteEngine on RewriteRule ^/galaxy$ /galaxy/ [R] RewriteRule >> > >> > ^/galaxy/static/style/(.*) >> > >> > /myplace/galaxy-dist/static/june_2007_style/blue/$1 [L] >> RewriteRule >> > >> > ^/galaxy/static/scripts/(.*) >> > >> > /myplace/galaxy-dist/static/scripts/packed/$1 >> > >> > [L] RewriteRule ^/galaxy/static/(.*) >> /myplace/galaxy-dist/static/$1 [L] >> > >> > RewriteRule ^/galaxy/favicon.ico >> /myplace/galaxy-dist/static/favicon.ico >> > >> > [L] >> > >> > RewriteRule ^/galaxy/robots.txt >> /myplace/galaxy-dist/static/robots.txt >> > >> > [L] >> > >> > RewriteRule ^/galaxy(.*) http://localhost:8080$1 [P] >> > >> > >> > >> > ...and re-started the apache server without a problem (note: I >> also >> > >> > tried it >> > >> > commenting out everything but the first, second and last line in >> case >> > >> > there >> > >> > was an issue with the static stuff). >> > >> > >> > >> > I then made sure the following lines were present and uncommented >> in my >> > >> > universe_wsgi.ini file >> > >> > >> > >> > [filter:proxy-prefix] >> > >> > use = egg:PasteDeploy#prefix >> > >> > prefix = /galaxy >> > >> > >> > >> > [app:main] >> > >> > >> > >> > filter-with = proxy-prefix >> > >> > cookie_path = /galaxy >> > >> > >> > >> > >> > >> > I start up Galaxy. And still, I can only reach it on >> > >> > http://mymachine:8080, >> > >> > not at http://mymachine/galaxy as I intend. >> > >> > >> > >> > Any help would be appreciated! Thanks! >> > >> > >> > >> > -Jeff >> > >> > >> > >> > >> > >> > ___________________________________________________________ >> > >> > 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/ >> > >> > >> > >> > To search Galaxy mailing lists use the unified search at: >> > >> > http://galaxyproject.org/search/mailinglists/ >> > >> >> > > >> > >> > >> > ___________________________________________________________ >> > 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/ >> > >> > To search Galaxy mailing lists use the unified search at: >> > http://galaxyproject.org/search/mailinglists/ >> >> >