On Apr 30, 2013, at 5:15 PM, Jeffrey Long wrote:
- 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.
- 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@uci.edu 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@uci.edu
On Mon, Apr 29, 2013 at 9:51 AM, Jeffrey Long jlong1@ualberta.ca 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.
Thanks for your help!
-Jeff
On Fri, Apr 26, 2013 at 10:11 PM, Adam Brenner aebrenne@uci.edu 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@uci.edu
On Fri, Apr 26, 2013 at 2:56 PM, Jeffrey Long jlong1@ualberta.ca 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
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