Ok, an update. I added the following to my httpd.conf... RewriteRule ^/static/style/(.*) /var/opt/galaxy/static/june_2007_style/ blue/$1 [L] RewriteRule ^/static/(.*) /var/opt/galaxy/static/$1 [L] RewriteRule ^/images/(.*) /var/opt/galaxy/static/images/$1 [L] RewriteRule ^/favicon.ico /var/opt/galaxy/static/favicon.ico [L] RewriteRule ^/robots.txt /var/opt/galaxy/static/robots.txt [L] As well as moving my galaxy directory to the appropriate location (/ var/opt/galaxy). Restarted galaxy process with some success. The only problem now is that the Tools and History panels are giving me 'Not Found' errors... "The requested URL /root/tool_menu was not found on this server" for the Tools pane and the same but for "/history" URL for the History pane. I would have thought that galaxy would have created these directories automatically during installation, but maybe I have to move some things around?? On Jun 4, 2009, at 10:08 AM, Nate Coraor wrote:

Andrew Stewart wrote:

...

sh run.sh seems to work okay until hitting this block of report... Any ideas what this socket business is about? It looks to me like possibly something python-specific.

Hi Andrew,

Please take a look and see if there are any old Galaxy processes around, or anything else on the system that would be using port 8080 (or whatever port is set in universe_wsgi.ini, if you changed it from the default). You may find the lsof(1) command useful for this:

% lsof -ti :8080

Invoked like this, it will return the PID of the process using port 8080.

--nate

Sorry, I forgot to mention that I have the 'RewriteRule ^(.*) http://localhost:8080 $1 [P]' rule in there as well. One odd symptom here appears to be that http://host:8080 is not working at all (yet http://host/galaxy does). Could this have something to do with it? On Jun 4, 2009, at 1:45 PM, Nate Coraor wrote:

Andrew Stewart wrote:

...

Ok, an update. I added the following to my httpd.conf... RewriteRule ^/static/style/(.*) /var/opt/galaxy/static/ june_2007_style/blue/$1 [L] RewriteRule ^/static/(.*) /var/opt/galaxy/static/$1 [L] RewriteRule ^/images/(.*) /var/opt/galaxy/static/images/$1 [L] RewriteRule ^/favicon.ico /var/opt/galaxy/static/favicon.ico [L] RewriteRule ^/robots.txt /var/opt/galaxy/static/robots.txt [L] As well as moving my galaxy directory to the appropriate location (/ var/opt/galaxy). Restarted galaxy process with some success. The only problem now is that the Tools and History panels are giving me 'Not Found' errors... "The requested URL /root/tool_menu was not found on this server" for the Tools pane and the same but for "/ history" URL for the History pane. I would have thought that galaxy would have created these directories automatically during installation, but maybe I have to move some things around??

Andrew,

The tool_menu and history are dynamic frames and the RewriteRules you've used above don't include the proxy to the Galaxy application itself. Essentially, your Apache server is serving all of the static content but not Galaxy. For that, you also need (after the other rules):

RewriteRule ^(.*) http://localhost:8080$1 [P]

Assuming your Galaxy server is running on port 8080.

--nate

Aha! galaxy only listening on 127.0.0.1 would certainly be a problem. Changing that value to 0.0.0.0 now allows for a working version Galaxy on http://host:8080 (thank you!) http://host/galaxy still wasn't working for a bit there at first, but I think I spotted a bug in the documentation at http://g2.trac.bx.psu.edu/wiki/HowToInstall/ApacheProxy RewriteEngine on ReWriteRule ^/galaxy$ /galaxy/ [R] RewriteRule ^/galaxy(.*) http://vm001:8080$1 [P] Notice 2nd line, 3rd character, =~ s/W/w/; I take it you were copy+pasting from that blurb just as I was. Sneaky typos! ;) Thanks for the help Nate. -Andrew On Jun 4, 2009, at 2:09 PM, Nate Coraor wrote:

Andrew Stewart wrote:

...

Sorry, I forgot to mention that I have the 'RewriteRule ^(.*) http://localhost:8080 $1 [P]' rule in there as well. One odd symptom here appears to be that http://host:8080 is not working at all (yet http://host/galaxy does). Could this have something to do with it?

Is your Galaxy URL not at the server root? If so, you'll also need to add the proxy-prefix options to the Galaxy config file and adjust your rewrite rules accordingly:

http://g2.trac.bx.psu.edu/wiki/HowToInstall/ApacheProxy

These would be suitable for a Galaxy instance rooted at http://host/galaxy :

ReWriteRule ^/galaxy$ /galaxy/ [R] RewriteRule ^/galaxy/static/style/(.*) /var/opt/galaxy/test/static/ june_2007_style/blue/$1 [L] RewriteRule ^/galaxy/static/(.*) /var/opt/galaxy/test/static/$1 [L] RewriteRule ^/galaxy/images/(.*) /var/opt/galaxy/test/static/images/ $1 [L] RewriteRule ^/galaxy/favicon.ico /var/opt/galaxy/test/static/ favicon.ico [L] RewriteRule ^/galaxy/robots.txt /var/opt/galaxy/test/static/ robots.txt [L] RewriteRule ^/galaxy(.*) http://localhost:8080$1 [P]

By default, Galaxy only listens on the localhost address (127.0.0.1). This can be changed in the config to 0.0.0.0 to listen on all available IPv4 interfaces.