Apache proxy to Galaxy
For various reasons (performance, authentication, etc.) in a production environment, it's recommended to run Galaxy behind a web server proxy. Although any proxy could work, Apache is the most common. Alternatively, we use nginx for our public sites, and details are available for it, too.
Currently the only recommended way to run Galaxy with Apache is using mod_rewrite and mod_proxy. fastcgi, AJP or similar connectors may be supported in the future.
To support proxying, the mod_proxy, mod_http_proxy and mod_rewrite modules must be enabled in the Apache config. The main proxy directives, ProxyRequests and ProxyVia do not need to be enabled.
Please note that Galaxy should never be located on disk inside Apache's DocumentRoot. By default, this would expose all of Galaxy (including datasets) to anyone on the web.
Serving Galaxy at the web server root (/)
For a default Galaxy configuration running on http://localhost:8080/, the following lines in the Apache configuration will proxy requests to the Galaxy application:
Thus, all requests on your server (for example, http://www.example.org/) are now redirected to Galaxy. Because this example uses the "root" of your web server, you may want to use a VirtualHost to be able to run other sites from this same server.
If your Apache server is set up to use mod_security, you may need to modify the value of the SecRequestBodyLimit. The default value on some systems will limit uploads to only a few kilobytes.
Since Apache is more efficient at serving static content, it is best to serve it directly, reducing the load on the Galaxy process and allowing for more effective compression (if enabled), caching, and pipelining. To do so, your configuration will now become:
1 RewriteEngine on 2 RewriteRule ^/static/style/(.*) /home/nate/galaxy-dist/static/june_2007_style/blue/$1 [L] 3 RewriteRule ^/static/scripts/(.*) /home/nate/galaxy-dist/static/scripts/packed/$1 [L] 4 RewriteRule ^/static/(.*) /home/nate/galaxy-dist/static/$1 [L] 5 RewriteRule ^/favicon.ico /home/nate/galaxy-dist/static/favicon.ico [L] 6 RewriteRule ^/robots.txt /home/nate/galaxy-dist/static/robots.txt [L] 7 RewriteRule ^(.*) http://localhost:8080$1 [P]
You'll need to ensure that filesystem permissions are set such that the user running your Apache server has access to the Galaxy static/ directory.
Serving Galaxy at a sub directory (such as /galaxy)
1 RewriteEngine on 2 RewriteRule ^/galaxy$ /galaxy/ [R] 3 RewriteRule ^/galaxy/static/style/(.*) /home/nate/galaxy-dist/static/june_2007_style/blue/$1 [L] 4 RewriteRule ^/galaxy/static/scripts/(.*) /home/nate/galaxy-dist/static/scripts/packed/$1 [L] 5 RewriteRule ^/galaxy/static/(.*) /home/nate/galaxy-dist/static/$1 [L] 6 RewriteRule ^/galaxy/favicon.ico /home/nate/galaxy-dist/static/favicon.ico [L] 7 RewriteRule ^/galaxy/robots.txt /home/nate/galaxy-dist/static/robots.txt [L] 8 RewriteRule ^/galaxy(.*) http://localhost:8080$1 [P]
Note the first rewrite rule deals with the missing trailing slash problem. If left out, http://www.example.org/galaxy will result in a 404 error.
Additionally, the Galaxy application needs to be aware that it is running with a prefix (for generating URLs in dynamic pages). This is accomplished by configuring a Paste proxy-prefix filter in the [app:main] section of config/galaxy.ini and restarting Galaxy:
cookie_prefix should be set to prevent Galaxy's session cookies from clobbering each other if running more than one instance of Galaxy in different subdirectories on the same hostname.
External user authentication
Moved to its own page, please check there.
Display sites such as UCSC work not by sending data directly from Galaxy to UCSC via the client's browser, but by sending UCSC a URL to the data in Galaxy that the UCSC server will retrieve data from. Since enabling authentication will place all of Galaxy behind authentication, such display sites will no longer be able to access data via that URL. If display_servers is set to a non-empty value in galaxy/config/galaxy.ini, this tells Galaxy it should allow the named servers access to data in Galaxy. However, you still need to configure Apache to allow access to the datasets. An example config is provided here that allows the UCSC Main/Test backends:
1 <Location "/root/display_as"> 2 Satisfy Any 3 Order deny,allow 4 Deny from all 5 Allow from hgw1.cse.ucsc.edu 6 Allow from hgw2.cse.ucsc.edu 7 Allow from hgw3.cse.ucsc.edu 8 Allow from hgw4.cse.ucsc.edu 9 Allow from hgw5.cse.ucsc.edu 10 Allow from hgw6.cse.ucsc.edu 11 Allow from hgw7.cse.ucsc.edu 12 Allow from hgw8.cse.ucsc.edu 13 </Location>
PLEASE NOTE that this introduces a security hole, the impact of which depends on whether you have restricted access to the dataset via Galaxy's internal dataset permissions.
- By default, data in Galaxy is public. Normally with a Galaxy server behind authentication in a proxy server this is of little concern since only clients who've authenticated can access Galaxy. However, if display site exceptions are made as shown above, anyone could use those public sites to bypass authentication and view any public dataset on your Galaxy server. If you have not changed from the default and most of your datasets are public, you should consider running your own display sites that are also behind authentication rather than using the public ones.
- For datasets for which access has been restricted to one or more roles (i.e. it is no longer "public"), access for reading via external browsers is only allowed for a brief period, when someone with access permission clicks the "display at..." link. During this period, anyone who has the dataset ID would then be able to use the browser to view this dataset. Although such a scenario is unlikely, it is technically possible.
If you place Galaxy behind a proxy address that uses SSL (e.g. https:// URLs), set the following in your Apache config:
Setting X-URL-SCHEME makes Galaxy aware of what type of URL it should generate for external sites like Biomart. This should be added to the existing <Location "/"> block if you already have one, and adjusted accordingly if you're serving Galaxy from a subdirectory.
Compression and caching
All of Galaxy's static content can be cached on the client side, and everything (including dynamic content) can be compressed on the fly. This will decrease download and page load times for your clients, as well as decrease server load and bandwidth usage. To enable, you'll need to load mod_deflate and mod_expires in your Apache configuration, and then set:
1 <Location "/"> 2 # Compress all uncompressed content. 3 SetOutputFilter DEFLATE 4 SetEnvIfNoCase Request_URI \.(?:gif|jpe?g|png)$ no-gzip dont-vary 5 SetEnvIfNoCase Request_URI \.(?:t?gz|zip|bz2)$ no-gzip dont-vary 6 SetEnvIfNoCase Request_URI /history/export_archive no-gzip dont-vary 7 </Location> 8 <Location "/static"> 9 # Allow browsers to cache everything from /static for 6 hours 10 ExpiresActive On 11 ExpiresDefault "access plus 6 hours" 12 </Location>
The contents of <Location "/"> should be added to the existing <Location "/"> block if you already have one, and adjusted accordingly if you're serving Galaxy from a subdirectory.
Sending files using Apache
Galaxy sends files (e.g. dataset downloads) by opening the file and streaming it in chunks through the proxy server. However, this ties up the Galaxy process, which can impact the performance of other operations (see Admin/Config/Performance/ProductionServer for a more in-depth explanation). Apache can assume this task instead and as an added benefit, speed up downloads. This is accomplished through the use of mod_xsendfile, a 3rd-party Apache module. Dataset security is maintained in this configuration because Apache will still check with Galaxy to ensure that the requesting user has permission to access the dataset before sending it.
To enable it, you must first download, compile and install mod_xsendfile. Once done, add the appropriate LoadModule directive to your Apache configuration to load the xsendfile module and the XSendFile directives to your proxy configuration:
This should be added to the existing <Location "/"> block if you already have one, and adjusted accordingly if you're serving Galaxy from a subdirectory.
Note: If you use a version of mod_xsendfile older than 0.10, use "XSendFileAllowAbove on" instead of "XSendFilePath /"
Finally, set apache_xsendfile = True in the [app:main] section of config/galaxy.ini and restart Galaxy.
Proxying multiple galaxy worker threads
If you've configured multiple threads for galaxy in the config/galaxy.ini file, you will need a ProxyBalancer to manage sending requests to each of the threads. You can do that with apache configuration as follows:
Allow Encoded Slashes in URLs
Some Galaxy URLs related to Data Managers contain encoded slashes (%2F) in the path and Apache will not serve these URLs by default. To configure Apache to serve URLs with encoded slashes in the path, add the following line to your Apache configuration file: