Galaxy
https://docs.rc.uab.edu/
Please use the new documentation url https://docs.rc.uab.edu/ for all Research Computing documentation needs.
As a result of this move, we have deprecated use of this wiki for documentation. We are providing read-only access to the content to facilitate migration of bookmarks and to serve as an historical record. All content updates should be made at the new documentation site. The original wiki will not receive further updates.
Thank you,
The Research Computing Team
Overview
Galaxy is an easy-to-use, open-source, scalable framework for tool and data integration. Galaxy provides access to tools (mainly comparative genomics) through an interface (e.g., a web-based interface). The Galaxy framework is implemented in the Python programming language.
End Users
A public instance of Galaxy maintained by Penn State University is at http://usegalaxy.org/
Developers
To get started with installing your own Galaxy instance, the only required component is Python (2.4,2.5, and 2.6). Four simple steps will get you started with your own Galaxy instance
- clone the mercurial galaxy distribution
hg clone http://www.bx.psu.edu/hg/galaxy galaxy_dist
or get a source tarball - execute setup.sh
- execute run.sh
- go to http://localhost:8080
- Galaxy runs on a local webserver, PasteScript written in Python. PasteScript is based on Python's library module simplehttpserverand implemented with the help of python package, WSGIUtils
- For deployment to production environments, Galaxy documentation suggests using a proxy server like Apache/Nginx to serve up static content and for handling authnz. As mentioned in Galaxy's ApacheProxy documentation, here's how to edit Apache's httpd.conf to proxy Galaxy on port 80
<Proxy http://localhost:8080>
Order deny,allow
Allow from all
</Proxy>
RewriteEngine on
RewriteRule ^/galaxy$ /galaxy/ [R]
RewriteRule ^/galaxy/static/style/(.*) /Users/pnm/project/galaxy_dist/static/june_2007_style/blue/$1 [L]
RewriteRule ^/galaxy/static/scripts/(.*) /Users/pnm/project/galaxy_dist/static/scripts/packed/$1 [L]
RewriteRule ^/galaxy/static/(.*) /Users/pnm/project/galaxy_dist/static/$1 [L]
RewriteRule ^/galaxy/favicon.ico /Users/pnm/project/galaxy_dist/static/favicon.ico [L]
RewriteRule ^/galaxy/robots.txt /Users/pnm/project/galaxy_dist/static/robots.txt [L]
RewriteRule ^/galaxy(.*) http://localhost:8080$1 [P]
- Change the path to where you have cloned/installed Galaxy
- http://localhost/galaxy should bring up Galaxy on port 80 now
Note: if you are using CentOS/RedHat as your platform, you may need to adjust or disable SELinux in order to allow Apache to access parts of the file system that are not part of the shipped default Directory directives of the Apache config. You will see unexplained "permission denied" errors in the errors.log if you are bitten by this.
Apache and Postgres Setup
In production mode it is reccomended that something other than SQLlite and the python web server be used, preferably postgres and apache. When setting up apache to proxy requests to the python web server on CentOS it is critical that the default CentOS security policy be overridden to allow proxying as shown below.
setsebool -P httpd_can_network_relay=1
Additionally, postgres ident privileges should be changed. One workaround is to set postgres to trust all local users as shown below in /var/lib/pgsql/data/pg_hba.conf
local all all trust