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.
To quickly create a production-like sandbox environment with Apache, one simple way is through XAMPP. Here's how to configure Apache to serve up Galaxy in your development environment
Mac OS X
- Install and configure XAMPP
- Edit /Applications/XAMPP/etc/httpd.conf to configure Apache for Galaxy
<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