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Galaxy Download and Installation

Note: You only need to download Galaxy if you plan to:

1. Develop it further
2. Add new tools
3. Plug-in new datasources, or
4. Run a local production server for your site

Otherwise, to simply use Galaxy, we maintain public sites: Galaxy Main and Galaxy Test.

The installation procedure is simple and is nearly identical for UNIX/Linux and Mac OS X. We are no longer supporting the Windows platform with our distribution, so you will have to build your own Python eggs if you want to install it on Windows (see Config/Windows for some tips). Of course, Windows users can use our public Galaxy server from their browsers.

You can also watch or stream a screencast of the installation process.

These instructions describe the basic setup procedure for a development environment, more detailed instructions on how to deploy a production server can be found at the bottom of this page.

0. Check your Python version:

Currently supported Python versions are 2.4 and 2.5. Support for Python 2.6 is in development. Before reporting bugs, please ensure that python -V reports one of these two versions. If this is not the case, a simple solution is to manipulate your shell's $PATH variable to place the correct version first. This can be done for only Python by creating a new directory at the front of $PATH and creating a symbolic link to python in that directory:

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% mkdir ~/galaxy-python
% ln -s /path/to/python2.5 ~/galaxy-python/python
% export PATH=~/galaxy-python:$PATH

Mac OS X Panther and Tiger (and Leopard/Snow Leopard on PPC) users should install Python 2.5 from python.org. For Leopard on Intel, you can use the system-provided Python 2.5. For Snow Leopard on Intel, please use the process above to symlink the system Python 2.5 to 'python', since the default Python 2.6 is not yet supported.

1. Get the latest copy from the repository:

The latest source code can be downloaded from the anonymous Mercurial repository with this command:

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% hg clone http://www.bx.psu.edu/hg/galaxy galaxy_dist

If you don't have Mercurial, tarballs can be downloaded instead: bzipped or gzipped. However, this makes it more difficult to stay updated in the future since there's no simple way to update your copy.

2. Enable configuration files and download eggs:

Once the source code is downloaded, cd to the galaxy_dist directory and run the setup.sh script. This will copy sample configuration files and download the proper eggs for your platform:

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% cd galaxy_dist
% sh setup.sh

3. Start it up:

At this point Galaxy is ready to run. Simply run the following command:

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% sh run.sh

This will start up the server on localhost and port 8080, so Galaxy can be accessed from your web browser at http://localhost:8080 . To stop the Galaxy server, just hit Ctrl-c in the terminal from which Galaxy is running.

As shown, Galaxy is run locally and developers do not need any special environment for running and developing its code.

To access Galaxy over the network, simply modify the universe_wsgi.ini file and change the host setting to host = 0.0.0.0. Upon restarting, Galaxy will bind to any available network interfaces instead of just the loopback.

Please note that some tools do have outside dependencies that cannot be provided with Galaxy for various reasons. The list of these dependencies can be found on the ToolDependencies page.

4. Join the Mailing List:

The best way to keep up on new features and bug fixes, as well as discuss future features is to join the Galaxy Developers mailing list. The list is low-to-medium volume.

Advanced Configuration

The above instructions are intended for those wishing to develop tools and the Galaxy framework. To deploy a local site installation of Galaxy, some changes from the default configuration are highly recommended. If nothing else, switching to PostgreSQL or MySQL (from the default SQLite) is highly recommended to prevent database locking issues that can arise with multiple users.

Please see the Running Galaxy in a production environment page for more details.