Locked History Actions


Galaxy Download and Installation

In addition to using the public Galaxy server (a.k.a. Main), you can install your own instance of Galaxy (what this page is about), or create a cloud-based instance of Galaxy. Another option is to use one of the ever-increasing number of public Galaxies hosted by other organizations.

See Big Picture: Choices for help on deciding which of these options may be best for your situation.

Reasons to Install Your Own Galaxy

You only need to download Galaxy if you plan to:


  • UNIX/Linux or Mac OS X (although you can try with Windows)

  • Python 2.7 (details here)

  • Git (optional - see below)
  • GNU Make, gcc to compile and install tool dependencies
  • Additional tool requirements as detailed in Tool Dependencies

Get the Code

Galaxy's source code is hosted in a GitHub repository. Below are your basic options on how to obtain the source code so you can use Galaxy. For more information see source code details.

For Production or Single User

If running a production Galaxy service or creating your own personal Galaxy server, you should use the latest release branch, which only receives stable code updates (list of releases).

  • If you do not have a Galaxy repository yet or you do not want to update the existing instance, run:

   1 $ git clone -b release_16.07 https://github.com/galaxyproject/galaxy.git
  • If you have an existing Galaxy repository you want to update, run:

   1 $ git checkout release_16.07 && git pull --ff-only origin release_16.07

For Development

If you are getting Galaxy for development, you want to use the default branch after cloning - dev. This is the branch that most pull requests should be made against, if you are contributing code back (unless you are fixing a bug in a Galaxy release).

   1 $ git clone https://github.com/galaxyproject/galaxy.git

Start It Up

Galaxy requires a few things to run - a virtualenv, configuration files, and dependent Python modules. However, starting the server for the first time will create/acquire these things as necessary. Simply run the following command:

   1 % 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 . Galaxy's server will start printing its output to your terminal. To stop the Galaxy server, just hit Ctrl-c in the terminal from which Galaxy is running.

To access Galaxy over the network, simply modify the config/galaxy.ini file and change the host setting to

   1 host =

Upon restarting, Galaxy will bind to any available network interfaces instead of just the loopback.

That's it - you have your very own Galaxy running. Congratulations!

What to do next

Become an Admin

In order to control your new Galaxy through the UI (installing tools, managing users, creating groups etc.) you have to become an administrator. First register as a new user and then give the user admin privileges like this: You add the Galaxy login ( email ) to the Galaxy configuration file (config/galaxy.ini). If the file does not exist you can copy it from the provided sample (config/galaxy.ini.sample). Note that you have to restart Galaxy after modifying the configuration for changes to take effect. More help with an example how-to.

# this should be a comma-separated list of valid Galaxy users
admin_users = user1@example.com,user2@example.com

Install More Tools

Your Galaxy came with the basic tools pre-installed. However, you probably want more. Installing tools to Galaxy is generally a very easy and pleasant experience. Please read Installing tools into Galaxy from ToolShed to get started.

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. See Mailing Lists for other options.

Keep your instance backed up

Like any other application, your Galaxy directory and your Galaxy database tables should be backed up and your disaster recovery plan should be regularly tested to make sure everything is working as expected.

Configure for production

The above instructions are intended for those wishing to develop Galaxy tools and the Galaxy itself. To deploy a production-ready 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 heavily endorsed to prevent database locking issues that can arise with multiple users.

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

Keep your code up to date

Galaxy development occurs in GitHub. Changes are stabilized in the release_YY.MM branches and then merged to master for each YY.MM.point release.

To be made aware of new Galaxy releases, please join the Galaxy Developers mailing list. Each release is accompanied by a news brief.

At any time, you can check to see if a new stable release is available by using the git log command:

   1 % git log ..origin/master
   2 commit 3f314974c9c3742b118518881a6d392123ccc05d
   3 Merge: d8eeaae c78b7b6
   4 Author: Nate Coraor <nate@bx.psu.edu>
   5 Date:   Mon Mar 9 22:26:54 2015 -0400
   7     Merge branch 'release_15.03' to master for v15.03
   9  ...

If you see no output, you are up to date. If you see a list of commits, a new version is available. We suggest checking the accompanying news brief first (if the release is to a newer major version of Galaxy), but you can also immediately pull the commits to your local Galaxy clone with:

% git pull

Note: After pulling changes, you will need to stop your Galaxy server and restart with the updated code. This will interrupt any running jobs, unless you are using a cluster configuration. For more information on how to make Galaxy restartable without interrupting users, see the production server documentation.

Note: Occasionally, updated code includes structural changes to the Galaxy database tables. The news brief will alert you if a release contains a database change. After updating Galaxy, if you attempt to restart, Galaxy will refuse to load, and will output an error message indicating that your database is the wrong version. The error message indicates that you should run backup your database and then run sh manage_db.sh upgrade - follow those instructions carefully - especially the part about backing up your database safely! Database updates are carefully tested before release, but it is always wise to be able to back out if something goes wrong during an update.

In the unlikely event that something goes wrong with updated code, you can return to an older release by guessing the release tag name from the news brief page and using the git checkout command. For example, to return to the latest version of the January 2015 release, use:

   1 % git checkout release_15.01

You can also use tags to check out specific releases:

   1 % git tag
   2 v13.01
   3 v13.01.1
   4 v13.02
   5  ...
   6 v14.10.1
   7 v15.01
   8 v15.01.1
   9 v15.01.2
  10 v15.03

Restore the fresh backup if a database update was required, and then restart Galaxy to get back to where you started.


  • Offline start: The initial Galaxy run requires internet access to download the pre-built Python wheels of Galaxy's dependencies.
  • The basic Galaxy install is a single-user instance and is only accessible by the local user. As with many web-based applications, enable cookies in the web-browser used for full functionality.
  • A common practice when using any web browser is to stay current with software updates to maximize performance and security. If moving forward to production server with login enabled, please make sure you and your end-users are current.

  • Some tools shipped with Galaxy have dependencies that need to be satisfied manually. Please see details here.


Get Galaxy without Git

  • Galaxy from an archive

    • If you don't have Git (and thus can't run the git command), you can download Galaxy in an archive instead: zipped or tar/gzipped.

    • Be aware that this makes it more difficult to stay up to date in the future since there's no simple way to update your copy.

Get Galaxy for Development

  • Fork Galaxy in GitHub

    • If you're doing development or making changes to Galaxy, it's typically a good idea to fork Galaxy in GitHub and update to/from your fork.

    • This changes the process slightly, see the GitHub fork documentation for details.

Become an Admin: Example

Follow these steps to edit config/galaxy.ini.sample for a brand new Galaxy.


  • Galaxy was installed Galaxy using Git.
  • Galaxy was started at least once using "sh run.sh".

  • Galaxy is now stopped. Help

Add yourself as an administrator while creating a config/galaxy.ini file

Check the config/galaxy.ini.sample file for the default settings. The result will be: #admin_users = None

   1 % grep "admin_users" config/galaxy.ini.sample

Make the changes

The command below will 1) remove the leading hash (#) character from the line, 2) replace "None" with the same email address you used or will use to register the admin account through the Galaxy web interface, 3) create a config/galaxy.ini file. Be careful to type the command exactly as written except for changing admin@email.edu to be your own admin email address.

   1 % sed 's/#admin_users = None/admin_users = admin@email.edu/' config/galaxy.ini.sample > config/galaxy.ini

Double check that the new config/galaxy.ini file has the replacement text correct. The result should be the first two changes above (the query is against the third change). For the example email address above, the result is: admin_users = admin@email.edu

   1 % grep "admin_users" config/galaxy.ini

That's it for the galaxy.ini file changes! Now start up Galaxy again and create an account - using the same email address - through the Galaxy web interface (if this hasn't been done already). The Admin tab will now appear in the Masthead for that account.

Shutting down Galaxy

Simplified instructions for users managing their own local Galaxy server. If your configuration is more complicated, getting help from an administrator is recommended.

  • The Galaxy process is running in the background

    • If Galaxy was the last process running within a terminal window, bring it into the foreground with the command fg. Now shut down with Ctrl-c.

    • If Galaxy is one of many processes running in the background within a terminal window, find it with the command jobs. The list of jobs will be numbered. Bring the galaxy job to the foreground with the command fg number_of_the_job. Now shut down with Ctrl-c.

  • I have lost the terminal window running Galaxy

    • From another terminal window, find all active processes with the command ps. The list of processes will each have a process ID (called PID). The target process will be named like "python ./scripts/paster.py serve config/galaxy.ini.sample". Stop it with the command kill PID, where "PID" is the actual process ID number.

    • If you kill only the process named "sh run.sh", this will result in conflicts and Galaxy will not restart. If you did this or are simply getting errors when trying to restart Galaxy, the solution is to kill the process "python ./scripts/paster.py serve config/galaxy.ini.sample" before restarting Galaxy again.

Other Resources

Galaxy administration, tool, and deployment search