Here you will find information on obtaining and setting up a Galaxy instance with default configuration.
- UNIX/Linux or Mac OSX
- Python 2.7
If setting up or running a production Galaxy service or creating your own personal Galaxy instance, use the latest release branch, which only receives stable code updates.
If you do not have a Galaxy repository yet or you do not want to update the existing instance, run:
$ git clone -b release_18.01 https://github.com/galaxyproject/galaxy.git
If you have an existing Galaxy repository and want to update it, run:
$ git fetch origin && git checkout release_18.01 && git pull --ff-only origin release_18.01
To obtain Galaxy for development, use the default branch after cloning:
dev. This is the branch that pull requests should be made against to contribute code (unless you are fixing a bug in a Galaxy release).
$ git clone https://github.com/galaxyproject/galaxy.git
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. To start Galaxy, simply run the following command in a terminal window:
$ sh run.sh
This will start up the Galaxy server on localhost and port 8080. Galaxy can then be accessed from a web browser at http://localhost:8080. After starting, Galaxy's server will print output to the terminal window. To stop the Galaxy server, use
Ctrl-C in the terminal window from which Galaxy is running. If galaxy does not start, you may be using the conda python. See the admin docs for more details.
To access Galaxy over the network, modify the
config/galaxy.ini file by changing the
host setting to
host = 0.0.0.0
Upon restarting, Galaxy will bind to any available network interfaces instead of the loopback.
To control Galaxy through the UI (installing tools, managing users, creating groups, etc.), users must become an administrator. Only registered users can become admins. To give a user admin privileges, complete the following steps:
- Add the user's Galaxy login email to the configuration file
config/galaxy.ini. As shown here:
# this should be a comma-separated list of valid Galaxy users admin_users = firstname.lastname@example.org,email@example.com
- If the file does not exist, copy it from the provided sample:
cp config/galaxy.ini.sample config/galaxy.ini
- Restart Galaxy after modifying the configuration file for changes to take effect.
- Additional details can be found below.
Galaxy comes with a small set of basic tools pre-installed. To install additional tools, follow the instructions on Installing tools into Galaxy from the Tool Shed.
Like any other application, Galaxy directories and Galaxy database tables should be backed up, and any disaster recovery plans should be regularly tested to make sure everything is working as expected.
The above instructions are intended for users wishing to develop Galaxy tools and 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.
Galaxy development occurs in GitHub. Changes are stabilized in the
release_YY.MM branches and then merged to
master for each
At any time, you can check to see if a new stable release is available by using the
git log command:
$ git log ..origin/master commit 3a2ff46c28172ef78510f4bea2f4be75ce660667 Merge: 8b538f17f 90de3f258 Author: Martin Cech <firstname.lastname@example.org> Date: Wed Feb 22 10:56:57 2017 -0500 Merge branch 'release_17.01'
git log produces no output, Galaxy is up-to-date. If
git log produces a list of commits, a new version is available. We suggest checking the accompanying release notes 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
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 good practice 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 using the release tag name from the release list page and the
git checkout command. For example, to return to the latest version of the January 2015 release, use:
$ git checkout release_15.01
You can also use tags to check out specific releases:
$ git tag v13.01 v13.01.1 v13.02 ... v16.01 v16.04 v16.07 v16.10 v17.01
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 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.
Be aware that using archives makes it more difficult to stay up-to-date with Galaxy code because there is no simple way to update the copy.
If you're doing development or making changes to Galaxy, it is best practice to fork Galaxy in GitHub and update to/from your fork. See the GitHub fork documentation for details.
Follow these steps to become an admin for a brand new Galaxy.
- Galaxy was installed using Git.
- Galaxy was started at least once using
- Galaxy is currently stopped. See our documentaion for help stopping Galaxy.
Check the default settings
The default setting for admin_users is:
#admin_users = None. You can check this by running the following command:
$ grep "admin_users" config/galaxy.ini.sample
config/galaxy.ini file and add yourself as an administrator
The following command will: 1) remove the leading hash (
#) character from the
admin_users line, 2) replace
None with the email address of the user being added as an admin, and 3) create a
config/galaxy.ini file with
admin_users changed. Be careful to type the command exactly as written except for changing
email@example.com to be the user's email address.
$ sed 's/#admin_users = None/admin_users = firstname.lastname@example.org/' config/galaxy.ini.sample > config/galaxy.ini
Confirm that the new
config/galaxy.ini file is correctly formatted
Running the command below should result in the following output:
admin_users = email@example.com
$ grep "admin_users" config/galaxy.ini
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.
Below are simplified instructions for shutting down local Galaxy server. If your configuration is more complicated, getting help from an administrator is recommended.
- If Galaxy was the last process running within a terminal window, bring it into the foreground with the command
fgand shut down with
- 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>and shut down with
- 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
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.samplebefore restarting Galaxy again.