Galaxy is an open, web-based platform for accessible, reproducible, and transparent computational research. Users can use the public instance of Galaxy, or at the Hutch, we provide acccess to self service installations with the following features:
- HutchNet ID authentication will be used
- The instance will run with the launching user’s permissions, these will be used for all data library access (e.g. file system)
- User maintains their own workflows (and thus can migratee them to newer installation of Galaxy if/when needed)
- User can self install the software as well as restart existing Galaxy servers, or make new ones if needed
- A simple database is provided (sqlite instead of Postgres)
- Each user can have access to multiple Galaxy instances (e.g. in case software updates need to be implemented)
- Galaxy server will run on a
gizmonode, thus compute capacity is limited to single node (36 cores)
Please check the Galaxy Documentation for more general information about using Galaxy.
How to use Galaxy on Gizmo:
Starting Galaxy is simple. You just run the
galaxy command on Rhino. Run this command in a new shell that won’t be canceled/closed for a while. We recommend tmux or NoMachine for long running shells.. When you run the command the first time, you may just the the “New Install” option, but in the future you can reconnect to a previous install by selecting one of the other options.
petersen@rhino03:~ galaxy Enter number to select your Galaxy install 1) /fh/fast/_HDC/user/petersen/galaxies/demo/ 2) /fh/fast/_HDC/user/petersen/galaxies/production/ 3) /fh/fast/_HDC/user/petersen/galaxies/latest/ 4) /fh/fast/_HDC/user/petersen/galaxies/solarsystem/ 5) New-Install #? 5 New Install: Enter a name for the Galaxy instance: brandnew
A few minutes after the installation has been started you receive an email like this:
Now you wait about 30 min. If you click on the link before Galaxy has finished installing you will see a proxy error:
Try again after a while. Then you should see the Galaxy login screen. Use your HutchnetID and password to login to the Galaxy interface:
To terminate the Galaxy instance just type Ctrl+c twice inside the terminal Window. It will cancel the cluster job that runs Galaxy.
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Updated: June 18, 2020Edit this Page via GitHub Comment by Filing an Issue Have Questions? Ask them here.