The UC Davis Bioinformatics Core
uses Galaxy and the command-line for our training workshops and courses, running in the Amazon Cloud
. We make the Amazon Machine Image (AMI) publicly available so that the community can use it for their projects. In addition to the standard software, our AMI contains customized software and interfaces that you will not find elsewhere; these tools are available through the Galaxy interface, or via the command-line under /share/apps. The AMI also contains all of the training materials from our week-long workshop. The current Bioinformatics Core AMI can be found by searching for UC Davis Bioinformatics
. It is located in the N. California Region. There is no charge for using this AMI to launch your own instances in the Amazon Cloud, but you will need an AWS account, and Amazon will charge you for running instances and storing/transferring data.
Notes on starting our AMI: If you are using Galaxy, you need to use the following rules in your security group:
Custom TCP Rule, port range 8080
Custom TCP Rule, port range 2200
Custom TCP Rule, port range 20-21
You can increase the size of your data partition by simply increasing the size of the EBS volume from 60Gb to whatever you want (up to 1024Gb) in the “Add Storage” step. We have added code in our AMI to automatically detect if the volume has increased capacity and to create a volume with that capacity. The steps to increase to maximum capacity can take a while depending upon the size increase, which means you may need to wait a while before the AMI is up and running. The default admin login for Galaxy is
and the password is
If you wish to use FTP to transfer files to your Galaxy instance, we have instructions on how to use FileZilla
to do so. FTP transfer is recommended for large files, however, you can use whatever FTP client you want.