How to set up your InterMine environment on the Amazon Cloud
This is where you should learn how to start your own MalariaMine web application on the Amazon Cloud. You could also use your InterMine Amazon instance to try building MalariaMine yourself or to build your own mine there.
You need an Amazon account. If you don't have one:
- Go to http://aws.amazon.com.
- Click on
- Follow the instructions on the page.
You will need to set up your key pair security mechanism (see step 7 below for an example). Alternatively, you will need your aws-access-key and your aws-secret-key to start your instance (not shown here).
#Starting a new Instance
InterMine is publicly available on Amazon Cloud as an Image (AMI), with an AMI ID ami-b1c7a9d8.
The image contains a ready deployed MalariaMine. To start a new instance:
Sign in at http://aws.amazon.com.
Go to the EC2 management console by following these steps:
AWS console --> https://console.aws.amazon.com/console/home --> EC2 console.
Set up a security group (if you don't have one) which allows access
to at least ports:
- 22 (SSH)
- 80 (HTTP)
- 8080 (TOMCAT)
you could also set up a few spare ones (20, 21, 8009).
Note You can do this also during step 7, but you cannot change the security group of an instance after starting it for the first time (unless you use a VPC instance, see User Guide).
Go to the IMAGES/AMI console.
Set the location on the top header (beside your username) to US
East (N. Virginia).
Set the filter to Public Images and search for InterMine.
Select BasicIntermine AMI (AMI ID = ami-b1c7a9d8).
Launch (and configure) instance
you can use all default options for the instance characteristics
and details, but use the security group you created in step 3.
when prompted, create a new key pair (
.pemfile), or use one
that you already own.
Go to the Instance console.
Select your new instance.
When public DNS appears (after checks, a couple of minutes), you can
open a terminal with:$ ssh -i your_pem_file ubuntu@the_instance_public_DNS
#Starting an existing Instance
If you are using an existing Instance, you need to:
- Sign in at http://aws.amazon.com.
- Go to the EC2 console (see step 2 above).
- Go to the Instance console.
- Select your instance.
- Start your instance (Actions --> Start).
#Working with your Instance
Open a terminal in your Instance
you will land in
Here, you can find these relevant directories:
git/intermine the InterMine code base
.intermine with the properties file
malaria sources for building MalariaMine
#Starting/stopping the existing MalariaMine web application
/webapp you'll find tomcat6. You can start the webapp using this command:
Your BioTestMine web application will then be available on
To stop the web application, use this command:
/home/ubuntu/git/intermine/malariamine/webapp, use this command:
/home/ubuntu/git/intermine/malariamine, use this command:
You can also follow all the steps in the build as illustrated in Tutorial.