tutorials

Tutorials

BioGrids on Amazon Web Services (AWS)

You can easily reproduce your bioinformatics working environment with the BioGrids installer.

The HMS Orchestra cluster makes available all BioGrids software packages by default.

With a few commands, you can install and use the same versions of bioinformatics software on your Mac laptop and AWS instances

As a simple example, here is the command to install samtools on your OS X based Mac:

biogrids install samtools

This same command can be used to install on an AWS EC2 instance. Here is a brief overview of installing BioGrids by command line on an AWS EC2 instance.

Start an AWS EC2 instance

aws ec2 run-instances --image-id ami-1609da7e [..other options..]

Log in to the instance

ssh -i "myaws.pem" centos@ec2-54-227-10-10.compute-1.amazonaws.com

Update the base software and install development tools

sudo yum update
sudo yum groupinstall "Development Tools"
sudo yum install wget

Get the BioGrids CLI installer

wget https://biogrids.org/wiki/downloads/biogrids-1.0.555-Linux.tgz
tar zxf  biogrids-1.0.555-Linux.tgz
cd biogrids-1.0.555-Linux

Activate the installer

./biogrids activate <your_site> <your_name> <your_key>

Install your tools

./biogrids install samtools
./biogrids install tophat
./biogrids install trimmomatic

Verify versions of installed tools:

./biogrids installed
Installed packages:
samtools (1.5)
tophat (2.1.1)
trimmomatic (0.36)

Launch the BioGrids environment:

 source /programs/biogrids.shrc

Your environment is now setup and ready for work.