tutorials

Tutorials

BioGrids on Amazon Web Services (AWS)

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

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

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

biogrids-cli 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-installation-manager.s3.amazonaws.com/2.4.5/biogrids-cli_2.4.5-linux.tar.gz
tar zxf biogrids-cli_2.4.5-linux.tar.gz

Activate the installer

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

Install your tools

./biogrids-cli  install samtools
./biogrids-cli  install tophat
./biogrids-cli  install trimmomatic

Verify versions of installed tools:

./biogrids-cli  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 set up and ready for work.