BioGrids on AWS

BioGrids provides identical software environments across Mac laptops, Linux workstations, and AWS EC2 instances, enabling reproducible bioinformatics workflows.

Setup Process

Launch an EC2 instance and connect via SSH. Update the system and install development tools with sudo yum update && sudo yum groupinstall "Development Tools" && sudo yum install wget.

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

Install bioinformatics tools and activate the environment:

./biogrids-cli install samtools tophat trimmomatic
source /programs/biogrids.shrc

Best Practices

Use t2.micro instances for free tier access and set up budget alerts to monitor costs. Store SSH keys in ~/.ssh/ with 400 permissions and consider EBS storage for large datasets.

For complete installation details, see the Installation Overview.