Using the BioGrids Environment
Support for Site Administrators
Hardware Support Notes
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-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" firstname.lastname@example.org
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
tar zxf biogrids-cli_2.4.5-linux.tar.gz
Activate the installer
./biogrids-cli activate <your_site> <your_name> <your_key>
./biogrids-cli install samtools
./biogrids-cli install tophat
./biogrids-cli install trimmomatic
Verify versions of installed tools:
Launch the BioGrids environment:
Your environment is now set up and ready for work.