AWS/Cloud Command Line Interface

AWS/ Cloud is an excellent method to run your pipeline if you are familiar with using a command line interface and have access to an AWS account. It is recommended to to use an S3 bucket to transfer your data to and from AWS. The Ion Mobility Dashboard utilizes EC2 instances to process data.

AWS EC2 Instance Specifications

  • Amazon Linux 2 (HVM)

  • Kernel 5.10

  • SSD Volume Type

  • Architecture: 64-bit x86

  • Minimum Instance type: t2.large - Higher CPU/Memory will result in faster processing.

  • Storage type: gp2

Storage depends on user needs:
SteppedField: we recommend allocating 14 times the storage that the input data takes up.
SingleField: we recommend allocating 5 times the storage that the input data takes up.
SLIM: Currently Unknown. To be updated by dev.

AWS Commands

Setup

sudo yum install git
git clone https://github.com/PNNL-CompBio/ion-mob-ms.git
sudo amazon-linux-extras install docker
sudo service docker start
sudo systemctl enable docker
sudo usermod -a -G docker ec2-user
cd ion-mob-ms
pip3 install -r requirements_py3.7_CLI.txt

Note: for docker engine to finish configuration, you must refresh the page. To check that docker is running correctly use the following command.

docker info

Run Test Data

cd UserInterfaceV2
python3 CLI.py --json sample.json