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Quick Start Deploy Nextflow Host on AWS

Sateesh Peri

1. Launch EC2 Instance

  • From the EC2 console, click on Launch Instance
  • For AMI, search for amzn2-ami-kernel-5.10-hvm-2.0.20230628.0-x86_64-gp2
  • For Instance type, choose t2.medium and provide key-pair
  • For Network Setting select existing default security-group
  • For Configure Storage, 8Gb of root volume is sufficient. Proceed to click on Launch Instance

2. SSH to Nextflow Host

  • From the EC2 console, get the public ip-address of the instance
  • Navigate to the directory with your key-pair and change permission for the pem file to read-only
chmod 400 sateesh_peri.pem
  • Connect to the instance
  • Open a terminal and SSH to the nextflow host from the directory with your key-pair pem file
ssh -i "sateesh_peri.pem" ec2-user@ec2-35-175-244-200.compute-1.amazonaws.com

3. Create Nextflow work directory S3 bucket

  • Navigate to S3 console & click on Create Bucket. Provide a name and choose the region for the bucket
  • Uncheck the Block all public access box and acknowledge in the checkbox
  • Leave defaults for the rest and click on Create Bucket

Retrieve security credentials for S3 bucket

  • Navigate to IAM console and select the user to retrieve security credentials and click on Create Access Key

  • Choose the use case of Command Line Interface (CLI), check the confirmation and click Next

  • Download the access key in csv format and save in secure location

4. Install MMC float CLI tool

wget https://<op_center_ip_address>/float --no-check-certificate
sudo mv float /usr/local/bin/
sudo chmod +x /usr/local/bin/float

example

wget https://34.205.19.185/float --no-check-certificate
sudo mv float /usr/local/bin/
sudo chmod +x /usr/local/bin/float
  • Connect float on Nextflow Host to the OpCenter (needs public ip address) with credentials below:

    username -> admin
    password -> memverge

5. Install Java & Nextflow

curl -s "https://get.sdkman.io" | bash
source "/home/ec2-user/.sdkman/bin/sdkman-init.sh"
  • Install Java 17.0.6
sdk install java 17.0.6-tem
java -version
  • Install Nextflow
curl -s https://get.nextflow.io | bash
sudo mv nextflow /usr/local/bin/

6. Install git & tmux

  • Install git
sudo yum install git
sudo yum install tmux