An example of a Nextflow Packer file in YAML

packer-nextflow.yaml

---

# Packer machine image configuration for a Nextflow/Docker machine.
#
# To use this file (Packer expects a JSON file) you need to
# use the project's yaml2json module to convert it to JSON.
# From this directory and a Suitable Python (see root's requirements.txt)
# you can run...
#
#   ../../../yaml2json.py < nextflow.yml > nextflow.json
#
# Then, to create the AMI for later use, run Packer...
#
#   packer build nextflow.json
#
# Your AMI will be seen and available at the end of the Packer run.

variables:

  aws_access_key: "{{env `TF_VAR_aws_access_key`}}"
  aws_secret_key: "{{env `TF_VAR_aws_secret_key`}}"
  aws_user: ec2-user
  aws_i_type: t2.micro
  our_name: Nextflow Base Image
  nextflow_dir: ../../nextflow
  base_ami_name: Nextflow
  base_description: |-
    Amazon Linux 2018.03.0 HVM EBS with Nextflow & Docker

builders:

# AWS Builder - Ireland

- access_key: "{{user `aws_access_key`}}"
  secret_key: "{{user `aws_secret_key`}}"
  type: amazon-ebs
  region: eu-west-1
  # Amazon Linux AMI 2018.03.0 (HVM), SSD Volume Type...
  source_ami: ami-e4515e0e
  instance_type: "{{user `aws_i_type`}}"
  ssh_username: "{{user `aws_user`}}"
  name: "{{user `our_name`}} Ireland"
  ami_name: "{{user `base_ami_name`}}"
  ami_description: "{{user `description`}}"

provisioners:

- type: shell
  inline:
  - sudo yum update -y
  # Cloud-Init and Docker
  # and nfs-utils for EFS mounting and git...
  - sudo yum install -y cloud-init docker nfs-utils git
  - sudo service docker start
  - sudo usermod -a -G docker ec2-user
  # Now move to Java 8...
  - sudo yum install -y java-1.8.0
  - sudo yum remove -y java-1.7.0-openjdk
  # And install Nextflow...
  - sudo wget -qO- https://get.nextflow.io | bash