A mostly reproducible, mostly persistent, quickly deployable, and portable custom bioinformatics environment built on-demand from anywhere with an SSH client.

This stack is what I use for carefree disposable development environments. Your mileage may vary greatly!

• Vagrant
• Ansible
• EC2 full-access
• direnv (optional)

Ensure you do a recursive clone otherwise you will not pull the submodules.

❯ git clone --recursive https://github.com/clintval/gimme.git

❯ vagrant plugin install vagrant-env
❯ vagrant plugin install vagrant-aws

We will install the miniconda role through ansible-galaxy:

❯ ansible-galaxy install andrewrothstein.miniconda

A dummy box is provided for the aws provider. This acts as a pass-through for Vagrant and could be created with defaults.

❯ address=https://github.com/clintval/gimme/raw/master/example-box/aws-dummy.box
❯ vagrant box add aws-dummy "${address}" --provider aws

Load the following variables into your environment.

export AWS_ACCESS_KEY_ID=YOURACCESSIDGOESHERE
export AWS_SECRET_ACCESS_KEY=YOURSECRETKEYGOESHERE

Edit and then source the file .envrc.

This project is set-up to provision an environment very specific to me and will later include some of my .dotfiles .

Read: hope you like Zsh!

The bioinformatics tools specified for install are also typical for an environment I use regularly.

Typically, Vagrant is used to spin-up virtual machines which are capable of recieving an SSH connection. In order to enable SSH connection for your EC2 instance we must attach a security group which gives the correct authority.

The security group SSH From Anywhere is referenced explicitly in the Vagrantfile.

Create the EC2 security group SSH From Anywhere:

[Inbound]
type=SSH
protocol=TCP
port-range=22
source=0.0.0.0/0

[Outbound]
type=All traffic
protocol=All
port-range=All
destination=0.0.0.0/0

# Connect to AWS, start and provision the instance
❯ vagrant up

# Provision the instance
❯ vagrant provision

# Do work
❯ vagrant ssh

# Halting the instance
❯ vagrant halt

# Terminating the instance
❯ vagrant destroy

Note the first few steps can be combined:

❯ vagrant --provision up && vagrant ssh