QuickStart.md

#Pancancer CLI

This quick-start guide will help you get started using the Pancancer CLI tool.

##Getting started

1. Launch a new VM in Amazon EC2 (This guide will assume you are using us-east-1 AKA North Virginia).
2. Download the bootstrap script
3. Execute the bootstrap script:

$ bash install_bootstrap

This script will install docker, the pancancer_launcher image, and collect some basic configuration info to get the launcher started.

##Inside the Pancancer Launcher.

The main tool for interacting with the Pancancer components is simply named pancancer. You can invoke Pancancer commands from the command line like this:

$ pancancer coordinator start

This example command will start the Pancancer coordinator service.

You can also work with the pancancer tool's interactive shell simply by executing the command pancancer:

$ pancancer
(pancancer) coordinator start

In this example, the user has started the interactive shell, as can be seen by the shell prompt, which has changed from $ to (pancancer).

To get a list of all pancancer commands, you can type pancancer -h and the help text will be displayed.

##Configuration

Once you are in the Pancancer Launcher docker container, you will to do some basic pancancer system configuration. You can do this using the command:

$ pancancer sysconfig

You should do this before you run any workflows.

##Running workflows

The Pancancer Launcher can generate a template INI file for workflows (you can see which workflows are available with the command pancancer workflows list), but you may want to edit these before executing the workflow.

To generate an INI file:

$ pancancer workflows config --workflow BWA

A new BWA-specific INI file should be generated in ~/ini-dir. You will want to edit this file before generating job requests.

To generate job requests for a workflow:

$ pancancer generator --workflow BWA

The generated jobs will use the INI files in ~/ini-dir so it is important to make any necessary edits before this step!