trajectoread builder

Overview

Builder is a module of the trajectoread suite of tools designed to simplify deployment of applets and workflows on DNAnexus. It is a command-line tool that allows users to automatically build DNAnexus workflows based on JSON configuration files.

Functions

• Use JSON file to manage DNAnexus build environments
• Use JSON files to codify workflow configurations
• Build workflows
• Build applets

Value

• Build workflows automatically
• Simplify new applet & workflow deployment
• Reduce deployment errors

Files

• builder.py: Python script used to build applets and workflows.
• builder.json: Configuration file with user-specific information describing DNAnexus build locations.
• workflows/fastqc_bwa-mem_gatk-genotyper.json: Sample configuration file used to generate a 3-step workflow.

Getting Started

This will guide you through the steps of installing builder, configuring the JSON file, and building a sample applet & workflow on DNAnexus.

1. Install the DNAnexus SDK

Visit https://wiki.dnanexus.com/Downloads and follow instructions to install dx-toolkit.

2. Clone the repository.

git clone git@github.com:StanfordBioinformatics/trjread-builder.git

3. Rename builder.json.template file.

mv builder.json.template builder.json

4. Populatate builder.json configuration data

Open builder.json file in a text editor and fill in DNAnexus environment information.

5. Build FastQC applet on DNAnexus

python builder.py -e develop -r aws:us-east-1 -a fastqc

6. Build sample workflow on DNAnexus

python builder.py -e develop -r aws:us-east-1 -w workflows/fastqc_bwa-mem_gatk-genotyper.json