boalang / bio

Boa for genomics

Boa_g: Boa for genomics

Boa_g is a domain-specific language and infrastructure on top of Hadoop for genomics data. Website: https://boalang.github.io/bio/

These instructions will get you a command line, jupyter notebook, Docker container, and Hadoop version of Boa_g. You can also set up a programming environment in Eclipse.

Prerequisites

You need to install Java. Boa_g compiler is written in java. It can be downloaded here.

Boa_g database schema and Data Generation

• Protobuffer schema and the step by step data generation is shown here.
• JSON files version of RefSeq for MongoDB

Run Boa_g

From Jupyter notebook

• Prerequisite is Jupyter: install
• Instructions on How to integrate Boa_g with Jupyter
• Jupyter notebook example

From command line

• Instructions on How to run Boa_g scripts on a command line

On a Docker container

• Instructions on How to run Boa_g scripts in a Docker container

On Hadoop

• Instructions on how to run Boa_g on Bridges

Boa_g Compiler source code

• Boa_g compiler is written in Java. See the source code
• This is a video on step by step instructions to set up programming environment on Eclipse for Boa compiler. link

Boa_g Query Script examples:

• Query over Refseq database

Download dataset and VirtualBox

• Google Drive Link
• Web interface is also implemented in the Ubuntu linux and it can be seen in the VirtualBox.