Overview

This program counts DNA bases in targeted sequencing data.

In the examples below, $ indicates the command line prompt.

Licence

This program is released as open source software under the terms of MIT License.

Installing

You can install base_counter directly from the source code or build and run it from within Docker container.

Installing directly from source code

Clone this repository:

$ git clone https://github.com/bjpop/base_counter

Move into the repository directory:

$ cd base_counter

Python 3 is required for this software.

Base_counter can be installed using pip in a variety of ways ($ indicates the command line prompt):

1. Inside a virtual environment:

$ python3 -m venv base_counter_dev
$ source base_counter_dev/bin/activate
$ pip install -U /path/to/base_counter

2. Into the global package database for all users:

$ pip install -U /path/to/base_counter

3. Into the user package database (for the current user only):

$ pip install -U --user /path/to/base_counter