Installation

Installation of ANGSD-wrapper is simple. The ANGSD-wrapper package has a built-in setup routine that downloads most dependencies, as well as a test dataset.

System Requirements

ANGSD-wrapper needs to be run on a UNIX-type operating system. This includes versions of Linux, BSD, and Mac OS X. It is strongly recommended that systems have at least a quad-core processor and 32 gigabytes of RAM.

Downloading

The easiest way to download ANGSD-wrapper is using Git. ANGSD-wrapper is hosted on GitHub. To download from GitHub using Git, use the following command:

git clone https://github.com/mojaveazure/angsd-wrapper.git

Alternatively, you may download a zipped archive of ANGSD-wrapper from the GitHub page.

Dependencies

There are some dependencies for ANGSD-wrapper that are not automatically installed during the setup routine. These dependencies are listed below:

• Git
• Wget
• SAMTools
• GNU Scientific Library

Most of these are available by default or through native package managers on Linux distributions. Mac OS X and BSD users will need to download all of these individually; Mac OS X users alternatively can use the Homebrew or another package manager.

Installation

The installation of ANGSD-wrapper is a two-command process. This must be done within the directory for ANGSD-wrapper:

./angsd-wrapper setup please
source ~/.bash_profile

This will download the primary dependencies for ANGSD-wrapper and install ANGSD-wrapper system-wide. This allows the user to be in any directory and call ANGSD-wrapper with the following command:

angsd-wrapper

To download the example dataset, we use the following command:

./angsd-wrapper setup data

Frequently asked questions