Installation

Welcome! 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.

Dependencies

The basic dependencies for ANGSD-wrapper are SAMTools, Wget, and Git. Most Linux distributions have Wget and Git installed by default, however some will not; users will need to download SAMTools, and it's dependency HTSlib from its GitHub page or your package manager.

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Note: Mac Users Have Special Installation Requirements

You will need to install all three of the basic dependencies to run, as well as the GNU Scientific Library. We recommend using Homebrew to manage the installation process. If you use Homebrew, you can install all of the required dependencies from anywhere in your terminal with the following commands:

brew install git
brew install samtools
brew install wget
brew install gsl

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Downloading and Installing ANGSD-wrapper

First, we need to clone the ANGSD-wrapper repository. You need to have git installed to do this. Alternatively, you can download a zip file from the releases page or use the download zip button on the home page of the repository.

We'll use Git to download ANGSD-wrapper. To do this, type the following commands:

git clone https://github.com/ANGSD-wrapper/angsd-wrapper.git
cd angsd-wrapper

ANGSD-wrapper comes with its own version of ANGSD, to prevent compatibility-breaking changes in ANGSD from affecting ANGSD-wrapper, as well as a few other programs. In order to compile these programs, you must run the following setup routine:

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

This will download and install ANGSD, ngsAdmix, ngsTools, and ngsF. All of these programs are downloaded to the dependencies directory.

If you would like to run through a tutorial with an example dataset, please go to the Tutorial page.

Recent Compilation Issues

Recently, some newer Unix-based systems (such as Ubuntu 20.04) have obsoleted libraries necessary for compiling ANGSD 0.935 and the contemporary versions of htslib and samtools. This shouldn't be an issue on HPC systems but may cause problems for personal workstations. Based upon a forum post here, a potential solution lies in adding an older OS version's packages to the list of sources for apt (a popular package manager in Ubuntu).

Summarily, the following steps should fix lib[...].so not found errors:

• Edit the package sources using sudo nano /etc/apt/sources.list
• Add deb http://security.ubuntu.com/ubuntu xenial-security main to end of the file
• sudo apt update to update the package manager's known package listings
• sudo apt install lib[...], such as sudo apt install libssl1.0.0