Installation

There has been some confusion about the versions of ANGSD.

• Even versions are freezes from the last odd giversion

• Odd versions are git versions. Once there has been enough commits we will increment and make a release.

Download and Installation

To download and use ANGSD you need to download the htslib and the angsd source folder

You can either download the angsd0.938.tar.gz which contains both. [1]

Or you can use github for the latest version of both htslib and angsd

Earlier versions from here: http://popgen.dk/software/download/angsd/ And here: https://github.com/ANGSD/angsd/releases

Install

Download and unpack the tarball, enter the directory and type make. Users on a mac computer, can use curl instead of wget.

Unix

The software can be compiled using make.

wget http://popgen.dk/software/download/angsd/angsd0.940.tar.gz
tar xf angsd0.940.tar.gz
cd htslib;make;cd ..
cd angsd
make HTSSRC=../htslib
cd ..

The executable then located in angsd/angsd.

Install from github

To install CRAM support you also need to install htslib and can be done using the following commands

git clone --recursive https://github.com/samtools/htslib.git
git clone https://github.com/ANGSD/angsd.git 
cd htslib;make;cd ../angsd ;make HTSSRC=../htslib

Systemwide installation of htslib

make HTSSRC="systemwide"