Installation

There has been some confusion about the versions of ANGSD. To simplify things we go like this from 0.912 onwards

1. Even versions are freezes from the last odd version 2. 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 angsd0.914.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. zlib needs to be installed on your system.

wget http://popgen.dk/software/download/angsd/angsd0.914.tar.gz
tar xf angsd0.914.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 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?

Then you just type make in the angsd directory