Revision as of 16:35, 26 February 2015

Download and Installation

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

You can either download the angsd0.700.tar.gz which contains both. [1]

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

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

The software can be compiled using make. zlib needs to be installed on your system.

wget http://popgen.dk/software/download/angsd/angsd0.615.tar.gz
tar xfz angsd0.615.tar.gz
cd angsd0.615
make
cd ..

The executable then located in angsd0.615/angsd.

NB the program also compiles a static version called angsd0.615/angsd.static which could be usefull.

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 --branch=withhtslib git://github.com/ANGSD/angsd.git 
cd angsd
make

@@ Line 1: / Line 1: @@
-=Download=
+=Download and Installation=
+To download and use ANGSD you need to download the htslib and the angsd source folder
-The latest stabile version of the source code is avaible as a tarball and be download here
+You can either download the angsd0.700.tar.gz which contains both.
-[http://popgen.dk/software/download/angsd/angsd0.615.tar.gz]
+[http://popgen.dk/software/download/angsd/angsd0.700.tar.gz]
+Or you can use github for the latest version of both htslib and angsd
 Earlier versions from here: http://popgen.dk/software/download/angsd/
-Latest dev version can be found on github: https://github.com/ANGSD/angsd
-The branch '''withhtslib''' now supports cram reading.
 =Install=