Revision as of 16:36, 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/angsd0.700.tar.gz
tar xfz angsd0.700.tar.gz
cd angsd0.700
make
cd ..

The executable then located in angsd0.615/angsd.

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 15: / Line 15: @@
 The software can be compiled using make. zlib needs to be installed on your system.
 <pre>
-wget http://popgen.dk/software/download/angsd/angsd0.615.tar.gz
+wget http://popgen.dk/software/download/angsd/angsd0.700.tar.gz
-tar xfz angsd0.615.tar.gz
+tar xfz angsd0.700.tar.gz
-cd angsd0.615
+cd angsd0.700
 make
 cd ..
 </pre>
 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.
 =Install CRAM version=
 To install CRAM support you also need to install htslib and can be done using the following commands