ANGSD: Analysis of next generation Sequencing Data
Latest tar.gz version is (0.938/0.939 on github), see Change_log for changes, and download it here.
Installation: Difference between revisions
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git clone https://github.com/ANGSD/angsd.git | git clone https://github.com/ANGSD/angsd.git | ||
cd htslib;make;cd ../angsd ;make HTSSRC=../htslib | cd htslib;make;cd ../angsd ;make HTSSRC=../htslib | ||
</pre> | </pre> | ||
=Systemwide installation of htslib?= | =Systemwide installation of htslib?= | ||
Then you just type make in the angsd directory | Then you just type make in the angsd directory | ||
Revision as of 18:12, 11 January 2016
Download and Installation
To download and use ANGSD you need to download the htslib and the angsd source folder
You can either download the angsd0.910.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/angsd0.910.tar.gz tar xfz angsd0.910.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