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.

Difference between revisions of "Installation"

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To download and use ANGSD you need to download the htslib and the angsd source folder
 
To download and use ANGSD you need to download the htslib and the angsd source folder
  
You can either download the angsd0.930.tar.gz which contains both.
+
You can either download the angsd0.934.tar.gz which contains both.
[http://popgen.dk/software/download/angsd/angsd0.930.tar.gz]
+
[http://popgen.dk/software/download/angsd/angsd0.934.tar.gz]
  
 
Or you can use github for the latest version of both htslib and angsd
 
Or you can use github for the latest version of both htslib and angsd
Line 22: Line 22:
 
The software can be compiled using make.
 
The software can be compiled using make.
 
<pre>
 
<pre>
wget http://popgen.dk/software/download/angsd/angsd0.930.tar.gz
+
wget http://popgen.dk/software/download/angsd/angsd0.934.tar.gz
tar xf angsd0.930.tar.gz
+
tar xf angsd0.934.tar.gz
 
cd htslib;make;cd ..
 
cd htslib;make;cd ..
 
cd angsd
 
cd angsd
Line 35: Line 35:
  
 
<pre>
 
<pre>
git clone https://github.com/samtools/htslib.git
+
git clone --recursive https://github.com/samtools/htslib.git
 
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

Revision as of 11:45, 15 March 2021

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 angsd0.934.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/angsd0.934.tar.gz
tar xf angsd0.934.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?

Then you just type make in the angsd directory