Latest revision as of 22:25, 8 December 2023

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 angsd0.938.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

Installation

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/angsd0.940.tar.gz
tar xf angsd0.940.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

Using htslib submodule

git clone https://github.com/ANGSD/angsd.git 
cd angsd
make

Systemwide installation of htslib

make HTSSRC="systemwide"

@@ Line 1: / Line 1: @@
-There has been some confusion about the versions of ANGSD. To simplify things we go like this from 0.912 onwards
+There has been some confusion about the versions of ANGSD.
-. Even versions are freezes from the last odd version
+* 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.
+* 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.
+You can either download the angsd0.938.tar.gz which contains both.
-[http://popgen.dk/software/download/angsd/angsd0.914.tar.gz]
+[http://popgen.dk/software/download/angsd/angsd0.938.tar.gz]
 Or you can use github for the latest version of both htslib and angsd
@@ Line 15: / Line 16: @@
 And here: https://github.com/ANGSD/angsd/releases
-=Install=
+=Installation=
 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.
+The software can be compiled using make.
 <pre>
-wget http://popgen.dk/software/download/angsd/angsd0.914.tar.gz
+wget http://popgen.dk/software/download/angsd/angsd0.940.tar.gz
-tar xf angsd0.914.tar.gz
+tar xf angsd0.940.tar.gz
 cd htslib;make;cd ..
 cd angsd
@@ Line 34: / Line 35: @@
 <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
 cd htslib;make;cd ../angsd ;make HTSSRC=../htslib
 </pre>
-=Systemwide installation of htslib?=
+=Using htslib submodule=
-Then you just type make in the angsd directory
+<pre>
+git clone https://github.com/ANGSD/angsd.git
+cd angsd
+make
+</pre>
+=Systemwide installation of htslib=
+<pre>
+make HTSSRC="systemwide"
+</pre>

Installation: Difference between revisions