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
No edit summary |
|||
| (6 intermediate revisions by the same user not shown) | |||
| Line 8: | Line 8: | ||
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. | You can either download the angsd0.934.tar.gz which contains both. | ||
[http://popgen.dk/software/download/angsd/angsd0. | [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 20: | Line 20: | ||
===Unix=== | ===Unix=== | ||
The software can be compiled using make | The software can be compiled using make. | ||
<pre> | <pre> | ||
wget http://popgen.dk/software/download/angsd/angsd0. | wget http://popgen.dk/software/download/angsd/angsd0.936.tar.gz | ||
tar xf angsd0. | tar xf angsd0.936.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 | 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 13:47, 8 February 2022
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/angsd0.936.tar.gz tar xf angsd0.936.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