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
(→Unix) |
No edit summary |
||
| (43 intermediate revisions by 2 users not shown) | |||
| Line 1: | Line 1: | ||
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= | =Download and Installation= | ||
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 angsd0.938.tar.gz which contains both. | ||
[http://popgen.dk/software/download/angsd/angsd0. | [http://popgen.dk/software/download/angsd/angsd0.938.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 | ||
Earlier versions from here: http://popgen.dk/software/download/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. | Download and unpack the tarball, enter the directory and type make. Users on a mac computer, can use curl instead of wget. | ||
===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/angsd0.940.tar.gz | ||
tar | tar xf angsd0.940.tar.gz | ||
cd htslib;make;cd .. | |||
cd angsd | cd angsd | ||
make | make HTSSRC=../htslib | ||
cd .. | cd .. | ||
</pre> | </pre> | ||
The executable then located in ''' | The executable then located in '''angsd/angsd'''. | ||
=Install from github= | =Install from github= | ||
| Line 27: | Line 35: | ||
<pre> | <pre> | ||
git clone https://github.com/samtools/htslib.git | git clone --recursive https://github.com/samtools/htslib.git | ||
git clone git://github.com/ANGSD/angsd.git | git clone https://github.com/ANGSD/angsd.git | ||
cd htslib;make;cd ../angsd ;make HTSSRC=../htslib | |||
</pre> | |||
=Using htslib submodule= | |||
<pre> | |||
git clone https://github.com/ANGSD/angsd.git | |||
cd angsd | cd angsd | ||
make | make | ||
</pre> | |||
=Systemwide installation of htslib= | |||
<pre> | |||
make HTSSRC="systemwide" | |||
</pre> | </pre> | ||
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"