INSTALL

# Installation
There are a few ways to install snp-sites. The simpliest way is using apt (Debian/Ubuntu) or Conda.

* Linux - Ubuntu/Debian
* OSX/Linux - using Bioconda
* OSX/Linux - from source
* OSX/Linux - from a release tarball

## Linux - Ubuntu/Debian
If you have a recent version of Ubuntu or Debian then you can install it using apt.
```
   apt-get install snp-sites
```

## OSX/Linux - using Bioconda
Install Conda and install the bioconda channels.
```
conda config --add channels conda-forge
conda config --add channels defaults
conda config --add channels r
conda config --add channels bioconda
conda install snp-sites
```

## OSX/Linux - from source
This is a difficult method and is only suitable for someone with advanced unix skills. No support is provided with this method, since you have advanced unix skills. Please consider using Conda instead. First install a standard development environment (e.g. gcc, automake, autoconf, libtool). Download the software from [GitHub](https://github.com/sanger-pathogens/snp-sites).

```
autoreconf -i -f
./configure
make
sudo make install
```

## OSX/Linux - from a release tarball
This is a difficult method and is only suitable for someone with advanced unix skills. No support is provided with this method, since you have advanced unix skills. Please consider using Conda instead. First install a standard development environment (e.g. gcc, automake, autoconf, libtool).

```
tar xzvf snp-sites-x.y.z.tar.gz
cd snp-sites-x.y.z
./configure
make
sudo make install
```

## All platforms - Docker
Bioconda produce a Docker container so you can use the software out of the box. Install Docker and then pull the container from Bioconda https://quay.io/repository/biocontainers/snp-sites