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add install instructions
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‎INSTALL‎

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== Installing from a git checkout ==
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$ autoreconf -i
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$ ./configure
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$ make
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$ su -
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$ make install
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== Installing from a released source tarball ==
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$ tar xzvf snp-sites-1.0.tar.gz
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$ cd snp-sites-1.0
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$ ./configure
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$ make
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$ su -
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$ make install
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# Installation
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There are a few ways to install snp-sites. The simpliest way is using apt (Debian/Ubuntu), HomeBrew (OSX) or LinuxBrew.
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## Linux - Ubuntu/Debian
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If you have a recent version of Ubuntu or Debian then you can install it using apt.
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apt-get install snp-sites
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## Linux - CentOS/RHEL
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The easiest way to install on CentOS/RHEL is to use [LinuxBrew](http://brew.sh/linuxbrew/). Enable EPEL and make sure compilers are installed.
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```
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sudo yum install epel-release gcc gcc-c++ automake ruby-irb
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```
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Install [LinuxBrew](http://brew.sh/linuxbrew/).
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```
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brew tap homebrew/science
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ln -s $(which gcc) ~/.linuxbrew/bin/gcc-4.4
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ln -s $(which g++) ~/.linuxbrew/bin/g++-4.4
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brew install snp-sites
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```
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## Linux - using LinuxBrew
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Install [LinuxBrew](http://brew.sh/linuxbrew/).
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```
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brew tap homebrew/science
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brew install snp-sites
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```
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## OSX - using HomeBrew
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Install [HomeBrew](http://brew.sh/). It requires a minimum of Xcode 5.1.1 (xcodebuild -version). Then run:
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```
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brew tap homebrew/science
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brew install snp-sites
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```
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## OSX/Linux - from source
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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 HomeBrew/LinuxBrew 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).
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```
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autoreconf -i -f
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./configure
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make
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sudo make install
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```
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## OSX/Linux - from a release tarball
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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 HomeBrew/LinuxBrew instead. First install a standard development environment (e.g. gcc, automake, autoconf, libtool).
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```
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tar xzvf snp-sites-x.y.z.tar.gz
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cd snp-sites-x.y.z
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./configure
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make
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sudo make install
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```

‎README.md‎

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### Relaxed Phylip format
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All the SNP sites in a format for RAxML and other tree building applications.
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# Installation
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There are a few ways to install snp-sites. The simpliest way is using apt (Debian/Ubuntu), HomeBrew (OSX) or LinuxBrew.
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## Linux - Ubuntu/Debian
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If you have a recent version of Ubuntu or Debian then you can install it using apt.
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apt-get install snp-sites
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## Linux - CentOS/RHEL
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The easiest way to install on CentOS/RHEL is to use [LinuxBrew](http://brew.sh/linuxbrew/). Enable EPEL and make sure compilers are installed.
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```
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sudo yum install epel-release gcc gcc-c++ automake ruby-irb
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```
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Install [LinuxBrew](http://brew.sh/linuxbrew/).
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```
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brew tap homebrew/science
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ln -s $(which gcc) ~/.linuxbrew/bin/gcc-4.4
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ln -s $(which g++) ~/.linuxbrew/bin/g++-4.4
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brew install snp-sites
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```
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## Linux - using LinuxBrew
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Install [LinuxBrew](http://brew.sh/linuxbrew/).
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```
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brew tap homebrew/science
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brew install snp-sites
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```
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## OSX - using HomeBrew
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Install [HomeBrew](http://brew.sh/). It requires a minimum of Xcode 5.1.1 (xcodebuild -version). Then run:
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```
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brew tap homebrew/science
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brew install snp-sites
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```
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## OSX/Linux - from source
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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 HomeBrew/LinuxBrew 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).
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```
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autoreconf -i -f
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./configure
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make
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sudo make install
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```
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## OSX/Linux - from a release tarball
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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 HomeBrew/LinuxBrew instead. First install a standard development environment (e.g. gcc, automake, autoconf, libtool).
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```
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tar xzvf snp-sites-x.y.z.tar.gz
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cd snp-sites-x.y.z
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./configure
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make
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sudo make install
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```
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