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remove homebrew
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@andrewjpage
andrewjpage committed Jan 12, 2018
1 parent 8a75d3e commit de698c6
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37 changes: 3 additions & 34 deletions INSTALL
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@@ -1,10 +1,7 @@
# Installation
There are a few ways to install snp-sites. The simpliest way is using apt (Debian/Ubuntu), Conda, HomeBrew (OSX) or LinuxBrew.
There are a few ways to install snp-sites. The simpliest way is using apt (Debian/Ubuntu) or Conda.

* Linux - Ubuntu/Debian
* Linux - CentOS/RHEL
* Linux - using LinuxBrew
* OSX - using HomeBrew
* OSX/Linux - using Bioconda
* OSX/Linux - from source
* OSX/Linux - from a release tarball
Expand All @@ -15,33 +12,6 @@ If you have a recent version of Ubuntu or Debian then you can install it using a
apt-get install snp-sites
```

## Linux - CentOS/RHEL
The easiest way to install on CentOS/RHEL is to use [LinuxBrew](http://brew.sh/linuxbrew/). Enable EPEL and make sure compilers are installed.
```
sudo yum install epel-release gcc gcc-c++ automake ruby-irb
```
Install [LinuxBrew](http://brew.sh/linuxbrew/).
```
brew tap homebrew/science
ln -s $(which gcc) ~/.linuxbrew/bin/gcc-4.4
ln -s $(which g++) ~/.linuxbrew/bin/g++-4.4
brew install snp-sites
```

## Linux - using LinuxBrew
Install [LinuxBrew](http://brew.sh/linuxbrew/).
```
brew tap homebrew/science
brew install snp-sites
```

## OSX - using HomeBrew
Install [HomeBrew](http://brew.sh/). It requires a minimum of Xcode 5.1.1 (xcodebuild -version). Then run:
```
brew tap homebrew/science
brew install snp-sites
```

## OSX/Linux - using Bioconda
Install Conda and install the bioconda channels.
```
Expand All @@ -52,9 +22,8 @@ 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 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).
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
Expand All @@ -64,7 +33,7 @@ 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 HomeBrew/LinuxBrew instead. First install a standard development environment (e.g. gcc, automake, autoconf, libtool).
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
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43 changes: 3 additions & 40 deletions README.md
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Expand Up @@ -62,52 +62,19 @@ This contains the position of each SNP in the reference sequence, and the occurr
All the SNP sites in a format for RAxML and other tree building applications.

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

* Linux - Ubuntu/Debian
* Linux - CentOS/RHEL
* Linux - using LinuxBrew
* OSX - using HomeBrew
* OSX/Linux - using Bioconda
* OSX/Linux - from source
* OSX/Linux - from a release tarball
* Windows/OSX/Linux - using a Virtual Machine
* Windows/OSX/Linux - using Docker


## 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
```

## Linux - CentOS/RHEL
The easiest way to install on CentOS/RHEL is to use [LinuxBrew](http://brew.sh/linuxbrew/). Enable EPEL and make sure compilers are installed.
```
sudo yum install epel-release gcc gcc-c++ automake ruby-irb
```
Install [LinuxBrew](http://brew.sh/linuxbrew/).
```
brew tap homebrew/science
ln -s $(which gcc) ~/.linuxbrew/bin/gcc-4.4
ln -s $(which g++) ~/.linuxbrew/bin/g++-4.4
brew install snp-sites
```

## Linux - using LinuxBrew
Install [LinuxBrew](http://brew.sh/linuxbrew/).
```
brew tap homebrew/science
brew install snp-sites
```

## OSX - using HomeBrew
Install [HomeBrew](http://brew.sh/). It requires a minimum of Xcode 5.1.1 (xcodebuild -version). Then run:
```
brew tap homebrew/science
brew install snp-sites
```

## OSX/Linux - using Bioconda
Install Conda and install the bioconda channels.
```
Expand All @@ -118,9 +85,8 @@ 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 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).
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
Expand All @@ -130,7 +96,7 @@ 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 HomeBrew/LinuxBrew instead. First install a standard development environment (e.g. gcc, automake, autoconf, libtool).
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
Expand All @@ -140,8 +106,5 @@ make
sudo make install
```

## Windows/OSX/Linux - using a Virtual Machine
A virtual machine (VM) is available containing the software. More details can be found on [the Pathogen VM page](http://sanger-pathogens.github.io/pathogens-vm/).

## 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

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