Software - lcoghill/phyloboost GitHub Wiki

• Python 2.7
• Numpy
• Sci-py
• Matplotlib
• Biopython
• IVY
• Muscle
• RAxML
• BLAST+
• vsearch
• Git
• Graph-tool

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These steps will show you how to get the needed requirements installed for a Debian / Ubuntu based Linux distribution.

• Python 2.7

$ sudo apt-get install python python-setuptools python-dev

• Git

$ sudo apt-get install git

• Numpy

$ sudo apt-get install numpy

• Sci-py

$ sudo apt-get install scipy

• Matplotlib

$ sudo apt-get install python-matplotlib

• Biopython

$ sudo apt-get install python-biopython python-biopython-doc

• MUSCLE

$ sudo apt-get install muscle

• RAxML

$ sudo apt-get install raxml

• Blast+

$ sudo apt-get install ncbi-blast+

• IVY

$ git clone https://github.com/rhr/ivy
$ cd ivy
$ sudo python setup.py install

• VSEARCH

cd ~
mkdir -p bin
cd ./bin/
wget https://github.com/torognes/vsearch/releases/download/v1.1.3/vsearch-1.1.3-linux-x86_64
ln -s vsearch-1.1.3-linux-x86_64 vsearch
***


#### Mac OS X Install Guide
These steps will show you how to get the needed software dependencies installed for Mac OS X. It can be a little tricky on OS X. MacOS X does not include integrated package management with automated dependency tracking, which means that the dependencies would have to be installed individually by hand. Instead we strongly recommend using a third-party package management system like [MacPorts](http://www.macports.org/).

* XCode
Install from the [MacApp Store](http://itunes.apple.com/us/app/xcode/id497799835)

• MacPorts

Install the correct [Package](https://www.macports.org/install.php) for your system.
$ sudo port selfupdate

• Python 2.7

$ sudo port install python27
$ port select --set python python27

• Git

Download and install the latest [Git package](http://git-scm.com/download/mac)

• Numpy

$ sudo port py27-numpy

• Sci-py

$ sudo port py27-scipy

• Matplotlib

$ sudo port py27-matplotlib

• Biopython

$ sudo port py27-biopython

• MUSCLE

Download [MUSCLE](http://www.drive5.com/muscle/downloads.htm) to a location of your choosing.
$ tar -xvf muscle3.8.31_i86darwin64.tar.gz
$ nano ~/.profile
$ export PATH=/Users/YourName/muscle3.8.31_i86darwin64/bin:${PATH}
Add MUSCLE to your path so the python wrappers can find it.

• RAxML

$ sudo port install raxml

• Blast+

Download Blast+ from NCBI.
$ tar -xvf blast-2.2.22-universal-macosx.tar.gz
$ mv blast-2.2.22 ~/
$ nano ~/.profile
$ export PATH=/Users/YourName/blast-2.2.22/bin:${PATH}

• IVY

$ git clone https://github.com/rhr/ivy
$ cd ivy
$ sudo python setup.py install

• VSEARCH

Download [https://github.com/torognes/vsearch/blob/master/bin/vsearch-1.1.3-osx-x86_64](https://github.com/torognes/vsearch/blob/master/bin/vsearch-1.1.3-osx-x86_64)