Spormann Lab:Protocols:InstallBiopython

• • Instructions for downloading and getting Biopython installed so you can do bioinformatics!

by Jess Grembi 23 Apr 2014

1. Install XCode - a program for developers to create apps for Mac ::

Download from (https://itunes.apple.com/us/app/xcode/id497799835?ls=1&mt=12)

Install XCode via normal install instructions

Install optional Command Line tool package

Open XCode

Open Preferences

Click on the Downloads icon

Install the Command Line Tools

2. Install Python (Already installed on the Mac, but you can upgrade to the latest version, if wanted)

3. Install NumPy - Numerical Python, a fundamental package for scientific computing with Python

Download the latest 'tar.gz' file from (http://sourceforge.net/projects/numpy/files/NumPy/)

Move NumPy into your user home directory

Open a terminal window make sure you are in your home directory and then type:

tar -zxvf numpy-1.8.1.tar.gz [This opens/unzips the tar file, you might need to change the 1.8.1 to reflect the version number from the file you downloaded]

cd numpy-1.8.1/ [This changes your working directory to the NumPy folder that was just unzipped]

python setup.py build

sudo python setup.py install [you need the 'sudo' at the beginning if your computer is password protected for installing new programs, remove 'sudo' if there are not restrictions on uploading to your machine]

*If password protected, you will be prompted for your password next*

Test to ensure it installed correctly. Type the following into the terminal command line:

python

import numpy [Note: NumPy is all lowercase in the command line!]

4. Install BioPython - tools for biological computation/ bioinformatics written in Python

Download the latest 'tar.gz' file from http://biopython.org/wiki/Download

Move BioPython into your user home directory

Type the following into the terminal window:

tar -zxvf biopython-1.63.tar.gz [This opens/unzips the tar file. Again, you might need to change the 1.8.1 to reflect your version number]

cd biopython-1.63 [Change your working directory to the new unzipped folder]

python setup.py build

python setup.py test

sudo python setup.py install [Again, 'sudo' not needed unless installing is password protected]

*If password protected, you will be prompted for your password next*