Something I realized when I began to work with the command line is that there are few extra additions that can be installed to make everything run smoothly within the terminal (Mac OSX 10.9).
1. Xcode 5.0 – This is an integrated development environment made by Apple Developer that provides a nice space to write and debug code. More importantly is that Xcode contains Command Line Tools that needed to properly compile and install packages you make need in the future. Note that you may need to have an Apple Developer ID to access the download site
5. Python – Python is a programming language extremely good at handling sequence data. Most Macs are already setup to use python version 2.7. To test if you have python simply open the terminal and type “python”