Installing and Running AltAnalyze via pip install

Requirements

• python 2.7 (not compatible with python 3+)
• Tkinter (Ubuntu users may not have by default)
• setup tools install (pip command)
• 5GB free hard-disk space

Installation

pip install altanalyze

Notes: * iGraph compatibility: See the igraph homepage for help. * pysam support: Pysam on Windows is not currently supported via the PyPi installer. Find the binary windows installer if you are processing BAM files. * Installation on Ubuntu: 1. Ensure all Ubuntu updates have been installed 1. Install Tkinter: apt-get install python-tk (restart after) 1. Install setuptools: sudo apt-get install python-setuptools

Running AltAnalyze

Graphical User Interface: type altanalyze and return on the command-prompt

Command-line Arguments: type altanalyze followed by appropriate command-line arguments. Example: altanalyze --update Official --species Sc --platform RNASeq --version EnsMart72