Eaton edited this page Jan 15, 2019 · 1 revision

Installing and Running AltAnalyze via pip install


  • 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


pip install altanalyze


  • 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
    2. Install Tkinter: apt-get install python-tk (restart after)
    3. 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

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