This page was last updated on Sunday, 16-Nov-2014 14:19:55 CST

Installation notes for fastStructure version 01e0183829 Nov. 13, 2014

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Prerequisites

• Numpy
  
  1. $ sudo apt-get install python-numpy
• Scipy
  
  1. $ sudo apt-get install python-scipy
• Cython
  
  1. $ sudo apt-get install cython
• GNU Scientific Library
  
  1. $ sudo apt-get install libgsl0-dev
• matplotlib
  
  1. $ sudo apt-get install python.matplotlib

Installation

1. $ cd /usr/local/bin/
2. $ git clone https://github.com/rajanil/fastStructure
3. $ cd fastStructure/vars
4. $ python setup.py build_ext --inplace
5. $ cd ..
6. $ python setup.py build_ext --inplace
7. Test
   $ python structure.py

   Here is how you can use this script
   
   Usage: python structure.py
   	 -K 
   	 --input=
   	 --output=
   	 --tol= (default: 10e-6)
   	 --prior={simple,logistic} (default: simple)
   	 --cv= (default: 0)
   	 --format={bed,str} (default: bed)
   	 --full (to output all variational parameters; optional)
   	 --seed= (optional)

8. None of the python scripts are executable. I made them all executable with
   $ for f in *.py ; do sed -i '1i#!/usr/bin/env python' "$f" ; chmod +x "$f" ; done
9. Then add this directory to the default PATH for all users
   $ sudo nano /etc/profile
   …
   PATH="$PATH:/usr/local/bin/fastStructure"
   …