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INSTALL.txt
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INSTALL.txt
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This software was tested on:
Operating systems: Ubuntu 14+, Debian 8, Windows 10
Environment: Python 2.7.X, Python 3.4+
Untested platforms/Upcoming support: MacOS
We strongly recommend running MotifGP under Ubuntu/Debian using python2.7+.
Core development is focused on Python2.7 as it is still the most popular version of Python to this date.
Support for Python3 and Windows is added for convinience, but we cannot guarantee optimal performance under non-Ubuntu/Debian and python2 systems.
We welcome any feedback that would help further cross-platform support. Please contact Manuel Belmadani <[email protected]> for support.
The code can be converted to Python3 using the 2to3 tool.
Command:
$ 2to3 --output-dir=motifgp_python3 -W -n motifgp/
=======================================================================================
INSTALL INSTRUCTIONS:
=======================================================================================
INSTALLING PYTHON 2.7
For Windows: Skip right to the Windows MotifGP installation as Python2.7 comes with miniconda.
For Unix systems: If you already have Python2.7, you can skip this step. You can find your default python version by typing:
Code:
$ python -V
> Python 2.7.10
If you get a version below Python2.7, please install a new version.
If python is already installed on your operating system, you should also have a version of Python2.x and Python3.x installed. try
Code:
$ python2 -V
or
$ python3 -V
And use python2 or python3 instead of python when following these instructions. If you install a package under python2, you will need to install it under python3 if you wish to use this version.
Python 2.7 is important for the fisher's exact test function provided by the scipy package. If your version of python is older than 2.7, you can install a local version:
-Download a version from Python.org (for example, https://www.python.org/ftp/python/2.7.11/Python-2.7.11.tgz)
Assuming Python-2.7.11,
Code:
$ tar zxf Python-2.7.11.tgz
$ cd Python-2.7.11
$ ./configure
$ make altinstall prefix=~ exec-prefix
$ cd ~/bin
$ ln -s python2.7 python
$ export PATH="/home/<YOURUSERNAME>/bin/:$PATH"
To make this python interpreter the default python interpreter, add
export PATH="/home/<YOURUSENAME>/bin/:$PATH"
to your ~/.bashrc file.
=======================================================================================
INSTALLING MotifGP
=======================================================================================
==============
= Linux =
==============
You can install all necessary packages through the python package manager pip. If you don't have the pip, install it by downloading the get-pip.py install script.
Code:
$ wget https://bootstrap.pypa.io/get-pip.py
$ python get-pip.py
Note that to get pip for python3, you will have to run python3 get-pip.py, and use "pip3" instead of "pip".
Install numpy:
$ pip install --user numpy
Install deap:
$ pip install --user deap
Install scipy (Optional, but required for scipy-based objectives)
$ pip install --user scipy
Test that MotifGP works:
$ python motifgp.py -h
Usage: motifgp.py [options]
Options:
(... list of program options ...)
Additional tests can be ran with the nosetests library
$ nosetests
(... runs tests. They *should* all pass ...)
================
= Windows =
================
The simplest way to install the dependencies on Windows is through the Anaconda/Miniconda Python distributions (http://conda.pydata.org/miniconda.html).
It includes Python, and makes it easy to install numpy, scipy, pip and deap without having to download additional build tools.
Install miniconda (a lightweight version of the Anaconda Python distribution.)
- If you don't already have Python, the graphical install will set its python binary as the default version
- If you do have Python, then the system will ask you if you want to make this the default Python through the PATH variable.
-- If you don't want to replace your existing Python by Anaconda's, just call Python, conda, and pip through:
C:\Users\<Your username>\Miniconda2\python
C:\Users\<Your username>\Miniconda2\Scripts\pip
C:\Users\<Your username>\Miniconda2\Scripts\conda
Install numpy:
> conda install numpy
Install scipy (Optional, but required for scipy-based objectives):
> conda install scipy
Install deap:
> pip install deap
Test that MotifGP works:
> python motifgp.py -h
Usage: motifgp.py [options]
Options:
(... list of program options ...)
=======================================================================================
USING MotifGP
=======================================================================================
- USAGE INSTRUCTIONS
See README.txt, EXAMPLES.txt