Installing

Before installing VirtualMicrobes, you need to have setuptools installed.

Quick install

Get VirtualMicrobes from the Python Package Index at http://pypi.python.org/pypi/VirtualMicrobes

or install it with

pip install VirtualMicrobes

and an attempt will be made to find and install an appropriate version that matches your operating system and Python version.

The project can be cloned from bitbucket with:

git clone https://thocu@bitbucket.org/thocu/virtualmicrobes.git

Requirements

Installing the project via pip, the required packages will be checked against your installation and installed if necessary.

Python

To use VirtualMicrobes you need Python 2.7

ete3

This is a package for drawing and manipulating phylogenetic trees. It is used to keep track of phylogenetic relationships between Virtual Microbes.

ete3 has its own dependency on pyqt.

Matplotlib

Used for generating various plots during the simulation.

Gnu Scientific Library

Other

  • networkx
  • attrdict
  • blessings
  • networkx
  • pandas
  • psutil
  • errand_boy
  • orderedset
  • pyparsing
  • setproctitle
  • sortedcontainers
  • mpl

Optional packages

Cython and CythonGSL

The package includes a few C Extension modules, originally written in the Cython language. If during the install both Cython and the CythonGSL package are detected, the extensions will be build from the original .pyx sources. Otherwise, the included pre-generated .c files will be used to build the extension.