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
.
- Download: http://etetoolkit.org/download/
ete3 has its own dependency on pyqt.
Matplotlib¶
Used for generating various plots during the simulation.
- Download: http://matplotlib.sourceforge.net/
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.
- Download: http://http://cython.org/#download
- Download: https://github.com/twiecki/CythonGSL (follow the
build
andinstall
instructions in the README)