Quick install

Requirements

VirtualMicrobes can be installed on a LINUX machine (tested on Ubuntu 16.04), and also functions fully on Ubuntu for Windows. We highly recommend installing it using a virtual python environment, which ensures all dependencies (and their version) do not conflict and break your current python projects 😉

Installation

Before you begin, make sure you have 1) python2.7, 2) numpy and 3) virtualenv installed, and 3) libgsl-dev installed

To install libgsl-dev, run:
sudo apt-get install libgsl-dev

Installation
From top to bottom: clone the code from bitbucket, make a virtual environment, activate it, and use pip to install virtualmicrobes in developer mode (-e), run it

user@computer: git clone -b develop https://thocu@bitbucket.org/thocu/virtual-microbes.git
user@computer: virtualenv ~/mypy --system-site-packages
user@computer: source ~/mypy/bin/activate
(mypy) user@computer: pip install -e virtual-microbes
(mypy) user@computer: virtualmicrobes.py evo --name MyFirstMicrobes

Trouble shooting

Trouble shooting:
Q: When I type virtualmicrobes.py it says ‘file not found’
Did pip install VirtualMicrobe run without errors? Does ‘which virtualmicrobes.py’ give a path to your virtual environment? Did you activate
your local environment (mypy in the above examples)
Q: I tried to use an option, but it says it doesn’t recognize it
General options (virtualmicrobes.py –help) go BEFORE the keyword evo, while other options go AFTER evo. If you use keyword options (such as mutation-rates) makes sure to include a dummy argument (-) before evo so it knows no more mutation-rates follow:
virtualmicrobes.py –mutation-rates point_mutation=0.8 tandem_dup=0.8 stretch_del=0.8 stretch_invert=0.8 stretch_translocate=0.8 – evo
–name Rediculous_Mutation_Rates