 
1. Requirements:
	sudo apt-get install \
		python-dev \
		python-setuptools \
		python-mysqldb \
		python-networkx \
		python-nose \
		python-lxml \
		sloccount \
		muscle;
	sudo easy_install poster;  # For Life Science Grid Portal 
	sudo easy_install coverage;
	sudo easy_install pylint;
		
	#BioPython
	sudo apt-get build-dep python-biopython; # Ubuntu 12.04 Precise has v1.58, which is fine 
	#Download & install 1.54 <= biopython

	#Other software
	MCL
	OrthoMCL
	NCBIBlast+
	TranslatorX
	PAML
	PHYLIP
	Galaxy
	
	#Galaxy plotting requirements
	sudo apt-get install \
	   python-gnuplot \
	   python-rpy;
	   
## Run requirements ##
# Galaxy
sudo apt-get install mercurial subversion
sudo apt-get install postgresql-client
# plotting requirements
sudo apt-get install python-gnuplot python-rpy;

# Python packages
sudo apt-get install python-biopython  # For sequence wrangling
sudo apt-get install python-lxml  # For download from MRS
sudo apt-get install python-mysqldb  # For OrthoMCL
sudo apt-get install python-poster  # For Life Science Grid Portal
sudo apt-get install python-networkx  # For drawing Phylo trees

# OrthoMCL
sudo apt-get install libdbd-mysql-perl

# TranslatorX
sudo apt-get install muscle

# Other software
MCL
NCBIBlast+
PAML
PHYLIP


## Build requirements ##
sudo apt-get install \
	python-dev \
	python-setuptools \
	python-nose \
	sloccount;

sudo easy_install coverage;
sudo easy_install pylint;

Update readme with additional requirements, and separation between run and dev reqs
Update readme with additional requirements, and separation between run and dev reqs

