Gene Lookup for denovo mutations in a set of studies.
First, clone the repository:
git clone https://github.com/michaelchess/gene-lookup [directory you want the code to go in]
And cd to the new directory:
cd [directory you said]
Now, create a new virtualenv, which allows us to install the same versions of python packages that Michael used, isolated away from the rest of your computer.
virtualenv env
This should create a new directory "env". Now activate the virutal environment:
source env/bin/activate
Your prompt should now start with (env), for example (env)Brett-Thomas:gene-lookup bt$
Okay, now time to actually install those packages:
pip install -r requirements.txt
One of the packages, rpy, requires R to be installed.
This is easy if you have a Mac, but first you have to install Homebrew
Do that, then:
brew install R
If that doesn't work, you're probably missing a recursive dependency, the GCC compiler. This bizarrely isn't preinstalled on mac os. Install XCode through the Mac App Store, then install Command Line Tools Here are some instructions
Okay - at this point pip install -r requirements.txt should run without error. If it does, you can run the site:
python GeneLookup.py
And check it out in your browser:
http://localhost:5000/
Win!
As a side note, this process could be totally skipped if we used a Vagrant virtual machine - but that poses its own challenges, so I think this is a good middle ground for now.