madprime / django-get-evidence

Django rewrite of GET-Evidence

django-get-evidence

Welcome to Madeleine's Django rewrite of GET-Evidence, a work in progress. This is a project to recreate the functionality of the current GET-Evidence, hosted at evidence.personalgenomes.org with code available at github.com/PersonalGenomeProject/get-evidence.

Installation

These instructions were written for Ubuntu Linux (since that's what I use). If you use another system, please go ahead and submit modifications to this file to describe alternate instructions. Thanks!

Clone the Git repository

• Navigate to the directory you want to have the code in, and clone the repository with: git clone git://github.com/madprime/django-get-evidence.

Install postgres, pip, virtualenv, and virtualenvwrapper

1. (Root user action) Install Postgres with: sudo apt-get install postgresql
2. (Root user action) Install pip: sudo apt-get install python-pip
3. (Root user action) Use pip to install virtualenv and virtualenvwrapper: sudo pip install virtualenv virtualenvwrapper.

Set up virtualenv and virtualenvwrapper

1. Make a directory to store your virtual environments: mkdir ~/.virtualenvs
2. To make virtualenv and virtualenvwrapper commands work in future terminals, add the following to your bashrc (or zshrc, as appropriate): export WORKON_HOME=$HOME/.virtualenvs and source /usr/local/bin/virtualenvwrapper.sh.

Make a virtual environment and install required Python packages

If you open a new terminal you should now be able to access the virtualenvwrapper commands listed below.

If you aren't familiar with pip and virtualenv: these are standard aspects of Python development, greatly facilitating package management. Whenever working on this software you should do so within the virtual environment (e.g. after performing step 2 below).

1. Create a new virtual environment for working on this code: mkvirtualenv getevidence
2. Start using this virtual environment: workon getevidence
3. Navigate to top directory in this project. (One of the subdirectories should be "requirements".) Install the Python packages required for development with pip install -r requirements/dev.txt.

Create and initialize database

1. (Postgres user action) Create a new Postgres user with: sudo -i -u postgres createuser getevidence -P with the password: glassworks. (This password a placeholder and is stored in the current settings, developing a real password is a TODO.) You should answer "n" to superuser, "y" to creating databases, and "n" to creating new roles.
2. (Postgres user action) Create a getevidence database with: sudo -i -u postgres createdb -O getevidence getevidence
3. Navigate to the django-get-evidence/getevidence/. Run python manage.py syncdb. You should probably create a superuser account for admin; set it to whatever you wish.
4. Add gene data by running: python manage.py add_external_gene_data ../external_data/getevidence_external_gene_data.csv
5. (Optional) Add sample data by running python manage.py sample_data.

Run server

• You can now run a local version with python manage.py runserver