README.md

MyGene.info

Description

MyGene.info is a web API for accessing gene annotation information (Gene Annotation Query as a Service). MyGene.info is part of BioThings API collection, together with MyVariant.info, MyChem.info and more.

For more information see this reference:

Xin J, Mark A, Afrasiabi C, Tsueng G, Juchler M, Gopal N, Stupp GS, Putman TE, Ainscough BJ, Griffith OL, Torkamani A, Whetzel PL, Mungall CJ, Mooney SD, Su AI, Wu C. High-performance web services for querying gene and variant annotation. Genome Biol. 2016 May 6;17(1):91. doi: 10.1186/s13059-016-0953-9. https://www.ncbi.nlm.nih.gov/pubmed/27154141

Setup Mygene.info Web Server Locally

1. Prerequisites

python (>=3.4)
git 

In Ubuntu/Debian system, you can install all prerequisites by

sudo apt-get install python-dev python-setuptools git 

2. Clone this repo:

git clone https://github.com/biothings/mygene.info.git

3. Setup a Python "virtualenv" (optional, but highly recommended):

sudo easy_install pip
sudo pip install virtualenv

virtualenv ~/opt/devpy

4. Install required python modules:

pip install -r ./requirements_web.txt

5. Make your own "config.py" file

cd src
vim config.py

from config_web import *
from config_hub import *
# And additional customizations

6. Run your dev server

python index.py --debug

or

python index.py --debug --port=9000