Local installation of LocusFocus

LocusFocus may be cloned from the GitHub repository and run as a local webserver in Mac or Linux distributions.

The GTEx database, and 1000 Genomes PLINK files are optional. GTEx may be built using the initdb_GTExV7.py and initdb_GTExV8.py scripts. The script pushes GTEx eQTL summary statistics into a NoSQL MongoDB database.

The app has been tested in Linux and Mac environments. For Windows, you may use the Windows Subsystem for Linux (WSL) to emulate a Linux environment. The app has been tested using the Ubuntu WSL system.

All required programs and packages are listed in a yml file and a conda spec file are also available for direct explicit installation of the exact conda virtual environment the app requires for a successful run.

To clone and install the required packages, simply run:

Clone and install required conda environment
> git clone https://github.com/naim-panjwani/LocusFocus.git
> conda create --name <env> --file spec-file.txt

Next, to run the application locally, simply run the app.py script:

Run the app
> python app.py

The above command will issue a web address to access the application locally. Simply type the address given in your browser.