AmpliconRepository

Authors: Forrest Kim, Jens Luebeck, Ted Liefeld, Edwin Huang, Thorin Tabor, Vineet Bafna

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This is the main repository for the AmpliconRepository. Currently in development.

How to set up the development server for AmpliconRepository

Requirements

• Anaconda (https://www.anaconda.com/products/distribution)

1. Clone the repository from GitHub

• Clone repo using https, ssh, or GitHub Desktop to your local machine

2. Set up the virtual environment and install packages:

• In a terminal window, move to the cloned Github repo
• Go to the caper top level directory (should see environment.yml and requirements.txt)
• Create a new Anaconda environment:

conda env create -f environment.yml

• Activate the new environment (you need to do this everytime before running the server):

conda activate caperenv

3. Set up MongoDB locally (for development)

• If you don't have a database location set up, set up a location:

mkdir ~/data/db/

• In a terminal window or tab with the caperenv environment active, run MongoDB locally:

mongod --dbpath ~/data/db or mongod --dbpath <DB_PATH>

3a. View MongoDB data in MongoDB Compass (Optional)

• Download MongoDB Compass: https://www.mongodb.com/docs/compass/current/install/#download-and-install-compass
• Open the MongoDB Compass app after starting MongoDB locally
• Connect to your local instance of MongoDB:

URI: mongodb://localhost:27017

• Relevant data will be located in /caper/projects/

4. Set up secret keys for OAuth2

• Open a terminal window or tab with the caperenv environment active
• Make sure you have the config.sh file from another developer (this contains secret key information)
• Run the command to initialize variables: source config.sh

5. Run development server (Django)

• Open a terminal window or tab with the caperenv environment active
• Move to the caper App folder (should see manage.py)
• Run the server locally:

python manage.py runserver

• Open the application on a web browser (recommend using a private/incognito window for faster development):

https://localhost:8000