P*R*O*P

Prerequisites

• Docker & docker-compose
  • https://www.digitalocean.com/community/tutorials/how-to-install-and-use-docker-on-ubuntu-18-04
  • https://www.digitalocean.com/community/tutorials/how-to-install-docker-compose-on-ubuntu-18-04
• npm
  • curl -sL https://deb.nodesource.com/setup_12.x | sudo -E bash -
  • sudo apt install nodejs

Installation

Backend

1. Pull this repo
2. cd PROP
3. sudo ./dc_script.sh Optional
4. Delete Angular Frontend Docker container if debugging is not needed.

  docker stop prop_frontend_1
  docker rm prop_frontend_1

Frontend (static)

1. Pull this repo

2. cd PROP

3. cd frontend

4. sudo npm install

5. copy/paste frontend/src/app/envDummy.json to frontend/src/app/env.json

6. In frontend/src/app/env.json, set "local_flag":"2" --> in that case, API Gateway endpoint is used instead of localhost

7. cd ../.. (so that you are in the folder frontend)

8. npx ng build --prod --output-path ../docs --base-href /bioinformatics/prop/

9. In frontend/src/app/header/header.component.html change src="/assets/canal_logo.svg" to src="/bioinformatics/prop/assets/canal_logo.svg"

10. open header.component.html

• Change from ../../assets/canal_logo.svg to /bioinformatics/prop/assets/canal_logo.svg

11. Host the docs folder on a hosting platform

local debugging

1. Pull this repo
2. cd PROP
3. copy/paste frontend/src/app/envDummy.json to frontend/src/app/env.json
4. create .env with BACKEND_APIKEY=DUMMY
5. sudo ./dc_script.sh
6. wait for the script to finish
7. open the website on https://localhost:4200/

How to update

MAFFT / ClustalW variables

• array length and count variables can be set in ./.env.fixedVariables
  • can set:
    • MAFFT array length & count
    • ClustalW array length & count

frontend only

1. sudo ./dc_script.sh --frontend-only

backend only

1. sudo ./dc_script.sh --backend-only

re-build / update everything

1. Rebuild: sudo ./dc_script.sh

Usage via browser

• local environment: https://localhost:4200/

• static hosting: domain provided by the hosting platform

This software is released under the MIT License, see LICENSE.txt.