Quickstart

The first execution could require several minutes, from the second one will be faster.

1 - Clone the repository:

$ git clone https://github.com/next-crs4/VariantAlert.git

2 - Cd into the docker directory:

$ cd VariantAlert

Local/Develop Environment

3 - Bring up the VariantAlert app

$ make EMAIL_HOST=smtp.yourserver.com \
    EMAIL_USER=your@yourserver.com \
    EMAIL_PASSWORD=your-email-account-password \
    EMAIL_PORT=your-server-port \
    HOST=0.0.0.0 \
    BATCH_SIZE=25 \
  start-local

4 - Point your browser to: http://0.0.0.0:8000

Production Environment (with SSL Certificate)

Put/link your SSL certificates in ./config/ssl/

./config/ssl/privkey.pem
./config/ssl/fullchain.pem

3 - Bring up the VariantAlert app

$ make EMAIL_HOST=smtp.yourserver.com \
    EMAIL_USER=your@yourserver.com \
    EMAIL_PASSWORD=your-email-account-password \
    EMAIL_PORT=your-server-port \
    HOST=your-variantalert-site.com \
    BATCH_SIZE=25 \
  start-prod

4 - Point your browser to: https://your-variantalert-site.com

Other commands

Bring down the VariantAlert app

$ make stop

From the second execution

$ make start-local

Remove VariantAlert app from your machine

$ make clean

Print the help message

$ make help

===================================================================================================

 VariantAlert - a tool to notify updates in genetic variant annotations
 https://github.com/next-crs4/VariantAlert
 
 Please use `make [options] <target>` where <target> is one of
                start-local             bring up the variant-alert app in your local/develop environment (0.0.0.0)
                start-prod              bring up the variant-alert app in production environment (with ssl)
                stop                    bring down the variant-alert app
                clean                   remove the variant-alert app from your computer
 
 options:
        VARIANT_ALERT_ROOT              deployment path (default: ~/variant-alert)
        EMAIL_HOST                      email host server (default: smtp.yourserver.com)
        EMAIL_USER                      email username (default: your@yourserver.com)
        EMAIL_PASSWORD                  email password (default: your-email-account-password)
        HOST                            variant alert host (default: 0.0.0.0)
        BATCH_SIZE                      number of variants for batch (default: 25)
                                        set zero to have no limitations
 
 variant-alert will be deployed into ~/variant-alert
 To set a different path, digit: 
  make VARIANT_ALERT_ROOT=/your/path [options] start-*
  
 Remember to configure your EMAIL_HOST: 
        make  EMAIL_HOST=smtp.yourserver.com \
              EMAIL_USER=your@yourserver.com \
              EMAIL_PASSWORD=your-email-account-password [options] start-*
  
 For production environment, configure HOST
        make    HOST=example.com [options] start-*
 
 Docs: https://next-crs4.github.io/VariantAlert