LANL-Bioinformatics/phame-app

Phame App

This Dockerized application contains all of the code you need to run PhaME as a standalone app. It has containers for the PhaME application, the web interface, Celery and Redis queues and a PostGREs database.

Step by step guide to running PhaME using a web interface on a local machine.

Docker and git are required.

1. clone the repo

   git clone git@github.com:LANL-Bioinformatics/phame-app.git

2. cd to the project root directory phame-app

   cd phame-app

3. run cp .envs/.local/.postgres_template phame-app/.envs/.local/.postgres and cp .envs/.local/.email_template phame-app/.envs/.local/.email.
   Edit the .postgres file and change the values for POSTGRES_USER and POSTGRES_PASSWORD

4. Create docker containers.

   docker-compose -f docker-compose-local.yml build

5. start docker

   docker-compose -f docker-compose-local.yml up -d

6. initialize the database.

   docker-compose -f docker-compose-local.yml run --rm web /bin/bash -c "python -c 'import database; database.init_db()'"

If all went well, you can go to localhost to see the phame webpage.

Step by step guide to running PhaME using a web interface on a production machine.

The user input files can require a lot of storage space. Use these instructions if you want to store the users' data on a data volume that is different from the main volume where the Docker container is created.

Go through steps 1-3 as for the local installation and then:

1. Run mkdir -p /path/to/api/uploads

2. Update paths in docker-compose-production.yml to the volume where you want to store the users' upload files for the phame and web containers.

   phame:
       volumes:
         - phame_data:/phame_api/media
         - /path/to/api/uploads:/api/static/uploads
   web:
       volumes:
         - phame_data:/phame_api/media
         - /path/to/api/uploads:/api/static/uploads
   

   For example set volumes to - /vol_d/api/uploads:/api/static/uploads if you want to store the upload files on /vol_d

3. Create docker containers.

   docker-compose -f docker-compose-production.yml build

4. start docker

   docker-compose -f docker-compose-production.yml up -d

Monitoring tasks

Browse to localhost:5555 to see the Flower Dashboard. Here you can see the status of the celery workers and their tasks.

You can look at projects run by other users if you create an admin account and login to that account. Click on the admin user icon in the upper right corner and select the username for the projects you would like to view.

Email notifications

If you would like users to receive email notifications with the error and execution logs when their projects have finished running:

1. Setup an email client. We use https://www.mailgun.com/

2. Edit the .email file and change the values for API_KEY, EMAIL_URL and SENDER

3. Edit phame-app/api/config.py and set SEND_NOTIFICATIONS = True