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 [email protected]:LANL-Bioinformatics/phame-api.git

2. create a .postegres file within the cloned directory phame-api/.envs/.local/.postgres, and add following lines to it.

   # PostgreSQL
   # ----------
   POSTGRES_HOST=postgres
   POSTGRES_PORT=5432
   POSTGRES_DB=phame_api01
   POSTGRES_USER=<username>
   POSTGRES_PASSWORD=<password>
   

3. cd to the project root directory phame-api

   cd phame-api

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.

Docker and git are required.

1. clone the repo

   git clone [email protected]:LANL-Bioinformatics/phame-api.git

2. create a .postegres file within the cloned directory phame-api/.envs/.local/.postgres, and add following lines to it.

   # PostgreSQL
   # ----------
   POSTGRES_HOST=postgres
   POSTGRES_PORT=5432
   POSTGRES_DB=phame_api01
   POSTGRES_USER=<username>
   POSTGRES_PASSWORD=<password>
   

3. cd to the project root directory phame-api

   cd phame-api

4. 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. For example: /vol_d/api/uploads:/api/static/uploads if you want to store the upload files on /vol_d

   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
   

5. Create docker containers.

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

6. 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.