Web Server

This is Team 2's web server repository.

Installation

We require that you use miniconda. This loads in the basic software and tools we will be using in our pipeline. To use our environment, type in

user@biosci:Team2-WebServer$ export PATH=$PATH:/home/projects/group-b/miniconda/condabin

If this is your first time using conda, type in

user@biosci:Team2-WebServer$ conda init bash

Then type in

user@biosci:Team2-WebServer$ conda activate group-b-conda

Execution

We will be calling a file called backbone.py in each directory of the 4 other steps of the pipeline. This ensures that a single file is running all of the code within a single pipeline step and centralizing the outputs. TODO: can we access these scripts if they are in different directories?

When a job is launched, each pipeline step's page will be created and will display a standby message. These pages will be filled with results as soon as they are available.

At the start, we will be checking if certain tools or inputs are present before the scripts are run.

Frameworks & Packages Used

• Django
• Celery (TODO: look for alternatives (celery not too good with errors or nonrepetitive & very long tasks)? async.io, etc.)
• SQLite

Data Usage

TODO:

  1. How will it be organized?
  
  2. How will we maintain it? 
  
  3. How do we use SQLite?
  
  4. Explore async tools other than Celery; Celery is our fall back option.
  
  5. See how sqlite works with Django.
  
  6. Figure out the organization of your group's data, how it's going to look, what intermittent stages are there in your group, and how would you store and display these intermittent results.