Getting Started With MICAS

Here are some of the programs that MICAS requires for it to function correctly. I have listed down the steps needed to get up and running with MICAS service as well.

Steps to get MICAS up and running

SOFTWARE REQUIRED

1. Centrifuge
2. Celery
3. Conda
4. Redis
5. Dustmasker (or as part of NCBI C++ toolkit)
6. NodeJS

SETTING UP THE BACKEND FLASK SERVER

1. Activate the right conda environment:

conda activate micas_env

2. Start up the Flask app

python server/micas.py

This hosts the back-end on http://127.0.0.1:5000

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SETTING UP THE DIRECTORIES

1. Create the main directory to hold all the other micas directories.

mkdir Files-MICAS

2. Create a directory to hold MICAS database related files

mkdir -p Files-MICAS/micas_data

3. Create a directory to hold MinION reads data.

mkdir -p Files-MICAS/minion_data

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START REDIS SERVER & CELERY WORKER

1. Start the Redis server for messaging between Python and Celery

redis-server

2. Start Celery Worker for given tasks

cd server/app/main/utils
celery -A tasks worker --loglevel=INFO

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