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QCDB Development

Prerequisites

Install Docker and docker-compose

Install dependencies

Pre-requisite of pipenv needed pipenv

pipenv install

Development

Contributing

Please, make sure to use commitizen to commit your messages. If you don't have commitizen installed:

pip install commitizen

To commit, instead of git commit -m use cz commit. For more information, read here.

Usage

All commands below need to be run from the top-level directory of this repository. All aspects related to starting and connection to the MySQL server are handled in the file params.yaml. The structure of the params.yaml file should look like the following:

db:
  name: qcdb
  params:
    host: 127.0.0.1
    port: 3306
    user: root
    password: password
files:
  - name: fastqc
    directory: /Users/aguang/CORE/qckit/qcdb/tests/data/
  - name: qckitfastq
    directory: /Users/aguang/CORE/qckit/qcdb/tests/data/
  - name: picardtools
    directory: /Users/aguang/CORE/qckit/qcdb/tests/data/

Each module run in the commands below also take a -f argument which by default is set to the top-level params.yaml. Thus no additional arguments need to be provided. However, if the user wishes to provide a yaml file from a different location, that is possible by providing commands like the following:

NOTE: to take advantage of the pipenv installation, enter a pipenv shell before running the python commands

python -m qcdb.db_create -f path/to/params.yaml

Additionally, code will likely only run for Python 3+.

Start MySQL Server

docker-compose up

Connect to Server

docker-compose exec mysql mysql -p

Password: password

Create database and tables

From another terminal window:

python -m qcdb.db_create

Load Data

If loading for the first time or adding a new metric/file type, run with the --buildref flag.

python -m qcdb.db_load

Running tests via Docker Compose

docker-compose run test

For testing the connection, create a .env file in the tests folder with MYSQLUSER and MYSQLPASSWORD used to connect to the datasci mysql server.

compbiocore / qcdb

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