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docker-compose-razi

Docker-compose to use compound database easily.

Docker image

db

PostgreSQL with RDKit database cartridge for compound database

  • PostsgreSQL (version 9.5)
  • RDKit database cartridge (latest)

web

Jupyter Notebook for creating database table and using database with Python

  • Python (version 3.6.0)
    • SQLAlchemy
    • Pillow (version 4.3.0)
    • RDKit (version 2017.03.1)
    • razi (latest)

How to use

1. git clone

git clone https://github.com/yamasakih/docker-compose-radi
cd docker-compose-django-radi

2. docker-compose up

docker-compose up -d

> $ docker-compose up -d
Creating network "dockercomposerazi_default" with the default driver
Creating dockercomposerazi_db_1 ... 
Creating dockercomposerazi_db_1 ... done
Creating dockercomposerazi_web_1 ... 
Creating dockercomposerazi_web_1 ... done

Please access http://0.0.0.0:8888 or http://localhost:8888, then you can run Jupyter Notebook.

If you can't, please restart docker-compose.

> $ docker-compose restart
Restarting dockercomposedjangordkit_web_1 ... done
Restarting dockercomposedjangordkit_db_1  ... done

3. Creating the database

If you want, create database by command createdb.
You can use postgresql command by simply adding docker-compose exec db at the beginning.
(Change YOUR_DATABASE_NAME to created database name)

> $ docker-compose exec db createdb -U postgres YOUR_DATABASE_NAME

4. Extend the database

Next, extend your database by command create extension rdkit for using RDKit database cartridge.
You can use postgresql command by simply adding docker-compose exec db at the beginning.
(Change YOUR_DATABASE_NAME to created database name or postgres (default database name))

> $ docker-compose exec db psql -U postgres -c 'create extension rdkit' YOUR_DATABASE_NAME
CREATE EXTENSION

5. Delete mount volume

This Docker-compose uses named volume.
If it becomes unnecessary, delete it with the following command.

> $ docker volume list
DRIVER              VOLUME NAME
local               dockercomposerazi_dbdata

> $ docker volume rm dockercomposerazi_dbdata 
dockercomposerazi_dbdata

> $ docker volume list                        
DRIVER              VOLUME NAME

For more information, please see tutorial.