Code Monkey home page Code Monkey logo

docker-postgres-rdkit's Introduction

PostgreSQL Docker Image with RDKit Cartridge

This is a PostgreSQL Docker image with the RDKit cartridge installed.

This image inherits from the official postgres image, and therefore has all the same environment variables for configuration, and can be extended by adding entrypoint scripts to the /docker-entrypoint-initdb.d directory to be run on first launch.

Running

Start Postgres server running in the background:

docker run --name mypostgres -p 5432:5432 -e POSTGRES_PASSWORD=mypassword -d mcs07/postgres-rdkit

Or run with an application via Docker Compose:

services:

  db:
    image: mcs07/postgres-rdkit
    restart: always
    environment:
      POSTGRES_PASSWORD: mypassword
    volumes:
      - /path/to/pgdata:/var/lib/postgresql/data

  adminer:
    image: adminer
    restart: always
    ports:
      - 8080:8080

This image exposes port 5432 (the postgres port), so standard container linking will make it automatically available to the linked containers.

Environment Variables

  • POSTGRES_PASSWORD: Superuser password for PostgreSQL.
  • POSTGRES_USER: Superuser username (default postgres).
  • POSTGRES_DB: Default database that is created when the image is first started.
  • PGDATA: Location for the database files (default /var/lib/postgresql/data).

See the official postgres image for more details.

Building

A multi-stage docker build is used to produce a lightweight production image without all the build dependencies. This image uses mcs07/rdkit as an earlier build stage to provide the RDKit libraries.

To build, run:

docker build -t postgres-rdkit .

docker-postgres-rdkit's People

Contributors

mcs07 avatar

Stargazers

 avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar

Watchers

 avatar  avatar  avatar

docker-postgres-rdkit's Issues

CMake Error in CMakeLists.txt:

We are seeing errors while trying to build the Postgres-rdkit. Not aware of this error. It was running fine previously. Please let us know the fix. whereas mcs07/docker-rdkit is building fine.

CMake Error in CMakeLists.txt:
Imported target "AvalonLib" includes a non-existent path

"/usr/include/python3.7m"

in its INTERFACE_INCLUDE_DIRECTORIES. Possible reasons include:

  • The path was deleted, renamed, or moved to another location.

  • An install or uninstall procedure did not complete successfully.

  • The installation package was faulty and references files it does not
    provide.

-- Generating done
CMake Generate step failed. Build files cannot be regenerated correctly.
The command '/bin/sh -c cmake -Wno-dev -D CMAKE_BUILD_TYPE=Release -D CMAKE_SYSTEM_PREFIX_PATH=/usr -D CMAKE_INSTALL_PREFIX=/usr -D CMAKE_MODULE_PATH=/rdkit/Code/cmake/Modules -D RDK_BUILD_AVALON_SUPPORT=ON -D RDK_BUILD_INCHI_SUPPORT=ON -D RDKit_DIR=/usr/lib -D PostgreSQL_ROOT=/usr -D PostgreSQL_TYPE_INCLUDE_DIR=/usr/include/postgresql/12/server/ .' returned a non-zero code: 1.

Patches

Hey, thanks for contributing this! I'm wondering if you could comment on what the purpose of the patches you use is. Is this something related to your needs or generally applicable?

Thanks!

Add docs on how to upgrade the image for future active maintainers

@mcs07 this project is really nice and useful. It's sad that it got unmaintained and is now causing errors when using jointly with newer versions of rdkit (in my case, this is in a django app context).

I would love to contribute and become a maintainer - any way you could help me start or write the docs about the process to upgrade to a newer version of rdkit?

your root image mcs07/rdkit image is easy to update, but this one seems a bit more difficult and is not just a matter of changing the versions in the dockerfile.

Any answer to this issue would help, thanks in advance ๐Ÿ‘

Recommend Projects

  • React photo React

    A declarative, efficient, and flexible JavaScript library for building user interfaces.

  • Vue.js photo Vue.js

    ๐Ÿ–– Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.

  • Typescript photo Typescript

    TypeScript is a superset of JavaScript that compiles to clean JavaScript output.

  • TensorFlow photo TensorFlow

    An Open Source Machine Learning Framework for Everyone

  • Django photo Django

    The Web framework for perfectionists with deadlines.

  • D3 photo D3

    Bring data to life with SVG, Canvas and HTML. ๐Ÿ“Š๐Ÿ“ˆ๐ŸŽ‰

Recommend Topics

  • javascript

    JavaScript (JS) is a lightweight interpreted programming language with first-class functions.

  • web

    Some thing interesting about web. New door for the world.

  • server

    A server is a program made to process requests and deliver data to clients.

  • Machine learning

    Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.

  • Game

    Some thing interesting about game, make everyone happy.

Recommend Org

  • Facebook photo Facebook

    We are working to build community through open source technology. NB: members must have two-factor auth.

  • Microsoft photo Microsoft

    Open source projects and samples from Microsoft.

  • Google photo Google

    Google โค๏ธ Open Source for everyone.

  • D3 photo D3

    Data-Driven Documents codes.