mcs07 / docker-rdkit

RDKit Docker images

RDKit Docker Image

RDKit is a collection of cheminformatics and machine-learning software written in C++ and Python.

This Docker image provides a Debian distribution with Python 3 and all other dependencies installed via the Debian package manager. RDKit is compiled from source.

This Docker image is designed to provide a lightweight RDKit installation, without any unnecessary build tools or package management infrastructure in the final image. Other images may inherit from it, or use it as an earlier stage in a multi-stage build process. See the mcs07/postgres-rdkit image for an example of this.

For a more complete environment that is easier to work with but results in a larger image, you may be better served by using a miniconda image and using conda install to add RDKit and other dependencies.

Running

Run rdkit container with an interactive shell:

docker run -it --rm mcs07/rdkit:latest /bin/bash

Or a python interpreter:

docker run -it --rm mcs07/rdkit:latest python3

Building

A multi-stage docker build is used to produce a lightweight production image without all the build dependencies. To build, run:

docker build -t rdkit .

Related Projects

• https://github.com/InformaticsMatters/docker-rdkit

docker-rdkit's Issues

Getting c++: fatal error: Killed signal terminated program cc1plus while builiding

Hi there,

First of all many thanks for this fenomenal clean Dockerfile and a great example of how to dockerize RDKit (or anything else really).

Bumped into a small problem, getting this error during builds

c++: fatal error: Killed signal terminated program cc1plus

It's not super clear from the error what the problem is – googling around it's clearly a memory error.

Fixed it by upping the docker accessible memory from 2GB to 3GB. Documenting it here in case other people stumble and get confused.