Make virtual machine for chemoinformatics #RDKit

Recently stable version of docker for mac is released. It’s good news for me. 😉
I used boot2docker before but, now I switched docker for mac. Because it’s easy to install and share the file with host OS.
Of course, I installed docker for mac !

Virtual machine is one of useful way to test my code and keep native environment clean.
Today I wrote sample Docker file for chemoinformatics.
The virtual machine can run rdkit and keras. It’s means the machine can do deep learning with rdkit.
My Docker file is following.
Linux environment can use new version of RDKit.

FROM ubuntu:16.04 
MAINTAINER iwatobipen <>
RUN apt-get -y update && apt-get -y install wget
RUN apt-get -y install bzip2
RUN apt-get -y install git-all
RUN apt-get -y install libfreetype6-dev libxft-dev
RUN wget
RUN bash ./ -b -p /opt/conda 
RUN rm ./
ENV PATH /bin:/usr/bin:/opt/conda/bin:PATH
RUN conda install -y -c rdkit rdkit=2016.03.3
RUN pip install seaborn
RUN conda install -y -c conda-forge keras=1.0.7
CMD /bin/bash

The run the image use docker run command.

 docker run -i -t iwatobipen/chemoinfo_test /bin/bash

OK check the VM.

root@b33953263220:/# ipython
Python 3.5.2 |Anaconda 4.1.1 (64-bit)| (default, Jul  2 2016, 17:53:06) 
Type "copyright", "credits" or "license" for more information.

IPython 4.2.0 -- An enhanced Interactive Python.
?         -> Introduction and overview of IPython's features.
%quickref -> Quick reference.
help      -> Python's own help system.
object?   -> Details about 'object', use 'object??' for extra details.

In [1]: from rdkit import Chem
In [2]: from rdkit import rdBase  
In [3]: rdBase.rdkitVersion
Out[3]: '2016.03.3'

In [4]: import keras
Using Theano backend.

In [5]: 

Hmm, my vm works well.
If user run the machine, it already to do deep learning.
My dockerhub repo is following.



Leave a Reply

Fill in your details below or click an icon to log in: Logo

You are commenting using your account. Log Out / Change )

Twitter picture

You are commenting using your Twitter account. Log Out / Change )

Facebook photo

You are commenting using your Facebook account. Log Out / Change )

Google+ photo

You are commenting using your Google+ account. Log Out / Change )

Connecting to %s