タグ: docker

Make virtual machine for chemoinformatics #RDKit

Recently stable version of docker for mac is released. It’s good news for me. 😉
https://www.docker.com/products/docker
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.
https://github.com/iwatobipen/docker4chmoinfo/blob/master/docker4chemoinfo/Dockerfile
Linux environment can use new version of RDKit.

FROM ubuntu:16.04 
MAINTAINER iwatobipen <seritaka@gmail.com>
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 http://repo.continuum.io/archive/Anaconda3-4.1.1-Linux-x86_64.sh
RUN bash ./Anaconda3-4.1.1-Linux-x86_64.sh -b -p /opt/conda 
RUN rm ./Anaconda3-4.1.1-Linux-x86_64.sh
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.
https://hub.docker.com/r/iwatobipen/chemoinfo_test/

Enjoy.