Dockerfile

# Build a CentOS based system
FROM mayoqin/grunt
LABEL maintainer "Korfiatis Panagiotis Korfiatis.Panagioits@mayo.edu"
USER root
#################################################################################################################
#			This builds a compute environment for developing medical image analysis applications	#
#################################################################################################################


#################################################################################################################
#						basic development tools						#
#################################################################################################################
RUN yum -y install git python-devel
RUN yum -y  install python-setuptools
RUN yum -y install gcc-gfortran libmpc-devel
RUN yum -y install wget
RUN yum -y install gcc-c++
RUN yum -y install Cython
RUN yum -y install epel-release
RUN yum -y install cmake
RUN yum -y install make
RUN yum install -y libjpeg-devel
RUN yum install -y zlib-dev openssl-devel sqlite-devel
RUN yum install -y glibmm24-devel gtkmm24-devel gsl-devel
# nifticlib dependencies
RUN yum install -y csh
# python dependencies for https, bzip2
RUN yum install -y bzip2-devel
# MITK dependencies
RUN yum install -y libtiff-devel tcp_wrappers-devel
RUN yum install -y telnet
RUN yum -y install python-pip
RUN pip install --upgrade pip
RUN mkdir ~/srcb && cd ~/srcb && \
  git clone https://github.com/xianyi/OpenBLAS && \
  cd ~/srcb/OpenBLAS && \
  make FC=gfortran && \
  make PREFIX=/opt/OpenBLAS install
# now update the library system:
RUN echo /opt/OpenBLAS/lib >  /etc/ld.so.conf.d/openblas.conf
RUN ldconfig
ENV LD_LIBRARY_PATH=/opt/OpenBLAS/lib:$LD_LIBRARY_PATH
RUN yum -y install freetype freetype-devel libpng-devel
RUN pip install matplotlib
# now install numpy source
RUN pwd
RUN ls
RUN cd ~/src && \
  git clone  -b maintenance/1.11.x https://github.com/numpy/numpy && \
  cd numpy && \
  touch site.cfg
RUN echo [default]  >                           ~/src/numpy/site.cfg && \
  echo include_dirs = /opt/OpenBLAS/include >>  ~/src/numpy/site.cfg && \
  echo library_dirs = /opt/OpenBLAS/lib >>      ~/src/numpy/site.cfg && \
  echo [openblas] >>                            ~/src/numpy/site.cfg && \
  echo openblas_libs = openblas >>              ~/src/numpy/site.cfg && \
  echo library_dirs = /opt/OpenBLAS/lib >>      ~/src/numpy/site.cfg && \
  echo [lapack]  >>                             ~/src/numpy/site.cfg && \
  echo lapack_libs = openblas >>                ~/src/numpy/site.cfg && \
  echo library_dirs = /opt/OpenBLAS/lib >>      ~/src/numpy/site.cfg
RUN cd ~/src/numpy && \
  python setup.py config && \
  python setup.py build --fcompiler=gnu95 && \
  python setup.py install
RUN pip install ipython
RUN pip install cython --upgrade
RUN pip install scipy
RUN pip install scikit-learn
RUN pip install scikit-image
# RUN pip install --trusted-host www.simpleitk.org -f http://www.simpleitk.org/SimpleITK/resources/software.html SimpleITK
RUN pip install pandas
RUN pip install argparse
RUN pip install pydicom
RUN pip install networkx
RUN pip install seaborn
RUN pip install tornado
RUN pip install nibabel
# RUN pip install nipype
RUN pip install wget
ENV OPENBLAS_NUM_THREADS=4
RUN pip install chainer
RUN pip install openpyxl
RUN pip install theano
RUN pip install keras

WORKDIR /
COPY unsuper.gruntfile.yml /grunt.d/unsuper.yml
COPY _kmeansseg.py _kmeansseg.py
COPY _classifierevaluation.py _classifierevaluation.py
COPY _featureSelection.py _featureSelection.py
COPY _analyticscalc.py _analyticscalc.py
COPY _model_application.py _model_application.py

# What do we run on startup?
CMD ["/bin/grunt", "/grunt.d/unsuper.yml"]
# We expose port 9901 by default
EXPOSE 9901:9901