# Generated by Porcupine
# Modelled after Neurodocker v0.2.0-dev. https://github.com/kaczmarj/neurodocker

FROM timvanmourik/porcupine

#----------------------------------------------------------
# Install common dependencies and create default entrypoint
#----------------------------------------------------------
ARG DEBIAN_FRONTEND=noninteractive
ENV LANG="C.UTF-8" \
    LC_ALL="C" \
    ND_ENTRYPOINT="/porcupine/startup.sh"
RUN apt-get update -qq && apt-get install -yq --no-install-recommends  \
    	bzip2 ca-certificates curl unzip \
    && apt-get clean \
    && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* \
    && chmod 777 /opt && chmod a+s /opt \
    && mkdir /porcupine \
    && echo '#!/usr/bin/env bash' >> $ND_ENTRYPOINT \
    && echo 'set +x' >> $ND_ENTRYPOINT \
    && echo 'if [ -z "$*" ]; then /usr/bin/env bash; else $*; fi' >> $ND_ENTRYPOINT \
    && chmod -R 777 /porcupine && chmod a+s /porcupine

#---------------
# Install Nipype
#---------------
RUN curl -sSLO https://repo.continuum.io/miniconda/Miniconda3-4.3.11-Linux-x86_64.sh && \
    bash Miniconda3-4.3.11-Linux-x86_64.sh -b -p /usr/local/miniconda && \
    rm Miniconda3-4.3.11-Linux-x86_64.sh

ENV PATH=/usr/local/miniconda/bin:$PATH \
    LANG=C.UTF-8 \
    LC_ALL=C.UTF-8

# Installing precomputed python packages
RUN conda install -y mkl=2017.0.1 mkl-service &&  \
    conda install -y numpy=1.12.0 \
                     scipy=0.18.1 \
                     scikit-learn=0.18.1 \
                     matplotlib=2.0.0 \
                     pandas=0.19.2 \
                     libxml2=2.9.4 \
                     libxslt=1.1.29\
                     traits=4.6.0 \
                     boto

RUN chmod +x /usr/local/miniconda/bin/* && conda clean --all -y
RUN echo 'export PATH=/usr/local/miniconda/bin:$PATH' >> /etc/profile
RUN pip install nipype
RUN apt-get update && apt-get install -y graphviz
#-----------------------------------------------------------
# Install FSL v5.0.10
# FSL is non-free. If you are considering commerical use
# of this Docker image, please consult the relevant license:
# https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/Licence
#-----------------------------------------------------------
RUN echo "Downloading FSL ..." \
    && curl -sSL https://fsl.fmrib.ox.ac.uk/fsldownloads/fsl-5.0.10-centos6_64.tar.gz \
    | tar zx -C /opt \
    && /bin/bash /opt/fsl/etc/fslconf/fslpython_install.sh -q -f /opt/fsl \
    && sed -i '$iecho Some packages in this Docker container are non-free' $ND_ENTRYPOINT \
    && sed -i '$iecho If you are considering commercial use of this container, please consult the relevant license:' $ND_ENTRYPOINT \
    && sed -i '$iecho https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/Licence' $ND_ENTRYPOINT \
    && sed -i '$isource $FSLDIR/etc/fslconf/fsl.sh' $ND_ENTRYPOINT
ENV FSLDIR=/opt/fsl \
    PATH=/opt/fsl/bin:$PATH

#--------------------------------
# Add custom analysis file as CMD
#--------------------------------

# THIS IS ONLY TEMPORARY (FIXES NIPYPE DEPENDENCY BUG)
RUN pip install --upgrade networkx==1.11

ADD skullstrip.py /skullstrip.py
ENTRYPOINT ["/skullstrip.py"]