Dockerfile

FROM neurodebian:stretch-non-free

ARG tag

MAINTAINER Soichi Hayashis <hayashis@iu.edu>

ENV DEBIAN_FRONTEND=noninteractive
RUN apt-get update && apt-get install -y g++ libeigen3-dev zlib1g-dev libqt4-opengl-dev libgl1-mesa-dev libfftw3-dev libtiff5-dev jq strace vim python3-tk

#libgomp1 seems to comes with pytorch so I don't need it

#RUN pip3 install --upgrade pip

# Libraries needed to compile python
RUN apt-get update -qq \
    && apt-get install -qq build-essential libbz2-dev zlib1g-dev libncurses5-dev libgdbm-dev \
    && apt-get install -qq libnss3-dev libssl-dev libreadline-dev libffi-dev wget \
    && apt-get install -qq software-properties-common git curl

# Compiling python 3.7
RUN cd /usr/src \
    && wget -q https://www.python.org/ftp/python/3.7.9/Python-3.7.9.tgz \
    && tar xzf Python-3.7.9.tgz \
    && cd Python-3.7.9 \
    && ./configure --enable-optimizations >/dev/null \
    && make install > /dev/null

# Install fsl (needed for bet and flirt)
RUN apt-get update -qq \
    && apt-get install -qq --no-install-recommends fsl-core \
    && apt-get clean -qq \
    && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*

## install and compile mrtrix3
RUN git clone https://github.com/MRtrix3/mrtrix3.git
RUN cd mrtrix3 && git fetch --tags && git checkout tags/3.0.0 && ./configure && ./build
ENV PATH=$PATH:/mrtrix3/bin

#RUN pip3 install seaborn numpy
#RUN pip3 install torch torchvision

RUN pip3.7 install -q --upgrade pip \
    && pip3.7 install -q wheel numpy scipy nilearn matplotlib scikit-image nibabel \
    && pip3.7 install -q torch==1.6.0+cpu -f https://download.pytorch.org/whl/torch_stable.html

#install batchgenerator/tractseg
#RUN pip install https://github.com/MIC-DKFZ/batchgenerators/archive/master.zip && pip install https://github.com/MIC-DKFZ/TractSeg/archive/v1.7.1.zip
#RUN pip3 install https://github.com/MIC-DKFZ/batchgenerators/archive/master.zip && pip3 install https://github.com/MIC-DKFZ/TractSeg/archive/v2.1.1.zip
#RUN pip3.7 install https://github.com/MIC-DKFZ/batchgenerators/archive/master.zip && pip3 install https://github.com/MIC-DKFZ/TractSeg/archive/v2.2.zip
RUN pip3.7 install https://github.com/MIC-DKFZ/batchgenerators/archive/master.zip && pip3 install https://github.com/MIC-DKFZ/TractSeg/archive/master.zip

RUN HOME=/ download_all_pretrained_weights

#make it work under singularity 
#RUN ldconfig && mkdir -p /N/u /N/home /N/dc2 /N/soft
RUN ldconfig && mkdir -p /N/u /N/home /N/soft

#https://wiki.ubuntu.com/DashAsBinSh 
RUN rm /bin/sh && ln -s /bin/bash /bin/sh