Dockerfile_CPU

# Neurodocker version 0.4.0
FROM neurodebian:stretch-non-free

ARG DEBIAN_FRONTEND="noninteractive"

# 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/*

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

RUN mkdir -p ~/.tractseg \
    && mkdir -p /code \
    && curl -sSL -o /code/mrtrix3_RC3.tar.gz https://zenodo.org/record/1415322/files/mrtrix3_RC3.tar.gz?download=1

RUN tar -zxf /code/mrtrix3_RC3.tar.gz -C code \
    && /code/mrtrix3/set_path

# Uncomment if we want to rebuild the following commands (otherwise using cache)
#RUN echo "rebuild"

RUN pip3.7 install -q --upgrade https://github.com/MIC-DKFZ/TractSeg/archive/master.zip

# Sometimes fails if running everything from cache -> uncomment line "RUN echo 'rebuild'"
RUN download_all_pretrained_weights

# Setup environment (make all commands available)
ENV ND_ENTRYPOINT="/code/startup.sh"
RUN touch "$ND_ENTRYPOINT" \
    && echo '#!/bin/bash' >> "$ND_ENTRYPOINT"  \
    && echo 'set -e' >> "$ND_ENTRYPOINT" \
    && echo 'source /etc/fsl/fsl.sh' >> "$ND_ENTRYPOINT" \
    && echo 'export PATH=/code/mrtrix3/bin:$PATH' >> "$ND_ENTRYPOINT" \
    && echo 'exec "$@"' >> "$ND_ENTRYPOINT" \
    && chmod -R 777 /code && chmod a+s /code

# This will be executed. Arguments passed on the command line will be passed as arguments to this
# script. So in this script we first setup the environment and then we execute (using exec) the
# commands which were provided on the command line (available via $@)
ENTRYPOINT ["/code/startup.sh"]