Dockerfile_v0.2

FROM pnilab/pumi:0.1

ENV C3DPATH="/opt/convert3d-1.0.0" \
    PATH="/opt/convert3d-1.0.0/bin:$PATH"

RUN conda install -y  --name base \
           "python=3.8" \
           "pytest" \
           "jupyter" \
           "jupyterlab" \
           "jupyter_contrib_nbextensions" \
           "traits" \
           "pandas" \
           "matplotlib" \
           "scikit-learn" \
           "scikit-image" \
           "seaborn" \
           "nbformat" \
           "nb_conda" \
           "numpy>=1.21.1" \
           "scipy>=1.7.1" \
           "numpydoc>=1.1.0" \
           "nbsphinx>=0.8.6" \
           "pytest>=7.1.2" \
           "nipype>=1.8.1" \
           "graphviz>=0.17" \
           "nilearn>=0.9.1" \
           "seaborn>=0.11.2" \
           "tensorflow" \
           "graphviz" \
           "numpydoc" \
           "nbsphinx" \
           "dot2tex"

RUN python -m pip install --no-cache-dir  \
             "pybids>=0.15.1" \
             "pydeface>=2.0.0" \
             "datalad[full]" \
             "nipy" \
             "duecredit" \
             "nbval" \
             "templateflow" \
    && sync && conda clean --all --yes && sync

RUN python -m pip install  git+https://github.com/MIC-DKFZ/HD-BET.git

RUN apt-get update -qq \
    && apt-get install -y -q --no-install-recommends \
           ca-certificates \
           curl \
    && rm -rf /var/lib/apt/lists/* \
    && echo "Downloading Convert3D ..." \
    && mkdir -p /opt/convert3d-1.0.0 \
    && curl -fsSL https://sourceforge.net/projects/c3d/files/c3d/1.0.0/c3d-1.0.0-Linux-x86_64.tar.gz/download \
    | tar -xz -C /opt/convert3d-1.0.0 --strip-components 1

ENV C3DPATH="/opt/convert3d-1.0.0" \
    PATH="/opt/convert3d-1.0.0/bin:$PATH"