Dockerfile_py3.11

FROM python:3.11-bullseye
SHELL ["/bin/bash", "-euxo", "pipefail", "-c"]

# Set up configuration envvars
ENV INSTALL_DIR=/usr/local \
    FSL_VERSION=6.0.7.9 \
    MRTRIX_VERSION=3.0.4 \
    VIRTUAL_ENV=/venv

# Initial update
RUN apt update && \
      apt install -y \
      apt-utils \
      wget \
      curl \
      nano \
      software-properties-common \
      jq \
      libblas-dev \
      liblapack-dev \
      libatlas-base-dev \
      gfortran \
      git \
      g++ \
      clang \
      libeigen3-dev \
      zlib1g-dev \
      libqt5opengl5-dev \
      libqt5svg5-dev \
      libgl1-mesa-dev \
      libfftw3-dev \
      libtiff5-dev \
      libpng-dev

# Install Poetry
ENV POETRY_HOME=${INSTALL_DIR}/poetry
RUN curl -sSL https://install.python-poetry.org | python3 -
ENV PATH=${PATH}:${POETRY_HOME}/bin

# Install UV
RUN pip install uv && \
    uv venv ${VIRTUAL_ENV} && \
    uv pip install -U pip setuptools wheel
ENV PATH=$PATH:${VIRTUAL_ENV}/bin

# Install FSL
RUN curl https://fsl.fmrib.ox.ac.uk/fsldownloads/fslinstaller.py -o /tmp/fslinstaller.py
RUN echo "/usr/local/fsl" | python /tmp/fslinstaller.py -V ${FSL_VERSION}

# Configure FSL Environment
ENV FSLDIR=${INSTALL_DIR}/fsl
ENV FSLOUTPUTTYPE=NIFTI_GZ
ENV PATH=$PATH:${FSLDIR}/bin
ENV LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${FSLDIR}

# Build and configure MRTRIX3
ENV MRTRIXDIR=${INSTALL_DIR}/mrtrix3
RUN git clone --branch ${MRTRIX_VERSION} https://github.com/MRtrix3/mrtrix3.git ${MRTRIXDIR}
ENV CXX=/usr/bin/clang++
ENV ARCH=native
RUN cd ${MRTRIXDIR} && \
      ./configure -nogui -openmp && \
      ./build
ENV PATH=$PATH:${MRTRIXDIR}/bin

# Remove unwanted packages
RUN apt autoremove && apt-get clean

CMD ["/bin/bash"]