Dockerfile

# ==============================================================================
# NeuroDock
# A docker container that contains all PyDesigner dependencies such as MRTRIX3,
# FSL, and Python to preprocess diffusion MRI images.
#
# Maintainer: Siddhartha Dhiman
# ------------------------------------------------------------------------------
# Current Dependencies
#    1.) FSL
#    2.) MRTRIX3
#    3.) Python 2.7
#    4.) Python 3.6
#    6.) PyDesigner
# ==============================================================================

# Load base Ubuntu image
FROM python:3.11-bullseye

# Labels
LABEL maintainer="Siddhartha Dhiman (siddhartha.dhiman@gmail.com)"
LABEL org.label-schema.schema-version="1.0.0-rc1"
LABEL org.label-schema.name="dmri/pydesigner"
LABEL org.label-schema.description="A state-of-the-art difusion and kurtosis MRI processing pipeline"
LABEL org.label-schema.url="https://github.com/m-ama/"
LABEL org.label-schema.vcs-url="https://github.com/m-ama/NeuroDock.git"
LABEL org.label-schema.vendor="MUSC BRIDGE"

# ARG DEBIAN_FRONTEND=noninteractive

# Initial update
RUN apt update && \
      apt-get install -y \
      apt-utils \
      wget \
      curl \
      nano \
      software-properties-common \
      python3 \
      python3-pip \
      jq \
      libblas-dev \
      liblapack-dev \
      libatlas-base-dev \
      gfortran \
      git \
      g++ \
      python \
      libeigen3-dev \
      zlib1g-dev \
      libqt5opengl5-dev \
      libqt5svg5-dev \
      libgl1-mesa-dev \
      libfftw3-dev \
      libtiff5-dev \
      libpng-dev

# Copy and install PyDesigner
RUN mkdir -p /pydesigner
COPY /pydesigner /app/pydesigner
COPY pyproject.toml app/
RUN ls
RUN ls -la /app
WORKDIR /app
ENV PYTHONPATH=${PYTHONPATH}:${PWD} 
RUN pip3 install poetry
RUN poetry config virtualenvs.create false
RUN poetry install --no-dev

# Install Python dependencies
RUN pip3 install --upgrade setuptools && \
            pip3 install numpy \
                        pandas \
                        scipy \
                        joblib \
                        multiprocess \
                        tqdm \
                        nibabel \
                        cvxpy

# Install FSL
RUN curl https://fsl.fmrib.ox.ac.uk/fsldownloads/fslinstaller.py -o /tmp/fslinstaller.py
RUN echo "/usr/local/fsl" | python2 /tmp/fslinstaller.py -V 6.0.3

# Configure FSL Environment
ENV FSLDIR=/usr/local/fsl
ENV FSLOUTPUTTYPE=NIFTI_GZ
ENV PATH=$PATH:$FSLDIR/bin
ENV LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$FSLDIR

# Build and Configure MRTRIX3
RUN git clone https://github.com/MRtrix3/mrtrix3.git /usr/lib/mrtrix3
ENV CXX=/usr/bin/clang++
ENV ARCH=native
RUN cd /usr/lib/mrtrix3 && \
      ./configure -nogui -openmp && \
      ./build && \
      ./set_path
ENV PATH=$PATH:/usr/lib/mrtrix3/bin

# Remove unwanted packages
RUN apt-get autoremove && apt-get clean
RUN rm /tmp/fslinstaller.py && rm -r /tmp/PyDesigner

USER bridge