Dockerfile

FROM ubuntu:jammy
# LABEL John Pellman <john.pellman@childmind.org>

ARG DEBIAN_FRONTEND="noninteractive"

ENV AFNIPATH /opt/afni/bin/
ENV PATH /code:/opt/afni/bin:/usr/local/bin/miniconda/bin:${PATH}

# install dependencies
RUN apt-get update -qq && \
    apt-get install -q --no-install-recommends -y \
            wget \
            pkg-config \
            graphviz \
            gsl-bin \
            libexpat1-dev \
            libgiftiio-dev \
            libglu1-mesa \
            libglu1-mesa-dev \
            libgsl0-dev \
            libjpeg-progs \
            libxml2 \
            libxml2-dev \
            libxext-dev \
            libxpm-dev \
            libxp6 \
            libxp-dev \
            mesa-common-dev \
            mesa-utils \
            netpbm \
            libpng-dev \
            libfreetype6-dev \
            libxml2-dev \
            libxslt1-dev \
            python-dev \
            build-essential \
            g++ \
            libxft2 \
            git && \
    apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*

# install miniconda
RUN wget --progress=dot:giga http://repo.continuum.io/miniconda/Miniconda-3.8.3-Linux-x86_64.sh && \
    bash Miniconda-3.8.3-Linux-x86_64.sh -b -p /usr/local/bin/miniconda && \
    rm -rf Miniconda-3.8.3-Linux-x86_64.sh && python -v

# install python requirements
RUN conda install -y pip scipy && \
    pip install --upgrade pip && \
    pip install \
        nipype \
        nibabel \
        nitime \
        pyyaml \
        pandas \
        seaborn \
        html5lib==1.0b8 \
        pyPdf2 \
        xhtml2pdf \
        indi-tools

# the first time nipype runs it will create a configuration directory, do it here
# to avoid problems in the future
RUN /usr/local/bin/miniconda/bin/python -c "import nipype" 2> /dev/null

# install afni
RUN wget --progress=dot:giga http://afni.nimh.nih.gov/pub/dist/tgz/linux_openmp_64.tgz && \
    tar xzvf linux_openmp_64.tgz && mkdir -p /opt/afni && \
    mv linux_openmp_64/ /opt/afni/bin && \
    rm -rf linux_openmp_64.tgz

#install latest version of qap
RUN cd /tmp/ && \
    git clone -b 1.0.8 https://github.com/preprocessed-connectomes-project/quality-assessment-protocol.git && \
    cd quality-assessment-protocol && \
    python setup.py build && \
    python setup.py install

## Install the validator
RUN apt-get update -qq && \
    apt-get install -q --no-install-recommends -y curl && \
    curl -sL https://deb.nodesource.com/setup_4.x | bash - && \
    apt-get remove -y curl && \
    apt-get install -y --no-install-recommends nodejs && \
    rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*

RUN npm install -g bids-validator

RUN mkdir /scratch && mkdir /local-scratch && mkdir -p /code && mkdir -p /qap_resources
COPY qap_templates.tar.gz /qap_resources/qap_templates.tar.gz
COPY default_pipeline.yml /qap_resources/default_pipeline.yml
COPY run.py /code/run.py
COPY bids_utils.py /code/bids_utils.py
RUN chmod +x /code/run.py && cd /qap_resources \
   && tar xzvf /qap_resources/qap_templates.tar.gz \
   && rm -f /qap_resources/qap_templates.tar.gz


ENTRYPOINT ["/code/run.py"]