Dockerfile

#flywheel/fmriprep

############################
# Get the image from DockerHub
FROM cookpa/antsct-aging:0.2.0

MAINTAINER Will Tackett <William.Tackett@pennmedicine.upenn.edu>

############################
# Install basic dependencies
RUN apt-get update && apt-get -y install \
    jq \
    tar \
    zip \
    curl \
    nano \
    build-essential
#RUN rm -f /usr/bin/python && ln -s /usr/bin/python /usr/bin/python3

############################
# Install conda environment
RUN curl -sSLO https://repo.continuum.io/miniconda/Miniconda3-4.5.11-Linux-x86_64.sh && \
    bash Miniconda3-4.5.11-Linux-x86_64.sh -b -p /usr/local/miniconda && \
    rm Miniconda3-4.5.11-Linux-x86_64.sh

ENV PATH=/usr/local/miniconda/bin:$PATH \
    LANG=C.UTF-8 \
    LC_ALL=C.UTF-8 \
    PYTHONNOUSERSITE=1

RUN conda install -y python=3.7.1 \
    chmod -R a+rX /usr/local/miniconda; sync && \
    chmod +x /usr/local/miniconda/bin/*; sync && \
    conda build purge-all; sync && \
    conda clean -tipsy && sync

############################
# Install the Flywheel SDK
RUN pip install flywheel-sdk
RUN pip install heudiconv
RUN pip install --upgrade fw-heudiconv ipython
RUN pip install pybids
RUN pip install -U templateflow
ENV TEMPLATEFLOW_HOME /flywheel/v0/.templateflow

############################
# Make directory for flywheel spec (v0)
ENV FLYWHEEL /flywheel/v0
RUN mkdir -p ${FLYWHEEL}
COPY run ${FLYWHEEL}/run
COPY prepare_run.py ${FLYWHEEL}/prepare_run.py
COPY manifest.json ${FLYWHEEL}/manifest.json
COPY BIDsDerivative.sh ${FLYWHEEL}/BIDsDerivative.sh
COPY .templateflow ${FLYWHEEL}/.templateflow
RUN chmod a+rx ${FLYWHEEL}/*

# Set the entrypoint
ENTRYPOINT ["/flywheel/v0/run"]
 
############################
# ENV preservation for Flywheel Engine
RUN env -u HOSTNAME -u PWD | \
  awk -F = '{ print "export " $1 "=\"" $2 "\"" }' > ${FLYWHEEL}/docker-env.sh

WORKDIR /flywheel/v0