Dockerfile

############################
# Get Freesurfer version in fMRIPrep 20.0.5
FROM ubuntu:xenial-20200114

MAINTAINER Ellyn Butler <ellyn.butler@pennmedicine.upenn.edu>
ENV FREESURFER_VERSION 6.0.1
ENV FREESURFER_HOME /opt/freesurfer


############################
# Install basic dependencies
RUN apt-get update && apt-get -y install \
    jq \
    tar \
    zip \
    build-essential

#COPY docker/files/neurodebian.gpg /usr/local/etc/neurodebian.gpg

# Prepare environment
RUN apt-get update && \
    apt-get install -y --no-install-recommends \
                    python2.7 \
                    curl \
                    bzip2 \
                    ca-certificates \
                    xvfb \
                    build-essential \
                    autoconf \
                    libtool \
                    pkg-config \
                    git && \
    curl -sL https://deb.nodesource.com/setup_10.x | bash - && \
    apt-get install -y --no-install-recommends \
                    nodejs && \
    apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
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

# Installing freesurfer
RUN curl -sSL https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.1/freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1.tar.gz | tar zxv --no-same-owner -C /opt \
    --exclude='freesurfer/diffusion' \
    --exclude='freesurfer/docs' \
    --exclude='freesurfer/fsfast' \
    --exclude='freesurfer/lib/cuda' \
    --exclude='freesurfer/lib/qt' \
    --exclude='freesurfer/matlab' \
    --exclude='freesurfer/mni/share/man' \
    --exclude='freesurfer/subjects/fsaverage_sym' \
    --exclude='freesurfer/subjects/fsaverage3' \
    --exclude='freesurfer/subjects/fsaverage4' \
    --exclude='freesurfer/subjects/cvs_avg35' \
    --exclude='freesurfer/subjects/cvs_avg35_inMNI152' \
    --exclude='freesurfer/subjects/bert' \
    --exclude='freesurfer/subjects/lh.EC_average' \
    --exclude='freesurfer/subjects/rh.EC_average' \
    --exclude='freesurfer/subjects/sample-*.mgz' \
    --exclude='freesurfer/subjects/V1_average' \
    --exclude='freesurfer/trctrain'

# Installing precomputed python packages # September 3, 2020: Ending up with pip v 10.1.1
RUN conda install -y python=3.7.1 \
                      pip=19.1 \
    chmod -R a+rX /usr/local/miniconda; sync && \
    chmod +x /usr/local/miniconda/bin/*; sync && \
    conda build purge-all; sync && \
    conda clean -tipsy && sync

RUN pip install pandas==1.1.3

############################
RUN mkdir -p /scripts
COPY stats2table_bash.sh /scripts/stats2table_bash.sh
COPY idcols.py /scripts/idcols.py
COPY run.sh /scripts/run.sh
RUN chmod +x /scripts/run.sh
RUN mkdir -p /output
RUN mkdir -p /input
RUN mkdir -p /input/data
RUN mkdir -p /input/license
RUN chmod +x /input

#RUN chmod +x ${FREESURFER_HOME} # Hopefully this will allow me to copy over the license... nope
#RUN chmod -R 777 ${FREESURFER_HOME} # Didn't work out

WORKDIR /home

ENTRYPOINT ["/scripts/run.sh"]