Dockerfile

# Use Ubuntu 18.04 LTS (compatible with python-mvpa2 package)
FROM ubuntu:18.04

MAINTAINER Sajjad Torabian <torabiansajjad@gmail.com>

# Prepare environment
RUN apt-get update && \
    apt-get install -y --no-install-recommends \
                    apt-utils \
                    autoconf \
                    build-essential \
                    bzip2 \
                    ca-certificates \
                    curl \
                    git \
                    libtool \
                    lsb-release \
                    netbase \
                    pkg-config \
                    unzip \
                    xvfb && \
    apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*

ENV DEBIAN_FRONTEND="noninteractive" \
    LANG="en_US.UTF-8" \
    LC_ALL="en_US.UTF-8"

# FSL 6.0.5.1
RUN apt-get update -qq \
    && apt-get install -y -q --no-install-recommends \
           bc \
           dc \
           file \
           libfontconfig1 \
           libfreetype6 \
           libgl1-mesa-dev \
           libgl1-mesa-dri \
           libglu1-mesa-dev \
           libgomp1 \
           libice6 \
           libxcursor1 \
           libxft2 \
           libxinerama1 \
           libxrandr2 \
           libxrender1 \
           libxt6 \
           sudo \
           wget \
    && apt-get clean \
    && rm -rf /var/lib/apt/lists/* \
    && echo "Downloading FSL ..." \
    && mkdir -p /opt/fsl-6.0.5.1 \
    && curl -fsSL --retry 5 https://fsl.fmrib.ox.ac.uk/fsldownloads/fsl-6.0.5.1-centos7_64.tar.gz \
    | tar -xz -C /opt/fsl-6.0.5.1 --strip-components 1 \
    --exclude "fsl/config" \
    --exclude "fsl/data/atlases" \
    --exclude "fsl/data/first" \
    --exclude "fsl/data/mist" \
    --exclude "fsl/data/possum" \
    --exclude "fsl/data/standard/bianca" \
    --exclude "fsl/data/standard/tissuepriors" \
    --exclude "fsl/doc" \
    --exclude "fsl/etc/default_flobs.flobs" \
    --exclude "fsl/etc/fslconf" \
    --exclude "fsl/etc/js" \
    --exclude "fsl/etc/luts" \
    --exclude "fsl/etc/matlab" \
    --exclude "fsl/extras" \
    --exclude "fsl/include" \
    --exclude "fsl/python" \
    --exclude "fsl/refdoc" \
    --exclude "fsl/src" \
    --exclude "fsl/tcl" \
    --exclude "fsl/bin/FSLeyes" \
    && find /opt/fsl-6.0.5.1/bin -type f -not \( \
        -name "applywarp" -or \
        -name "bet" -or \
        -name "bet2" -or \
        -name "convert_xfm" -or \
        -name "fast" -or \
        -name "flirt" -or \
        -name "fsl_regfilt" -or \
        -name "fslhd" -or \
        -name "fslinfo" -or \
        -name "fslmaths" -or \
        -name "fslmerge" -or \
        -name "fslroi" -or \
        -name "fslsplit" -or \
        -name "fslstats" -or \
        -name "imtest" -or \
        -name "mcflirt" -or \
        -name "melodic" -or \
        -name "prelude" -or \
        -name "remove_ext" -or \
        -name "susan" -or \
        -name "topup" -or \
        -name "fslval" -or \
        -name "zeropad" \) -delete \
    && find /opt/fsl-6.0.5.1/data/standard -type f -not -name "MNI152_T1_2mm_brain.nii.gz" -delete
ENV FSLDIR="/opt/fsl-6.0.5.1" \
    PATH="/opt/fsl-6.0.5.1/bin:$PATH" \
    FSLOUTPUTTYPE="NIFTI_GZ" \
    FSLMULTIFILEQUIT="TRUE" \
    FSLLOCKDIR="" \
    FSLMACHINELIST="" \
    FSLREMOTECALL="" \
    FSLGECUDAQ="cuda.q" \
    LD_LIBRARY_PATH="/opt/fsl-6.0.5.1/lib:$LD_LIBRARY_PATH"

# PyMVPA
RUN apt-get update && \
    apt-get install -y --no-install-recommends python2.7

RUN apt-get update && \
    mkdir /dev/fuse && \
    chmod 777 /dev/fuse && \
    apt-get install -y python-mvpa2 && \
    apt-get remove -f -y --purge fuse

RUN mkdir -p /code

COPY run.py /code/run.py
RUN chmod +x /code/run.py

COPY version /code/version

ENTRYPOINT ["/code/run.py"]