Dockerfile

# Docker file for fshack ChRIS plugin app
#
# Build with
#
#   docker build -t <name> .
#
# For example if building a local version, you could do:
#
#   docker build -t local/pl-fshack .
#
# In the case of a proxy (located at say 10.41.13.4:3128), do:
#
#    export PROXY="http://10.41.13.4:3128"
#    docker build --build-arg http_proxy=${PROXY} --build-arg UID=$UID -t local/pl-fshack .
#
# To run an interactive shell inside this container, do:
#
#   docker run -ti --entrypoint /bin/bash local/pl-fshack
#
# To pass an env var HOST_IP to container, do:
#
#   docker run -ti -e HOST_IP=$(ip route | grep -v docker | awk '{if(NF==11) print $9}') --entrypoint /bin/bash local/pl-fshack
#
# Versions of FreeSurfer post 7.4.1 weigh in at 15GB and exceed build space on
# Github Actions. To build/push manually, do
#
#    docker tag local/pl-fshack docker.io/fnndsc/pl-fshack:1.5.0
#    docker push docker.io/fnndsc/pl-fshack:1.5.0
#
# obviously changing the 1.5.0 to whatever version number is appropriate. Then,
# upload to the ChRIS store at https://chrisstore.co/create
#
#    docker run --rm docker.io/fnndsc/pl-fshack:1.5.0 fshack.py --json > fshack.json
#
# either manually via the web ui, or from the CLI
#
#    http -a fnndsc:<fnndscpasswd> -f POST https://chrisstore.co/api/v1/plugins/    \
#    dock_image=fnndsc/pl-fshack                                                    \
#    descriptor_file@fshack.json                                                    \
#    public_repo=https://github.com/FNNDSC/pl-fshack                                \
#    name=pl-fshack
#


#FROM fnndsc/ubuntu-python3:latest
FROM fnndsc/ubuntu-python3@sha256:612b88b00d167c28a2bff5d7759f99112a5987463683362cd87d2e4c1726183d
LABEL maintainer="dev@babymri.org"

ARG UID=1001
ENV APPROOT="/usr/src/fshack"
ENV UID=$UID DEBIAN_FRONTEND=noninteractive
COPY ["fshack/", "requirements.txt", "license.txt", "${APPROOT}/"]

WORKDIR $APPROOT

ARG FREESURFER_VERSION=7.4.1
RUN pip install -r requirements.txt                         \
    && apt-get update -q &&                                 \
    apt-get -qq install bc binutils libgomp1 perl psmisc curl tar tcsh uuid-dev vim-common libjpeg62-dev \
    libglu1-mesa libxmu6 libglib2.0-0 qt5-default &&        \
    curl "https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/${FREESURFER_VERSION}/freesurfer-linux-ubuntu20_$(dpkg --print-architecture)-${FREESURFER_VERSION}.tar.gz" | \
    tar -C /usr/local -xz                                   \
    && mv license.txt /usr/local/freesurfer                 \
    && apt-get install -y locales                           \
    && export LANGUAGE=en_US.UTF-8                          \
    && export LANG=en_US.UTF-8                              \
    && export LC_ALL=en_US.UTF-8                            \
    && locale-gen en_US.UTF-8                               \
    && dpkg-reconfigure locales                             \
    && useradd -u $UID -ms /bin/bash localuser

ENV PATH="/usr/local/freesurfer/bin:/usr/local/freesurfer/fsfast/bin:/usr/local/freesurfer/tktools:/usr/local/freesurfer/mni/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:" \
    FREESURFER_HOME="/usr/local/freesurfer"                 \
    SUBJECTS_DIR="/outgoing"                                \
    MINC_LIB_DIR="/usr/local/freesurfer/mni/lib"            \
    MNI_DATAPATH="/usr/local/freesurfer/mni/data"           \
    PERL5LIB="/usr/local/freesurfer/mni/share/perl5"        \
    MINC_BIN_DIR="/usr/local/freesurfer/mni/bin"            \
    MNI_PERL5LIB="/usr/local/freesurfer/mni/share/perl5"    \
    FMRI_ANALYSIS_DIR="/usr/local/freesurfer/fsfast"        \
    FUNCTIONALS_DIR="/usr/local/freesurfer/sessions"        \
    LOCAL_DIR="/usr/local/freesurfer/local"                 \
    FSFAST_HOME="/usr/local/freesurfer/fsfast"              \
    MNI_DIR="/usr/local/freesurfer/mni"                     \
    FSF_OUTPUT_FORMAT="nii.gz"

# duct tape programming
WORKDIR /usr/local/src/pl-fshack
COPY . .
RUN pip install .
RUN rm /bin/sh && ln -s /bin/bash /bin/sh
WORKDIR $APPROOT

CMD ["fshack.py", "--help"]