# Use Ubuntu 22.04 LTS
FROM ubuntu:22.04

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

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 \
xorg \
unzip \
wget \
cmake \
make \
xvfb && \
apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*


# Installing ANTs 2.3.3 (NeuroDocker build)
# Note: the URL says 2.3.4 but it is actually 2.3.3
ENV ANTSPATH="/opt/ants" \
PATH="/opt/ants:$PATH"
WORKDIR $ANTSPATH
RUN curl -sSL "https://dl.dropbox.com/s/gwf51ykkk5bifyj/ants-Linux-centos6_x86_64-v2.3.4.tar.gz" \
| tar -xzC $ANTSPATH --strip-components 1


# Installing niftyreg
WORKDIR "/opt"
RUN git clone https://github.com/KCL-BMEIS/niftyreg.gi...
RUN mkdir niftyreg-build
RUN cd ./niftyreg-build && cmake ../niftyreg && make

# setup niftyreg
RUN rm -rf ./niftyreg && mv ./niftyreg-build /opt/niftyreg
ENV PATH="/opt/niftyreg/reg-io:/opt/niftyreg/reg-apps:$PATH"


# Install matlab-runtime
# Modified from https://github.com/dafnifacility/matlab-...
# Install pre-requisites
RUN mkdir -p /matlab-runtime /opt/matlab-runtime/v94/archives /code/model

# Download and install Matlab runtime
RUN wget https://ssd.mathworks.com/supportfiles/d... && \
unzip MCR_R2018a_glnxa64_installer.zip && \
rm -rf MCR_R2018a_glnxa64_installer.zip && \
./install -destinationFolder /opt/matlab-runtime -agreeToLicense yes -mode silent -outputFile /log.txt $$ \
rm -rf /matlab-runtime
ENV MCRROOT=/opt/matlab-runtime/v94

# Point to the newly installed Matlab runtime binaries
ENV LD_LIBRARY_PATH $MCRROOT:$MCRROOT/runtime/glnxa64:$MCRROOT/bin/glnxa64:$MCRROOT/sys/os/glnxa64:$MCRROOT/sys/opengl/lib/glnxa64:$MCRROOT/extern/bin/glnxa64

# Add mri_reface
COPY * /opt/mri_reface/
ENV PATH="/opt/mri_reface:$PATH"

WORKDIR "/home"