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Dockerfile
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FROM ubuntu:16.04
# Create a base docker container that can execute the new version 2.1 of brainageR
# https://github.com/james-cole/brainageR
# Authors: Daniela Furlan and Ferran Prados
#
# Example usage:
#
# docker run --rm -it -v ${PWD}/your_data:/data -w /data \
# docker.io/library/brainimage:latest brainageR \
# -f sub-01_T1w_defaced.nii -o subj01_brain_predicted.age.csv
#
# Build the docker:
#
# docker build . -f Dockerfile -t brainimage
#
# Install the needed basic packages
RUN apt-get update
RUN apt-get install -y --fix-missing \
unzip\
git \
wget
# Install R-package
RUN apt-get update \
&& apt-get install -y --no-install-recommends \
software-properties-common \
dirmngr \
ed \
less \
locales \
vim-tiny \
wget \
ca-certificates \
&& add-apt-repository --enable-source --yes "ppa:marutter/rrutter4.0" \
&& add-apt-repository --enable-source --yes "ppa:c2d4u.team/c2d4u4.0+"
# Configure default locale, see https://github.com/rocker-org/rocker/issues/19
RUN echo "en_US.UTF-8 UTF-8" >> /etc/locale.gen \
&& locale-gen en_US.utf8 \
&& /usr/sbin/update-locale LANG=en_US.UTF-8
ENV LC_ALL en_US.UTF-8
ENV LANG en_US.UTF-8
# This was not needed before but we need it now
ENV DEBIAN_FRONTEND noninteractive
# Otherwise timedatectl will get called which leads to 'no systemd' inside Docker
ENV TZ UTC
# Now install R and littler, and create a link for littler in /usr/local/bin
# Default CRAN repo is now set by R itself, and littler knows about it too
# r-cran-docopt is not currently in c2d4u so we install from source
RUN apt-get update \
&& apt-get install -y --no-install-recommends \
littler \
r-base \
r-base-dev \
r-recommended \
&& ln -s /usr/lib/R/site-library/littler/examples/install.r /usr/local/bin/install.r \
&& ln -s /usr/lib/R/site-library/littler/examples/install2.r /usr/local/bin/install2.r \
&& ln -s /usr/lib/R/site-library/littler/examples/installGithub.r /usr/local/bin/installGithub.r \
&& ln -s /usr/lib/R/site-library/littler/examples/testInstalled.r /usr/local/bin/testInstalled.r \
&& install.r docopt \
&& rm -rf /tmp/downloaded_packages/ /tmp/*.rds \
&& rm -rf /var/lib/apt/lists/*
# Install packages kernlab,RNifti and stringr
RUN R -e "install.packages('kernlab',dependencies=TRUE, repos='http://cran.rstudio.com/')"
RUN R -e "install.packages('RNifti',dependencies=TRUE, repos='http://cran.rstudio.com/')"
RUN R -e "install.packages('stringr',dependencies=TRUE, repos='http://cran.rstudio.com/')"
# Install SMP12 and Octave
RUN apt-get update && DEBIAN_FRONTEND=noninteractive apt-get -y install \
build-essential \
curl \
octave \
liboctave-dev \
&& apt-get clean \
&& rm -rf \
/tmp/hsperfdata* \
/var/*/apt/*/partial \
/var/lib/apt/lists/* \
/var/log/apt/term*
RUN mkdir /opt/spm12 \
&& curl -SL https://github.com/spm/spm12/archive/refs/tags/r7219.tar.gz \
| tar -xzC /opt/spm12 --strip-components 1 \
&& curl -SL https://raw.githubusercontent.com/spm/spm-docker/687c160b9d50100079c8a7decd696d07cf66251a/octave/spm12_r7771.patch
RUN make -C /opt/spm12/src PLATFORM=octave distclean \
&& make -C /opt/spm12/src PLATFORM=octave \
&& make -C /opt/spm12/src PLATFORM=octave install \
&& ln -s /opt/spm12/bin/spm12-octave /usr/local/bin/spm12
# Install FSL
RUN apt-get update
# setup FSL using debian
ENV NDEB_URL http://neuro.debian.net/lists/xenial.us-ca.full
COPY neurodebian.gpg /root/.neurodebian.gpg
RUN apt-get install -y software-properties-common python-software-properties
RUN add-apt-repository universe
RUN apt-get update
RUN \
curl -sSL $NDEB_URL >> /etc/apt/sources.list.d/neurodebian.sources.list && \
apt-key add /root/.neurodebian.gpg && \
(apt-key adv --refresh-keys --keyserver hkp://ha.pool.sks-keyservers.net 0xA5D32F012649A5A9 || true) && \
apt-get update
RUN \
apt-get update && \
apt-get install -y \
fsl-5.0-core \
fsl-mni152-templates=5.0.7-2
# Configure environment
ENV \
FSLDIR=/usr/share/fsl/5.0 \
FSLOUTPUTTYPE=NIFTI_GZ \
FSLMULTIFILEQUIT=TRUE \
POSSUMDIR=/usr/share/fsl/5.0 \
LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/lib/fsl/5.0 \
FSLTCLSH=/usr/bin/tclsh \
FSLWISH=/usr/bin/wish
ENV PATH=$FSLDIR/bin:$PATH
ENV PATH=.:$PATH
ENV PATH=/opt/brainageR/software:$PATH
RUN \
echo ". $FSLDIR/etc/fslconf/fsl.sh" >> ~/.bashrc && \
echo "export FSLDIR PATH" >> ~/.bashrc
# Install brainageR
# Install brainageR zip v2.1 from github
RUN cd /opt && \
wget https://github.com/james-cole/brainageR/archive/refs/tags/2.1.zip
# BrainageR directory
RUN cd /opt && \
mkdir brainageR
# Unzip 2.1 in brainageR directory
RUN cd /opt && \
unzip 2.1.zip -d /opt/brainageR
# Rename unzipped 2.1 folder (brainageR-2.1)
RUN cd /opt/brainageR &&\
mv brainageR-2.1 software
# Substituting brainageR script by a brainageR script with new software directories
# Edited variables: brainageR_dir, spm_dir, matlab_path,FSLDIR
ADD brainageR /opt/brainageR/software
# Data directory for input and output
RUN mkdir -p /data
# Download PCAs
# pca_center.rds
RUN cd /opt/brainageR/software &&\
wget https://github.com/james-cole/brainageR/releases/download/2.1/pca_center.rds
# pca_rotation.rds
RUN cd /opt/brainageR/software &&\
wget https://github.com/james-cole/brainageR/releases/download/2.1/pca_rotation.rds
# pca_scale.rds
RUN cd /opt/brainageR/software &&\
wget https://github.com/james-cole/brainageR/releases/download/2.1/pca_scale.rds
# Install the needed packages
RUN apt-get update
RUN apt-get install -y --fix-missing \
cmake \
gcc \
g++ \
git \
libeigen3-dev \
zlib1g-dev \
libpng-dev \
openssl* \
doxygen \
xvfb \
curl
# Install NiftyReg and NiftySeg from QNI bitbucket account
RUN cd /opt && \
git clone https://github.com/KCL-BMEIS/niftyreg.git niftyreg && \
cd niftyreg && \
mkdir build-reg && \
cd build-reg && \
cmake \
-D \
CMAKE_BUILD_TYPE=Release \
BUILD_SHARED_LIBS=ON \
BUILD_ALL_DEP=ON \
USE_OPENMP=ON \
/opt/niftyreg && \
make && \
make install && \
cd /opt && \
git clone https://github.com/KCL-BMEIS/niftyseg.git niftyseg && \
cd niftyseg && \
mkdir build-seg && \
cd build-seg && \
cmake \
-D \
CMAKE_BUILD_TYPE=Release \
BUILD_SHARED_LIBS=ON \
USE_OPENMP=ON \
/opt/niftyseg && \
make && \
make install
RUN chmod +x /opt/brainageR/software/brainageR