Bootstrap: docker
From: ubuntu:16.04
Stage: spython-base

%files
neurodebian.gpg /root/.neurodebian.gpg
brainageR /opt/tmp/brainageR

%post
# 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
apt-get update
apt-get install -y --fix-missing \
unzip \
git \
wget \
openssl \
libssl-dev \
libxml2 \
libcurl4-openssl-dev

# Install R-package
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
echo "en_US.UTF-8 UTF-8" >> /etc/locale.gen \
&& locale-gen en_US.utf8 \
&& /usr/sbin/update-locale LANG=en_US.UTF-8

LC_ALL=en_US.UTF-8
LANG=en_US.UTF-8

# This was not needed before but we need it now
DEBIAN_FRONTEND=noninteractive

# Otherwise timedatectl will get called which leads to 'no systemd' inside Docker
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
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
R -e "install.packages('kernlab',dependencies=TRUE, repos='http://cran.rstudio.com/')"
R -e "install.packages('RNifti',dependencies=TRUE, repos='http://cran.rstudio.com/')"
R -e "install.packages('stringr',dependencies=TRUE, repos='http://cran.rstudio.com/')"

# Install SMP12 and Octave
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*

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/main/octave/spm12_r7771.patch \
| patch -p0 \
&& 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
apt-get update

# setup FSL using debian
NDEB_URL=http://neuro.debian.net/lists/xenial.us-ca.full

apt-get install -y software-properties-common python-software-properties
add-apt-repository universe
apt-get update

\
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
\
apt-get update && \
apt-get install -y \
fsl-5.0-core \
fsl-mni152-templates=5.0.7-2

# Configure environment
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

PATH=$FSLDIR/bin:$PATH
PATH=.:$PATH
PATH=/opt/brainageR/software:$PATH

\
echo ". $FSLDIR/etc/fslconf/fsl.sh" >> ~/.bashrc && \
echo "export FSLDIR PATH" >> ~/.bashrc

# Install brainageR
# Install brainageR zip v2.1 from github
cd /opt && \
wget https://github.com/james-cole/brainageR/archive/refs/tags/2.1.zip

# BrainageR directory
cd /opt && \
pwd
ls -al
mkdir brainageR

# Unzip 2.1 in brainageR directory
cd /opt && \
unzip 2.1.zip -d /opt/brainageR
      
# Rename unzipped 2.1 folder (brainageR-2.1)
cd /opt/brainageR &&\
mv brainageR-2.1 software

# Data directory for input and output
mkdir -p /data

# Download PCAs
# pca_center.rds 
cd /opt/brainageR/software &&\
wget  https://github.com/james-cole/brainageR/releases/download/2.1/pca_center.rds

# pca_rotation.rds
cd /opt/brainageR/software &&\
wget  https://github.com/james-cole/brainageR/releases/download/2.1/pca_rotation.rds
# pca_scale.rds 
cd /opt/brainageR/software &&\
wget  https://github.com/james-cole/brainageR/releases/download/2.1/pca_scale.rds

# Install the needed packages
apt-get update
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
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

# Substituting brainageR script by a brainageR script with new software directories·
# Edited variables: brainageR_dir, spm_dir, matlab_path,FSLDIR
mv /opt/tmp/brainageR /opt/brainageR/software/brainageR
chmod +x /opt/brainageR/software/brainageR

%environment
export LC_ALL=en_US.UTF-8
export LANG=en_US.UTF-8
export DEBIAN_FRONTEND=noninteractive
export TZ=UTC
export NDEB_URL=http://neuro.debian.net/lists/xenial.us-ca.full
export FSLDIR=/usr/share/fsl/5.0
export FSLOUTPUTTYPE=NIFTI_GZ
export FSLMULTIFILEQUIT=TRUE
export POSSUMDIR=/usr/share/fsl/5.0
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/lib/fsl/5.0
export FSLTCLSH=/usr/bin/tclsh
export FSLWISH=/usr/bin/wish
export PATH=$FSLDIR/bin:$PATH
export PATH=.:$PATH
export PATH=/opt/brainageR/software:$PATH
%runscript
exec /bin/bash "$@"
%startscript
exec /bin/bash "$@"