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MICe-container.def
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MICe-container.def
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Bootstrap: debootstrap
OSVersion: focal
MirrorURL: http://us.archive.ubuntu.com/ubuntu/
%environment
export ANTSPATH=/usr/local/bin
# remember the system manpath (from /etc/manpath.config) when prepending:
export MANPATH="::"
export MINC_COMPRESS=6
export MINC_FORCE_V2=1
# prevent arbitrary growth in memory use when processing many minc files:
export VOLUME_CACHE_THRESHOLD=-1
# stuff installed by python3 setup.py install rather than pip ends up here:
export PYTHONPATH=/usr/lib/python3.8/site-packages:$PYTHONPATH
export R_LIBS_SITE=/usr/local/R/packratting/packrat/lib/x86_64-pc-linux-gnu/3.6.3 R
%post -c /bin/bash
export BUILD_CORES=8
export MINC_TOOLKIT_COMMIT="b98e4972bdac2b78e3c1e412d75c97e2e7c5f6b9"
export MINC_TOOLKIT_VERSION="1.9.18.2"
export RSTUDIO_VERSION="2022.07.1-554-amd64"
export ANTS_VERSION="aacdc61e35a5ea4a4f93f6ac6b04f71d091d6b6d"
export MINC2_SIMPLE_COMMIT="6382802dd6e3f712d394c7d708281d05b7e9a82b"
export CCTOOLS_VERSION="release/7.4.7"
export PYDPIPER_COMMIT="7277fad53b08157df50c0a3ab502b729854f4c62"
export PYEZMINC_COMMIT="4a1c16f834f1bbe4ebbef2985f42dac1ebd30dd2"
export RMINC_VERSION="1.5.3.0"
export MICE_LAB_COMMIT="78a54d7c34022aed28af05d2c625e1fe0e3b4778"
export F3D_VERSION=1.1.1
export SLICER_VERSION=v4.11.20210226
export DEBIAN_FRONTEND=noninteractive
# according to the Singularity documentation "best practice" is to install system packages
# here rather than via the 'Include' keyword (why?)
cat <<EOF > /etc/apt/sources.list
deb http://ca.archive.ubuntu.com/ubuntu/ focal main restricted
deb http://ca.archive.ubuntu.com/ubuntu/ focal-updates main restricted
deb http://ca.archive.ubuntu.com/ubuntu/ focal universe
deb http://ca.archive.ubuntu.com/ubuntu/ focal-updates universe
deb http://ca.archive.ubuntu.com/ubuntu/ focal multiverse
deb http://ca.archive.ubuntu.com/ubuntu/ focal-updates multiverse
deb http://security.ubuntu.com/ubuntu focal-security main restricted
deb http://security.ubuntu.com/ubuntu focal-security universe
deb http://security.ubuntu.com/ubuntu focal-security multiverse
EOF
apt-get -y update
apt-get install -y ca-certificates gnupg
# NeuroDebian (removed because this repo is down)
apt-get -y update
apt-get install -y \
build-essential \
locales \
autoconf \
automake \
cmake \
libtool \
m4 \
flex \
bison \
gdb \
dpkg-sig \
gdebi-core \
swig \
texinfo \
g++ \
gfortran \
golang-go \
curl \
wget \
git \
lsof \
emacs \
neovim \
blender \
fsl \
gimp \
imagej \
imagemagick \
inkscape \
itksnap \
mencoder \
meshlab \
mplayer \
octave \
octave-openems \
openems \
pandoc \
parallel \
paraview \
python3 \
python3-pip \
r-base-core \
texlive-latex-extra \
texlive-science \
vlc \
freeglut3-dev \
libbz2-dev \
libcurl4-openssl-dev \
libeigen3-dev \
liblzma-dev \
libgl-dev \
libglu-dev \
libopenblas-dev \
libpcre2-dev \
libreadline-dev \
libssl-dev \
libssh-dev \
libsqlite3-dev \
libxml2-dev \
zlib1g-dev \
# update locales
locale-gen en_US.UTF-8 en_US en_CA.UTF-8 en_CA
#dpkg-reconfigure locales
pip3 install --upgrade pip setuptools wheel
# some other Python packages have broken builds,
# and require numpy already present
pip3 install --upgrade numpy cython
pip3 install attrdict # missing wxPython==4.2.0 dep
pip3 install --upgrade \
balsam-flow \
batchgenerators \
bids-validator \
cvxopt \
dask[complete] \
datalad \
dicom2nifti \
dipy \
disptools \
hyppo \
h5py \
imageio \
intensity-normalization \
ipython \
joblib \
jupyter \
matplotlib \
meshio \
mne \
neo \
networkx \
nibabel \
nilearn \
nipy \
nipype \
nitime \
nitransforms \
numexpr \
opencv-python \
openpyxl \
pandas \
pillow \
pybids \
pydicom \
pynrrd \
pyosf \
pytest \
pywavelets \
pyxnat \
scikit-build \
scikit-image \
scikit-learn \
scipy \
SimpleITK \
seaborn \
simpy \
statsmodels \
sympy \
tables \
transforms3d \
#pytorch-lightning \
#pytorch-metric-learning \
#skorch \
#tensorboardx \
#torch \
#torchvision \
#psychopy \ wxPython/wxwidgets install fails
# TODO pysurfer/visbrain/vispy - Mayavi build hangs
# TODO install torch, torchvision according to CPU, CUDA etc.?
# numba # broken due to numpy bounds
# TODO itk - no wheel for 22.04 ?
# TODO vtk - borked
# TODO onnx and/or onnxruntime - borked
# install cctools
(git clone https:/cooperative-computing-lab/cctools.git
pushd cctools
git checkout ${CCTOOLS_VERSION}
./configure --prefix=/usr && make && make install
popd
rm -rf cctools)
# f3d # TODO vtk 9
#(git clone https:/f3d-app/f3d
# cd f3d
# git checkout "v${F3D_VERSION}"
# mkdir build
# cd build
# cmake ..
# make
# make install)
# slicer
#apt-get install -y qt5-default qtmultimedia5-dev qttools5-dev libqt5xmlpatterns5-dev libqt5svg5-dev qtwebengine5-dev qtscript5-dev qtbase5-private-dev libqt5x11extras5-dev libxt-dev
#(git clone https:/Slicer/Slicer.git
# cd Slicer
# git checkout ${SLICER_VERSION}
# ./Utilities/SetupForDevelopment.sh
# mkdir build
# cd build
# cmake -DCMAKE_BUILD_TYPE=Release ..
# make -j${BUILD_CORES}
# (cd Slicer-build
# make package
# #ctest -j4
# )
# ln -s /Slicer/build/Slicer-build/Slicer /usr/bin/Slicer
# )
# install rstudio desktop
gpg --keyserver keys.openpgp.org --recv-keys 3F32EE77E331692F
(wget https://download1.rstudio.org/desktop/bionic/amd64/rstudio-${RSTUDIO_VERSION}.deb
dpkg-sig --verify rstudio-${RSTUDIO_VERSION}.deb
gdebi -n rstudio-${RSTUDIO_VERSION}.deb
rm rstudio-${RSTUDIO_VERSION}.deb)
# to install rstudio-server (needs adaptation for container?):
(wget https://download2.rstudio.org/server/bionic/amd64/rstudio-server-${RSTUDIO_VERSION}.deb
dpkg-sig --verify rstudio-server-${RSTUDIO_VERSION}.deb
gdebi -n rstudio-server-${RSTUDIO_VERSION}.deb
rm rstudio-server-${RSTUDIO_VERSION}.deb)
apt-get autoclean
rm -rf /var/lib/apt/lists/*
# minc-toolkit-v2
(git clone --recursive https:/BIC-MNI/minc-toolkit-v2.git
mkdir minc-toolkit-v2/build
pushd minc-toolkit-v2/build
git checkout ${MINC_TOOLKIT_COMMIT}
git submodule update --recursive
# TODO build updated external c3d and set -DMT_BUILD_C3D=OFF
cmake -DMT_BUILD_SHARED_LIBS=ON -DMT_BUILD_ANTS=OFF -DMT_BUILD_VISUAL_TOOLS=ON -DMT_BUILD_ELASTIX=OFF ..
make -j${BUILD_CORES}
#make test
make install
popd
rm -rf minc-toolkit-v2)
# TODO -DCMAKE_BUILD_TYPE=RelWithDebugInfo
# TODO Elastix - separate build?
export MINC_TOOLKIT_CONFIG=/usr/local/minc-toolkit-config.sh
sed -i '/LD_LIBRARY_PATH/d' ${MINC_TOOLKIT_CONFIG}
. ${MINC_TOOLKIT_CONFIG}
echo "source ${MINC_TOOLKIT_CONFIG}" >> $SINGULARITY_ENVIRONMENT
# install ANTs
(git clone https:/ANTsX/ANTs.git
mkdir ANTs/build
pushd ANTs/build
git checkout ${ANTS_VERSION}
cmake -DITK_BUILD_MINC_SUPPORT=ON -DBUILD_TESTING=OFF -DCMAKE_INSTALL_PREFIX=/usr/local ..
make -j${BUILD_CORES}
cd ANTS-build && make install
popd
rm -rf ANTs)
# install minc-stuffs (automatically installs Pyminc)
(git clone --recursive https:/Mouse-Imaging-Centre/minc-stuffs.git
cd minc-stuffs
./autogen.sh
./configure --with-minc2 --with-build-path=/usr/local
make
make install
pip3 install .
cd ..
rm -rf minc-stuffs)
# install pyezminc
(git clone https:/BIC-MNI/pyezminc.git
cd pyezminc
git checkout ${PYEZMINC_COMMIT}
pip3 install .
#python3 setup.py install
cd ..
rm -rf pyezminc)
# install minc2-simple
(git clone https:/NIST-MNI/minc2-simple.git
mkdir minc2-simple/build
pushd minc2-simple/build
pushd build
git checkout ${MINC2_SIMPLE_COMMIT}
cmake ..
make
make install
python3 ../python/setup.py install
#pip3 install .
popd
rm -rf minc2-simple)
# install Pydpiper
(git clone https:/Mouse-Imaging-Centre/pydpiper.git
pushd pydpiper
git checkout ${PYDPIPER_COMMIT}
pip3 install .
popd
rm -rf pydpiper)
# install mice-lab
(git clone https:/Mouse-Imaging-Centre/MICe-lab.git
cd MICe-lab
git checkout ${MICE_LAB_COMMIT}
./autogen.sh
./configure
make
make install
#python3 setup.py install
pip3 install .
cd ..
rm -rf MICe-lab.git)
# TODO install more viewers (openvv, f3d, seg3d, mango/papaya, slicer)
# install RMINC and R packages:
(wget https:/Mouse-Imaging-Centre/RMINC/files/8307296/packratting-2022-03-18.tar.gz
mkdir -p /usr/local/R
Rscript -e 'install.packages("packrat"); library(packrat); packrat::unbundle("packratting-2022-03-18.tar.gz", where="/usr/local/R")'
export R_LIBS_SITE=/usr/local/R/packratting/packrat/lib/x86_64-pc-linux-gnu/3.6.3 R
Rscript -e 'library(devtools); devtools::install_github("Mouse-Imaging-Centre/RMINC@807ffc5886ae8ec407ecbbff81271e5476c08a41", upgrade="never"); devtools::install_github("Mouse-Imaging-Centre/MRIcrotome", upgrade="never")'
rm packratting-2022-03-18.tar.gz)
#(Rscript -e 'update.packages(repos="https://cloud.r-project.org",ask=F)'
# Rscript -e 'install.packages(c("lme4", "lmerTest", "tidyverse", "batchtools", "Rcpp", "rjson", "igraph", "jsonlite", "shiny", "visNetwork", "DT", "testthat", "bigstatsr", "data.table", "data.tree", "gridBase", "plotrix", "rgl", "rstanarm", "brms", "tidymodels", "vtreat", "dagitty", "lenses", "qvalue", "reticulate"), repos="https://cloud.r-project.org", ask=F)'
# wget https:/Mouse-Imaging-Centre/RMINC/archive/v${RMINC_VERSION}.tar.gz
# R CMD INSTALL v${RMINC_VERSION}.tar.gz --configure-args='--with-build-path=/usr/local'
# rm -f RMINC_${RMINC_VERSION}.tar.gz)
%labels
Maintainer Ben Darwin
Author [email protected]
Version 20240726
%help
MICe imaging packages. Loosely based on Vlad's minc-toolkit-containers repository.