Singularity.v1.3.4

Bootstrap: docker
From: ubuntu:20.04

%help
  First level fMRI analysis for specific GenFac tasks
  Info and usage:
    /opt/gf-fmri/README.md


%setup
  mkdir -p ${SINGULARITY_ROOTFS}/opt/gf-fmri


%files
  src                          /opt/gf-fmri
  matlab                       /opt/gf-fmri
  README.md                    /opt/gf-fmri
  test_container.sh            /opt/gf-fmri

 
%labels
  Maintainer baxter.rogers@vanderbilt.edu


%post
  apt-get update > /dev/null 2>&1
  apt-get install -y wget unzip zip xvfb ghostscript imagemagick bc > /dev/null 2>&1   # Misc tools
  apt-get install -y openjdk-8-jre                                  > /dev/null 2>&1   # Matlab
  apt-get install -y libopenblas-base language-pack-en              > /dev/null 2>&1   # FSL
  
  # Fix imagemagick policy to allow PDF output and text read. See https://usn.ubuntu.com/3785-1/
  sed -i 's/rights="none" pattern="PDF"/rights="read | write" pattern="PDF"/' \
    /etc/ImageMagick-6/policy.xml
  sed -i 's/rights="none" pattern="@\*"/rights="read" pattern="@*"/' \
    /etc/ImageMagick-6/policy.xml
  
  # Download the Matlab Compiled Runtime installer, install, clean up
  mkdir /MCR
  wget -nv -P /MCR https://ssd.mathworks.com/supportfiles/downloads/R2019b/Release/6/deployment_files/installer/complete/glnxa64/MATLAB_Runtime_R2019b_Update_6_glnxa64.zip
  unzip -qq /MCR/MATLAB_Runtime_R2019b_Update_6_glnxa64.zip -d /MCR/MATLAB_Runtime_R2019b_Update_6_glnxa64
  /MCR/MATLAB_Runtime_R2019b_Update_6_glnxa64/install -mode silent -agreeToLicense yes > /dev/null 2>&1
  rm -r /MCR/MATLAB_Runtime_R2019b_Update_6_glnxa64 /MCR/MATLAB_Runtime_R2019b_Update_6_glnxa64.zip
  rmdir /MCR

  # FSL. We need 6.0.4 for the b02b01_1.sch topup schedule. See
  # https://fsl.fmrib.ox.ac.uk/fsldownloads/manifest.csv
  # And, the centos7 version suits for Ubuntu 14-20.
  fslver=6.0.4
  cd /usr/local
  wget -nv https://fsl.fmrib.ox.ac.uk/fsldownloads/fsl-${fslver}-centos7_64.tar.gz
  tar -zxf fsl-${fslver}-centos7_64.tar.gz
  rm fsl-${fslver}-centos7_64.tar.gz

  # FSL setup
  export FSLDIR=/usr/local/fsl
  . ${FSLDIR}/etc/fslconf/fsl.sh
  export PATH=${FSLDIR}/bin:${PATH}
  
  # Run the FSL python installer. A clue that we forgot this is an imglob error at runtime
  ${FSLDIR}/etc/fslconf/fslpython_install.sh
  
  # Create input/output directories for binding
  mkdir /INPUTS && mkdir /OUTPUTS

  # Singularity-hub doesn't work with github LFS (it gets the pointer info instead 
  # of the actual file) so we get the compiled matlab executable via direct download.
  rm /opt/gf-fmri/matlab/bin/spm12.ctf
  wget -nv -P /opt/gf-fmri/matlab/bin https://github.com/baxpr/gf-fmri/raw/master/matlab/bin/spm12.ctf

  # We need to run the matlab executable now to extract the CTF, because
  # now is the only time the container is writeable
  /opt/gf-fmri/matlab/bin/run_spm12.sh /usr/local/MATLAB/MATLAB_Runtime/v97 quit


%environment

  # Matlab shell. We don't need to set the Matlab library path here, because 
  # Matlab's auto-generated run_??.sh script does it for us.
  MATLAB_SHELL=/bin/bash

  # FSL
  export FSLDIR=/usr/local/fsl
  
  # Path
  export PATH=/opt/gf-fmri/src:/opt/gf-fmri/matlab/bin:/usr/local/fsl/bin:${PATH}


%runscript
  wrapper.sh "$@"