baxpr/freesurfer-singularity:dev2

$ singularity pull shub://baxpr/freesurfer-singularity:dev2

Singularity Recipe

Bootstrap: docker
From: centos:7.5.1804

%help

Freesurfer development version. Runs recon-all plus hippocampus, thalamus, 
brainstem modules. Requires a valid license file at runtime.

Useful information within the container:
  /opt/README.md                          Summary and references
  /opt/USAGE.md                           Detailed instructions
  /usr/local/freesurfer/build-stamp.txt   Specific Freesurfer version


%files

  # Freesurfer development version, if we are going to download manually and 
  # reference a local copy during the build
  # https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/freesurfer-linux-centos7_x86_64-dev.tar.gz
  #freesurfer-linux-centos7_x86_64-dev.tar.gz /usr/local

  # Matlab runtime, if we are going to download manually and ref the local copy
  # http://ssd.mathworks.com/supportfiles/downloads/R2014b/deployment_files/R2014b/installers/glnxa64/MCR_R2014b_glnxa64_installer.zip
  #MCR_R2014b_glnxa64_installer.zip /opt

  # FSL archive, if we are going to download manually and ref the local copy
  # https://fsl.fmrib.ox.ac.uk/fsldownloads/fsl-6.0.0-centos7_64.tar.gz
  #fsl-6.0.0-centos7_64.tar.gz /opt

  # Default run scripts
  src /opt

  # Usage and Readme
  USAGE.md /opt
  README.md /opt
  

%post
  
  # For installs
  yum -y install unzip wget
  
  # For Freesurfer
  yum -y install tcsh bc mesa-libGLU libgomp perl mesa-dri-drivers libicu
  
  # For FSL
  yum -y install epel-release
  yum -y install openblas-devel
  
  # For matlab runtime
  yum -y install java-1.8.0-openjdk
  
  # For X
  yum -y install xorg-x11-server-Xvfb xorg-x11-xauth which

  # For PDF outputs
  yum -y install ImageMagick
  
  # Python modules
  yum -y install python-pip
  pip install pandas numpy
  
  # We need a piece of FSL (fslstats)
  wget -nv -P /opt https://fsl.fmrib.ox.ac.uk/fsldownloads/fsl-6.0.0-centos7_64.tar.gz
  cd /opt
  tar -zxf fsl-6.0.0-centos7_64.tar.gz
  mkdir -p /usr/local/fsl/bin
  cp fsl/bin/fslstats /usr/local/fsl/bin
  rm -r fsl fsl-6.0.0-centos7_64.tar.gz
  
  # Matlab runtime for brainstem, hippocampus, thalamus modules
  wget -nv -P /opt http://ssd.mathworks.com/supportfiles/downloads/R2014b/deployment_files/R2014b/installers/glnxa64/MCR_R2014b_glnxa64_installer.zip
  unzip -q /opt/MCR_R2014b_glnxa64_installer.zip -d /opt/MCR_R2014b_glnxa64_installer
  /opt/MCR_R2014b_glnxa64_installer/install -mode silent -agreeToLicense yes
  rm -r /opt/MCR_R2014b_glnxa64_installer
  rm /opt/MCR_R2014b_glnxa64_installer.zip

  # Install Freesurfer
  # Make our own build stamp since FS dev seems to not provide it sometimes
  wget -nv -P /usr/local https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/freesurfer-linux-centos7_x86_64-dev.tar.gz
  cd /usr/local
  tar -zxf freesurfer-linux-centos7_x86_64-dev.tar.gz
  md5sum freesurfer-linux-centos7_x86_64-dev.tar.gz > freesurfer/build-hash.txt
  rm freesurfer-linux-centos7_x86_64-dev.tar.gz
  cd /usr/local/freesurfer
  H=$(cat build-hash.txt)
  echo ${H% freesurfer-linux-centos7_x86_64-dev.tar.gz} > build-hash.txt
  cat build-hash.txt build-stamp.txt > build-info.txt

  # Freeview needs a machine id here
  dbus-uuidgen > /etc/machine-id
  
  # Tell freesurfer where to find the MCR
  ln -s /usr/local/MATLAB/MATLAB_Compiler_Runtime/v84 /usr/local/freesurfer/MCRv84

  # Create input/output directories for binding
  mkdir /INPUTS && mkdir /OUTPUTS


%environment

  # FSL (we only use fslstats so no need for the full setup)
  export FSLOUTPUTTYPE=NIFTI_GZ
  
  # Freesurfer
  export FREESURFER_HOME=/usr/local/freesurfer


%runscript
  xvfb-run --server-num=$(($$ + 99)) \
  --server-args='-screen 0 1600x1200x24 -ac +extension GLX' \
  bash /opt/src/run_everything.sh "$@"

Collection

• Name: baxpr/freesurfer-singularity
• License: None

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