baxpr/fmri_modularity:v1.0.0

$ singularity pull shub://baxpr/fmri_modularity:v1.0.0

Singularity Recipe

Bootstrap: docker
From: ubuntu:16.04

%help
fmri_modularity

FMRI functional connectivity processing - compute modularity from a connectivity
matrix.

See the associated YAML for inputs, outputs, and run command.

%files
  bin /matlab_bin

%labels
  Maintainer baxter.rogers@vanderbilt.edu

%post
  apt-get update
  apt-get install -y wget unzip zip xvfb ghostscript openjdk-8-jre imagemagick
    
  # Fix imagemagick policy to allow PDF output. See https://usn.ubuntu.com/3785-1/
  sed -i 's/rights="none" pattern="PDF"/rights="read | write" pattern="PDF"/' \
    /etc/ImageMagick-6/policy.xml

  # Download the Matlab Compiled Runtime installer, install, clean up
  mkdir /MCR
  wget -nv -P/MCR http://ssd.mathworks.com/supportfiles/downloads/R2017a/deployment_files/R2017a/installers/glnxa64/MCR_R2017a_glnxa64_installer.zip
  unzip /MCR/MCR_R2017a_glnxa64_installer.zip -d /MCR/MCR_R2017a_glnxa64_installer
  /MCR/MCR_R2017a_glnxa64_installer/install -mode silent -agreeToLicense yes
  rm -fr /MCR/MCR_R2017a_glnxa64_installer /MCR/MCR_R2017a_glnxa64_installer.zip
  rmdir /MCR

  # 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 /matlab_bin/fmri_modularity
  wget -nv -P /matlab_bin https://github.com/baxpr/fmri_modularity/raw/master/bin/fmri_modularity
  chmod ugo+rx /matlab_bin/fmri_modularity
  
%environment
  # Set Matlab library path
  LD_LIBRARY_PATH=/usr/local/MATLAB/MATLAB_Runtime/v92/runtime/glnxa64:/usr/local/MATLAB/MATLAB_Runtime/v92/bin/glnxa64:/usr/local/MATLAB/MATLAB_Runtime/v92/sys/os/glnxa64:${LD_LIBRARY_PATH}
  export LD_LIBRARY_PATH

%runscript
    xvfb-run --server-num=$(($$ + 99)) \
    --server-args='-screen 0 1600x1200x24 -ac +extension GLX' \
    sh /matlab_bin/run_fmri_modularity.sh \
    /usr/local/MATLAB/MATLAB_Runtime/v92 "$@"

Collection


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key value
id /containers/baxpr-fmri_modularity-v1.0.0
collection name baxpr/fmri_modularity
branch master
tag v1.0.0
commit cf5b733276949992622cdc95022b52e0668dffe9
version (container hash) e3041514ab02ee78339f74b0e09c92f8
build date 2018-10-26T11:06:03.712Z
size (MB) 3589
size (bytes) 1581309983
SIF Download URL (please use pull with shub://)
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