a build specification file for a Singularity bootstrap for Joke

Singularity

Bootstrap: docker
From: joke/hcppipelines

%runscript

exec /run.py "$@"

%post

# Make script executable
chmod +x /run.py

# add variables to the environment file
echo "" >> /environment
echo "export FSLDIR=/usr/share/fsl/5.0" >> /environment
echo 'export FSL_DIR="${FSLDIR}"' >> /environment
echo "export FSLOUTPUTTYPE=NIFTI_GZ" >> /environment
echo "export PATH=/usr/lib/fsl/5.0:$PATH" >> /environment
echo "export FSLMULTIFILEQUIT=TRUE" >> /environment
echo "export POSSUMDIR=/usr/share/fsl/5.0" >> /environment
echo "export LD_LIBRARY_PATH=/usr/lib/fsl/5.0:$LD_LIBRARY_PATH" >> /environment
echo "export FSLTCLSH=/usr/bin/tclsh" >> /environment
echo "export FSLWISH=/usr/bin/wish" >> /environment
echo "export FSLOUTPUTTYPE=NIFTI_GZ" >> /environment
echo "export CARET7DIR=/usr/bin" >> /environment
echo "export HCPPIPEDIR=/opt/HCP-Pipelines" >> /environment
echo "export HCPPIPEDIR_Templates=${HCPPIPEDIR}/global/templates" >> /environment
echo "export HCPPIPEDIR_Bin=${HCPPIPEDIR}/global/binaries" >> /environment
echo "export HCPPIPEDIR_Config=${HCPPIPEDIR}/global/config" >> /environment
echo "export HCPPIPEDIR_PreFS=${HCPPIPEDIR}/PreFreeSurfer/scripts" >> /environment
echo "export HCPPIPEDIR_FS=${HCPPIPEDIR}/FreeSurfer/scripts" >> /environment
echo "export HCPPIPEDIR_PostFS=${HCPPIPEDIR}/PostFreeSurfer/scripts" >> /environment
echo "export HCPPIPEDIR_fMRISurf=${HCPPIPEDIR}/fMRISurface/scripts" >> /environment
echo "export HCPPIPEDIR_fMRIVol=${HCPPIPEDIR}/fMRIVolume/scripts" >> /environment
echo "export HCPPIPEDIR_tfMRI=${HCPPIPEDIR}/tfMRI/scripts" >> /environment
echo "export HCPPIPEDIR_dMRI=${HCPPIPEDIR}/DiffusionPreprocessing/scripts" >> /environment
echo "export HCPPIPEDIR_dMRITract=${HCPPIPEDIR}/DiffusionTractography/scripts" >> /environment
echo "export HCPPIPEDIR_Global=${HCPPIPEDIR}/global/scripts" >> /environment
echo "export HCPPIPEDIR_tfMRIAnalysis=${HCPPIPEDIR}/TaskfMRIAnalysis/scripts" >> /environment
echo "export MSMBin=${HCPPIPEDIR}/MSMBinaries" >> /environment
echo "export PYTHONPATH=''" >> /environment