Singularity.0.0.1h

Bootstrap: docker
From: ubuntu:xenial

#note: install_afni_fsl_sudo.sh solves error message when run itksnap: LibGlu.so.1

#run freesurfer's freeview 
# if libQtOpenGL.so.4, run sudo apt-get libqt4-dev
# if missing:  libjpeg.so.62, run apt-get install libjpeg62

#create image
#rm ~/neuroglia/neuroglia.img && singularity create  --size 20000 ~/neuroglia/neuroglia.img && sudo singularity bootstrap ~/neuroglia/neuroglia.img Singularity

#########
%setup
#########
mkdir -p $SINGULARITY_ROOTFS/gradcorrect
cp -Rv . $SINGULARITY_ROOTFS/gradcorrect

#########
%post
#########

cd /gradcorrect/deps

export DEBIAN_FRONTEND=noninteractive
bash 00.install_basics_sudo.sh
bash 03.install_anaconda2_nipype_dcmstack_by_binary.sh /opt
bash 10.install_afni_fsl_sudo.sh
bash 12.install_c3d_by_binary.sh
bash 16.install_ants_by_binary.sh /opt
bash 25.install_niftyreg_by_source.sh /opt
bash 28.install_gradunwarp_by_source.sh /opt




#########
%environment

#anaconda2
export PATH=/opt/anaconda2/bin/:$PATH

#fsl
export FSLDIR=/usr/share/fsl/5.0
export POSSUMDIR=$FSLDIR
export PATH=/usr/lib/fsl/5.0:$PATH
export FSLOUTPUTTYPE=NIFTI_GZ
export FSLMULTIFILEQUIT=TRUE
export FSLTCLSH=/usr/bin/tclsh
export FSLWISH=/usr/bin/wish
export FSLBROWSER=/etc/alternatives/x-www-browser
export LD_LIBRARY_PATH=/usr/lib/fsl/5.0:${LD_LIBRARY_PATH}

#c3d
export PATH=/opt/c3d/bin:$PATH

#ants
export PATH=/opt/ants:$PATH
export ANTSPATH=/opt/ants


#niftyreg
export LD_LIBRARY_PATH=/opt/niftyreg-1.3.9/lib:$LD_LIBRARY_PATH 
export PATH=/opt/niftyreg-1.3.9/bin:$PATH

#this app:
export PATH=/gradcorrect:$PATH

%runscript
exec /gradcorrect/run.sh $@