khanlab/gradcorrect:0.0.1f

$ singularity pull shub://khanlab/gradcorrect:0.0.1f

Singularity Recipe

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 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}

#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 $@

Collection

• Name: khanlab/gradcorrect
• License: GNU General Public License v3.0

Metrics

Feedback

Was this page helpful?

Glad to hear it! Please tell us how we can improve.

Sorry to hear that. Please tell us how we can improve.