khanlab/neuroglia-core-minc:v1.0.0

$ singularity pull shub://khanlab/neuroglia-core-minc:v1.0.0

Singularity Recipe

Bootstrap: docker
From: ubuntu:xenial

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

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

cd /src/install_scripts

export DEBIAN_FRONTEND=noninteractive
bash 00.install_basics_sudo.sh
bash 10.install_afni_fsl_sudo.sh
bash 16.install_ants_by_binary.sh /opt
bash 25.install_niftyreg_by_source.sh /opt
bash 22.install_minc_by_deb.sh /opt


#remove all install scripts
rm -rf /src


#########
%environment


#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

#minc
export MINC_TOOLKIT=/opt/minc/1.9.15
export MINC_TOOLKIT_VERSION="1.9.15-20170529"
export PATH=/opt/minc/1.9.15/bin:/opt/minc/1.9.15/pipeline:${PATH}
export PERL5LIB=/opt/minc/1.9.15/perl:/opt/minc/1.9.15/pipeline:${PERL5LIB}
export LD_LIBRARY_PATH=/opt/minc/1.9.15/lib:/opt/minc/1.9.15/lib/InsightToolkit:${LD_LIBRARY_PATH}
export MNI_DATAPATH=/opt/minc/1.9.15/share
export MINC_FORCE_V2=1
export MINC_COMPRESS=4
export VOLUME_CACHE_THRESHOLD=-1
export MANPATH=/opt/minc/1.9.15/man:${MANPATH}

Collection

• Name: khanlab/neuroglia-core-minc
• License: None

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