Singularity.v0.0.4

Bootstrap: shub
From: khanlab/neuroglia-dwi:v1.0.0


%labels
Maintainer "Ali Khan"

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%setup
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mkdir -p $SINGULARITY_ROOTFS/opt/vasst-dev
cp -Rv . $SINGULARITY_ROOTFS/opt/vasst-dev

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%post
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echo addpath\(genpath\(\'/opt/vasst-dev/tools/matlab\'\)\)\; >> /etc/octave.conf 

cd /opt/vasst-dev/install_scripts
export DEBIAN_FRONTEND=noninteractive

bash 05.install_MCR.sh /opt v92 R2017a
bash 27.install_vasst_dev_atlases_by_source.sh /opt


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%environment



#vasst-dev
export VASST_DEV_HOME=/opt/vasst-dev
export PIPELINE_ATLAS_DIR=/opt/atlases
export PIPELINE_DIR=$VASST_DEV_HOME/pipeline
export PIPELINE_TOOL_DIR=$VASST_DEV_HOME/tools
MIAL_DEPENDS_DIR=$VASST_DEV_HOME/mial-depends
#MIAL_DEPENDS_LIBS=$VASST_DEV_HOME/mial-depends/lib
#export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$MIAL_DEPENDS_LIBS
export PIPELINE_CFG_DIR=$PIPELINE_DIR/cfg
export PATH=$PIPELINE_TOOL_DIR:$MIAL_DEPENDS_DIR:$PATH
export MCRBINS=$VASST_DEV_HOME/mcr/v92
for name in `ls -d $PIPELINE_DIR/*`; do  export PATH=$name:$PATH; done
#mcr - vasst-dev dependency
export MCRROOT=/opt/mcr/v92