khanlab/neuroglia-core:v1.0.0

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

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/src
cp -Rv . $SINGULARITY_ROOTFS/src

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

cd /src

# checkout specific git release 
SINGULARITY_TAG=${SINGULARITY_BUILDDEF#Singularity.}
if [ ! "$SINGULARITY_TAG" = "Singularity" ]
then
  apt-get install -y git
  git checkout $SINGULARITY_TAG
fi

cd /src/install_scripts

export DEBIAN_FRONTEND=noninteractive
bash 00.install_basics_sudo.sh
bash 03.install_anaconda2_nipype_dcmstack_by_binary.sh /opt
bash 04.install_octave_sudo.sh 
bash 10.install_afni_fsl_sudo.sh
bash 12.install_c3d_by_binary.sh /opt
bash 15.install_freesurfer_minimal_by_binary.sh /opt
bash 16.install_ants_by_binary.sh /opt
bash 17.install_dcm2niix_by_binary.sh /opt
bash 23.install_heudiconv_by_source.sh /opt
bash 24.install_bids-validator_sudo.sh
bash 25.install_niftyreg_by_source.sh /opt



#remove all install scripts
rm -rf /src


#########
%environment

#export PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin

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

#c3d
export PATH=/opt/c3d/bin:$PATH
#leave out deps for c3d gui to avoid conflicts
#export LD_LIBRARY_PATH=/opt/c3d/lib/c3d_gui-1.1.0:$LD_LIBRARY_PATH 

#itksnap
#export PATH=/opt/itksnap/bin:$PATH
#export LD_LIBRARY_PATH=/opt/itksnap/lib/snap-3.6.0:$LD_LIBRARY_PATH

#dicom_retrieve.py use dcm4che's getscu. So, put dcm4che's PATH before dcmtk's PATH
#dcm4che
#export PATH=/opt/dcm4che-3.3.8/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

#dcm2niix
export PATH=/opt/mricrogl_lx:$PATH

#heudiconv
export PYTHONPATH=/opt/heudiconv:$PYTHONPATH

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

#matlab on graham (requires user to be on sharcnet matlab users list)
export JAVA_HOME=/cvmfs/soft.computecanada.ca/easybuild/software/2017/Core/java/1.8.0_121
export MLM_LICENSE_FILE=/cvmfs/restricted.computecanada.ca/config/licenses/matlab/inst_uwo/graham.lic
export PATH=/cvmfs/restricted.computecanada.ca/easybuild/software/2017/Core/matlab/2017a:/cvmfs/restricted.computecanada.ca/easybuild/software/2017/Core/matlab/2017a/bin:/cvmfs/soft.computecanada.ca/easybuild/software/2017/Core/java/1.8.0_121:/cvmfs/soft.computecanada.ca/easybuild/software/2017/Core/java/1.8.0_121/bin:$PATH
export _JAVA_OPTIONS=-Xmx256m
export LIBRARY_PATH=/cvmfs/soft.computecanada.ca/easybuild/software/2017/Core/java/1.8.0_121/lib

#freesurfer - minimal
export FREESURFER_HOME=/opt/freesurfer_minimal
export PATH=$FREESURFER_HOME/bin:$PATH

Collection

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

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