Singularity.centos7

Bootstrap: docker
From: centos:7.5.1804


%labels
    Maintainer: Tashrif Billah <tbillah@bwh.harvard.edu>
    Organization: PNL-BWH-HMS


%help
    Singularity recipe for FSL and FSLeyes


%post
    # set up user and working directory

    cd /


    # libraries and commands for FSL

    yum -y update
    yum -y install epel-release wget file bzip2 openblas-devel which libmng libpng12 libSM gtk2 mesa-dri-drivers


    # install FSL, -V 5.0.11, you are welcome to change it below

    wget https://fsl.fmrib.ox.ac.uk/fsldownloads/fslinstaller.py -O fslinstaller.py
    python fslinstaller.py -V 6.0.1 -d `pwd`/fsl-5.0.11-centos7 -p


    # setup FSL environment

    export FSLDIR=/fsl-5.0.11-centos7
    # export PATH=$FSLDIR/bin/:$PATH
    # source $FSLDIR/etc/fslconf/fsl.sh

    # apply patch

    $FSLDIR/fslpython/bin/conda install -y -n fslpython -c conda-forge deprecation==1.*


%environment
    
    export FSLDIR=/fsl-5.0.11-centos7
    export PATH=$FSLDIR/bin/:$PATH
    source $FSLDIR/etc/fslconf/fsl.sh