Singularity.centos7

Bootstrap: docker
From: centos:7.5.1804


%labels
    Maintainer: Tashrif Billah <tbillah@bwh.harvard.edu>
    Organization: PNL-BWH-HMS
    Version: 0.0.0


%help
    Singularity recipe for FSL and TBSS
    https://github.com/pnlbwh/tbss/README.md


%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 libmng libpng12


    # install FSL

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


    # setup FSL environment

    export FSLDIR=/fsl-6.0.1-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.*


    # install python

    wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh \
	-O Miniconda3-latest-Linux-x86_64.sh \
    && /bin/bash Miniconda3-latest-Linux-x86_64.sh -b -p miniconda3/


    # activate miniconda3

    source /miniconda3/bin/activate
    export ANTSPATH=/miniconda3/bin/

    # install ANTs=2.3.0
    conda install -y -c pnlbwh ants

    # libraries and commands for TBSS
    yum -y install git bc unzip gcc

    # clone TBSS
    git clone https://github.com/pnlbwh/tbss.git

    # install TBSS
    /bin/bash tbss/install.sh setup

    # run tests
    /bin/bash tbss/install.sh test


%environment
    
    export FSLDIR=/fsl-6.0.1-centos7
    export PATH=$FSLDIR/bin/:$PATH
    export ANTSPATH=/miniconda3/bin/
    source $FSLDIR/etc/fslconf/fsl.sh
    source /miniconda3/bin/activate