higgsPheno.def

####
# to build me
# sudo singularity build higgsPheno.sif higgsPheno.def
####
# to run me do
# singularity run --containall --bind /my/out/dir/ higgsPheno.sif
#     the "--containall" flag prevents interactions with your system
#     the "--bind /my/out/dir/" mounts a directory in your system
#     this allows scripts in that directory to be accessed from the image
#     and results from the image to persist in the directory
#     It also allows the run script to call .bashrc

BootStrap: docker
From: ubuntu:18.04
    
# commands on the host system
# try to avoid doing stuff here
%setup

# get files from the host (but we dont need any)
%files

# what is done when the container is built
%post
    # make print colour #
    GREEN='\033[0;32m'
    NOCOLOUR='\033[0m'
    # start
    echo "${GREEN}~~~ install apt packages ~~~ ${NOCOLOUR}"
    apt -y update
    apt -y install python2.7 git wget vim-tiny nano make libgsl-dev g++

    #echo "${GREEN}~~~ Give the user permission and control ~~~ ${NOCOLOUR}"
    umask 000

    echo "${GREEN}~~~ Getting modified packages from github ~~~ ${NOCOLOUR}"
    PACKAGES=$SINGULAITY_ROOTFS/packages
    git clone https://github.com/HenryDayHall/higgsPhenoPackages.git $PACKAGES

    echo "${GREEN}~~~ Making the packages ~~~ ${NOCOLOUR}"
    echo "${GREEN}~~~ 2HDMC ~~~ ${NOCOLOUR}"
    cd $PACKAGES/2HDMC
    # for some reason the lib dir is not automaticaly constructed
    mkdir lib
    make

    echo "${GREEN}~~~ Set up a .bashrc ~~~ ${NOCOLOUR}"
    BASHRC=/home/.bashrc
    touch $BASHRC
    # will be called in run

    echo "${GREEN}~~~ Create sylinks for programs ~~~ ${NOCOLOUR}"
    ln -s $(which vim-tiny) /usr/local/bin/vim
    ln -s $(which python2.7) /usr/local/bin/python


# enviroment variabels instide the container
# sourced at run time not build time
%environment
    export PACKAGES=/packages/
    export BASHRC=/home/.bashrc


# this is executed when the contain is launched with
# singularity run higgsPheno.sif
%runscript
    # make print colour #
    GREEN='\033[0;32m'
    NOCOLOUR='\033[0m'
    echo "${GREEN}~~~ Link packages to the users home directory ~~~ ${NOCOLOUR}"
    ln -s /packages/2HDMC ~/
    /bin/bash --rcfile $BASHRC
    

# this would be executed just after build
%test
    echo I havent written any tests

# metadata
%labels
    Author HenryDayHall
    Version v1.0

%help
    to build me
    > sudo singularity build higgsPheno.sif higgsPheno.def
    to run me do
    > singularity run --containall --bind /my/out/dir/ higgsPheno.sif
        the "--containall" flag prevents interactions with your system
        the "--bind /my/out/dir/" mounts a directory in your system
        this allows scripts in that directory to be accessed from the image
        and results from the image to persist in the directory
        It also allows the run script to call .bashrc