easybuild_bootstrap_install.sh

#!/bin/bash

# Define help function
function help(){
    echo "EasyBuild Bootstrap - Bootstrap method of installing easybuild";
    echo "Usage example:";
    echo "easybuild-bootstrap (-e|--easybuild_install_base) char [(-h|--help) boolean] [(-E|--environment_modules)] [(-L|--lmod)] [(-b|--eb_version) char] [(-l|--lmod_version) char] [(-m|--em_version) char]";
    echo "Options:";
    echo "-h or --help boolean: Displays this information.";
    echo "-E or --environment_modules: Include Environment Modules.";
    echo "-e or --easybuild_install_base char: Easybuild software base. Required.";
    echo "-L or --lmod: Include Lmod.";
    echo "-b or --eb_version char: Easybuild Version  - Default 3.1.0.";
    echo "-l or --lmod_version char: Lmod Version - Default 7.3.16.";
    echo "-m or --em_version char: Environment Modules Version - Default 3.2.10.";
    exit 1;
}

EASYBUILD_BASE=0

# Declare vars. Flags initalizing to 0.
environment_modules=0
lmod=0

eb_version="3.1.0";
lmod_version="7.3.16";
em_version="3.2.10";

# Execute getopt
ARGS=$(getopt -o "h:Ee:Lb:l:m:" -l "help:,environment_modules,easybuild_install_base:,lmod,eb_version:,lmod_version:,em_version:" -n "EasyBuild Bootstrap" -- "$@");

#Bad arguments
if [[ $? -ne 0 ]];
then
    help;
fi

eval set -- "$ARGS";

while true; do
    case "$1" in
        -h|--help)
            shift;
                    if [[ -n "$1" ]];
                    then
                        help="$1";
                        shift;
                    fi
            ;;
        -E|--environment_modules)
            shift;
                    environment_modules="1";
            ;;
        -e|--easybuild_install_base)
            shift;
                    if [[ -n "$1" ]];
                    then
                        EASYBUILD_BASE="$1";
                        shift;
                    fi
            ;;
        -L|--lmod)
            shift;
                    lmod="1";
            ;;
        -b|--eb_version)
            shift;
                    if [[ -n "$1" ]];
                    then
                        eb_version="$1";
                        shift;
                    fi
            ;;
        -l|--lmod_version)
            shift;
                    if [[ -n "$1" ]];
                    then
                        lmod_version="$1";
                        shift;
                    fi
            ;;
        -m|--em_version)
            shift;
                    if [[ -n "$1" ]];
                    then
                        em_version="$1";
                        shift;
                    fi
            ;;

        --)
            shift;
            break;
            ;;
    esac
done


# Check required arguments
if [[ $EASYBUILD_BASE == 0 ]]
then
    echo "easybuild_base is required";
    help;
fi

echo "Beginning install."
echo ""

if [[ $lmod == 1 ]] && [[ $environment_modules == 1 ]]; then
  echo "You must specify either lmod or environment modules."
  exit 1
fi

if [[ $lmod == 0 ]] && [[ $environment_modules == 0 ]]; then
  echo "You have not specified either lmod or environment_modules."
  echo ""
fi

EASYBUILD_NAME="eb--${eb_version}"
LMOD_NAME="lmod--${lmod_version}"
EM_NAME="em--${em_version}"

if [[ "$lmod" -eq "1" ]]
then
    echo "We are including ${LMOD_NAME}";
    T="${EASYBUILD_NAME}_${LMOD_NAME}"
    EASYBUILD_NAME=$T
fi

if [[ "$environment_modules" -eq "1" ]]
then
    echo "We are including ${EM_NAME}";
    T="${EASYBUILD_NAME}_${EM_NAME}"
    EASYBUILD_NAME=$T
fi

EASYBUILD_PACKAGE="easybuild=${eb_version}"
LMOD_PACKAGE="lmod=${lmod_version}"
EM_PACKAGE="environment-modules=${em_version}"
EB_CONDA_INSTALL="${EASYBUILD_PACKAGE}"

if [[ "$lmod" -eq "1" ]]
then
    T="${EB_CONDA_INSTALL} ${LMOD_PACKAGE}"
    EB_CONDA_INSTALL=$T
fi

if [[ "$environment_modules" -eq "1" ]]
then
    T="${EB_CONDA_INSTALL} ${EM_PACKAGE}"
    EB_CONDA_INSTALL=$T
fi

export EASYBUILD_PREFIX="${EASYBUILD_BASE}"

##################################################################
## Anaconda Setup
## We are using miniconda3/python3 from anaconda
##################################################################
echo "===================================================================="
echo ""
echo "Installing Anaconda3. This could take some time..."
export ANACONDA3_BASE="${EASYBUILD_BASE}/anaconda3"

curl -s -L https://repo.continuum.io/miniconda/Miniconda3-4.2.12-Linux-x86_64.sh  > miniconda.sh && \
    openssl md5 miniconda.sh | grep 'd0c7c71cc5659e54ab51f2005a8d96f3'

chmod 777 miniconda.sh ; bash miniconda.sh -b -p $ANACONDA3_BASE
rm miniconda.sh && \
    export PATH=${ANACONDA3_BASE}/bin:$PATH && \
    conda config --set show_channel_urls True && \
    conda config --add channels conda-forge && \
    conda config --add channels defaults && \
    conda update --all --yes && \
    conda clean -tipy

echo "Finished installing Anaconda3."
echo "It is located in ${ANACONDA3_BASE}."
echo ""

export PATH="${ANACONDA3_BASE}/bin:${PATH}"
export EB_ENV="${EASYBUILD_BASE}/${EASYBUILD_NAME}"
export MODULEPATH="${EASYBUILD_PREFIX}/modules/all"
export EB_CONFIG="${HOME}/.config/easybuild"

##################################################################
## Add Easybuild Config
##################################################################

echo "===================================================================="
echo ""
echo "Creating configuration directory."
echo "${EB_CONFIG}"

mkdir -p "${EB_CONFIG}"

if [[ "$environment_modules" -eq "1" ]]
then
  echo "You have opted to use environment modules for you module system."
  echo "Please see: https://github.com/easybuilders/easybuild/blob/master/docs/Configuration.rst"
  echo "Under 'Modules Tool' and 'Module File Syntax'"
  echo "You will need to update your easybuild config accordingly."
  echo "Additionally, please see this gist: https://gist.github.com/jerowe/99b4ca875c642ebac7c5feced8acb7f2"
  echo "Which is a minimal configuration for easybuild with environment modules"
fi

##################################################################
## Install Easybuild and Lmod
## Create a conda env with easybuild and lmod - and nothing else
##################################################################


echo "===================================================================="
echo ""
echo "Creating easybuild conda env."
echo "conda create -p $EB_ENV $EB_CONDA_INSTALL"
echo ""

rm -rf $EB_ENV
conda create -p $EB_ENV $EB_CONDA_INSTALL

echo "===================================================================="
echo "Complete! You can load EasyBuild at any time with:"
echo "source activate ${EB_ENV}"
echo ""

echo "===================================================================="
echo "Please keep these variables!"
echo "The following are helpful environmental variables that you probably want to include in your ~/.bashrc or other shell."
echo "They will be stored in ${EASYBUILD_BASE}/source_eb for future use."
echo "Invoke as source ${EASYBUILD_BASE}/source_eb"
echo "In order to change where Easybuild deploys modules - please change the EASYBUILD_PREFIX."
echo ""
echo "export PATH=${ANACONDA3_BASE}/bin:\${PATH}"
echo "export MODULEPATH=${EASYBUILD_PREFIX}/modules/all:\${MODULEPATH}"
echo "export EASYBUILD_PREFIX=${EASYBUILD_PREFIX}"
echo "source activate ${EB_ENV}"
echo ""

echo "export PATH=${ANACONDA3_BASE}/bin:\${PATH}" >> ${EASYBUILD_BASE}/source_eb
echo "export MODULEPATH=${EASYBUILD_PREFIX}/modules/all:\${MODULEPATH}" >> ${EASYBUILD_BASE}/source_eb
echo "export EASYBUILD_PREFIX=${EASYBUILD_PREFIX}" >> ${EASYBUILD_BASE}/source_eb
echo "source activate ${EB_ENV}" >> ${EASYBUILD_BASE}/source_eb