AAD2/install at main · GLYCAM-Web/AAD2 · GitHub

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#!/usr/bin/env bash

noS="    0.configure/setup_AD_Directory \
    3.prepare_docking_directories/prepare_AD_docking_directory \
    4.run_docking/start_all_docking_jobs \
    5.analyze_results/generate_AD_results_view \
    6.check_status/archive_AD_logs \
    6.check_status/get_AD_docking_replica_status \
    6.check_status/check_AD_status \
    7.package_results/generate_zip_file \
    99.cluster_utilities/monitor_and_analyze \
    99.cluster_utilities/run_cluster_AAD2_from_CLI.bash \
    99.cluster_utilities/submit_and_spawn_monitor \
    AD_Get_Status  \
    AD_Help  \
    AD_Setup  \
    AD_Validate "

onlyS=" 1.prepare_antibody/align_antibody/align  \
    1.prepare_antibody/generate_antibody_pdbqt  \
    2.prepare_glycan/generate_glycan_pdbqt \
    2.prepare_glycan/get_flexible_bond_info \
    4.run_docking/run_AD_docking \
    5.analyze_results/clustering \
    5.analyze_results/plot_results \
    5.analyze_results/reorderpdb \
    5.analyze_results/write_output \
    AD_Evaluate  \
    AD_Prep_Glycan  \
    AD_Run_AD  \
    AD_Run_Core_Serial  \
    AD_Analyze "


USAGE="""
Usage:

    Install <install path> [what to install]

    For example,

        Install /usr/local

    	... will install all executables into /usr/local/bin.

    And:

        Install /programs no-S

    	... will install executables that do not require the special environment into /programs/bin.

        Install ./  only-S

    	... will install executables that require the special environment into ./bin.

    What to Install:

        Some executables are able to run on modern machines that are used as controllers for the jobs
        that will run on machines with older code. Some executables depend on the older code.

           no-S  -  Do not install executables that needs the special, older, operating environment.

         only-S  -  Only install executables that needs the special, older, operating environment.

        [empty]  -  Same as 'all'.

            all  -  Install all the executables.
"""

if [[ -z "${1}" ]] ; then
	echo "Must supply location for installation."
	echo "${USAGE}"
	exit 1
fi

if [ ! -d "${1}/bin" ] ; then
	mkdir ${1}/bin || echo "Cannot make directory ${1}/bin." && exit 1
fi

if [ -z "${2}" ] ; then
	toInstall='all'
elif [ "${2}" == "all" ] ; then
	toInstall='all'
elif [ "${2}" == "only-S" ] ; then
	toInstall='only-S'
elif [ "${2}" == "no-S" ] ; then
	toInstall='no-S'
else
	echo "Unknown install option: ${2}"
        echo "${USAGE}"
        exit 1
fi

if [ "${toInstall}" == "only-S" ] ; then
	copyMe="${onlyS}"
elif [ "${toInstall}" == "no-S" ] ; then
	copyMe="${noS}"
else
	copyMe="${noS} \
${onlyS}"
fi

#COMMAND=" cp \\
#${copyMe}
#${1}/bin"

#echo "Command is"
#echo "${COMMAND}"

#eval ${COMMAND}

cp \
${copyMe} \
${1}/bin