installkSNP

#!/bin/bash

cat > /dev/null <<IGNOREME

This is a simple script to install kSNP4 onto a computer system in a reliable,
and repeatable way.

In addition, I intend it to be possible for the user to update the links in 
the BINDIR in bulk and automatically, e.g. if the user wishes to install more
than one copy of kSNP.

The general policy is:

Put all files in PACKAGEDIR.
Create symbolic links in BINDIR for all scripts or executables that the user is
likely to want to use.
Run the kSNPConfig program to get an initial configuration.

IGNOREME
######################
######################
#
# VARIABLES
#
######################
######################

# The other binaries are all in the kSNP4 directory once it is unpacked.
ARCHIVE=kSNP4

# Default install paths:
# This is the directory where distribution files will be stored.  They may be
# referenced from other locations.
PACKAGEDIR=/usr/local/kSNP4Pkg

# This is a directory in the PATH where we will create symbolic links to the
# executables.
BINDIR=/usr/local/bin

# Variables containing lists of files that are required for kSNP to function
USERBINS="checkFileNames checkGenbankFromNCBI extractNthLocus4 fixOldFastaHeaders genomeNames4 getFastaGenomes Kchooser4 kSNP4 ksnpConfig MakeKSNP4infile nodeChiSquare2tree4 parseNCBIcsv rmNodeNamesFromTree4 selectNodeAnnotations4"

# A program to manipulate the kSNP configuration (if any)
RECONFIGURE=ksnpConfig


######################
######################
#
# MAIN
#
######################
######################

SYMLINKS=TRUE
CONFIGURE=TRUE
INSTALL=TRUE
CMDLINE_ERROR=FALSE
USAGE=FALSE


while [ ${#} -gt 0 ]  # While we have more arguments to process...
do
    case "${1}" in    # "switch" / case  based on what the argument is.
	--symlinks-only) # This is used if the binaries are already in place.
	    INSTALL=FALSE
	    CONFIGURE=FALSE
	    shift
	    ;;

	--configure-only) # This is used if we just want to re-configure.
	    INSTALL=FALSE
	    SYMLINKS=FALSE
	    shift
	    ;;

	--install-only) # This is used if the user wants to place the symlinks and configure themselves.
	    SYMLINKS=FALSE
	    CONFIGURE=FALSE
	    shift
	    ;;
	
	--installdir)
	    PACKAGEDIR="${2}"
	    shift 2 # Argument and value
	    ;;

	--bindir)
	    BINDIR="${2}"
	    if [ ! -d "${BINDIR}" ]
	    then
		CMDLINE_ERROR=TRUE
		echo "Specified target directory ${BINDIR} for binary symlinks does not yet exist."
		echo "Did you specify the directory correctly?"
	    fi
	    shift 2
	    ;;
	
	--help)
	    USAGE=TRUE
	    break
	    ;;

	--debug)
	    DEBUG=1
	    # Same as specifying -x on the shell shebang above.
	    set -o xtrace
	    # Same as specifying -v on the shell shebang above.
	    set -o verbose
	    shift # Argument
	    ;;

	*)  # All other values are errors.          
	    CMDLINE_ERROR=TRUE
	    USAGE=TRUE
	    echo "Error: Unrecognized argument (no valid argument: ${1})"
	    shift
	    ;;
    esac

done # Processing arguments

if [ "${USAGE}" = "TRUE" ]
then
    cat <<HERETEXT
Usage: installkSNP [--bindir <directory in PATH>] [--installdir <install target>] [--install-only] [--symlinks-only] [--configure-only] [--help] [--debug]

This script is designed to install and initially configure kSNP for your use.
You likely will need to run it as an administrator to install to the default
systemwide folders / directories.

Optional arguments:
 --bindir <directory>    Directory to place symbolic links to kSNP binaries.
 --installdir <directory>  Directory to place kSNP binaries and support data.
 --install-only          Instruct the script to only install binaries without
                         placing symbolic links or configuring kSNP.
 --symlinks-only         Replace symbolic links into the --bindir directory.
 --configure-only        Configure kSNP for the current user, no installation.
 --help                  This text.
 --debug                 Verbose debugging information.  Probably useless.


Typical usage is to run without arguments.  You may also use it to re-
configure kSNP from the defaults, or to restore the symbolic links if
something happened to disturb them (like another kSNP install)
HERETEXT
    # And after displaying help, don't do anything.
    exit 0
fi


if [ "${CMDLINE_ERROR}" = "TRUE" ]
then
   exit 1 # Error
fi


if [ "${INSTALL}" = "TRUE" ]
then
    mkdir -p "${PACKAGEDIR}"
    cp "${ARCHIVE}/"* "${PACKAGEDIR}/"
    # Make this installer available going forward.
    cp "${0}" "${PACKAGEDIR}/"
fi


if [ "${SYMLINKS}" = "TRUE" ]
then
    
    for BINARY in ${USERBINS}
    do
	ln -s "${PACKAGEDIR}/${BINARY}" "${BINDIR}/${BINARY}"
    done
fi

if [ "${CONFIGURE}" = "TRUE" ]
then
    "${PACKAGEDIR}/${RECONFIGURE}"
fi