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#!/bin/bash

processEcho () {

	echo ""

	echo "#####"

	echo "# $1"

	echo "#####"

	echo ""

}

installApt () {

	# check [$1=binName; $2=aptName]

	if hash $1 2>/dev/null; then

		processEcho "$1 is already installed!"

	else

		if [[ $1 == gt ]]; then

			processEcho "Installing libgenometools0, libgenometools-dev and genometools"

			apt-get install libgenometools0 libgenometools0-dev genometools	

		else

			apt-get install $2

		fi

	fi

}

installPip3Modul () {

	processEcho "Installing $1"

	pip3 install $1

}

# apt dependencies

aptBinNames=(build-essential gcc pip3 git gt blastx)

aptNames=(build-essential gcc python3-pip git genometools blast2)

# add also libgenometools0 libgenometools0-dev  for gt

# pip3 dependencies

pip3Moduls=(setuptools biopython bcbio-gff click decorator networkx numpy PyYAML six)

# main process

if [[ $EUID -ne 0 ]]; then

	echo "You should run as root!"

	exit 1

else

	# Prequisites installation

	processEcho "CHECKING AND INSTALLING DEPENDENCIES"

	processEcho "APT PACKAGES"

	apt-get update

	for i in "${!aptBinNames[@]}"

		do

		installApt "${aptBinNames[$i]}" "${aptNames[$i]}"

	done

	processEcho "PYTHON3 PACKAGES"

	for pckg in "${pip3Moduls[@]}"

		do

		processEcho "Installing $pckg"

		pip3 install $pckg

	done

	# LTR_Finder installation

	# check

	processEcho "LTR_FINDER CHECK & INSTALLATION"

	path2LtrFinder=""

	if hash ltr_finder 2>/dev/null; then

		processEcho "$1 is already installed!"

		path2LtrFinder="ltr_finder"

	else

		processEcho "LTR_Finder installation"

		git clone https://github.com/xzhub/LTR_Finder.git

		cd LTR_Finder/source

		make

		path=$(pwd)

		path2LtrFinder=$(pwd)"/ltr_finder"

		cd ../../

	fi

	# Setup paths in 'config.yml'

	processEcho "GENERATING 'config.yml'"

	# strings to be changed

	ltrFinder="/path/to/ltr_finder_repository/LTR_Finder/source/ltr_finder"

	prosite="path/to/repository/dbs/prosite"

	tRNAs="/path/to/ltr_finder_repository/LTR_Finder/source/tRNA/Athal-tRNAs.fa"

	gtStyle="/path/to/nested/nested/config/gt.style"

	domDb="path/to/repository/dbs/gydb_arh_chdcr/gydb_arh_chdcr.fa"

	origPaths=($ltrFinder $prosite $tRNAs $gtStyle $domDb)

	# real paths	

	path2prosite=$(pwd)"/dbs/prosite"

	path2tRNAs=$(pwd)"/LTR_Finder/source/tRNA/Athal-tRNAs.fa"

	path2gtStyle=$(pwd)"/nested/config/gt.style"

	path2domDb=$(pwd)"/dbs/gydb_arh_chdcr/gydb_arh_chdcr.fa"

	realPaths=($path2LtrFinder $path2prosite $path2tRNAs $path2gtStyle $path2domDb)

	# replacing paths

	IFS=''

	while read -r line

	do

		line=${line//$(echo $ltrFinder | sed 's_/_\\/_g')/$(echo $path2LtrFinder)}

		line=${line//$(echo $prosite | sed 's_/_\\/_g')/$(echo $path2prosite)}

		line=${line//$(echo $tRNAs | sed 's_/_\\/_g')/$(echo 	$path2tRNAs)}

		line=${line//$(echo $gtStyle | sed 's_/_\\/_g')/$(echo $path2gtStyle)}

		line=${line//$(echo $domDb | sed 's_/_\\/_g')/$(echo $path2domDb)}

		echo $line >> config.yml

	done<config_template.yml

	processEcho "'config.yml' was generated"

	# installing nester

	processEcho "INSTALLING Te-greedy-nester"

	./setup.sh

	processEcho "Te-greedy-nester has been installed"

fi