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#!/usr/bin/env python3

#

# run this script within */nested/. path as follows:

# $ sudo python3 teGreedyNester_Installation.py

import os

import apt

import subprocess

import sys

# check installed tools:

def returnToolDict():

    toolDict = {}

    toolDict = {'build-essential':False, 'gcc':False, 'pip3':False, 'git':False, 'ltr_finder':False, 'blastx':False,

                'gt': False}

    return toolDict

def checkTool(tool, boolVar):    

    result = subprocess.run(['which', '{}'.format(tool)], stdout=subprocess.PIPE)

    path = result.stdout.decode('utf-8').rstrip()

    if tool in path:

        boolVar = True

        return boolVar

    else:

        return boolVar

def runCheck(toolDict):    

    for t in toolDict.keys():

        toolDict[t] = checkTool(t, toolDict[t])

    return toolDict

# 1. installation of apts

# 1.1 'installed or not' check:

def installCheck(toolDict):

    aptList = ['build-essential', 'gcc', 'blast2', 'genometools', 'libgenometools0', 'libgenometools0-dev',

               'python3-pip', 'git']

    if toolDict['build-essential']:

        aptList.remove('build-essential')

        print("'build-essential' is already installed.")

        print()

    if toolDict['gcc']:

        aptList.remove('blast2')

        print("'gcc' is already installed.")

        print()

    if toolDict['blastx']:

        aptList.remove('blast2')

        print("'blastx' is already installed.")

        print()

    if toolDict['gt']:

        aptList.remove('genometools')

        print("'genometools' are already installed.")

        print()

    if toolDict['pip3']:

        aptList.remove('python3-pip')

        print("'python3-pip' is already installed.")

        print()

    if toolDict['git']:

        aptList.remove('git')

        print("'git' is already installed.")

        print()    

    return aptList

# 1.2 Installation:    

def installPckg(apt_name):

    pkg_name = apt_name

    cache = apt.cache.Cache()

    cache.update()

    cache.open()

    pkg = cache[pkg_name]

    if pkg.is_installed:

        print("{pkg_name} is already installed".format(pkg_name = pkg_name))

        print()

    else:

        pkg.mark_install()

        try:

            cache.commit()

        except Exception (arg):

            print("Sorry, package installation failed [{err}]".format(err=str(arg)), file=sys.stderr)

            print()

def runInstallation(aptList):

    for apt_name in aptList:

        installPckg(apt_name)

        print()

# 2. ltr_finder

def compileLtrFinder():

    presentPath = os.getcwd()

    os.chdir(presentPath + "/LTR_Finder/source")

    subprocess.check_call(["make"])

    os.chdir(presentPath)

    print()

def installLtrFinder(toolDict):

    path2LtrFinder = ""

    if not toolDict['ltr_finder']:

        path2LtrFinder = ""

        if not os.path.exists("LTR_Finder/source/ltr_finder"):

            subprocess.check_call(["git", "clone", "https://github.com/xzhub/LTR_Finder.git"])

            compileLtrFinder()

            path2LtrFinder = os.getcwd() + "/LTR_Finder/source/ltr_finder"

        else:

            compileLtrFinder()

            path2LtrFinder = os.getcwd() + "/LTR_Finder/source/ltr_finder"

        print("'LTR_Finder' has been installed.")

        print()

    else:

        print("'LTR_Finder' is already installed.")

        print()

        result = subprocess.run(['which', 'ltr_finder'], stdout=subprocess.PIPE)

        path2LtrFinder = result.stdout.decode('utf-8').rstrip()

    return path2LtrFinder

# 3. python3 packages:

def installPyPckgs():

    pckgList = ['setuptools', 'biopython', 'bcbio-gff', 'click', 'decorator', 'networkx', 'numpy',

    'PyYAML', 'six']

    for pckg in pckgList:

        subprocess.check_call(['pip3', 'install', '{}'.format(pckg), '--no-cache-dir'])

        print()

# 4. teGreedyNester:

# 4.1 setup paths in 'config.yml':

def getPaths(path2LtrFinder):

    path2prosite = os.getcwd() + "/dbs/prosite"

    path2tRNA = os.getcwd() + "/LTR_Finder/source/tRNA/Athal-tRNAs.fa"

    path2style = os.getcwd() + "/nested/config/gt.style"

    path2db = os.getcwd() + "/dbs/gydb_arh_chdcr/gydb_arh_chdcr.fa"

    with open("config.yml", "w") as out:

        with open("config_template.yml") as cfg:

            for l in cfg:

                if "/path/to/ltr_finder_repository/LTR_Finder/source/ltr_finder" in l:

                    lNew = l.replace("/path/to/ltr_finder_repository/LTR_Finder/source/ltr_finder",

                              path2LtrFinder)

                    out.write(lNew)

                elif "path/to/repository/dbs/prosite" in l:

                    lNew = l.replace("path/to/repository/dbs/prosite", path2prosite)

                    out.write(lNew)

                elif "/path/to/ltr_finder_repository/LTR_Finder/source/tRNA/Athal-tRNAs.fa" in l:

                    lNew = l.replace("/path/to/ltr_finder_repository/LTR_Finder/source/tRNA/Athal-tRNAs.fa",

                              path2tRNA)

                    out.write(lNew)

                elif "/path/to/nested/nested/config/gt.style" in l:

                    lNew = l.replace("/home/xvanat/nested/nested/config/gt.style", path2style)

                    out.write(lNew)

                elif "path/to/repository/dbs/gydb_arh_chdcr/gydb_arh_chdcr.fa" in l:

                    lNew = l.replace("path/to/repository/dbs/gydb_arh_chdcr/gydb_arh_chdcr.fa", path2db)

                    out.write(lNew)

                else:

                    out.write(l)

    print("Paths in 'config.yml' have been set.")

    print()

# 4.2 install nester

def installNester():

    subprocess.check_call(["./setup.sh"])

    print()

    print("Te-greedy-nester has been installed.")

    print()

# Whole process:

if __name__ == "__main__":

    # check installed tools:

    toolDict = returnToolDict()

    toolDictChecked = runCheck(toolDict)

    # 1. apts

    # 1.1 installed or not check:

    # &&

    # 1.2 installation:    

    runInstallation(installCheck(toolDictChecked))

    # 2. ltr_finder installation:

    path2LtrFinder = installLtrFinder(toolDictChecked)

    # 3. python3 packages:

    installPyPckgs()

    # 4. teGreedyNester:

    # 4.1 setup paths in 'config.yml':

    getPaths(path2LtrFinder)

    # 4.2 install nester:

    installNester()