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teGreedyNester_installation.py

+#!/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()