--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/TEisotools-1.0/setup_TEiso.py	Wed Jul 20 05:00:24 2016 -0400
@@ -0,0 +1,139 @@
+import os, shutil, glob, re, sys, time
+from distutils.util import convert_path
+from distutils.core import setup
+from distutils.core import Command
+
+class Devtools(object):
+    
+    @staticmethod
+    def find_sub_packages(lrootPackage, lExclude=()):
+        lPackages = Devtools.find_packages(exclude=lExclude)
+        lSubPackage = []
+        for package in lPackages:
+                for rootPackage in lrootPackage:
+                        if package.startswith(rootPackage):
+                                lSubPackage.append(package)         
+        return lSubPackage
+    
+    @staticmethod
+    def find_packages(where='.', exclude=()):
+        out = []
+        stack=[(convert_path(where), '')]
+        while stack:
+            where,prefix = stack.pop(0)
+            for name in os.listdir(where):
+                fn = os.path.join(where,name)
+                if ('.' not in name and os.path.isdir(fn) and os.path.isfile(os.path.join(fn,'__init__.py'))):
+                    out.append(prefix+name); stack.append((fn,prefix+name+'.'))
+        for pat in list(exclude)+['ez_setup', 'distribute_setup']:
+            from fnmatch import fnmatchcase
+            out = [item for item in out if not fnmatchcase(item,pat)]
+        return out
+    
+    @staticmethod
+    def findall(directory = os.curdir):
+        all_files = []
+        for base, dirs, files in os.walk(directory):
+            if base==os.curdir or base.startswith(os.curdir+os.sep):
+                base = base[2:]
+            if base:
+                files = [os.path.join(base, f) for f in files]
+            all_files.extend(filter(os.path.isfile, files))
+        return all_files
+
+
+class Install(Command):
+    description = "Install TEiso_tools"
+    user_options = []
+ 
+    def initialize_options(self):
+        """Use this to set option defaults before parsing."""
+        pass
+ 
+    def finalize_options(self):
+        """Code to validate/modify command-line/config input goes here."""
+        pass
+
+    def _isToLink(self, fileName):
+        if re.search("__\w*.py", fileName):
+            return False
+        elif re.search("Test\w*.py", fileName):
+            return False
+        elif re.search("\w*.py$", fileName):
+            return True
+        return False        
+
+    def run(self):
+        cwd = os.getcwd()
+        print "Build TEiso in %s" % (cwd)
+        if not os.path.isdir("bin"):
+            os.mkdir("bin")
+        os.chdir("bin")
+        lPackages = ["TEiso"]
+        for package in lPackages:
+            if os.path.isdir("../%s" % package):
+                print "processing %s/..." % package
+                [os.symlink(i, os.path.basename(i)) for i in Devtools.findall("../%s" % package) if self._isToLink(os.path.basename(i))]
+        os.system("chmod 0755 *")
+        print "TEiso is ready to use"
+
+class PublicRelease(Command):
+    description = "public release for TEiso_tools"
+    user_options = []
+ 
+    def initialize_options(self):
+        """Use this to set option defaults before parsing."""
+        pass
+ 
+    def finalize_options(self):
+        """Code to validate/modify command-line/config input goes here."""
+        pass
+ 
+    def run(self):
+        
+        print "START Releasing (%s)" % time.strftime("%Y-%m-%d %H:%M:%S")
+        sys.stdout.flush()
+
+        cwd = os.getcwd()
+        
+        print "Removing all '.pyc' files and dead symlinks in bin, then adding execution rights to all 'py' files (%s)" % time.strftime("%Y-%m-%d %H:%M:%S")
+        sys.stdout.flush()
+        
+        os.system("find . -name '*.pyc' -exec rm {} \;")
+        os.system("find . -name '*.py' -exec chmod +x {} \;")
+        os.system("find -L ./bin -type l -exec rm {} +")
+
+#        lSetupFiles = FileUtils.getFileNamesList(cwd, "setup_.*.py")
+#        lSetupFiles.remove("setup_REPET.py")
+#        FileUtils.removeFilesFromList(lSetupFiles)
+
+        os.chdir("..")
+        os.system("tar -czf %s.tar.gz %s" % (os.path.basename(cwd), os.path.basename(cwd)))
+
+        print "END Releasing (%s)" % time.strftime("%Y-%m-%d %H:%M:%S")
+        sys.stdout.flush()
+    
+setup(
+      name = "TEisotools",
+      version = "1.0",
+      description='Set of tools to analyse RNA_seq for the France Genomics projects.',
+      author='URGI team',
+      author_email='urgi-support@versailles.inra.fr',
+      url='https://urgi.versailles.inra.fr/Projects/TEiso',
+      packages=[],
+      #Additionnal Files
+      data_files=[('TEiso',["TEiso/LaunchTEiso.py", "TEiso/Tophat.py", "TEiso/Cufflinks.py", "TEiso/Cuffcompare.py", "TEiso/Bowtie_build.py", "TEiso/Bedtools_closest.py","TEiso/ClosestToStartSite.py", "TEiso/GFFToBed.py", "TEiso/CufflinksGTFToBed.py"]),
+                  ("commons/core", glob.glob("commons/core/*.py")),
+                  ("commons", glob.glob("commons/*.py")),
+                  ("commons/core/utils", glob.glob("commons/core/utils/*.py")),
+                  ("commons/core/checker", glob.glob("commons/core/checker/*.py")),
+                  ("commons/core/seq", glob.glob("commons/core/seq/*.py")),
+                  ("commons/core/coord", glob.glob("commons/core/coord/*.py")),
+                  ('commons/core/parsing',["commons/core/parsing/GtfParser.py", "commons/core/parsing/TranscriptListParser.py", "commons/core/parsing/GffParser.py", "commons/core/parsing/__init__.py"]),
+                  ('',['TEiso/doc/README_TEiso.txt']),('',['LICENSE'])],
+      cmdclass={
+     'install' : Install
+        }
+      )
+
+