diff --git a/Modules/Ensembl/ActivityCategorizer.py b/bin/Modules/Ensembl/ActivityCategorizer.py similarity index 100% rename from Modules/Ensembl/ActivityCategorizer.py rename to bin/Modules/Ensembl/ActivityCategorizer.py diff --git a/Modules/Ensembl/ActivityTable.py b/bin/Modules/Ensembl/ActivityTable.py similarity index 100% rename from Modules/Ensembl/ActivityTable.py rename to bin/Modules/Ensembl/ActivityTable.py diff --git a/Modules/Ensembl/ActivityTableGenerator.py b/bin/Modules/Ensembl/ActivityTableGenerator.py similarity index 100% rename from Modules/Ensembl/ActivityTableGenerator.py rename to bin/Modules/Ensembl/ActivityTableGenerator.py diff --git a/Modules/Ensembl/Ensembl.py b/bin/Modules/Ensembl/Ensembl.py similarity index 100% rename from Modules/Ensembl/Ensembl.py rename to bin/Modules/Ensembl/Ensembl.py diff --git a/Modules/Ensembl/FTPHandling/FTPEntry.py b/bin/Modules/Ensembl/FTPHandling/FTPEntry.py similarity index 100% rename from Modules/Ensembl/FTPHandling/FTPEntry.py rename to bin/Modules/Ensembl/FTPHandling/FTPEntry.py diff --git a/Modules/Ensembl/FTPHandling/URLRetrieve.py b/bin/Modules/Ensembl/FTPHandling/URLRetrieve.py similarity index 100% rename from Modules/Ensembl/FTPHandling/URLRetrieve.py rename to bin/Modules/Ensembl/FTPHandling/URLRetrieve.py diff --git a/Modules/Ensembl/FTPHandling/VersionChecker.py b/bin/Modules/Ensembl/FTPHandling/VersionChecker.py similarity index 100% rename from Modules/Ensembl/FTPHandling/VersionChecker.py rename to bin/Modules/Ensembl/FTPHandling/VersionChecker.py diff --git a/Modules/Ensembl/FTPHandling/__init__.py b/bin/Modules/Ensembl/FTPHandling/__init__.py similarity index 100% rename from Modules/Ensembl/FTPHandling/__init__.py rename to bin/Modules/Ensembl/FTPHandling/__init__.py diff --git a/Modules/Ensembl/GTFGen.py b/bin/Modules/Ensembl/GTFGen.py similarity index 100% rename from Modules/Ensembl/GTFGen.py rename to bin/Modules/Ensembl/GTFGen.py diff --git a/Modules/Ensembl/__init__.py b/bin/Modules/Ensembl/__init__.py similarity index 100% rename from Modules/Ensembl/__init__.py rename to bin/Modules/Ensembl/__init__.py diff --git a/Modules/Ensembl/checksums.py b/bin/Modules/Ensembl/checksums.py similarity index 100% rename from Modules/Ensembl/checksums.py rename to bin/Modules/Ensembl/checksums.py diff --git a/Modules/SaveResults.py b/bin/Modules/SaveResults.py similarity index 100% rename from Modules/SaveResults.py rename to bin/Modules/SaveResults.py diff --git a/Modules/Uniquifier.py b/bin/Modules/Uniquifier.py similarity index 100% rename from Modules/Uniquifier.py rename to bin/Modules/Uniquifier.py diff --git a/Modules/__init__.py b/bin/Modules/__init__.py similarity index 100% rename from Modules/__init__.py rename to bin/Modules/__init__.py diff --git a/Modules/ucsc/__init__.py b/bin/Modules/ucsc/__init__.py similarity index 100% rename from Modules/ucsc/__init__.py rename to bin/Modules/ucsc/__init__.py diff --git a/Modules/ucsc/bigBedToBed b/bin/Modules/ucsc/bigBedToBed old mode 100755 new mode 100644 similarity index 100% rename from Modules/ucsc/bigBedToBed rename to bin/Modules/ucsc/bigBedToBed diff --git a/Modules/ucsc/ucsc.py b/bin/Modules/ucsc/ucsc.py similarity index 100% rename from Modules/ucsc/ucsc.py rename to bin/Modules/ucsc/ucsc.py diff --git a/RegGTFExtractor.py b/bin/RegGTFExtractor.py old mode 100755 new mode 100644 similarity index 100% rename from RegGTFExtractor.py rename to bin/RegGTFExtractor.py