diff --git a/bin/make_tracks_file b/bin/make_tracks_config
similarity index 63%
rename from bin/make_tracks_file
rename to bin/make_tracks_config
index af77414e..3ba56176 100755
--- a/bin/make_tracks_file
+++ b/bin/make_tracks_config
@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 
-from pygenometracks.makeTracksFile import main
+from pygenometracks.makeTracksConfig import main
 
 if __name__ == "__main__":
     main()
diff --git a/pygenometracks/makeTracksFile.py b/pygenometracks/makeTracksConfig.py
similarity index 100%
rename from pygenometracks/makeTracksFile.py
rename to pygenometracks/makeTracksConfig.py
diff --git a/pygenometracks/tracksClass.py b/pygenometracks/tracks/tracksClass.py
old mode 100644
new mode 100755
similarity index 99%
rename from pygenometracks/tracksClass.py
rename to pygenometracks/tracks/tracksClass.py
index cbbb5f8d..8ae0accf
--- a/pygenometracks/tracksClass.py
+++ b/pygenometracks/tracks/tracksClass.py
@@ -12,10 +12,10 @@
 import matplotlib.gridspec
 import matplotlib.cm
 import mpl_toolkits.axisartist as axisartist
-from . utilities import file_to_intervaltree, change_chrom_names
+from .. utilities import file_to_intervaltree, change_chrom_names
 from collections import OrderedDict
-from pygenometracks.tracks.GenomeTrack import GenomeTrack
-from pygenometracks.utilities import InputError
+from . GenomeTrack import GenomeTrack
+from .. utilities import InputError
 
 import warnings
 
diff --git a/setup.py b/setup.py
old mode 100644
new mode 100755
index 382492bd..0a4a33a1
--- a/setup.py
+++ b/setup.py
@@ -16,7 +16,6 @@
 __version__ = '%s'
 """
 
-
 def update_version_py():
     if not os.path.isdir(".git"):
         print("This does not appear to be a Git repository.")
@@ -108,7 +107,7 @@ def checkProgramIsInstalled(self, program, args, where_to_download,
     version=get_version(),
     author='Lucille Lopez-Delisle, Leily Rabbani, Joachim Wolf, Björn Grüning',
     packages=find_packages(exclude=['tests']),
-    scripts=['bin/make_tracks_file', 'bin/pgt', 'bin/pyGenomeTracks'],
+    scripts=['bin/make_tracks_config', 'bin/pgt', 'bin/pyGenomeTracks'],
     include_package_data=True,
     package_dir={'pygenometracks': 'pygenometracks'},
     url='http://pygenometracks.readthedocs.io',