diff --git a/debian/clean b/debian/clean
deleted file mode 100644
index 574116c..0000000
--- a/debian/clean
+++ /dev/null
@@ -1 +0,0 @@
-ctdconverter.egg-info/
diff --git a/debian/patches/add_setup.py.patch b/debian/patches/add_setup.py.patch
index 9a575b5..7d1636c 100644
--- a/debian/patches/add_setup.py.patch
+++ b/debian/patches/add_setup.py.patch
@@ -1,30 +1,10 @@
 From: Michael R. Crusoe <michael.crusoe@gmail.com>
 Subject: Add setup.py
 Forwarded: https://github.com/WorkflowConversion/CTDConverter/pull/40
---- ctdconverter.orig/common/utils.py
-+++ ctdconverter/common/utils.py
-@@ -7,7 +7,7 @@
- from string import strip
- from logger import info, error, warning
- 
--from common.exceptions import ApplicationException
-+from .exceptions import ApplicationException
- from CTDopts.CTDopts import CTDModel, ParameterGroup
- 
- 
 --- ctdconverter.orig/convert.py
 +++ ctdconverter/convert.py
-@@ -1,14 +1,14 @@
- import os
- import sys
- import traceback
--import common.utils as utils
-+import .common.utils as utils
- 
- from argparse import ArgumentParser
- from argparse import RawDescriptionHelpFormatter
--from common.exceptions import ApplicationException, ModelError
-+from . import common.exceptions as exceptions
+@@ -8,7 +8,7 @@
+ from common.exceptions import ApplicationException, ModelError
  
  __all__ = []
 -__version__ = 2.0
@@ -32,38 +12,6 @@
  __date__ = '2014-09-17'
  __updated__ = '2017-08-09'
  
-@@ -222,13 +222,13 @@
-         print("Interrupted...")
-         return 0
- 
--    except ApplicationException, e:
-+    except exceptions.ApplicationException, e:
-         traceback.print_exc()
-         utils.error("CTDConverter could not complete the requested operation.", 0)
-         utils.error("Reason: " + e.msg, 0)
-         return 1
- 
--    except ModelError, e:
-+    except exceptions.ModelError, e:
-         traceback.print_exc()
-         utils.error("There seems to be a problem with one of your input CTDs.", 0)
-         utils.error("Reason: " + e.msg, 0)
-@@ -250,13 +250,13 @@
-     # if input is a single file, we expect output to be a file (and not a dir that already exists)
-     if len(args.input_files) == 1:
-         if os.path.isdir(args.output_destination):
--            raise ApplicationException("If a single input file is provided, output (%s) is expected to be a file "
-+            raise exceptions.ApplicationException("If a single input file is provided, output (%s) is expected to be a file "
-                                        "and not a folder.\n" % args.output_destination)
- 
-     # if input is a list of files, we expect output to be a folder
-     if len(args.input_files) > 1:
-         if not os.path.isdir(args.output_destination):
--            raise ApplicationException("If several input files are provided, output (%s) is expected to be an "
-+            raise exceptions.ApplicationException("If several input files are provided, output (%s) is expected to be an "
-                                        "existing directory.\n" % args.output_destination)
- 
-     # check that the provided input files, if provided, contain a valid file path
 @@ -269,4 +269,4 @@
  
  
@@ -71,42 +19,9 @@
 -    sys.exit(main())
 \ No newline at end of file
 +    sys.exit(main())
---- ctdconverter.orig/cwl/converter.py
-+++ ctdconverter/cwl/converter.py
-@@ -12,7 +12,7 @@
- import ruamel.yaml as yaml
- 
- from CTDopts.CTDopts import _InFile, _OutFile, ParameterGroup, _Choices, _NumericRange, _FileFormat, ModelError, _Null
--from common import utils, logger
-+from ..common import utils, logger
- 
- # all cwl-related properties are defined here
- 
---- ctdconverter.orig/galaxy/converter.py
-+++ ctdconverter/galaxy/converter.py
-@@ -8,8 +8,8 @@
- from lxml import etree
- from lxml.etree import SubElement, Element, ElementTree, ParseError, parse
- 
--from common import utils, logger
--from common.exceptions import ApplicationException, InvalidModelException
-+from ..common import utils, logger
-+from ..common.exceptions import ApplicationException, InvalidModelException
- 
- from CTDopts.CTDopts import _InFile, _OutFile, ParameterGroup, _Choices, _NumericRange, _FileFormat, ModelError, _Null
- 
---- /dev/null
-+++ ctdconverter/__main__.py
-@@ -0,0 +1,6 @@
-+from __future__ import absolute_import
-+import sys
-+
-+from . import convert
-+
-+sys.exit(convert.main())
 --- /dev/null
 +++ ctdconverter/setup.py
-@@ -0,0 +1,167 @@
+@@ -0,0 +1,170 @@
 +"""A setuptools based setup module.
 +
 +See:
@@ -163,8 +78,7 @@
 +    # This is a one-line description or tagline of what your project does. This
 +    # corresponds to the "Summary" metadata field:
 +    # https://packaging.python.org/specifications/core-metadata/#summary
-+    description='Convert CTD files into Galaxy tool and CWL CommandLineTool '
-+                'files',  # Required
++    description='Convert CTD files into Galaxy tool and CWL CommandLineTool files',  # Required
 +
 +    # This is an optional longer description of your project that represents
 +    # the body of text which users will see when they visit PyPI.
@@ -174,17 +88,17 @@
 +    #
 +    # This field corresponds to the "Description" metadata field:
 +    # https://packaging.python.org/specifications/core-metadata/#description-optional
-+    long_description=long_description,
++    long_description=long_description,  # Optional
 +
 +    # This should be a valid link to your project's main homepage.
 +    #
 +    # This field corresponds to the "Home-Page" metadata field:
 +    # https://packaging.python.org/specifications/core-metadata/#home-page-optional
-+    url='https://github.com/WorkflowConversion/CTDConverter',
++    url='https://github.com/WorkflowConversion/CTDConverter',  # Optional
 +
 +    # This should be your name or the name of the organization which owns the
 +    # project.
-+    author='The WorkflowConversion team',
++    author='The WorkflowConversion team',  # Optional
 +
 +    # This should be a valid email address corresponding to the author listed
 +    # above.
@@ -194,7 +108,7 @@
 +    #
 +    # For a list of valid classifiers, see
 +    # https://pypi.python.org/pypi?%3Aaction=list_classifiers
-+    classifiers=[
++    classifiers=[  # Optional
 +        # How mature is this project? Common values are
 +        #   3 - Alpha
 +        #   4 - Beta
@@ -224,12 +138,16 @@
 +    # Note that this is a string of words separated by whitespace, not a list.
 +    keywords='CTD CWL CommonWL Galaxy Workflows WorkflowConversion',  # Optional
 +
-+    packages=['ctdconverter', 'ctdconverter.common', 'ctdconverter.galaxy',
-+              'ctdconverter.cwl'],  # Required
-+    package_dir={ 'ctdconverter': '.',
-+                  'ctdconverter.common': 'common',
-+                  'ctdconverter.galaxy': 'galaxy',
-+                  'ctdconverter.cwl': 'cwl'},
++    # You can just specify package directories manually here if your project is
++    # simple. Or you can use find_packages().
++    #
++    # Alternatively, if you just want to distribute a single Python file, use
++    # the `py_modules` argument instead as follows, which will expect a file
++    # called `my_module.py` to exist:
++    #
++    py_modules=["convert"],
++    #
++    packages=find_packages(exclude=['contrib', 'docs', 'tests']),  # Required
 +
 +    # This field lists other packages that your project depends on to run.
 +    # Any package you put here will be installed by pip when your project is
@@ -257,7 +175,7 @@
 +    #
 +    # If using Python 2.6 or earlier, then these have to be included in
 +    # MANIFEST.in as well.
-+    package_data={
++    package_data={  # Optional
 +        'ctdconverter': ['galaxy/macros.xml'],
 +    },
 +
@@ -270,7 +188,7 @@
 +    # executes the function `main` from this package when invoked:
 +    entry_points={  # Optional
 +        'console_scripts': [
-+            'CTDConverter=ctdconverter',
++            'CTDConverter=convert:main',
 +        ],
 +    },
 +)
diff --git a/debian/patches/upgrade_deprecated_strip b/debian/patches/upgrade_deprecated_strip
index 4caf8dd..d39b370 100644
--- a/debian/patches/upgrade_deprecated_strip
+++ b/debian/patches/upgrade_deprecated_strip
@@ -2,14 +2,16 @@
 Subject: Upgrade deprecated using of string.strip()
 --- ctdconverter.orig/common/utils.py
 +++ ctdconverter/common/utils.py
-@@ -4,7 +4,6 @@
+@@ -4,8 +4,7 @@
  import os
  
  from lxml import etree
 -from string import strip
- from logger import info, error, warning
+-from logger import info, error, warning
++from logger import info, error, warning
  
- from .exceptions import ApplicationException
+ from common.exceptions import ApplicationException
+ from CTDopts.CTDopts import CTDModel, ParameterGroup
 @@ -73,9 +72,9 @@
      if member_value is not None:
          if isinstance(member_value, list):
@@ -22,3 +24,4 @@
  
          for path_to_check in paths_to_check:
              validate_path_exists(path_to_check)
+
diff --git a/debian/rules b/debian/rules
index 993d904..1d00b1a 100755
--- a/debian/rules
+++ b/debian/rules
@@ -3,7 +3,6 @@
 # DH_VERBOSE := 1
 export LC_ALL=C.UTF-8
 export PYBUILD_NAME = ctdconverter
-export PYBUILD_SYSTEM = distutils
 
 include /usr/share/dpkg/default.mk
 # this provides:
@@ -31,9 +30,3 @@
 
 override_dh_installman: debian/CTDConverter.1
 	dh_installman
-
-override_dh_auto_test:
-	dh_auto_install
-	PYBUILD_SYSTEM=custom PYBUILD_TEST_ARGS="export \
-		PYTHONPATH={build_dir} && {interpreter} -m \
-		ctdconverter.convert --help" dh_auto_test