diff --git a/debian/clean b/debian/clean
new file mode 100644
index 0000000..574116c
--- /dev/null
+++ b/debian/clean
@@ -0,0 +1 @@
+ctdconverter.egg-info/
diff --git a/debian/patches/add_setup.py.patch b/debian/patches/add_setup.py.patch
index 7d1636c..9a575b5 100644
--- a/debian/patches/add_setup.py.patch
+++ b/debian/patches/add_setup.py.patch
@@ -1,10 +1,30 @@
 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
-@@ -8,7 +8,7 @@
- from common.exceptions import ApplicationException, ModelError
+@@ -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
  
  __all__ = []
 -__version__ = 2.0
@@ -12,6 +32,38 @@
  __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 @@
  
  
@@ -19,9 +71,42 @@
 -    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 +1,170 @@
+@@ -0,0 +1,167 @@
 +"""A setuptools based setup module.
 +
 +See:
@@ -78,7 +163,8 @@
 +    # 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.
@@ -88,17 +174,17 @@
 +    #
 +    # This field corresponds to the "Description" metadata field:
 +    # https://packaging.python.org/specifications/core-metadata/#description-optional
-+    long_description=long_description,  # Optional
++    long_description=long_description,
 +
 +    # 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',  # Optional
++    url='https://github.com/WorkflowConversion/CTDConverter',
 +
 +    # This should be your name or the name of the organization which owns the
 +    # project.
-+    author='The WorkflowConversion team',  # Optional
++    author='The WorkflowConversion team',
 +
 +    # This should be a valid email address corresponding to the author listed
 +    # above.
@@ -108,7 +194,7 @@
 +    #
 +    # For a list of valid classifiers, see
 +    # https://pypi.python.org/pypi?%3Aaction=list_classifiers
-+    classifiers=[  # Optional
++    classifiers=[
 +        # How mature is this project? Common values are
 +        #   3 - Alpha
 +        #   4 - Beta
@@ -138,16 +224,12 @@
 +    # Note that this is a string of words separated by whitespace, not a list.
 +    keywords='CTD CWL CommonWL Galaxy Workflows WorkflowConversion',  # Optional
 +
-+    # 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
++    packages=['ctdconverter', 'ctdconverter.common', 'ctdconverter.galaxy',
++              'ctdconverter.cwl'],  # Required
++    package_dir={ 'ctdconverter': '.',
++                  'ctdconverter.common': 'common',
++                  'ctdconverter.galaxy': 'galaxy',
++                  'ctdconverter.cwl': 'cwl'},
 +
 +    # 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
@@ -175,7 +257,7 @@
 +    #
 +    # If using Python 2.6 or earlier, then these have to be included in
 +    # MANIFEST.in as well.
-+    package_data={  # Optional
++    package_data={
 +        'ctdconverter': ['galaxy/macros.xml'],
 +    },
 +
@@ -188,7 +270,7 @@
 +    # executes the function `main` from this package when invoked:
 +    entry_points={  # Optional
 +        'console_scripts': [
-+            'CTDConverter=convert:main',
++            'CTDConverter=ctdconverter',
 +        ],
 +    },
 +)
diff --git a/debian/patches/upgrade_deprecated_strip b/debian/patches/upgrade_deprecated_strip
index d39b370..4caf8dd 100644
--- a/debian/patches/upgrade_deprecated_strip
+++ b/debian/patches/upgrade_deprecated_strip
@@ -2,16 +2,14 @@
 Subject: Upgrade deprecated using of string.strip()
 --- ctdconverter.orig/common/utils.py
 +++ ctdconverter/common/utils.py
-@@ -4,8 +4,7 @@
+@@ -4,7 +4,6 @@
  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 common.exceptions import ApplicationException
- from CTDopts.CTDopts import CTDModel, ParameterGroup
+ from .exceptions import ApplicationException
 @@ -73,9 +72,9 @@
      if member_value is not None:
          if isinstance(member_value, list):
@@ -24,4 +22,3 @@
  
          for path_to_check in paths_to_check:
              validate_path_exists(path_to_check)
-
diff --git a/debian/rules b/debian/rules
index 1d00b1a..993d904 100755
--- a/debian/rules
+++ b/debian/rules
@@ -3,6 +3,7 @@
 # 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:
@@ -30,3 +31,9 @@
 
 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