diff --git a/.gitignore b/.gitignore
new file mode 100644
index 000000000..ecc32fec7
--- /dev/null
+++ b/.gitignore
@@ -0,0 +1,3 @@
+*pyc
+.tox
+cwltool.egg-info/
\ No newline at end of file
diff --git a/cwltool/builder.py b/cwltool/builder.py
index 5352f915a..fa28dd018 100644
--- a/cwltool/builder.py
+++ b/cwltool/builder.py
@@ -3,15 +3,18 @@
 import expression
 import avro
 import schema_salad.validate as validate
+from .errors import WorkflowException
 
 CONTENT_LIMIT = 64 * 1024
 
+
 def substitute(value, replace):
     if replace[0] == "^":
         return substitute(value[0:value.rindex('.')], replace[1:])
     else:
         return value + replace
 
+
 class Builder(object):
 
     def bind_input(self, schema, datum, lead_pos=[], tail_pos=[]):
diff --git a/cwltool/cwlrdf.py b/cwltool/cwlrdf.py
index 02b42bf91..59a9b8c71 100644
--- a/cwltool/cwlrdf.py
+++ b/cwltool/cwlrdf.py
@@ -1,24 +1,25 @@
 import json
-from rdflib import Graph, plugin
-from rdflib.serializer import Serializer
+from rdflib import Graph
+
 
 def printrdf(workflow, wf, ctx, sr):
     wf["@context"] = ctx
     g = Graph().parse(data=json.dumps(wf), format='json-ld', location=workflow)
     print(g.serialize(format=sr))
 
+
 def printdot(workflow, wf, ctx, sr):
     wf["@context"] = ctx
     g = Graph().parse(data=json.dumps(wf), format='json-ld', location=workflow)
 
     print "digraph {"
 
-    #g.namespace_manager.qname(predicate)
+    # g.namespace_manager.qname(predicate)
 
     def lastpart(uri):
         uri = str(uri)
         if "/" in uri:
-            return uri[uri.rindex("/")+1:]
+            return uri[uri.rindex("/") + 1:]
         else:
             return uri
 
@@ -76,5 +77,4 @@ def lastpart(uri):
     for (inp,) in qres:
         print '"%s" [shape=octagon]' % (lastpart(inp))
 
-
     print "}"
diff --git a/cwltool/cwltest.py b/cwltool/cwltest.py
index 919f5b8d8..219e5da64 100755
--- a/cwltool/cwltest.py
+++ b/cwltool/cwltest.py
@@ -17,6 +17,7 @@
 
 UNSUPPORTED_FEATURE = 33
 
+
 def compare(a, b):
     try:
         if isinstance(a, dict):
@@ -47,6 +48,7 @@ def compare(a, b):
     except:
         return False
 
+
 def run_test(args, i, t):
     out = {}
     outdir = None
@@ -92,7 +94,7 @@ def run_test(args, i, t):
         _logger.error(outstr)
         _logger.error("Parse error %s", str(e))
 
-    pwd = os.path.abspath(os.path.dirname(t["job"]))
+    os.path.abspath(os.path.dirname(t["job"]))
     # t["args"] = map(lambda x: x.replace("$PWD", pwd), t["args"])
     # if "stdin" in t:
     #     t["stdin"] = t["stdin"].replace("$PWD", pwd)
@@ -110,9 +112,9 @@ def run_test(args, i, t):
                 _logger.warn(t.get("doc"))
                 failed = True
             _logger.warn("%s expected %s\n%s      got %s", key,
-                                                            t.get(key),
-                                                            " " * len(key),
-                                                            out.get(key))
+                         t.get(key),
+                         " " * len(key),
+                         out.get(key))
 
     if outdir:
         shutil.rmtree(outdir)
@@ -144,14 +146,14 @@ def main():
 
     if args.n is not None:
         sys.stderr.write("\rTest [%i/%i] " % (args.n, len(tests)))
-        rt = run_test(args, args.n-1, tests[args.n-1])
+        rt = run_test(args, args.n - 1, tests[args.n - 1])
         if rt == 1:
             failures += 1
         elif rt == UNSUPPORTED_FEATURE:
             unsupported += 1
     else:
         for i, t in enumerate(tests):
-            sys.stderr.write("\rTest [%i/%i] " % (i+1, len(tests)))
+            sys.stderr.write("\rTest [%i/%i] " % (i + 1, len(tests)))
             sys.stderr.flush()
             rt = run_test(args, i, t)
             if rt == 1:
@@ -160,8 +162,8 @@ def main():
                 unsupported += 1
 
     if failures == 0 and unsupported == 0:
-         _logger.info("All tests passed")
-         return 0
+        _logger.info("All tests passed")
+        return 0
     else:
         _logger.warn("%i failures, %i unsupported features", failures, unsupported)
         return 1
diff --git a/cwltool/docker.py b/cwltool/docker.py
index e9a56f418..4790f563c 100644
--- a/cwltool/docker.py
+++ b/cwltool/docker.py
@@ -9,6 +9,7 @@
 
 _logger = logging.getLogger("cwltool")
 
+
 def get_image(dockerRequirement, pull_image, dry_run=False):
     found = False
 
diff --git a/cwltool/draft2tool.py b/cwltool/draft2tool.py
index 75ba80d72..37452077d 100644
--- a/cwltool/draft2tool.py
+++ b/cwltool/draft2tool.py
@@ -1,4 +1,3 @@
-import avro.schema
 import json
 import copy
 from flatten import flatten
@@ -7,23 +6,19 @@
 from pathmapper import PathMapper, DockerPathMapper
 from job import CommandLineJob
 import yaml
-import glob
 import logging
 import hashlib
-import random
 from process import Process, shortname
 from errors import WorkflowException
 import schema_salad.validate as validate
 from aslist import aslist
-import expression
-import re
-import urlparse
 import tempfile
 from builder import CONTENT_LIMIT, substitute
 import shellescape
 
 _logger = logging.getLogger("cwltool")
 
+
 class ExpressionTool(Process):
     def __init__(self, toolpath_object, **kwargs):
         super(ExpressionTool, self).__init__(toolpath_object, **kwargs)
@@ -106,12 +101,11 @@ def job(self, joborder, input_basedir, output_callback, **kwargs):
         j.hints = self.hints
 
         _logger.debug("[job %s] initializing from %s%s",
-                     id(j),
-                     self.tool.get("id", ""),
-                     " as part of %s" % kwargs["part_of"] if "part_of" in kwargs else "")
+                      id(j),
+                      self.tool.get("id", ""),
+                      " as part of %s" % kwargs["part_of"] if "part_of" in kwargs else "")
         _logger.debug("[job %s] %s", id(j), json.dumps(joborder, indent=4))
 
-
         builder.pathmapper = None
 
         if self.tool.get("stdin"):
@@ -246,7 +240,6 @@ def collect_output(self, schema, builder, outdir):
                     if not builder.fs_access.exists(sf["path"]):
                         raise WorkflowException("Missing secondary file of '%s' of primary file '%s'" % (sf["path"], r["path"]))
 
-
         if not r and schema["type"] == "record":
             r = {}
             for f in schema["fields"]:
diff --git a/cwltool/expression.py b/cwltool/expression.py
index a5f8b7e5e..b0bf76fa1 100644
--- a/cwltool/expression.py
+++ b/cwltool/expression.py
@@ -3,22 +3,20 @@
 import json
 from aslist import aslist
 import logging
-import os
 from errors import WorkflowException
 import process
-import yaml
-import schema_salad.validate as validate
 import schema_salad.ref_resolver
 
 _logger = logging.getLogger("cwltool")
 
+
 def exeval(ex, jobinput, requirements, outdir, tmpdir, context, pull_image):
     if ex["engine"] == "https://w3id.org/cwl/cwl#JsonPointer":
         try:
             obj = {"job": jobinput, "context": context, "outdir": outdir, "tmpdir": tmpdir}
             return schema_salad.ref_resolver.resolve_json_pointer(obj, ex["script"])
         except ValueError as v:
-            raise WorkflowException("%s in %s" % (v,  obj))
+            raise WorkflowException("%s in %s" % (v, obj))
 
     for r in reversed(requirements):
         if r["class"] == "ExpressionEngineRequirement" and r["id"] == ex["engine"]:
@@ -56,13 +54,13 @@ class DR(object):
 
             _logger.debug("Invoking expression engine %s with %s",
                           runtime + aslist(r["engineCommand"]),
-                                           json.dumps(inp, indent=4))
+                          json.dumps(inp, indent=4))
 
             sp = subprocess.Popen(runtime + aslist(r["engineCommand"]),
-                             shell=False,
-                             close_fds=True,
-                             stdin=subprocess.PIPE,
-                             stdout=subprocess.PIPE)
+                                  shell=False,
+                                  close_fds=True,
+                                  stdin=subprocess.PIPE,
+                                  stdout=subprocess.PIPE)
 
             (stdoutdata, stderrdata) = sp.communicate(json.dumps(inp) + "\n\n")
             if sp.returncode != 0:
@@ -72,6 +70,7 @@ class DR(object):
 
     raise WorkflowException("Unknown expression engine '%s'" % ex["engine"])
 
+
 def do_eval(ex, jobinput, requirements, outdir, tmpdir, context=None, pull_image=True):
     if isinstance(ex, dict) and "engine" in ex and "script" in ex:
         return exeval(ex, jobinput, requirements, outdir, tmpdir, context, pull_image)
diff --git a/cwltool/job.py b/cwltool/job.py
index d6d7109c7..0f02ff639 100644
--- a/cwltool/job.py
+++ b/cwltool/job.py
@@ -1,12 +1,8 @@
 import subprocess
 import os
-import tempfile
-import glob
 import json
-import yaml
 import logging
 import sys
-import requests
 import docker
 from process import get_feature, empty_subtree
 from errors import WorkflowException
@@ -20,6 +16,7 @@
 
 needs_shell_quoting = re.compile(r"""(^$|[\s|&;()<>\'"$@])""").search
 
+
 def deref_links(outputs):
     if isinstance(outputs, dict):
         if outputs.get("class") == "File":
@@ -33,12 +30,13 @@ def deref_links(outputs):
         for v in outputs:
             deref_links(v)
 
+
 class CommandLineJob(object):
     def run(self, dry_run=False, pull_image=True, rm_container=True, rm_tmpdir=True, move_outputs=True, **kwargs):
         if not os.path.exists(self.outdir):
             os.makedirs(self.outdir)
 
-        #with open(os.path.join(outdir, "cwl.input.json"), "w") as fp:
+        # with open(os.path.join(outdir, "cwl.input.json"), "w") as fp:
         #    json.dump(self.joborder, fp)
 
         runtime = []
@@ -74,7 +72,7 @@ def run(self, dry_run=False, pull_image=True, rm_container=True, rm_tmpdir=True,
 
             runtime.append("--env=TMPDIR=/tmp/job_tmp")
 
-            for t,v in self.environment.items():
+            for t, v in self.environment.items():
                 runtime.append("--env=%s=%s" % (t, v))
 
             runtime.append(img_id)
diff --git a/cwltool/main.py b/cwltool/main.py
index 4461399cc..16f6cf659 100755
--- a/cwltool/main.py
+++ b/cwltool/main.py
@@ -1,6 +1,5 @@
 #!/usr/bin/env python
 
-import draft2tool
 import argparse
 from schema_salad.ref_resolver import Loader
 import json
@@ -15,7 +14,6 @@
 import yaml
 import urlparse
 import process
-import job
 from cwlrdf import printrdf, printdot
 import pkg_resources  # part of setuptools
 import update
@@ -27,6 +25,7 @@
 _logger.addHandler(defaultStreamHandler)
 _logger.setLevel(logging.INFO)
 
+
 def arg_parser():
     parser = argparse.ArgumentParser()
     parser.add_argument("--conformance-test", action="store_true")
@@ -40,17 +39,17 @@ def arg_parser():
 
     parser.add_argument("--preserve-environment", type=str, nargs='+',
                         help="Preserve specified environment variables when running CommandLineTools",
-                        metavar=("VAR1","VAR2"),
+                        metavar=("VAR1", "VAR2"),
                         dest="preserve_environment")
 
     exgroup = parser.add_mutually_exclusive_group()
     exgroup.add_argument("--rm-container", action="store_true", default=True,
-                        help="Delete Docker container used by jobs after they exit (default)",
-                        dest="rm_container")
+                         help="Delete Docker container used by jobs after they exit (default)",
+                         dest="rm_container")
 
     exgroup.add_argument("--leave-container", action="store_false",
-                        default=True, help="Do not delete Docker container used by jobs after they exit",
-                        dest="rm_container")
+                         default=True, help="Do not delete Docker container used by jobs after they exit",
+                         dest="rm_container")
 
     parser.add_argument("--tmpdir-prefix", type=str,
                         help="Path prefix for temporary directories",
@@ -62,28 +61,28 @@ def arg_parser():
 
     exgroup = parser.add_mutually_exclusive_group()
     exgroup.add_argument("--rm-tmpdir", action="store_true", default=True,
-                        help="Delete intermediate temporary directories (default)",
-                        dest="rm_tmpdir")
+                         help="Delete intermediate temporary directories (default)",
+                         dest="rm_tmpdir")
 
     exgroup.add_argument("--leave-tmpdir", action="store_false",
-                        default=True, help="Do not delete intermediate temporary directories",
-                        dest="rm_tmpdir")
+                         default=True, help="Do not delete intermediate temporary directories",
+                         dest="rm_tmpdir")
 
     exgroup = parser.add_mutually_exclusive_group()
     exgroup.add_argument("--move-outputs", action="store_true", default=True,
-                        help="Move output files to the workflow output directory and delete intermediate output directories (default).",
-                        dest="move_outputs")
+                         help="Move output files to the workflow output directory and delete intermediate output directories (default).",
+                         dest="move_outputs")
 
     exgroup.add_argument("--leave-outputs", action="store_false", default=True,
-                        help="Leave output files in intermediate output directories.",
-                        dest="move_outputs")
+                         help="Leave output files in intermediate output directories.",
+                         dest="move_outputs")
 
     exgroup = parser.add_mutually_exclusive_group()
     exgroup.add_argument("--enable-pull", default=True, action="store_true",
-                        help="Try to pull Docker images", dest="enable_pull")
+                         help="Try to pull Docker images", dest="enable_pull")
 
     exgroup.add_argument("--disable-pull", default=True, action="store_false",
-                        help="Do not try to pull Docker images", dest="enable_pull")
+                         help="Do not try to pull Docker images", dest="enable_pull")
 
     parser.add_argument("--dry-run", action="store_true",
                         help="Load and validate but do not execute")
@@ -94,7 +93,7 @@ def arg_parser():
 
     exgroup = parser.add_mutually_exclusive_group()
     exgroup.add_argument("--print-rdf", action="store_true",
-                        help="Print corresponding RDF graph for workflow and exit")
+                         help="Print corresponding RDF graph for workflow and exit")
     exgroup.add_argument("--print-dot", action="store_true", help="Print workflow visualization in graphviz format and exit")
     exgroup.add_argument("--print-pre", action="store_true", help="Print CWL document after preprocessing.")
     exgroup.add_argument("--version", action="store_true", help="Print version and exit")
@@ -114,6 +113,7 @@ def arg_parser():
 
     return parser
 
+
 def single_job_executor(t, job_order, input_basedir, args, **kwargs):
     final_output = []
     final_status = []
@@ -166,6 +166,7 @@ def output_callback(out, processStatus):
 
         return final_output[0]
 
+
 def create_loader(ctx):
     loader = Loader()
     url_fields = []
@@ -176,19 +177,24 @@ def create_loader(ctx):
     loader.idx["cwl:JsonPointer"] = {}
     return loader
 
+
 class FileAction(argparse.Action):
+
     def __init__(self, option_strings, dest, nargs=None, **kwargs):
         if nargs is not None:
             raise ValueError("nargs not allowed")
         super(FileAction, self).__init__(option_strings, dest, **kwargs)
+
     def __call__(self, parser, namespace, values, option_string=None):
         setattr(namespace, self.dest, {"class": "File", "path": values})
 
+
 class FileAppendAction(argparse.Action):
     def __init__(self, option_strings, dest, nargs=None, **kwargs):
         if nargs is not None:
             raise ValueError("nargs not allowed")
         super(FileAppendAction, self).__init__(option_strings, dest, **kwargs)
+
     def __call__(self, parser, namespace, values, option_string=None):
         g = getattr(namespace, self.dest)
         if not g:
@@ -196,6 +202,7 @@ def __call__(self, parser, namespace, values, option_string=None):
             setattr(namespace, self.dest, g)
         g.append({"class": "File", "path": values})
 
+
 def generate_parser(toolparser, tool, namemap):
     toolparser.add_argument("job_order", nargs="?", help="Job input json file")
     namemap["job_order"] = "job_order"
@@ -253,6 +260,7 @@ def generate_parser(toolparser, tool, namemap):
 
     return toolparser
 
+
 def load_tool(argsworkflow, updateonly, strict, makeTool, debug, print_pre=False):
     (document_loader, avsc_names, schema_metadata) = process.get_schema()
 
@@ -296,6 +304,7 @@ def load_tool(argsworkflow, updateonly, strict, makeTool, debug, print_pre=False
 
     return t
 
+
 def main(args=None,
          executor=single_job_executor,
          makeTool=workflow.defaultMakeTool,
@@ -410,7 +419,7 @@ def main(args=None,
             else:
                 job_order_object = {}
 
-            job_order_object.update({namemap[k]: v for k,v in cmd_line.items()})
+            job_order_object.update({namemap[k]: v for k, v in cmd_line.items()})
             _logger.debug("Parsed job order from command line: %s", job_order_object)
         else:
             job_order_object = None
diff --git a/cwltool/pathmapper.py b/cwltool/pathmapper.py
index 7fbb40c68..621bc7ae9 100644
--- a/cwltool/pathmapper.py
+++ b/cwltool/pathmapper.py
@@ -5,6 +5,7 @@
 
 _logger = logging.getLogger("cwltool")
 
+
 def abspath(src, basedir):
     if src.startswith("file://"):
         ab = src[7:]
@@ -12,6 +13,7 @@ def abspath(src, basedir):
         ab = src if os.path.isabs(src) else os.path.join(basedir, src)
     return ab
 
+
 class PathMapper(object):
     """Mapping of files from relative path provided in the file to a tuple of
     (absolute local path, absolute container path)"""
@@ -29,10 +31,11 @@ def files(self):
         return self._pathmap.keys()
 
     def reversemap(self, target):
-        for k,v in self._pathmap.items():
+        for k, v in self._pathmap.items():
             if v[1] == target:
                 return (k, v[0])
 
+
 class DockerPathMapper(PathMapper):
     def __init__(self, referenced_files, basedir):
         self._pathmap = {}
@@ -44,8 +47,8 @@ def __init__(self, referenced_files, basedir):
             subdir = False
             for d in self.dirs:
                 if dir.startswith(d):
-                  subdir = True
-                  break
+                    subdir = True
+                    break
 
             if not subdir:
                 for d in list(self.dirs):
diff --git a/cwltool/process.py b/cwltool/process.py
index 993d703f8..8ebc09896 100644
--- a/cwltool/process.py
+++ b/cwltool/process.py
@@ -4,13 +4,10 @@
 import schema_salad.validate as validate
 import copy
 import yaml
-import copy
 import logging
-import pprint
 from aslist import aslist
 import schema_salad.schema
 import urlparse
-import pprint
 from pkg_resources import resource_stream
 import stat
 from builder import Builder
@@ -31,12 +28,14 @@
                                 "MultipleInputFeatureRequirement",
                                 "ShellCommandRequirement"]
 
+
 def get_schema():
     f = resource_stream(__name__, 'schemas/draft-3/cwl-avro.yml')
     j = yaml.load(f)
     j["name"] = "https://w3id.org/cwl/cwl"
     return schema_salad.schema.load_schema(j)
 
+
 def get_feature(self, feature):
     for t in reversed(self.requirements):
         if t["class"] == feature:
@@ -46,10 +45,12 @@ def get_feature(self, feature):
             return (t, False)
     return (None, None)
 
+
 def shortname(inputid):
     (_, d) = urlparse.urldefrag(inputid)
     return d.split("/")[-1].split(".")[-1]
 
+
 class StdFsAccess(object):
     def __init__(self, basedir):
         self.basedir = basedir
@@ -66,6 +67,7 @@ def open(self, fn, mode):
     def exists(self, fn):
         return os.path.exists(self._abs(fn))
 
+
 def checkRequirements(rec, supportedProcessRequirements):
     if isinstance(rec, dict):
         if "requirements" in rec:
@@ -81,6 +83,7 @@ def checkRequirements(rec, supportedProcessRequirements):
         for d in rec:
             checkRequirements(d, supportedProcessRequirements)
 
+
 def adjustFiles(rec, op):
     """Apply a mapping function to each File path in the object `rec`."""
 
@@ -93,6 +96,7 @@ def adjustFiles(rec, op):
         for d in rec:
             adjustFiles(d, op)
 
+
 class Process(object):
     def __init__(self, toolpath_object, **kwargs):
         (_, self.names, _) = get_schema()
@@ -149,7 +153,6 @@ def __init__(self, toolpath_object, **kwargs):
         except avro.schema.SchemaParseException as e:
             raise validate.ValidationException("Got error `%s` while prcoessing outputs of %s:\n%s" % (str(e), self.tool["id"], json.dumps(self.outputs_record_schema, indent=4)))
 
-
     def _init_job(self, joborder, input_basedir, **kwargs):
         builder = Builder()
         builder.job = copy.deepcopy(joborder)
@@ -189,7 +192,6 @@ def _init_job(self, joborder, input_basedir, **kwargs):
 
         return builder
 
-
     def validate_hints(self, hints, strict):
         for r in hints:
             try:
@@ -203,6 +205,7 @@ def validate_hints(self, hints, strict):
     def get_requirement(self, feature):
         return get_feature(self, feature)
 
+
 def empty_subtree(dirpath):
     # Test if a directory tree contains any files (does not count empty
     # subdirectories)
diff --git a/cwltool/schemas/draft-2/draft-2/search.py b/cwltool/schemas/draft-2/draft-2/search.py
index 002a627e3..20e44fc76 100755
--- a/cwltool/schemas/draft-2/draft-2/search.py
+++ b/cwltool/schemas/draft-2/draft-2/search.py
@@ -4,7 +4,6 @@
 # appears.
 
 import sys
-import os
 
 mainfile = sys.argv[1]
 indexfile = sys.argv[1] + ".idx"
diff --git a/cwltool/schemas/site/generate.py b/cwltool/schemas/site/generate.py
index ae4adc84d..a1d90bc35 100644
--- a/cwltool/schemas/site/generate.py
+++ b/cwltool/schemas/site/generate.py
@@ -1,11 +1,10 @@
 import cwltool.avro_ld.schema
 import cwltool.avro_ld.makedoc
-import mistune
+
 import sys
 
 with open(sys.argv[1]) as f:
     cwltool.avro_ld.makedoc.avrold_doc([{"name": " ",
-                                "type": "doc",
-                                "doc": f.read().decode("utf-8")
-                            }],
-                               sys.stdout)
+                                         "type": "doc",
+                                         "doc": f.read().decode("utf-8")}],
+                                       sys.stdout)
diff --git a/cwltool/update.py b/cwltool/update.py
index 1f1698fb1..c68ed65d5 100644
--- a/cwltool/update.py
+++ b/cwltool/update.py
@@ -1,7 +1,7 @@
-import sys
 import urlparse
 import json
 
+
 def findId(doc, frg):
     if isinstance(doc, dict):
         if "id" in doc and doc["id"] == frg:
@@ -18,6 +18,7 @@ def findId(doc, frg):
                 return f
     return None
 
+
 def fixType(doc):
     if isinstance(doc, list):
         return [fixType(f) for f in doc]
@@ -27,6 +28,7 @@ def fixType(doc):
             return "#" + doc
     return doc
 
+
 def _draft2toDraft3(doc, loader, baseuri):
     try:
         if isinstance(doc, dict):
@@ -61,7 +63,6 @@ def _draft2toDraft3(doc, loader, baseuri):
                                 doc["requirements"] = []
                             doc["requirements"].append({"class": "MultipleInputFeatureRequirement"})
 
-
             for a in doc:
                 doc[a] = _draft2toDraft3(doc[a], loader, baseuri)
 
@@ -77,9 +78,11 @@ def _draft2toDraft3(doc, loader, baseuri):
             err = doc["name"]
         raise Exception("Error updating '%s'\n  %s" % (err, e))
 
+
 def draft2toDraft3(doc, loader, baseuri):
     return (_draft2toDraft3(doc, loader, baseuri), "https://w3id.org/cwl/cwl#draft-3.dev1")
 
+
 def update(doc, loader, baseuri):
     updates = {
         "https://w3id.org/cwl/cwl#draft-2": draft2toDraft3,
diff --git a/cwltool/workflow.py b/cwltool/workflow.py
index 9fc08ef91..fb74418b8 100644
--- a/cwltool/workflow.py
+++ b/cwltool/workflow.py
@@ -1,26 +1,22 @@
-import job
 import draft2tool
 from aslist import aslist
-from process import Process, get_feature, empty_subtree, shortname
+from process import Process, empty_subtree, shortname
 from errors import WorkflowException
 import copy
 import logging
 import random
 import os
 from collections import namedtuple
-import pprint
 import functools
 import schema_salad.validate as validate
-import urlparse
-import pprint
 import tempfile
 import shutil
-import json
 
 _logger = logging.getLogger("cwltool")
 
 WorkflowStateItem = namedtuple('WorkflowStateItem', ['parameter', 'value'])
 
+
 def defaultMakeTool(toolpath_object, **kwargs):
     if not isinstance(toolpath_object, dict):
         raise WorkflowException("Not a dict: `%s`" % toolpath_object)
@@ -34,6 +30,7 @@ def defaultMakeTool(toolpath_object, **kwargs):
 
     raise WorkflowException("Missing or invalid 'class' field in %s, expecting one of: CommandLineTool, ExpressionTool, Workflow" % toolpath_object["id"])
 
+
 def findfiles(wo, fn=None):
     if fn is None:
         fn = []
@@ -100,7 +97,7 @@ def object_from_state(state, parms, frag_only, supportsMultipleInput):
             for src in connections:
                 if src in state and state[src] is not None:
                     if not match_types(inp["type"], state[src], iid, inputobj,
-                                            inp.get("linkMerge", ("merge_nested" if len(connections) > 1 else None))):
+                                       inp.get("linkMerge", ("merge_nested" if len(connections) > 1 else None))):
                         raise WorkflowException("Type mismatch between source '%s' (%s) and sink '%s' (%s)" % (src, state[src].parameter["type"], inp["id"], inp["type"]))
                 elif src not in state:
                     raise WorkflowException("Connect source '%s' on parameter '%s' does not exist" % (src, inp["id"]))
@@ -126,6 +123,7 @@ def job(self, joborder, basedir, output_callback, **kwargs):
         for j in self.step.job(joborder, basedir, output_callback, **kwargs):
             yield j
 
+
 class WorkflowJob(object):
     def __init__(self, workflow, **kwargs):
         self.workflow = workflow
@@ -203,7 +201,7 @@ def try_make_job(self, step, basedir, **kwargs):
                 yield j
         except WorkflowException:
             raise
-        except Exception as e:
+        except Exception:
             _logger.exception("Unhandled exception")
             self.processStatus = "permanentFail"
             step.completed = True
@@ -264,7 +262,7 @@ def job(self, joborder, basedir, output_callback, move_outputs=True, **kwargs):
                 for a in output_dirs:
                     if f["path"].startswith(a):
                         src = f["path"]
-                        dst = os.path.join(self.outdir, src[len(a)+1:])
+                        dst = os.path.join(self.outdir, src[len(a) + 1:])
                         if dst in targets:
                             conflicts.add(dst)
                         else:
@@ -274,7 +272,7 @@ def job(self, joborder, basedir, output_callback, move_outputs=True, **kwargs):
                 for a in output_dirs:
                     if f["path"].startswith(a):
                         src = f["path"]
-                        dst = os.path.join(self.outdir, src[len(a)+1:])
+                        dst = os.path.join(self.outdir, src[len(a) + 1:])
                         if dst in conflicts:
                             sp = os.path.splitext(dst)
                             dst = "%s-%s%s" % (sp[0], str(random.randint(1, 1000000000)), sp[1])
@@ -302,8 +300,8 @@ def __init__(self, toolpath_object, **kwargs):
         kwargs["requirements"] = self.requirements
         kwargs["hints"] = self.hints
 
-        makeTool = kwargs.get("makeTool")
-        self.steps = [WorkflowStep(step, n, **kwargs) for n,step in enumerate(self.tool.get("steps", []))]
+        kwargs.get("makeTool")
+        self.steps = [WorkflowStep(step, n, **kwargs) for n, step in enumerate(self.tool.get("steps", []))]
         random.shuffle(self.steps)
 
         # TODO: statically validate data links instead of doing it at runtime.
@@ -386,7 +384,7 @@ def __init__(self, toolpath_object, pos, **kwargs):
             self.tool["outputs"] = outputparms
 
     def receive_output(self, output_callback, jobout, processStatus):
-        #_logger.debug("WorkflowStep output from run is %s", jobout)
+        # _logger.debug("WorkflowStep output from run is %s", jobout)
         output = {}
         for i in self.tool["outputs"]:
             field = shortname(i["id"])
@@ -422,7 +420,7 @@ def __init__(self, output_callback, dest):
         self.output_callback = output_callback
 
     def receive_scatter_output(self, index, jobout, processStatus):
-        for k,v in jobout.items():
+        for k, v in jobout.items():
             self.dest[k][index] = v
 
         if processStatus != "success":
@@ -500,6 +498,7 @@ def crossproduct_size(joborder, scatter_keys):
             sum += crossproduct_size(joborder, scatter_keys[1:])
     return sum
 
+
 def flat_crossproduct_scatter(process, joborder, basedir, scatter_keys, output_callback, startindex, **kwargs):
     scatter_key = scatter_keys[0]
     l = len(joborder[scatter_key])
diff --git a/setup.cfg b/setup.cfg
new file mode 100644
index 000000000..3363abe67
--- /dev/null
+++ b/setup.cfg
@@ -0,0 +1,3 @@
+[flake8]
+max-line-length = 200
+max-complexity = 38
diff --git a/tox.ini b/tox.ini
new file mode 100644
index 000000000..1143a5418
--- /dev/null
+++ b/tox.ini
@@ -0,0 +1,7 @@
+[tox]
+envlist = py27-lint
+
+[testenv:py27-lint]
+commands = flake8 cwltool
+skip_install = True
+deps = flake8