diff --git a/.flake8 b/.flake8
deleted file mode 100644
index 9b65fe6..0000000
--- a/.flake8
+++ /dev/null
@@ -1,2 +0,0 @@
-[flake8]
-exclude = *_pb2.py
diff --git a/.travis.yml b/.travis.yml
index 8df7032..43777be 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -22,7 +22,7 @@ before_script:
 # run_tests.py runs everything under the script: tag so only put commands
 # under it that we want to run (and want to be able to run) as local tests
 script: 
-  - flake8 *.py ga4gh_common tests
+  - flake8 run_tests_dev.py setup.py ga4gh_common tests
   - nosetests tests
         --with-coverage --cover-package ga4gh_common
         --cover-inclusive --cover-min-percentage=70
diff --git a/ga4gh_common/run_tests.py b/ga4gh_common/run_tests.py
index a94ffa6..2a8a0cd 100644
--- a/ga4gh_common/run_tests.py
+++ b/ga4gh_common/run_tests.py
@@ -24,7 +24,7 @@ def runTests(self):
         testCommands = self.parseTestCommands()
         for command in testCommands:
             self.log('Running: "{}"'.format(command))
-            utils.runCommand(command, shell=True)
+            utils.runCommand(command)
         self.log('SUCCESS')
 
     def log(self, logStr):