Merge pull request #355 from broadinstitute/dp-fix-tool-patch

fix Tool._patch

tools/__init__.py

@@ -324,12 +324,8 @@ def executable_path(self):
  return os.path.join(self.bin_path, self.executable)
 
  def apply_patches(self):
- result = None
  for path, patch in self.patches:
- result = self._patch(path, patch)
- if result.returncode != 0:
- return result
- return result
+ self._patch(path, patch)
 
 
  def _patch(self, path, patch):
@@ -340,7 +336,7 @@ def _patch(self, path, patch):
  file_path = os.path.join(self.env_path, path)
  patch_path = os.path.join(
  util.file.get_project_path(), 'tools', 'patches', patch)
- return subprocess.check_call(['patch', file_path, patch_path])
+ subprocess.check_call(['patch', file_path, patch_path])
 
  @property
  def _package_installed(self):
@@ -533,10 +529,7 @@ def install_package(self):
 
  if data["success"] == True:
  _log.debug("Package installed.")
- result = self.apply_patches()
- if result and result.returncode != 0:
- _log.error("Failed to apply patches.")
- return
+ self.apply_patches()
 
  else:
  if "success" in data.keys() and data["success"]: