Merge pull request #598 from galaxyproject/docker_galaxy

Try to make planemo work with docker_galaxy

planemo/commands/cmd_conda_lint.py

@@ -1,8 +1,8 @@
 """Module describing the planemo ``conda_lint`` command."""
 import click
 
-from planemo import options
 from planemo import conda_lint
+from planemo import options
 from planemo.cli import command_function
 
 

planemo/commands/cmd_travis_init.py

@@ -5,8 +5,8 @@
 
 from galaxy.tools.deps.commands import shell
 
-from planemo import options
 from planemo import RAW_CONTENT_URL
+from planemo import options
 from planemo.cli import command_function
 from planemo.io import info, warn
 

planemo/engine/factory.py

@@ -20,7 +20,7 @@ def build_engine(ctx, **kwds):
     engine_type_str = kwds.get("engine", "galaxy")
     if engine_type_str == "galaxy":
         engine_type = GalaxyEngine
-    elif engine_type_str == "dockerize_galaxy":
+    elif engine_type_str == "docker_galaxy":
         engine_type = DockerizedGalaxyEngine
     elif engine_type_str == "cwltool":
         engine_type = CwlToolEngine

planemo/galaxy/test/structures.py

@@ -1,6 +1,6 @@
 """Utilities for reasoning about Galaxy test results."""
-from __future__ import print_function
 from __future__ import absolute_import
+from __future__ import print_function
 
 import os
 import xml.etree.ElementTree as ET

planemo/glob.py

@@ -1,5 +1,5 @@
-from __future__ import print_function
 from __future__ import absolute_import
+from __future__ import print_function
 
 NO_GLOB_2 = "glob2 library unavailabile, please install with pip install glob2."
 

planemo/shed2tap/base.py

@@ -9,8 +9,8 @@
 from ftplib import all_errors as FTPErrors  # tuple of exceptions
 from xml.etree import ElementTree
 
-from six import string_types
 from six import iteritems
+from six import string_types
 from six.moves import map as imap
 from six.moves.urllib.error import URLError
 from six.moves.urllib.request import urlretrieve