From 50d3c4ae9540c4f2a4ffc78f96b260c5b72a69d2 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= Date: Mon, 31 Oct 2016 19:02:37 +0100 Subject: [PATCH 1/6] Try to make planemo work with docker_galaxy --- planemo/engine/factory.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/planemo/engine/factory.py b/planemo/engine/factory.py index 8e9cf8d8d..989288a2b 100644 --- a/planemo/engine/factory.py +++ b/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 From 3263d9039d202db4f8193adfe43a9a18a1bf3368 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= Date: Mon, 31 Oct 2016 20:22:20 +0100 Subject: [PATCH 2/6] lint fixes --- planemo/glob.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/planemo/glob.py b/planemo/glob.py index e03e3a5b8..63adb9f0c 100644 --- a/planemo/glob.py +++ b/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." From 135d38cc9828d483f3d7fb98f6ec166360335e58 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= Date: Mon, 31 Oct 2016 20:24:06 +0100 Subject: [PATCH 3/6] lint fixes --- planemo/commands/cmd_conda_lint.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/planemo/commands/cmd_conda_lint.py b/planemo/commands/cmd_conda_lint.py index 984c0bd7c..566e7c486 100644 --- a/planemo/commands/cmd_conda_lint.py +++ b/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 From 7d77c4b068618ef0cbb54a03d62059d5361a20a5 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= Date: Mon, 31 Oct 2016 20:26:34 +0100 Subject: [PATCH 4/6] lint fixes --- planemo/commands/cmd_travis_init.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/planemo/commands/cmd_travis_init.py b/planemo/commands/cmd_travis_init.py index 193fe197d..c60ee011f 100644 --- a/planemo/commands/cmd_travis_init.py +++ b/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 From 58e3fe4977f263ba7695d27fa3fdfa9bb6ac99f9 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= Date: Mon, 31 Oct 2016 20:27:00 +0100 Subject: [PATCH 5/6] lint fixes --- planemo/galaxy/test/structures.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/planemo/galaxy/test/structures.py b/planemo/galaxy/test/structures.py index aa7240eb5..dccb19fc9 100644 --- a/planemo/galaxy/test/structures.py +++ b/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 From 9d4f5fd03afb2249b39a44dee21c605e5e67ec3c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= Date: Mon, 31 Oct 2016 20:27:37 +0100 Subject: [PATCH 6/6] lint fixes --- planemo/shed2tap/base.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/planemo/shed2tap/base.py b/planemo/shed2tap/base.py index f4de640e8..3e13ea9bd 100644 --- a/planemo/shed2tap/base.py +++ b/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