Branch: refs/heads/release_18.01
Home: https://github.com/galaxyproject/galaxy
Commit: 8806030f53c2b9d0002505bf5193be88d7cff8f9
https://github.com/galaxyproject/galaxy/commit/8806030f53c2b9d0002505bf5193…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2018-02-22 (Thu, 22 Feb 2018)
Changed paths:
M lib/galaxy/datatypes/converters/sam_to_bam.py
M lib/galaxy/dependencies/pinned-requirements.txt
M lib/galaxy/dependencies/requirements.txt
M lib/galaxy/jobs/runners/pulsar.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/deps/conda_util.py
M lib/galaxy/tools/deps/mulled/util.py
M lib/galaxy/tools/toolbox/lineages/interface.py
M lib/galaxy/visualization/data_providers/genome.py
Log Message:
-----------
Replace distutils.version with packaging.version
distutils under Python3 has this bug:
https://bugs.python.org/issue14894
which causes this traceback:
```
Traceback (most recent call last):
File "lib/galaxy/webapps/galaxy/buildapp.py", line 49, in app_factory
app = galaxy.app.UniverseApplication(global_conf=global_conf, **kwargs)
File "lib/galaxy/app.py", line 125, in __init__
self._configure_toolbox()
File "lib/galaxy/config.py", line 930, in _configure_toolbox
self.toolbox = tools.ToolBox(tool_configs, self.config.tool_path, self)
File "lib/galaxy/tools/__init__.py", line 232, in __init__
app=app,
File "lib/galaxy/tools/toolbox/base.py", line 1056, in __init__
super(BaseGalaxyToolBox, self).__init__(config_filenames, tool_root_dir, app)
File "lib/galaxy/tools/toolbox/base.py", line 84, in __init__
self._load_tool_panel()
File "lib/galaxy/tools/toolbox/base.py", line 358, in _load_tool_panel
self.__add_tool_to_tool_panel(section_val, section, section=True)
File "lib/galaxy/tools/toolbox/base.py", line 278, in __add_tool_to_tool_panel
related_tool = self._lineage_in_panel(panel_dict, tool=tool)
File "lib/galaxy/tools/toolbox/base.py", line 961, in _lineage_in_panel
lineage_tool_versions = reversed(tool_lineage.get_versions())
File "lib/galaxy/tools/toolbox/lineages/interface.py", line 77, in get_versions
return [ToolLineageVersion(tool_id, tool_version) for tool_id, tool_version in zip(self.tool_ids, self.tool_versions)]
File "lib/galaxy/tools/toolbox/lineages/interface.py", line 55, in tool_ids
return ["%s/%s" % (tool_id, version) for version in self.tool_versions]
File "lib/galaxy/tools/toolbox/lineages/interface.py", line 49, in tool_versions
return sorted(self._tool_versions, key=LooseVersion)
File "/usr/lib/python3.4/distutils/version.py", line 58, in __lt__
c = self._cmp(other)
File "/usr/lib/python3.4/distutils/version.py", line 343, in _cmp
if self.version < other.version:
TypeError: unorderable types: str() < int()
```
when a tool version contains a letter in the "wrong" place (e.g. in the first position).
Fix https://github.com/galaxyproject/galaxy/issues/5408 .
Commit: fc52fe5c62700b4f8527e4edead0fba4e7cfe33f
https://github.com/galaxyproject/galaxy/commit/fc52fe5c62700b4f8527e4edead0…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2018-02-22 (Thu, 22 Feb 2018)
Changed paths:
M lib/galaxy/datatypes/converters/sam_to_bam.py
M lib/galaxy/dependencies/pinned-requirements.txt
M lib/galaxy/dependencies/requirements.txt
M lib/galaxy/jobs/runners/pulsar.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/deps/conda_util.py
M lib/galaxy/tools/deps/mulled/util.py
M lib/galaxy/tools/toolbox/lineages/interface.py
M lib/galaxy/visualization/data_providers/genome.py
Log Message:
-----------
Merge pull request #5588 from jmchilton/backport_packaging
[18.01] Replace distutils.version with packaging.version
Compare: https://github.com/galaxyproject/galaxy/compare/ce3b40cfc10e...fc52fe5c6270