Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: 8806030f53c2b9d0002505bf5193be88d7cff8f9 https://github.com/galaxyproject/galaxy/commit/8806030f53c2b9d0002505bf5193b... Author: Nicola Soranzo <nicola.soranzo@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/fc52fe5c62700b4f8527e4edead0f... Author: Martin Cech <marten@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