Commit Graph
1067 Commits
Author SHA1 Message Date
mvdbeek 746d0ba724 Merge branch 'release_20.01' into dev 2020-04-01 11:45:12 +02:00
John Chilton 6a0253499d Rebuild config. 2020-03-26 09:39:39 -04:00
Nicola Soranzo 401b163e71 Fix docs to update conda from conda-forge 2020-03-22 17:08:04 +00:00
Anup Kumar 71f657565f Merge branch 'dev' of github.com:anuprulez/galaxy into recommend_tools_run 2020-03-17 23:49:47 +01:00
Anup Kumar 8d8d3d08f5 Update model path 2020-03-17 22:36:52 +01:00
Dannon c5efa01b10 Merge pull request #9455 from ic4f/dev_sanitized_whitelist_move
Move sanitize_whitelist into mutable_config_dir
2020-03-13 14:44:33 -04:00
Anup Kumar 6b77c0ada4 Merge branch 'dev' of github.com:anuprulez/galaxy into recommend_tools_run 2020-03-12 15:01:31 +01:00
John Chilton 9ec4638d75 Merge pull request #9512 from astrovsky01/patch-4
Fixed tool locations
2020-03-11 19:35:33 -04:00
Dannon Baker 302df392d7 typo: juypter/jupyter 2020-03-10 17:13:24 -04:00
Dannon Baker cbecde300f Fix IT wrapper filenames. 2020-03-10 17:11:52 -04:00
Alex Ostrovsky 39a8c0ca63 Fixed tool locations 2020-03-10 12:52:13 -04:00
Anup Kumar 30e6728787 Merge branch 'dev' of github.com:anuprulez/galaxy into recommend_tools_run 2020-03-10 09:09:36 +01:00
Daniel Blankenberg 486d633cde run make config-rebuild 2020-03-06 16:46:05 -05:00
MiguelJulia 64e4cfe19e updated documentation with new priority over lists 2020-03-06 21:21:34 +01:00
MiguelJulia 70f0a4dc89 make config-rebuild 2020-03-06 18:37:23 +01:00
MiguelJulia e7f086c334 Added documentation generated with make 2020-03-06 16:45:35 +01:00
mvdbeek e954807275 Merge branch 'release_20.01' into dev 2020-03-05 12:52:43 +01:00
Helena Rasche 09bfa57ab9 rebuild 2020-03-03 17:26:02 +01:00
Anup Kumar e3d028c186 Merge branch 'dev' of github.com:anuprulez/galaxy into recommend_tools_run 2020-03-03 17:09:04 +01:00
mvdbeek a8cbd36d90 Drop manage_dependency_relationships altogether
Probably didn't work for some time and seems unnecessary.

Fixes
```
galaxy.tool_shed.galaxy_install.installed_repository_manager DEBUG 2020-02-28 10:57:01,109 [p:94029,w:0,m:0] [MainThread] Adding an entry for version 2.2.4 of package bowtie2 to runtime_tool_dependencies_of_installed_tool_dependencies.
Traceback (most recent call last):
  File "lib/galaxy/webapps/galaxy/buildapp.py", line 48, in app_factory
    app = galaxy.app.UniverseApplication(global_conf=global_conf, **kwargs)
  File "lib/galaxy/app.py", line 95, in __init__
    self.installed_repository_manager = InstalledRepositoryManager(self)
  File "lib/galaxy/tool_shed/galaxy_install/installed_repository_manager.py", line 84, in __init__
    self.load_dependency_relationships()
  File "lib/galaxy/tool_shed/galaxy_install/installed_repository_manager.py", line 734, in load_dependency_relationships
    self.add_entry_to_runtime_tool_dependencies_of_installed_tool_dependencies(tool_dependency)
  File "lib/galaxy/tool_shed/galaxy_install/installed_repository_manager.py", line 218, in add_entry_to_runtime_tool_dependencies_of_installed_tool_dependencies
    status=None)
  File "lib/galaxy/tool_shed/galaxy_install/installed_repository_manager.py", line 604, in get_runtime_dependent_tool_dependency_tuples
    required_env_shell_file_path = tool_dependency.get_env_shell_file_path(self.app)
  File "lib/galaxy/model/tool_shed_install/__init__.py", line 522, in get_env_shell_file_path
    installation_directory = self.installation_directory(app)
  File "lib/galaxy/model/tool_shed_install/__init__.py", line 534, in installation_directory
    return os.path.join(app.tool_dependency_dir,
  File "lib/galaxy/config/__init__.py", line 1186, in tool_dependency_dir
    return self.toolbox.dependency_manager.default_base_path
AttributeError: 'UniverseApplication' object has no attribute 'toolbox'
```
reported by @scholtalbers
2020-02-29 17:36:42 +01:00
Sergey Golitsynskiy b31d63e92f Run make config-rebuild 2020-02-28 11:42:07 -05:00
Sergey Golitsynskiy 4a847a2fab Merge pull request #9444 from ic4f/dev_managed_config_dir2
Make mutable_config_dir configurable + rename
2020-02-27 20:54:04 -05:00
mvdbeek 36ab948087 Merge branch 'release_20.01' into dev 2020-02-27 21:54:30 +01:00
mvdbeek a974d02b23 Fix newlines in final release notes 2020-02-27 21:03:20 +01:00
mvdbeek a02480f35b Merge branch 'release_20.01' into dev 2020-02-27 17:51:34 +01:00
mvdbeek b6d05e3d09 Update for new 20.01 PRs 2020-02-26 16:19:32 +01:00
Marius van den BeekandNicola Soranzo 0aa5c4b21c One more version change
Co-Authored-By: Nicola Soranzo <nicola.soranzo@gmail.com>
2020-02-26 14:25:10 +01:00
mvdbeek 4f0cce0c27 Adjust docs for when we started preferring python3 2020-02-26 14:06:55 +01:00
Anup Kumar cf54ae1beb Fix linting issues 2020-02-26 12:29:46 +01:00
mvdbeek 9fdbad7247 Mention that more distribution tools/converters need dependencies now 2020-02-26 11:13:45 +01:00
mvdbeek 48e015d362 Link to Python upgrade instructions 2020-02-26 11:02:39 +01:00
mvdbeek 1169db7c9e Mention that database/compiled_templates needs to be removed when upgrading python 2020-02-26 11:02:24 +01:00
Nicola Soranzo 99bc25f4cc Add more details 2020-02-26 10:54:56 +01:00
Alex Ostrovsky 4c712f0f2d Added conda python update 2020-02-26 10:54:56 +01:00
Nicola Soranzo 58ae3e43e3 Python3: decode the output of `subprocess.check_output()` 2020-02-26 10:53:49 +01:00
Nicola Soranzo 765f59175c Create Python3 virtualenv by default
- Allow specifying Python to use to create virtualenv using GALAXY_PYTHON
  environment variable.
- Integrate Python support docs from https://galaxyproject.org/admin/python/
- Update virtualenv installation to use v16.7.9
2020-02-26 10:53:43 +01:00
mvdbeek 9748452b1b Merge followup PR into original announcement 2020-02-26 10:24:52 +01:00
mvdbeek 05d5fd1da8 Update with latest PRs 2020-02-26 10:23:22 +01:00
mvdbeek 07a6922105 Update with new 20.01 PRs 2020-02-26 10:15:33 +01:00
mvdbeek fe68dede4d Pahes typo 2020-02-26 10:15:33 +01:00
mvdbeek 3d22c726fc Fix RST formatting 2020-02-26 10:15:33 +01:00
mvdbeek 090bef14fb Tweak image size and add 20.01_annouce to index 2020-02-26 10:15:33 +01:00
mvdbeek b76e29a267 Add workflow report and email button screenshots 2020-02-26 10:15:33 +01:00
mvdbeek 722c2f251a First pass at user announements 2020-02-26 10:15:33 +01:00
mvdbeek d217b6d117 Edit to 20.01_announce.rst 2020-02-26 10:15:33 +01:00
Marius van den BeekandHelena Rasche 8619c2d01f Update doc/source/releases/20.01_announce.rst
Co-Authored-By: Helena Rasche <hxr@hx42.org>
2020-02-26 10:15:33 +01:00
mvdbeek 08e97198c9 Release notes for 20.01 2020-02-26 10:15:33 +01:00
Sergey Golitsynskiy ed19b91941 Run make config-rebuild 2020-02-25 22:28:46 -05:00
Anup Kumar 91c2676946 Add tool recommendations for tool run 2020-02-25 17:28:31 +01:00
Sergey Golitsynskiy c54836e984 Remove '.sample' from default value; rebuild schema 2020-02-25 10:01:10 +01:00