- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 063605: Use pgcalc when possible
by GitHub 20 Mar '17

20 Mar '17

Branch: refs/heads/usegalaxy Home: https://github.com/galaxyproject/galaxy Commit: 0636053901545a26662ed8f42a15bb67407f2231 https://github.com/galaxyproject/galaxy/commit/0636053901545a26662ed8f42a15… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-24 (Fri, 24 Feb 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/user.py Log Message: ----------- Use pgcalc when possible Commit: 895351cdf8e8867452d28dffb89a2067eabfadb3 https://github.com/galaxyproject/galaxy/commit/895351cdf8e8867452d28dffb89a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-24 (Fri, 24 Feb 2017) Changed paths: M lib/galaxy/queue_worker.py M lib/galaxy/webapps/galaxy/controllers/user.py Log Message: ----------- initial working async recalc Commit: 45d75e3da55e43a4444c1a7982e1ea31e1aa5cb7 https://github.com/galaxyproject/galaxy/commit/45d75e3da55e43a4444c1a7982e1… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-24 (Fri, 24 Feb 2017) Changed paths: M lib/galaxy/queue_worker.py M lib/galaxy/webapps/galaxy/controllers/user.py Log Message: ----------- Encode userid in messages. Commit: c373bf27e79e48bc2e8ba983e9f08abde16db4df https://github.com/galaxyproject/galaxy/commit/c373bf27e79e48bc2e8ba983e9f0… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-24 (Fri, 24 Feb 2017) Changed paths: M lib/galaxy/queue_worker.py Log Message: ----------- Change handling of declare in queue_async_task Commit: 00b1591f05af4743d8b16b7d1bbbbc99a3974adb https://github.com/galaxyproject/galaxy/commit/00b1591f05af4743d8b16b7d1bbb… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-24 (Fri, 24 Feb 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/user.py Log Message: ----------- Fix inline doc Commit: 5a5dbb97f1e04dfe15fbf71c441eb50ae4b70b11 https://github.com/galaxyproject/galaxy/commit/5a5dbb97f1e04dfe15fbf71c441e… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-02-25 (Sat, 25 Feb 2017) Changed paths: M doc/source/releases/17.01_announce.rst Log Message: ----------- improve 17.01 get galaxy release notes Commit: 53c00df805e7ae7e509c08374bc941d31d20000d https://github.com/galaxyproject/galaxy/commit/53c00df805e7ae7e509c08374bc9… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-25 (Sat, 25 Feb 2017) Changed paths: M lib/galaxy/queue_worker.py M lib/galaxy/webapps/galaxy/controllers/user.py Log Message: ----------- Rename send_local_controL_task, add at least a tiny bit of documentation. Commit: d4b677bc38b221678bc991e0fddc43622accb928 https://github.com/galaxyproject/galaxy/commit/d4b677bc38b221678bc991e0fddc… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-02-27 (Mon, 27 Feb 2017) Changed paths: M lib/galaxy/queue_worker.py M lib/galaxy/webapps/galaxy/controllers/user.py Log Message: ----------- Merge pull request #3669 from dannon/logout-recalc-improvements [17.01] Logout recalc improvements Commit: 28875de584ac1967a8f2c0cdc8f5fa7b37e70f21 https://github.com/galaxyproject/galaxy/commit/28875de584ac1967a8f2c0cdc8f5… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2017-02-28 (Tue, 28 Feb 2017) Changed paths: M doc/source/releases/17.01_announce.rst Log Message: ----------- Merge pull request #3670 from martenson/fix-RN1701 [17.01] improve 17.01 get galaxy release notes Commit: 0997348a1c0a450986d376a96af024c73d4c7f37 https://github.com/galaxyproject/galaxy/commit/0997348a1c0a450986d376a96af0… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-02-28 (Tue, 28 Feb 2017) Changed paths: M lib/galaxy/tools/search/__init__.py Log Message: ----------- fix tool search idnex building for tools with / in id and not from TS Commit: c11cb3dd4572e7a4f1f814a31a45477f9ecd5ae9 https://github.com/galaxyproject/galaxy/commit/c11cb3dd4572e7a4f1f814a31a45… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-02-28 (Tue, 28 Feb 2017) Changed paths: M lib/galaxy/tools/search/__init__.py Log Message: ----------- fix typo spotted by :beer: :eyes: Commit: 169b45b138685164010043be95cefe8148c6f713 https://github.com/galaxyproject/galaxy/commit/169b45b138685164010043be95ce… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-28 (Tue, 28 Feb 2017) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Fix step name display for 17.01 Commit: e23facb966c9962bb5bd1fdd07bf6ee28d7d5930 https://github.com/galaxyproject/galaxy/commit/e23facb966c9962bb5bd1fdd07bf… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-02-28 (Tue, 28 Feb 2017) Changed paths: M lib/galaxy/tools/search/__init__.py Log Message: ----------- Merge pull request #3680 from martenson/fix-id-indexing [17.01] fix tool search index building for tools with slash in id and not from TS Commit: 7824cd31fd7b9351efa1cf8274b89b2b9a0d811d https://github.com/galaxyproject/galaxy/commit/7824cd31fd7b9351efa1cf8274b8… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-03-01 (Wed, 01 Mar 2017) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Merge pull request #3681 from guerler/fix_name_display [17.01] Fix step name display for 17.01 Commit: dda11d21c2e88f6b935f9f90f270a7aeccd929da https://github.com/galaxyproject/galaxy/commit/dda11d21c2e88f6b935f9f90f270… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-03-01 (Wed, 01 Mar 2017) Changed paths: M lib/galaxy/tools/deps/container_resolvers/__init__.py M lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/tools/deps/requirements.py Log Message: ----------- [17.01] Fix container resolver log statements exposing pointers. These log statements: ``` 2017-02-27 12:11:50,959 INFO [galaxy.tools.deps.containers] Checking with container resolver [<galaxy.tools.deps.container_resolvers.explicit.ExplicitContainerResolver object at 0x10b211590>] found description [None] 2017-02-27 12:11:51,062 INFO [galaxy.tools.deps.containers] Checking with container resolver [<galaxy.tools.deps.container_resolvers.mulled.CachedMulledContainerResolver object at 0x10b2115d0>] found description [None] 2017-02-27 12:11:51,490 INFO [galaxy.tools.deps.containers] Checking with container resolver [<galaxy.tools.deps.container_resolvers.mulled.MulledContainerResolver object at 0x10b211610>] found description [<galaxy.tools.deps.requirements.ContainerDescription object at 0x10d6f1550>] ``` Become: ``` 2017-02-27 13:19:06,201 INFO [galaxy.tools.deps.containers] Checking with container resolver [ExplicitContainerResolver[]] found description [None] 2017-02-27 13:19:06,251 INFO [galaxy.tools.deps.containers] Checking with container resolver [CachedMulledContainerResolver[namespace=None]] found description [None] 2017-02-27 13:19:06,679 INFO [galaxy.tools.deps.containers] Checking with container resolver [MulledContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/seqtk:1.2--0,type=docker]] ``` Rebased with suggestion from @nsoranzo :eagle::eyes: Commit: ca5bb99ee043587fe37cc9354885d3de6fbd5ce3 https://github.com/galaxyproject/galaxy/commit/ca5bb99ee043587fe37cc9354885… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-03-01 (Wed, 01 Mar 2017) Changed paths: M lib/galaxy/tools/deps/container_resolvers/__init__.py M lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/tools/deps/requirements.py Log Message: ----------- Merge pull request #3679 from jmchilton/fix_logs [17.01] Fix container resolver log statements exposing pointers. Commit: ce7f9e91ca8893ce290aeeac4836e18db07af3a5 https://github.com/galaxyproject/galaxy/commit/ce7f9e91ca8893ce290aeeac4836… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-03-01 (Wed, 01 Mar 2017) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Annotate converters that appear to need galaxy on PYTHONPATH. Should fix #3499 (thanks for the explicit heads up @mvdbeek). Commit: 93a802bd450658f0c66d4226c626112e8163d5a6 https://github.com/galaxyproject/galaxy/commit/93a802bd450658f0c66d4226c626… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-03-02 (Thu, 02 Mar 2017) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Merge pull request #3690 from jmchilton/converter_galaxy_lib_fixes [17.01] Annotate converters that appear to need galaxy on PYTHONPATH. Commit: 02f3a2737dd1c48574df9bf8e51ce43e6789bf1e https://github.com/galaxyproject/galaxy/commit/02f3a2737dd1c48574df9bf8e51c… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-03-08 (Wed, 08 Mar 2017) Changed paths: M client/galaxy/scripts/layout/menu.js M static/maps/layout/menu.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/menu.js Log Message: ----------- Bug fix for masthead webhook if Galaxy.page is undefined for workflow, data libraries etc pages Commit: 7988ae59f5b94b952bd1965b76250ad3f21525d6 https://github.com/galaxyproject/galaxy/commit/7988ae59f5b94b952bd1965b7625… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-03-09 (Thu, 09 Mar 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py R templates/admin/tool_shed_repository/select_shed_tool_panel_config.mako M templates/admin/tool_shed_repository/select_tool_panel_section.mako Log Message: ----------- Allow display of install_resolver_checkbox when installing data manager tools by merging select_shed_tool_panel_config.mako functionality into select_tool_panel_section.mako (thx @nsoranzo for this suggestion). Commit: e8922295bd5753e0be262f141b25a05622972ee6 https://github.com/galaxyproject/galaxy/commit/e8922295bd5753e0be262f141b25… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-03-09 (Thu, 09 Mar 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py Log Message: ----------- Remove checks for `includes_tools_for_display_in_tool_panel` and `includes_tools_for_display_in_tool_panel` when determining if initiate_repository_installation.mako should be posted to. It is sufficient to check that select_tool_panel_section_button has been clicked. Commit: 2df727cb05d8d15e14a23a4f8c1da920bfde999d https://github.com/galaxyproject/galaxy/commit/2df727cb05d8d15e14a23a4f8c1d… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-03-09 (Thu, 09 Mar 2017) Changed paths: M test/shed_functional/functional/test_1150_datatype_converters.py Log Message: ----------- Adjust wording of datatype converter install test. Commit: 1b9a2868a17899787bf65181f96892596b16b51b https://github.com/galaxyproject/galaxy/commit/1b9a2868a17899787bf65181f968… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-03-09 (Thu, 09 Mar 2017) Changed paths: M client/galaxy/scripts/layout/menu.js M static/maps/layout/menu.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/menu.js Log Message: ----------- Merge pull request #3728 from martenson/backport-masthead-fix [16.10] backport of webhook masthead fix for datalibs and workflows Commit: fa37f67786b88b5d1c4138a142efccf3cc42d219 https://github.com/galaxyproject/galaxy/commit/fa37f67786b88b5d1c4138a142ef… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-03-17 (Fri, 17 Mar 2017) Changed paths: M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Merge branch 'release_16.10' into release_17.01 Conflicts: static/maps/layout/menu.js.map static/scripts/bundled/libs.bundled.js static/scripts/bundled/libs.bundled.js.map static/scripts/layout/menu.js Commit: 7429ded33e1af8214f2ca20563698f73dd3869d3 https://github.com/galaxyproject/galaxy/commit/7429ded33e1af8214f2ca2056369… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-03-17 (Fri, 17 Mar 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/users.py Log Message: ----------- fix datetime import Commit: aaafbe956f343eb6d34dbdcec0b8b937e439334a https://github.com/galaxyproject/galaxy/commit/aaafbe956f343eb6d34dbdcec0b8… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-03-17 (Fri, 17 Mar 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/users.py Log Message: ----------- add the activation functionality to API users controller it was invoked but not included resulting in errors Commit: 642956a899ea2b97348be698bd81dd11a85d113e https://github.com/galaxyproject/galaxy/commit/642956a899ea2b97348be698bd81… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-03-17 (Fri, 17 Mar 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/users.py Log Message: ----------- remove unused import Commit: 54fb1a433d061d398d67a0cb3e80ea1406226898 https://github.com/galaxyproject/galaxy/commit/54fb1a433d061d398d67a0cb3e80… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-03-17 (Fri, 17 Mar 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/users.py Log Message: ----------- only request verificaion when needed thanks @nsoranzo Commit: 56c710adbc1f10579511c506503493241df4176c https://github.com/galaxyproject/galaxy/commit/56c710adbc1f10579511c5065034… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-03-17 (Fri, 17 Mar 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/users.py Log Message: ----------- reqork the activation logic when email is changed thanks to @nsoranzo for help Commit: cfa3e29cadf0960f01735a2ad43b64ac9c17e031 https://github.com/galaxyproject/galaxy/commit/cfa3e29cadf0960f01735a2ad43b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-17 (Fri, 17 Mar 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py R templates/admin/tool_shed_repository/select_shed_tool_panel_config.mako M templates/admin/tool_shed_repository/select_tool_panel_section.mako M test/shed_functional/functional/test_1150_datatype_converters.py Log Message: ----------- Merge pull request #3686 from mvdbeek/datamanager_conda_install [17.01] Allow display of install_resolver_checkbox when installing data manag… Commit: 6ab5cc1caf8c9fc0d4ce311c43988d12ea2ae6bb https://github.com/galaxyproject/galaxy/commit/6ab5cc1caf8c9fc0d4ce311c4398… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-18 (Sat, 18 Mar 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/users.py Log Message: ----------- Merge pull request #3771 from martenson/fix-users-api [17.01] Fixes for users API Commit: f76e0921d7d24b05920036e9fb64555ebbe4633b https://github.com/galaxyproject/galaxy/commit/f76e0921d7d24b05920036e9fb64… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-20 (Mon, 20 Mar 2017) Changed paths: M doc/source/releases/17.01_announce.rst M lib/galaxy/managers/workflows.py M lib/galaxy/queue_worker.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/container_resolvers/__init__.py M lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/tools/deps/requirements.py M lib/galaxy/tools/search/__init__.py M lib/galaxy/webapps/galaxy/api/users.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/user.py M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map R templates/admin/tool_shed_repository/select_shed_tool_panel_config.mako M templates/admin/tool_shed_repository/select_tool_panel_section.mako M test/shed_functional/functional/test_1150_datatype_converters.py Log Message: ----------- Merge pull request #3772 from galaxyproject/release_17.01 [usegalaxy] Merge release 17.01 Compare: https://github.com/galaxyproject/galaxy/compare/a352b3c490c7...f76e0921d7d2

1 0

[galaxyproject/galaxy] 7429de: fix datetime import
by GitHub 18 Mar '17

18 Mar '17

Branch: refs/heads/release_17.01 Home: https://github.com/galaxyproject/galaxy Commit: 7429ded33e1af8214f2ca20563698f73dd3869d3 https://github.com/galaxyproject/galaxy/commit/7429ded33e1af8214f2ca2056369… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-03-17 (Fri, 17 Mar 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/users.py Log Message: ----------- fix datetime import Commit: aaafbe956f343eb6d34dbdcec0b8b937e439334a https://github.com/galaxyproject/galaxy/commit/aaafbe956f343eb6d34dbdcec0b8… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-03-17 (Fri, 17 Mar 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/users.py Log Message: ----------- add the activation functionality to API users controller it was invoked but not included resulting in errors Commit: 642956a899ea2b97348be698bd81dd11a85d113e https://github.com/galaxyproject/galaxy/commit/642956a899ea2b97348be698bd81… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-03-17 (Fri, 17 Mar 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/users.py Log Message: ----------- remove unused import Commit: 54fb1a433d061d398d67a0cb3e80ea1406226898 https://github.com/galaxyproject/galaxy/commit/54fb1a433d061d398d67a0cb3e80… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-03-17 (Fri, 17 Mar 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/users.py Log Message: ----------- only request verificaion when needed thanks @nsoranzo Commit: 56c710adbc1f10579511c506503493241df4176c https://github.com/galaxyproject/galaxy/commit/56c710adbc1f10579511c5065034… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-03-17 (Fri, 17 Mar 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/users.py Log Message: ----------- reqork the activation logic when email is changed thanks to @nsoranzo for help Commit: 6ab5cc1caf8c9fc0d4ce311c43988d12ea2ae6bb https://github.com/galaxyproject/galaxy/commit/6ab5cc1caf8c9fc0d4ce311c4398… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-18 (Sat, 18 Mar 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/users.py Log Message: ----------- Merge pull request #3771 from martenson/fix-users-api [17.01] Fixes for users API Compare: https://github.com/galaxyproject/galaxy/compare/cfa3e29cadf0...6ab5cc1caf8c

1 0

[galaxyproject/galaxy] 7988ae: Allow display of install_resolver_checkbox when in...
by GitHub 17 Mar '17

17 Mar '17

Branch: refs/heads/release_17.01 Home: https://github.com/galaxyproject/galaxy Commit: 7988ae59f5b94b952bd1965b76250ad3f21525d6 https://github.com/galaxyproject/galaxy/commit/7988ae59f5b94b952bd1965b7625… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-03-09 (Thu, 09 Mar 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py R templates/admin/tool_shed_repository/select_shed_tool_panel_config.mako M templates/admin/tool_shed_repository/select_tool_panel_section.mako Log Message: ----------- Allow display of install_resolver_checkbox when installing data manager tools by merging select_shed_tool_panel_config.mako functionality into select_tool_panel_section.mako (thx @nsoranzo for this suggestion). Commit: e8922295bd5753e0be262f141b25a05622972ee6 https://github.com/galaxyproject/galaxy/commit/e8922295bd5753e0be262f141b25… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-03-09 (Thu, 09 Mar 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py Log Message: ----------- Remove checks for `includes_tools_for_display_in_tool_panel` and `includes_tools_for_display_in_tool_panel` when determining if initiate_repository_installation.mako should be posted to. It is sufficient to check that select_tool_panel_section_button has been clicked. Commit: 2df727cb05d8d15e14a23a4f8c1da920bfde999d https://github.com/galaxyproject/galaxy/commit/2df727cb05d8d15e14a23a4f8c1d… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-03-09 (Thu, 09 Mar 2017) Changed paths: M test/shed_functional/functional/test_1150_datatype_converters.py Log Message: ----------- Adjust wording of datatype converter install test. Commit: cfa3e29cadf0960f01735a2ad43b64ac9c17e031 https://github.com/galaxyproject/galaxy/commit/cfa3e29cadf0960f01735a2ad43b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-17 (Fri, 17 Mar 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py R templates/admin/tool_shed_repository/select_shed_tool_panel_config.mako M templates/admin/tool_shed_repository/select_tool_panel_section.mako M test/shed_functional/functional/test_1150_datatype_converters.py Log Message: ----------- Merge pull request #3686 from mvdbeek/datamanager_conda_install [17.01] Allow display of install_resolver_checkbox when installing data manag… Compare: https://github.com/galaxyproject/galaxy/compare/fa37f67786b8...cfa3e29cadf0

1 0

[galaxyproject/galaxy] b1429d: Mirror latest galaxy-lib changes for Conda and CWL...
by GitHub 17 Mar '17

17 Mar '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b1429d4340f11591768bb853fd646508e32e0501 https://github.com/galaxyproject/galaxy/commit/b1429d4340f11591768bb853fd64… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-03-14 (Tue, 14 Mar 2017) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/cwl/cwltool_deps.py M lib/galaxy/tools/cwl/parser.py M lib/galaxy/tools/cwl/representation.py M lib/galaxy/tools/cwl/runtime_actions.py M lib/galaxy/tools/cwl/schema.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/mulled/invfile.lua M lib/galaxy/tools/deps/mulled/mulled_build.py M lib/galaxy/tools/deps/resolvers/conda.py A lib/galaxy/tools/fetcher.py M lib/galaxy/tools/loader_directory.py A lib/galaxy/tools/locations/__init__.py A lib/galaxy/tools/locations/dockstore.py A lib/galaxy/tools/locations/file.py A lib/galaxy/tools/locations/http.py M lib/galaxy/tools/parser/cwl.py M lib/galaxy/tools/parser/factory.py Log Message: ----------- Mirror latest galaxy-lib changes for Conda and CWL improvements. - I added more flexibility to mulled operations to work around bugs on OS X (galaxyproject/galaxy-lib#50). - I added the ability to use local packages with the Conda resolver (galaxyproject/galaxy-lib#47) - this allows Galaxy when used with Planemo to use locally built packages. Including Nicola's suggested changes here (https://github.com/galaxyproject/galaxy-lib/commit/6d53fc7dec6c48ea8fb00fa3…) - I switched the default Conda prefix to miniconda3 so the name matches what Galaxy is actually installing. galaxyproject/galaxy-lib#48. This would never actually be used with Galaxy since we decided it should maintain its own prefix rather than using the default - it is important for Planemo though. - I synced the galaxy.tools.cwl package with my latest downstream work that provides updates for latest developments in cwltool. https://github.com/galaxyproject/galaxy-lib/pull/53 - I added the ability to load tools via URI-like strings in addition to simple paths - this allows referencing URLs and Dockstore/GA4GH tools directly from the command-line with Planemo. https://github.com/galaxyproject/galaxy-lib/pull/52 There are some other bug fixes outside of these three main PRs related to the second point - minor refinements to get conda-build dependencies working and working automatically. - galaxyproject/galaxy-lib@bdacc4d - galaxyproject/galaxy-lib@1b7bca6 - galaxyproject/galaxy-lib@36b2e65 Commit: 031ce2307367f021646c2a1640112599320076fc https://github.com/galaxyproject/galaxy/commit/031ce2307367f021646c2a164011… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-17 (Fri, 17 Mar 2017) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/cwl/cwltool_deps.py M lib/galaxy/tools/cwl/parser.py M lib/galaxy/tools/cwl/representation.py M lib/galaxy/tools/cwl/runtime_actions.py M lib/galaxy/tools/cwl/schema.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/mulled/invfile.lua M lib/galaxy/tools/deps/mulled/mulled_build.py M lib/galaxy/tools/deps/resolvers/conda.py A lib/galaxy/tools/fetcher.py M lib/galaxy/tools/loader_directory.py A lib/galaxy/tools/locations/__init__.py A lib/galaxy/tools/locations/dockstore.py A lib/galaxy/tools/locations/file.py A lib/galaxy/tools/locations/http.py M lib/galaxy/tools/parser/cwl.py M lib/galaxy/tools/parser/factory.py Log Message: ----------- Merge pull request #3742 from jmchilton/galaxy-lib-20170311 Mirror latest galaxy-lib changes for Conda and CWL improvements. Compare: https://github.com/galaxyproject/galaxy/compare/d50ca25a822a...031ce2307367

1 0

[galaxyproject/infrastructure-playbook] 4da043: Add redirect for advanced-workflow/vars, second pa...
by GitHub 17 Mar '17

17 Mar '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 4da0439a30d5fc902cc3720faebac6fd21175773 https://github.com/galaxyproject/infrastructure-playbook/commit/4da0439a30d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-17 (Fri, 17 Mar 2017) Changed paths: M galaxyenv/templates/nginx/wiki_hub_rewrites.conf.j2 Log Message: ----------- Add redirect for advanced-workflow/vars, second page Commit: 03c88af472db2d53ebb20688b3721c7e56f84337 https://github.com/galaxyproject/infrastructure-playbook/commit/03c88af472d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-17 (Fri, 17 Mar 2017) Changed paths: M galaxyenv/templates/nginx/wiki_hub_rewrites.conf.j2 Log Message: ----------- variables-edit should not have existed, this should just be variables; was a mistake in translation taking the wrong copy of the page. Compare: https://github.com/galaxyproject/infrastructure-playbook/compare/b2e5e3265d…

1 0

[galaxyproject/galaxy] 7bf6a5: Remove outdated items from tool cache
by GitHub 17 Mar '17

17 Mar '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 7bf6a581249ec409d33ccc060816b9f505185165 https://github.com/galaxyproject/galaxy/commit/7bf6a581249ec409d33ccc060816… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-03-09 (Thu, 09 Mar 2017) Changed paths: M lib/galaxy/queue_worker.py M lib/galaxy/tools/toolbox/cache.py Log Message: ----------- Remove outdated items from tool cache Commit: 0d80b8807a70ff94a6f8dbee6279207c53869755 https://github.com/galaxyproject/galaxy/commit/0d80b8807a70ff94a6f8dbee6279… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-03-09 (Thu, 09 Mar 2017) Changed paths: M lib/galaxy/tools/toolbox/cache.py Log Message: ----------- Remove hash when expiring tool from tool cache and rename `clean_paths` to `paths_to_cleanup` (thx @nsoranzo). Commit: 7b375664634075c1ad261eff42a2355637cfc363 https://github.com/galaxyproject/galaxy/commit/7b375664634075c1ad261eff42a2… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-03-09 (Thu, 09 Mar 2017) Changed paths: M lib/galaxy/tools/toolbox/cache.py Log Message: ----------- Use config_filename throughout ToolCache Commit: d50ca25a822a48e58b08c404fca1c25dfdc2bbd3 https://github.com/galaxyproject/galaxy/commit/d50ca25a822a48e58b08c404fca1… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-17 (Fri, 17 Mar 2017) Changed paths: M lib/galaxy/queue_worker.py M lib/galaxy/tools/toolbox/cache.py Log Message: ----------- Merge pull request #3729 from mvdbeek/cleanup_tool_cache Remove outdated items from tool cache when reloading the toolbox Compare: https://github.com/galaxyproject/galaxy/compare/4f749098d56b...d50ca25a822a

1 0

[galaxyproject/galaxy] 02f3a2: Bug fix for masthead webhook if Galaxy.page is und...
by GitHub 17 Mar '17

17 Mar '17

Branch: refs/heads/release_17.01 Home: https://github.com/galaxyproject/galaxy Commit: 02f3a2737dd1c48574df9bf8e51ce43e6789bf1e https://github.com/galaxyproject/galaxy/commit/02f3a2737dd1c48574df9bf8e51c… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-03-08 (Wed, 08 Mar 2017) Changed paths: M client/galaxy/scripts/layout/menu.js M static/maps/layout/menu.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/menu.js Log Message: ----------- Bug fix for masthead webhook if Galaxy.page is undefined for workflow, data libraries etc pages Commit: 1b9a2868a17899787bf65181f96892596b16b51b https://github.com/galaxyproject/galaxy/commit/1b9a2868a17899787bf65181f968… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-03-09 (Thu, 09 Mar 2017) Changed paths: M client/galaxy/scripts/layout/menu.js M static/maps/layout/menu.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/menu.js Log Message: ----------- Merge pull request #3728 from martenson/backport-masthead-fix [16.10] backport of webhook masthead fix for datalibs and workflows Commit: fa37f67786b88b5d1c4138a142efccf3cc42d219 https://github.com/galaxyproject/galaxy/commit/fa37f67786b88b5d1c4138a142ef… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-03-17 (Fri, 17 Mar 2017) Changed paths: M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Merge branch 'release_16.10' into release_17.01 Conflicts: static/maps/layout/menu.js.map static/scripts/bundled/libs.bundled.js static/scripts/bundled/libs.bundled.js.map static/scripts/layout/menu.js Compare: https://github.com/galaxyproject/galaxy/compare/93a802bd4506...fa37f67786b8

1 0

[galaxyproject/galaxy] 986134: Should exit immediately to avoid index error
by GitHub 17 Mar '17

17 Mar '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 986134d766e69344c511e2627739a51f9d8cf044 https://github.com/galaxyproject/galaxy/commit/986134d766e69344c511e2627739… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2017-03-17 (Fri, 17 Mar 2017) Changed paths: M scripts/secret_decoder_ring.py Log Message: ----------- Should exit immediately to avoid index error Commit: 4f749098d56b282125bf5644620f0bf5a273e5a3 https://github.com/galaxyproject/galaxy/commit/4f749098d56b282125bf5644620f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-17 (Fri, 17 Mar 2017) Changed paths: M scripts/secret_decoder_ring.py Log Message: ----------- Merge pull request #3770 from erasche/index-error Should exit immediately to avoid index error Compare: https://github.com/galaxyproject/galaxy/compare/caf0675176ae...4f749098d56b

1 0

[galaxyproject/galaxy] 277c4e: Pull build_sites out of datatypes conf.
by GitHub 17 Mar '17

17 Mar '17

Branch: refs/heads/usegalaxy Home: https://github.com/galaxyproject/galaxy Commit: 277c4ed20bdf8d38e6b98dc5e8d4d1d350ea4d2f https://github.com/galaxyproject/galaxy/commit/277c4ed20bdf8d38e6b98dc5e8d4… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-02-21 (Tue, 21 Feb 2017) Changed paths: A config/build_sites.yml.sample M config/datatypes_conf.xml.sample M lib/galaxy/config.py M lib/galaxy/datatypes/registry.py M scripts/common_startup.sh Log Message: ----------- Pull build_sites out of datatypes conf. So deployers may modify these paths and stil use the default datatypes config. This should speed up set_metadata also since each of these config files won't be loaded as part of that. Commit: a352b3c490c7f5d7fbcf4e28a129bc8a537d3b53 https://github.com/galaxyproject/galaxy/commit/a352b3c490c7f5d7fbcf4e28a129… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-02-23 (Thu, 23 Feb 2017) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/__init__.py M lib/galaxy/version.py M lib/galaxy/webapps/galaxy/controllers/user.py A templates/webapps/galaxy/user/manage_info.mako Log Message: ----------- Merge branch 'release_17.01' into usegalaxy Compare: https://github.com/galaxyproject/galaxy/compare/277c4ed20bdf^...a352b3c490c7

1 0

[galaxyproject/galaxy] 59526d: update logo URL
by GitHub 17 Mar '17

17 Mar '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 59526d82e8c1ce8e796b461d3e69eb8c03cc3030 https://github.com/galaxyproject/galaxy/commit/59526d82e8c1ce8e796b461d3e69… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-03-17 (Fri, 17 Mar 2017) Changed paths: M README.rst Log Message: ----------- update logo URL Commit: caf0675176ae9b8a0b578fb8de3cba97695e9ad4 https://github.com/galaxyproject/galaxy/commit/caf0675176ae9b8a0b578fb8de3c… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-17 (Fri, 17 Mar 2017) Changed paths: M README.rst Log Message: ----------- Merge pull request #3768 from martenson/logo-url-update update logo URL Compare: https://github.com/galaxyproject/galaxy/compare/0e7a71596d85...caf0675176ae

1 0