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
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
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
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
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