Branch: refs/heads/release_16.01
Home: https://github.com/galaxyproject/galaxy
Commit: bf4e736c3ca8e129ff8c75f8261c08f303c76080
https://github.com/galaxyproject/galaxy/commit/bf4e736c3ca8e129ff8c75f8261c…
Author: pavanvidem <videmp(a)informatik.uni-freiburg.de>
Date: 2016-02-09 (Tue, 09 Feb 2016)
Changed paths:
M tools/phenotype_association/linkToDavid.xml
Log Message:
-----------
Update david identifier types
David identifier types seem to be changed. Some of them are no more available on david web server.
Branch: refs/heads/master
Home: https://github.com/galaxyproject/usegalaxy-playbook
Commit: be043f30573a4e205f3a0801307dcc674a38ffd3
https://github.com/galaxyproject/usegalaxy-playbook/commit/be043f30573a4e20…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-02-08 (Mon, 08 Feb 2016)
Changed paths:
M stage/files/interactive_environments/plugins/.ansible_ie_role_current_version
A stage/files/interactive_environments/plugins/phinch/config/phinch.ini.sample
A stage/files/interactive_environments/plugins/phinch/config/phinch.xml
A stage/files/interactive_environments/plugins/phinch/static/js/phinch.js
A stage/files/interactive_environments/plugins/phinch/templates/phinch.mako
M stage/files/interactive_environments/proxy/.ansible_ie_role_current_version
M stage/group_vars/all.yml
Log Message:
-----------
update Test and mutable confs
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: bf989f6051303658c6bc537fc1e00c877c55c6e1
https://github.com/galaxyproject/galaxy/commit/bf989f6051303658c6bc537fc1e0…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-02-03 (Wed, 03 Feb 2016)
Changed paths:
M lib/galaxy/datatypes/text.py
Log Message:
-----------
correct typo in text datatype
Commit: 04af1ae1c609c0b73afabaf2aeb58110043847e6
https://github.com/galaxyproject/galaxy/commit/04af1ae1c609c0b73afabaf2aeb5…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2016-02-03 (Wed, 03 Feb 2016)
Changed paths:
M scripts/common_startup.sh
Log Message:
-----------
Always use the python hashlib for verifying the virtualenv download in
common_startup.sh rather than attempting to use sha256sum. Older
versions of coreutils (such as in RHEL 6) did not include the --strict
argument to sha256sum.
Commit: 2641f0af9ac84f91ea0cf3e849b6e8348da8909d
https://github.com/galaxyproject/galaxy/commit/2641f0af9ac84f91ea0cf3e849b6…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-02-03 (Wed, 03 Feb 2016)
Changed paths:
M scripts/common_startup.sh
Log Message:
-----------
Merge pull request #1668 from natefoo/venv-checksum
[16.01] Always use the python hashlib method for verifying the virtualenv download
Commit: bb95a65b2201509ce950d6c3c578f8d417f83cc4
https://github.com/galaxyproject/galaxy/commit/bb95a65b2201509ce950d6c3c578…
Author: Aysam Guerler <aysam.guerler(a)gmail.com>
Date: 2016-02-03 (Wed, 03 Feb 2016)
Changed paths:
M lib/galaxy/datatypes/text.py
Log Message:
-----------
Merge pull request #1666 from martenson/correct-datatype-typo
[16.01] correct typo in text datatype
Commit: 9551fc07b475b4095b7d002315cbc05bdf0925b5
https://github.com/galaxyproject/galaxy/commit/9551fc07b475b4095b7d002315cb…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2016-02-03 (Wed, 03 Feb 2016)
Changed paths:
M scripts/binary_compatibility.py
Log Message:
-----------
Add the `scientific` platform (Scientific Linux) as binary compatible
with RHEL.
Commit: 9ead68aeca6722f62d3d6fabae6484aa00246615
https://github.com/galaxyproject/galaxy/commit/9ead68aeca6722f62d3d6fabae64…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-02-03 (Wed, 03 Feb 2016)
Changed paths:
M scripts/binary_compatibility.py
Log Message:
-----------
Merge pull request #1669 from natefoo/scientificlinux-tag-compat
[16.01] Add the `scientific` platform (Scientific Linux) as binary compatible with RHEL
Commit: 4b24d95f6f95124f357b72434a29113fa9bacf73
https://github.com/galaxyproject/galaxy/commit/4b24d95f6f95124f357b72434a29…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2016-02-04 (Thu, 04 Feb 2016)
Changed paths:
M doc/source/admin/framework_dependencies.rst
Log Message:
-----------
Improve documentation about binary-compatibility.cfg. Resolves #1672.
Commit: ada39dea6ab68be543f53feb7a30e97167d96013
https://github.com/galaxyproject/galaxy/commit/ada39dea6ab68be543f53feb7a30…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-02-04 (Thu, 04 Feb 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/api/lda_datasets.py
Log Message:
-----------
handle correctly application/json pased in POST
Commit: 530501c682be85b595bd8115bc2fc0ebc53f57a0
https://github.com/galaxyproject/galaxy/commit/530501c682be85b595bd8115bc2f…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-02-04 (Thu, 04 Feb 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/api/libraries.py
Log Message:
-----------
fix setting library permissions to accept JSON correctly
Commit: 5dd839960e1ca5170b528c4c88ad8965eebde08b
https://github.com/galaxyproject/galaxy/commit/5dd839960e1ca5170b528c4c88ad…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-02-04 (Thu, 04 Feb 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/api/libraries.py
Log Message:
-----------
unify api for library creation; support POST with url params
Commit: edd8b222acac34cd2e35e768ab1cbd888b2fc824
https://github.com/galaxyproject/galaxy/commit/edd8b222acac34cd2e35e768ab1c…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-02-04 (Thu, 04 Feb 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/api/libraries.py
Log Message:
-----------
catch value errors from id decoding
Commit: 0398aafb1cf0aa0863d0867d20dd79a09bc2fb85
https://github.com/galaxyproject/galaxy/commit/0398aafb1cf0aa0863d0867d20dd…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-02-04 (Thu, 04 Feb 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/api/libraries.py
Log Message:
-----------
fix updating library API to not require payload
and to properly handle optional params
Commit: 4b51be57d114d840112970baccb979ec1876663b
https://github.com/galaxyproject/galaxy/commit/4b51be57d114d840112970baccb9…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-02-04 (Thu, 04 Feb 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/api/libraries.py
Log Message:
-----------
allow specifying DELETE params in JSON
Commit: c288b43627d3da925c5fe4b2fd0ebd5a7bc752b2
https://github.com/galaxyproject/galaxy/commit/c288b43627d3da925c5fe4b2fd0e…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-02-04 (Thu, 04 Feb 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/api/folders.py
Log Message:
-----------
allow creating folders with JSON payload
Commit: 7867f3e0835a2cbd99658ad25debd9be278300f2
https://github.com/galaxyproject/galaxy/commit/7867f3e0835a2cbd99658ad25deb…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-02-04 (Thu, 04 Feb 2016)
Changed paths:
M client/galaxy/scripts/mvc/library/library-folder-view.js
M lib/galaxy/webapps/galaxy/api/folders.py
M static/maps/mvc/library/library-folder-view.js.map
M static/scripts/mvc/library/library-folder-view.js
Log Message:
-----------
accept json as input for setting permissions;
fix inconsistency by leveraging role_manager
Commit: a4c2098da010d79a70a9425e8ccb6c1e69807442
https://github.com/galaxyproject/galaxy/commit/a4c2098da010d79a70a9425e8ccb…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-02-04 (Thu, 04 Feb 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/api/folders.py
Log Message:
-----------
allow PATCHing with payload in urlparams
Commit: b46636a53f579fc6ffa63fbca888196bb0ff99f6
https://github.com/galaxyproject/galaxy/commit/b46636a53f579fc6ffa63fbca888…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-02-04 (Thu, 04 Feb 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/api/libraries.py
Log Message:
-----------
remove deletion of the payload dict item
it is not necessary and the key does not have to exist
Commit: 170c83e6c283e97b1e399bc122ee94ddb8cb34b4
https://github.com/galaxyproject/galaxy/commit/170c83e6c283e97b1e399bc122ee…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-02-04 (Thu, 04 Feb 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/api/folders.py
M lib/galaxy/webapps/galaxy/api/libraries.py
Log Message:
-----------
fix unused imports and unused vars
Commit: 9c7c75b7661989b5fe6f2e4819b04ae6e7b901a1
https://github.com/galaxyproject/galaxy/commit/9c7c75b7661989b5fe6f2e4819b0…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2016-02-05 (Fri, 05 Feb 2016)
Changed paths:
M doc/source/admin/framework_dependencies.rst
Log Message:
-----------
Typo
Commit: c693b69b344461bd428a0ef314b3ec985e1a60d9
https://github.com/galaxyproject/galaxy/commit/c693b69b344461bd428a0ef314b3…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-02-05 (Fri, 05 Feb 2016)
Changed paths:
M doc/source/admin/framework_dependencies.rst
Log Message:
-----------
Merge pull request #1677 from natefoo/admin-docs
[16.01] Improve documentation about binary-compatibility.cfg
Commit: 134d792c1fcfba5d09e2937074c3263792bea991
https://github.com/galaxyproject/galaxy/commit/134d792c1fcfba5d09e2937074c3…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-02-05 (Fri, 05 Feb 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/api/libraries.py
Log Message:
-----------
delete the 'payload' if it is in kwd so it is not supplied twice
Commit: e7b6b4b13bd93a8520942c94d0ed28d110af261b
https://github.com/galaxyproject/galaxy/commit/e7b6b4b13bd93a8520942c94d0ed…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-02-05 (Fri, 05 Feb 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/api/libraries.py
Log Message:
-----------
Revert "delete the 'payload' if it is in kwd so it is not supplied twice"
This reverts commit 134d792c1fcfba5d09e2937074c3263792bea991.
Commit: 5301269fbb54753e75969ecd446b8cb74c6093b6
https://github.com/galaxyproject/galaxy/commit/5301269fbb54753e75969ecd446b…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-02-05 (Fri, 05 Feb 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/api/folder_contents.py
M lib/galaxy/webapps/galaxy/api/folders.py
M lib/galaxy/webapps/galaxy/api/lda_datasets.py
M lib/galaxy/webapps/galaxy/api/libraries.py
Log Message:
-----------
update docs of the data libraries API
Commit: 5e77af198a9b81646dbe59a02b991d496b334967
https://github.com/galaxyproject/galaxy/commit/5e77af198a9b81646dbe59a02b99…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2016-02-08 (Mon, 08 Feb 2016)
Changed paths:
M client/galaxy/style/less/base.less
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/style/blue/base.css
Log Message:
-----------
Update help text rST note/warning/error box styling for change in div
class from toolHelpBody to ui-form-help.
Commit: ef6bd90f20394f6fb74b1bdedbd0f94ecb752018
https://github.com/galaxyproject/galaxy/commit/ef6bd90f20394f6fb74b1bdedbd0…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-02-08 (Mon, 08 Feb 2016)
Changed paths:
M client/galaxy/scripts/mvc/library/library-folder-view.js
M lib/galaxy/webapps/galaxy/api/folder_contents.py
M lib/galaxy/webapps/galaxy/api/folders.py
M lib/galaxy/webapps/galaxy/api/lda_datasets.py
M lib/galaxy/webapps/galaxy/api/libraries.py
M static/maps/mvc/library/library-folder-view.js.map
M static/scripts/mvc/library/library-folder-view.js
Log Message:
-----------
Merge pull request #1641 from martenson/libraries-load-handle-payload
[16.01] libraries: handle correctly application/json pased in POST
Commit: 054c04f490fe5e641c1dec8c4f8af53cf02daffd
https://github.com/galaxyproject/galaxy/commit/054c04f490fe5e641c1dec8c4f8a…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-02-08 (Mon, 08 Feb 2016)
Changed paths:
M client/galaxy/style/less/base.less
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/style/blue/base.css
Log Message:
-----------
Merge pull request #1695 from natefoo/help-message-css
[16.01] Update help text rST note/warning/error box styling for change in div class from toolHelpBody to ui-form-help.
Commit: 308402235fe4d3d3bb85e350181ab5ab11df87f2
https://github.com/galaxyproject/galaxy/commit/308402235fe4d3d3bb85e350181a…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-02-08 (Mon, 08 Feb 2016)
Changed paths:
M client/galaxy/scripts/mvc/library/library-folder-view.js
M client/galaxy/style/less/base.less
M doc/source/admin/framework_dependencies.rst
M lib/galaxy/datatypes/text.py
M lib/galaxy/webapps/galaxy/api/folder_contents.py
M lib/galaxy/webapps/galaxy/api/folders.py
M lib/galaxy/webapps/galaxy/api/lda_datasets.py
M lib/galaxy/webapps/galaxy/api/libraries.py
M scripts/binary_compatibility.py
M scripts/common_startup.sh
M static/maps/mvc/library/library-folder-view.js.map
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/library/library-folder-view.js
M static/style/blue/base.css
Log Message:
-----------
Merge release_16.01 into dev
Commit: 8acc7ebc048d58165d3a02b21446cc5674f6aefd
https://github.com/galaxyproject/galaxy/commit/8acc7ebc048d58165d3a02b21446…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-02-08 (Mon, 08 Feb 2016)
Changed paths:
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/style/blue/base.css
Log Message:
-----------
repack client
Commit: d331b54b99cdc9f07bf0e53f284adf1fa4398ce0
https://github.com/galaxyproject/galaxy/commit/d331b54b99cdc9f07bf0e53f284a…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-02-08 (Mon, 08 Feb 2016)
Changed paths:
M client/galaxy/scripts/mvc/library/library-folder-view.js
M client/galaxy/style/less/base.less
M doc/source/admin/framework_dependencies.rst
M lib/galaxy/datatypes/text.py
M lib/galaxy/webapps/galaxy/api/folder_contents.py
M lib/galaxy/webapps/galaxy/api/folders.py
M lib/galaxy/webapps/galaxy/api/lda_datasets.py
M lib/galaxy/webapps/galaxy/api/libraries.py
M scripts/binary_compatibility.py
M scripts/common_startup.sh
M static/maps/mvc/library/library-folder-view.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/library/library-folder-view.js
M static/style/blue/base.css
Log Message:
-----------
Merge pull request #1697 from martenson/merge-1601-dev
merge 16.01 into dev
Compare: https://github.com/galaxyproject/galaxy/compare/ae372ae33b67...d331b54b99cd
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 055f180d20bfe70c0edd7f550e0332b0a79e228f
https://github.com/galaxyproject/galaxy/commit/055f180d20bfe70c0edd7f550e03…
Author: carlfeberhard <carlfeberhard(a)gmail.com>
Date: 2016-01-22 (Fri, 22 Jan 2016)
Changed paths:
M lib/galaxy/managers/annotatable.py
M lib/galaxy/managers/base.py
M lib/galaxy/managers/datasets.py
M lib/galaxy/managers/deletable.py
M lib/galaxy/managers/hdas.py
M lib/galaxy/managers/histories.py
M lib/galaxy/managers/pages.py
M lib/galaxy/managers/ratable.py
M lib/galaxy/managers/sharable.py
M lib/galaxy/managers/visualizations.py
M lib/galaxy/webapps/galaxy/api/histories.py
Log Message:
-----------
Managers: fix sharable.list_published's incorrect use of query, add manager getter to base serializer, deserializer, and filter parser; Managers, ratable: implement and attach to history
Commit: de42737c44d93684f3b6e83b385beab2c0a5ea21
https://github.com/galaxyproject/galaxy/commit/de42737c44d93684f3b6e83b385b…
Author: carlfeberhard <carlfeberhard(a)gmail.com>
Date: 2016-01-22 (Fri, 22 Jan 2016)
Changed paths:
M client/galaxy/scripts/mvc/list/list-view.js
M lib/galaxy/managers/base.py
M lib/galaxy/managers/containers.py
M lib/galaxy/managers/histories.py
A lib/galaxy/managers/history_contents.py
M static/maps/mvc/list/list-view.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/list/list-view.js
M templates/show_params.mako
M test/docker/base/run_test_wrapper.sh
A test/unit/managers/test_HistoryContentsManager.py
M test/unit/managers/test_HistoryManager.py
Log Message:
-----------
Merge remote-tracking branch 'upstream/dev' into managers.ratable
Commit: 4d75d1c6418a363f56700b2f3afd9c32c6d60516
https://github.com/galaxyproject/galaxy/commit/4d75d1c6418a363f56700b2f3afd…
Author: carlfeberhard <carlfeberhard(a)gmail.com>
Date: 2016-01-29 (Fri, 29 Jan 2016)
Changed paths:
M lib/galaxy/managers/base.py
M lib/galaxy/managers/ratable.py
M test/unit/managers/test_HistoryManager.py
Log Message:
-----------
Managers, ratable: clean up, test, and fix
Commit: 05a3d04b60bf9512a2fd9ebe07bc978a295e6865
https://github.com/galaxyproject/galaxy/commit/05a3d04b60bf9512a2fd9ebe07bc…
Author: carlfeberhard <carlfeberhard(a)gmail.com>
Date: 2016-02-08 (Mon, 08 Feb 2016)
Changed paths:
M lib/galaxy/managers/annotatable.py
M lib/galaxy/managers/base.py
M lib/galaxy/managers/datasets.py
M lib/galaxy/managers/deletable.py
M lib/galaxy/managers/hdas.py
M lib/galaxy/managers/histories.py
M lib/galaxy/managers/pages.py
M lib/galaxy/managers/ratable.py
M lib/galaxy/managers/sharable.py
M lib/galaxy/managers/visualizations.py
Log Message:
-----------
Managers: extract manager() code and move into class with property accessor
Commit: d07677bba16d535a67a2e4517f29ab28a8bb6c04
https://github.com/galaxyproject/galaxy/commit/d07677bba16d535a67a2e4517f29…
Author: carlfeberhard <carlfeberhard(a)gmail.com>
Date: 2016-02-08 (Mon, 08 Feb 2016)
Changed paths:
M lib/galaxy/managers/base.py
M lib/galaxy/managers/configuration.py
M lib/galaxy/managers/datasets.py
M lib/galaxy/managers/hdas.py
M lib/galaxy/managers/users.py
M lib/galaxy/managers/visualizations.py
Log Message:
-----------
Managers: bit of cleanup for 05a3d04b
Commit: 427909929296ccf5c24389aace39057225f4b2da
https://github.com/galaxyproject/galaxy/commit/427909929296ccf5c24389aace39…
Author: carlfeberhard <carlfeberhard(a)gmail.com>
Date: 2016-02-08 (Mon, 08 Feb 2016)
Changed paths:
A .ci/first_startup.sh
M .travis.yml
M client/galaxy/scripts/apps/analysis.js
M client/galaxy/scripts/layout/menu.js
M client/galaxy/scripts/layout/page.js
M client/galaxy/scripts/mvc/form/form-input.js
M client/galaxy/scripts/mvc/form/form-section.js
M client/galaxy/scripts/mvc/form/form-select-content.js
M client/galaxy/scripts/mvc/library/library-folderlist-view.js
M client/galaxy/scripts/mvc/library/library-folderrow-view.js
M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js
M client/galaxy/scripts/mvc/library/library-libraryrow-view.js
M client/galaxy/scripts/mvc/tours.js
M client/galaxy/scripts/mvc/ui/ui-select-default.js
M client/galaxy/scripts/mvc/upload/default/default-row.js
M client/galaxy/scripts/mvc/visualization/visualization-model.js
M client/galaxy/scripts/mvc/workflow/workflow-view.js
M client/galaxy/scripts/onload.js
M client/galaxy/style/less/base.less
M client/galaxy/style/less/library.less
M client/galaxy/style/less/tour.less
M config/galaxy.ini.sample
M config/plugins/visualizations/charts/Gruntfile.js
M config/plugins/visualizations/charts/templates/charts.mako
M config/plugins/visualizations/scatterplot/templates/scatterplot.mako
A doc/source/admin/framework_dependencies.rst
M doc/source/admin/index.rst
M doc/source/project/issues.rst
A doc/source/releases/16.01.rst
M doc/source/releases/16.01_announce.rst
A doc/source/releases/16.04_announce.rst
M doc/source/releases/index.rst
M lib/galaxy/app.py
M lib/galaxy/config.py
M lib/galaxy/datatypes/binary.py
M lib/galaxy/datatypes/data.py
M lib/galaxy/datatypes/interval.py
M lib/galaxy/datatypes/tabular.py
A lib/galaxy/dependencies/conda-environment.txt
M lib/galaxy/dependencies/pinned-hashed-requirements.txt
M lib/galaxy/dependencies/pinned-requirements.txt
M lib/galaxy/dependencies/requirements.txt
M lib/galaxy/jobs/__init__.py
M lib/galaxy/jobs/actions/post.py
M lib/galaxy/jobs/runners/__init__.py
M lib/galaxy/jobs/runners/condor.py
M lib/galaxy/jobs/runners/drmaa.py
M lib/galaxy/managers/workflows.py
M lib/galaxy/model/__init__.py
M lib/galaxy/objectstore/__init__.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/actions/__init__.py
M lib/galaxy/tools/evaluation.py
M lib/galaxy/tools/execute.py
M lib/galaxy/tools/imp_exp/__init__.py
M lib/galaxy/tools/linters/inputs.py
M lib/galaxy/tools/parameters/__init__.py
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/tools/parameters/dynamic_options.py
M lib/galaxy/tools/parameters/grouping.py
M lib/galaxy/tools/parameters/validation.py
M lib/galaxy/tools/parameters/wrapped.py
M lib/galaxy/tools/special_tools.py
M lib/galaxy/tools/toolbox/base.py
M lib/galaxy/tools/wrappers.py
M lib/galaxy/util/__init__.py
M lib/galaxy/util/heartbeat.py
M lib/galaxy/visualization/data_providers/genome.py
M lib/galaxy/webapps/galaxy/api/folder_contents.py
M lib/galaxy/webapps/galaxy/api/lda_datasets.py
M lib/galaxy/webapps/galaxy/controllers/user.py
M lib/galaxy/work/context.py
M lib/galaxy/workflow/extract.py
M lib/galaxy/workflow/modules.py
M lib/galaxy/workflow/scheduling_manager.py
M lib/tool_shed/galaxy_install/install_manager.py
M scripts/bootstrap_history.py
M scripts/common_startup.sh
M static/maps/layout/menu.js.map
M static/maps/layout/page.js.map
R static/maps/libs/backbone/backbone.js.map
M static/maps/mvc/form/form-input.js.map
M static/maps/mvc/form/form-section.js.map
M static/maps/mvc/form/form-select-content.js.map
M static/maps/mvc/library/library-folderlist-view.js.map
M static/maps/mvc/library/library-folderrow-view.js.map
M static/maps/mvc/library/library-foldertoolbar-view.js.map
M static/maps/mvc/library/library-libraryrow-view.js.map
M static/maps/mvc/tours.js.map
M static/maps/mvc/ui/ui-select-default.js.map
M static/maps/mvc/upload/default/default-row.js.map
M static/maps/mvc/visualization/visualization-model.js.map
M static/maps/mvc/workflow/workflow-view.js.map
M static/maps/onload.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/bundled/login.bundled.js
M static/scripts/bundled/login.bundled.js.map
M static/scripts/layout/menu.js
M static/scripts/layout/page.js
R static/scripts/libs/backbone/backbone.js
M static/scripts/mvc/form/form-input.js
M static/scripts/mvc/form/form-section.js
M static/scripts/mvc/form/form-select-content.js
M static/scripts/mvc/library/library-folderlist-view.js
M static/scripts/mvc/library/library-folderrow-view.js
M static/scripts/mvc/library/library-foldertoolbar-view.js
M static/scripts/mvc/library/library-libraryrow-view.js
M static/scripts/mvc/tours.js
M static/scripts/mvc/ui/ui-select-default.js
M static/scripts/mvc/upload/default/default-row.js
M static/scripts/mvc/visualization/visualization-model.js
M static/scripts/mvc/workflow/workflow-view.js
M static/scripts/onload.js
M static/style/blue/base.css
M static/style/blue/library.css
M templates/user/info.mako
M templates/user/username.mako
M templates/webapps/galaxy/workflow/editor_tool_form.mako
M templates/webapps/galaxy/workflow/run.mako
M test-data/3.bam
M test/api/test_workflows.py
M test/api/workflows_format_2/converter.py
A test/functional/tools/for_workflows/1.bam
A test/functional/tools/for_workflows/mapper.xml
A test/functional/tools/for_workflows/pileup.xml
A test/functional/tools/paths_as_file.xml
M test/functional/tools/samples_tool_conf.xml
M test/unit/tools/test_data_parameters.py
M test/unit/tools/test_evaluation.py
M test/unit/tools/test_execution.py
M test/unit/tools/test_select_parameters.py
M test/unit/tools_support.py
M tools/data_source/upload.xml
M tox.ini
Log Message:
-----------
Merge remote-tracking branch 'upstream/dev' into managers.ratable
Commit: ae372ae33b67fb2b50d45f79dfed1e54452d60d0
https://github.com/galaxyproject/galaxy/commit/ae372ae33b67fb2b50d45f79dfed…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-02-08 (Mon, 08 Feb 2016)
Changed paths:
M lib/galaxy/managers/base.py
M lib/galaxy/managers/configuration.py
M lib/galaxy/managers/datasets.py
M lib/galaxy/managers/hdas.py
M lib/galaxy/managers/histories.py
M lib/galaxy/managers/ratable.py
M lib/galaxy/managers/sharable.py
M lib/galaxy/managers/users.py
M lib/galaxy/managers/visualizations.py
M lib/galaxy/webapps/galaxy/api/histories.py
M test/unit/managers/test_HistoryManager.py
Log Message:
-----------
Merge pull request #1618 from carlfeberhard/managers.ratable
Implement the ratable mixin
Compare: https://github.com/galaxyproject/galaxy/compare/eab2f1ff5c53...ae372ae33b67
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 20f18793cd53c6c0c5c43838b7368eb14809188e
https://github.com/galaxyproject/galaxy/commit/20f18793cd53c6c0c5c43838b736…
Author: Zipho Mashologu <zipho(a)trustpay.biz>
Date: 2016-02-01 (Mon, 01 Feb 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/api/tool_dependencies.py
M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
M templates/admin/tool_shed_repository/manage_repository.mako
M templates/webapps/tool_shed/repository/common.mako
Log Message:
-----------
added resolver dependency display to the tool view page
Commit: 95cb53a2fb28c214a9191ba2f8758914efe1d151
https://github.com/galaxyproject/galaxy/commit/95cb53a2fb28c214a9191ba2f875…
Author: Zipho Mashologu <zipho(a)trustpay.biz>
Date: 2016-02-02 (Tue, 02 Feb 2016)
Changed paths:
M .travis.yml
M client/galaxy/scripts/mvc/form/form-select-content.js
M client/galaxy/scripts/mvc/library/library-folderlist-view.js
M client/galaxy/scripts/mvc/library/library-folderrow-view.js
M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js
M client/galaxy/scripts/mvc/library/library-libraryrow-view.js
M client/galaxy/scripts/mvc/list/list-view.js
M client/galaxy/scripts/mvc/tours.js
M client/galaxy/scripts/mvc/ui/ui-select-default.js
M client/galaxy/scripts/mvc/upload/default/default-row.js
M client/galaxy/scripts/mvc/visualization/visualization-model.js
M client/galaxy/scripts/mvc/workflow/workflow-view.js
M client/galaxy/scripts/onload.js
M client/galaxy/style/less/library.less
M client/galaxy/style/less/tour.less
M config/galaxy.ini.sample
M config/plugins/visualizations/charts/Gruntfile.js
M config/plugins/visualizations/charts/templates/charts.mako
M config/plugins/visualizations/scatterplot/templates/scatterplot.mako
A doc/source/admin/framework_dependencies.rst
M doc/source/admin/index.rst
M doc/source/project/issues.rst
A doc/source/releases/16.01.rst
M doc/source/releases/16.01_announce.rst
A doc/source/releases/16.04_announce.rst
M doc/source/releases/index.rst
M lib/galaxy/app.py
M lib/galaxy/config.py
M lib/galaxy/datatypes/interval.py
A lib/galaxy/dependencies/conda-environment.txt
M lib/galaxy/jobs/__init__.py
M lib/galaxy/jobs/actions/post.py
M lib/galaxy/jobs/runners/__init__.py
M lib/galaxy/jobs/runners/condor.py
M lib/galaxy/jobs/runners/drmaa.py
M lib/galaxy/managers/base.py
M lib/galaxy/managers/containers.py
M lib/galaxy/managers/histories.py
A lib/galaxy/managers/history_contents.py
M lib/galaxy/managers/workflows.py
M lib/galaxy/model/__init__.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/actions/__init__.py
M lib/galaxy/tools/evaluation.py
M lib/galaxy/tools/execute.py
M lib/galaxy/tools/imp_exp/__init__.py
M lib/galaxy/tools/linters/inputs.py
M lib/galaxy/tools/parameters/__init__.py
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/tools/parameters/dynamic_options.py
M lib/galaxy/tools/parameters/grouping.py
M lib/galaxy/tools/parameters/validation.py
M lib/galaxy/tools/special_tools.py
M lib/galaxy/tools/toolbox/base.py
M lib/galaxy/util/heartbeat.py
M lib/galaxy/webapps/galaxy/api/folder_contents.py
M lib/galaxy/webapps/galaxy/api/lda_datasets.py
M lib/galaxy/webapps/galaxy/controllers/user.py
M lib/galaxy/work/context.py
M lib/galaxy/workflow/extract.py
M lib/galaxy/workflow/modules.py
M lib/galaxy/workflow/scheduling_manager.py
M lib/tool_shed/galaxy_install/install_manager.py
M scripts/bootstrap_history.py
M scripts/common_startup.sh
R static/maps/libs/backbone/backbone.js.map
M static/maps/mvc/form/form-select-content.js.map
M static/maps/mvc/library/library-folderlist-view.js.map
M static/maps/mvc/library/library-folderrow-view.js.map
M static/maps/mvc/library/library-foldertoolbar-view.js.map
M static/maps/mvc/library/library-libraryrow-view.js.map
M static/maps/mvc/list/list-view.js.map
M static/maps/mvc/tours.js.map
M static/maps/mvc/ui/ui-select-default.js.map
M static/maps/mvc/upload/default/default-row.js.map
M static/maps/mvc/visualization/visualization-model.js.map
M static/maps/mvc/workflow/workflow-view.js.map
M static/maps/onload.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
R static/scripts/libs/backbone/backbone.js
M static/scripts/mvc/form/form-select-content.js
M static/scripts/mvc/library/library-folderlist-view.js
M static/scripts/mvc/library/library-folderrow-view.js
M static/scripts/mvc/library/library-foldertoolbar-view.js
M static/scripts/mvc/library/library-libraryrow-view.js
M static/scripts/mvc/list/list-view.js
M static/scripts/mvc/tours.js
M static/scripts/mvc/ui/ui-select-default.js
M static/scripts/mvc/upload/default/default-row.js
M static/scripts/mvc/visualization/visualization-model.js
M static/scripts/mvc/workflow/workflow-view.js
M static/scripts/onload.js
M static/style/blue/base.css
M static/style/blue/library.css
M templates/show_params.mako
M templates/webapps/galaxy/workflow/editor_tool_form.mako
M templates/webapps/galaxy/workflow/run.mako
M test/api/test_workflows.py
M test/api/workflows_format_2/converter.py
M test/docker/base/run_test_wrapper.sh
A test/functional/tools/for_workflows/1.bam
A test/functional/tools/for_workflows/mapper.xml
A test/functional/tools/for_workflows/pileup.xml
M test/functional/tools/samples_tool_conf.xml
A test/unit/managers/test_HistoryContentsManager.py
M test/unit/managers/test_HistoryManager.py
M test/unit/tools/test_data_parameters.py
M test/unit/tools/test_evaluation.py
M test/unit/tools/test_execution.py
M test/unit/tools/test_select_parameters.py
M test/unit/tools_support.py
M tools/data_source/upload.xml
Log Message:
-----------
Merge branch 'dev' into resolver_dependencies
Commit: 0a440f60ae3f9443599eb234f32fa3c149f05c61
https://github.com/galaxyproject/galaxy/commit/0a440f60ae3f9443599eb234f32f…
Author: Zipho Mashologu <zipho(a)trustpay.biz>
Date: 2016-02-02 (Tue, 02 Feb 2016)
Changed paths:
M templates/webapps/tool_shed/repository/common.mako
Log Message:
-----------
fixed variable names and making user feedback friendlier
Commit: 7a60f669fa5fd9603ddbf30153cb8e17dbe8a1a8
https://github.com/galaxyproject/galaxy/commit/7a60f669fa5fd9603ddbf30153cb…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-02-08 (Mon, 08 Feb 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/api/tool_dependencies.py
M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
M templates/admin/tool_shed_repository/manage_repository.mako
M templates/webapps/tool_shed/repository/common.mako
Log Message:
-----------
Merge pull request #1632 from zipho/resolver_dependencies
added resolver dependency display to the tool view page
Compare: https://github.com/galaxyproject/galaxy/compare/6a3452afff49...7a60f669fa5f
Branch: refs/heads/release_16.01
Home: https://github.com/galaxyproject/galaxy
Commit: 5e77af198a9b81646dbe59a02b991d496b334967
https://github.com/galaxyproject/galaxy/commit/5e77af198a9b81646dbe59a02b99…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2016-02-08 (Mon, 08 Feb 2016)
Changed paths:
M client/galaxy/style/less/base.less
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/style/blue/base.css
Log Message:
-----------
Update help text rST note/warning/error box styling for change in div
class from toolHelpBody to ui-form-help.
Commit: 054c04f490fe5e641c1dec8c4f8af53cf02daffd
https://github.com/galaxyproject/galaxy/commit/054c04f490fe5e641c1dec8c4f8a…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-02-08 (Mon, 08 Feb 2016)
Changed paths:
M client/galaxy/style/less/base.less
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/style/blue/base.css
Log Message:
-----------
Merge pull request #1695 from natefoo/help-message-css
[16.01] Update help text rST note/warning/error box styling for change in div class from toolHelpBody to ui-form-help.
Compare: https://github.com/galaxyproject/galaxy/compare/ef6bd90f2039...054c04f490fe