- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] f9f7ba: use dictobj as standard dependency
by GitHub 31 Mar '16

31 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f9f7ba49fe5a78a6d78e63c9af13ba02573623f3 https://github.com/galaxyproject/galaxy/commit/f9f7ba49fe5a78a6d78e63c9af13… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-30 (Wed, 30 Mar 2016) Changed paths: M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt M lib/galaxy/util/jstree.py Log Message: ----------- use dictobj as standard dependency Commit: 36df74be2fd1418d5ba7b403a2d70ae51ffa741b https://github.com/galaxyproject/galaxy/commit/36df74be2fd1418d5ba7b403a2d7… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-30 (Wed, 30 Mar 2016) Changed paths: R lib/galaxy/util/dictobj.py Log Message: ----------- remove dictobj.py as we now import it properly Commit: 8681b5f83160a04f05284f57fc04bb29bf3c7721 https://github.com/galaxyproject/galaxy/commit/8681b5f83160a04f05284f57fc04… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-30 (Wed, 30 Mar 2016) Changed paths: M lib/galaxy/util/object_wrapper.py Log Message: ----------- remove import from dictobj and move func to the wrapper itself Commit: b160cd52f30165b511bd44911eab88492079444b https://github.com/galaxyproject/galaxy/commit/b160cd52f30165b511bd44911eab… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-30 (Wed, 30 Mar 2016) Changed paths: M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt R lib/galaxy/util/dictobj.py M lib/galaxy/util/jstree.py M lib/galaxy/util/object_wrapper.py Log Message: ----------- Merge pull request #2046 from martenson/jstree-dictobj use dictobj as standard dependency Compare: https://github.com/galaxyproject/galaxy/compare/9214acb96b75...b160cd52f301

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[galaxyproject/galaxy] cba0e0: Fix workflow importing (when missing tools) broken...
by GitHub 31 Mar '16

31 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: cba0e01b7310a4994395a79c2599bde7a06ac300 https://github.com/galaxyproject/galaxy/commit/cba0e01b7310a4994395a79c2599… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-30 (Wed, 30 Mar 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- Fix workflow importing (when missing tools) broken in 0dac0c207757cf160901df387214dcfc56016469 Commit: 4e5a9df7a1f1084b89275e22c0060fc440262978 https://github.com/galaxyproject/galaxy/commit/4e5a9df7a1f1084b89275e22c006… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-30 (Wed, 30 Mar 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- py3 exception 'as' syntax. Commit: 9214acb96b7592c86f08e52688e30ee49dc23a86 https://github.com/galaxyproject/galaxy/commit/9214acb96b7592c86f08e52688e3… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-30 (Wed, 30 Mar 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- Merge pull request #2048 from dannon/workflow_import_fix Workflow import fix when tools are missing. Compare: https://github.com/galaxyproject/galaxy/compare/853fed9b9fff...9214acb96b75

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[galaxyproject/infrastructure-playbook] c8c20d: Properly update access list...
by GitHub 30 Mar '16

30 Mar '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: c8c20d2ffad15c1c632cd1c410cdfc6223274cce https://github.com/galaxyproject/infrastructure-playbook/commit/c8c20d2ffad… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-03-30 (Wed, 30 Mar 2016) Changed paths: M galaxyenv/secret_host_vars/orval.galaxyproject.org.yml Log Message: ----------- Properly update access list...

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[galaxyproject/infrastructure-playbook] 4428c7: Update common_roles
by GitHub 30 Mar '16

30 Mar '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 4428c72eea944e7a5eab52e4c8544779b5a1434b https://github.com/galaxyproject/infrastructure-playbook/commit/4428c72eea9… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-03-30 (Wed, 30 Mar 2016) Changed paths: M common_roles Log Message: ----------- Update common_roles Commit: af4fb4984e66643dcd1ba8373b025b22ed2b6878 https://github.com/galaxyproject/infrastructure-playbook/commit/af4fb4984e6… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-03-30 (Wed, 30 Mar 2016) Changed paths: M common_roles Log Message: ----------- Update common_roles Commit: 3041f30d89aed34b39e47c62aa9ca22eab3509c1 https://github.com/galaxyproject/infrastructure-playbook/commit/3041f30d89a… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-03-30 (Wed, 30 Mar 2016) Changed paths: M galaxyenv/secret_host_vars/orval.galaxyproject.org.yml Log Message: ----------- Update access list for orval Compare: https://github.com/galaxyproject/infrastructure-playbook/compare/b55fdbafe0…

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[galaxyproject/galaxy]
by GitHub 30 Mar '16

30 Mar '16

Branch: refs/heads/revert-1537-handlebars.removal Home: https://github.com/galaxyproject/galaxy

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[galaxyproject/galaxy]
by GitHub 30 Mar '16

30 Mar '16

Branch: refs/heads/revert-2033-remove-hg-direct-api Home: https://github.com/galaxyproject/galaxy

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[galaxyproject/galaxy] a218b6: Revert "disable 'hg push' to TS repositories"
by GitHub 30 Mar '16

30 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a218b6ed2a2ee32b03b2fbbeb22199a6d5adf25e https://github.com/galaxyproject/galaxy/commit/a218b6ed2a2ee32b03b2fbbeb221… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-30 (Wed, 30 Mar 2016) Changed paths: M config/tool_shed.ini.sample M lib/galaxy/webapps/tool_shed/config.py M lib/galaxy/webapps/tool_shed/framework/middleware/hg.py R test/tool_shed/functional/test_0310_hg_clone.py A test/tool_shed/functional/test_0310_hg_push_from_api.py Log Message: ----------- Revert "disable 'hg push' to TS repositories" Commit: 853fed9b9fffd04cceb8f0af5db5764bfd5bf435 https://github.com/galaxyproject/galaxy/commit/853fed9b9fffd04cceb8f0af5db5… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-30 (Wed, 30 Mar 2016) Changed paths: M config/tool_shed.ini.sample M lib/galaxy/webapps/tool_shed/config.py M lib/galaxy/webapps/tool_shed/framework/middleware/hg.py R test/tool_shed/functional/test_0310_hg_clone.py A test/tool_shed/functional/test_0310_hg_push_from_api.py Log Message: ----------- Merge pull request #2040 from galaxyproject/revert-2033-remove-hg-direct-api Revert "disable 'hg push' to TS repositories" Compare: https://github.com/galaxyproject/galaxy/compare/9a12c14d22ce...853fed9b9fff

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[galaxyproject/galaxy] a218b6: Revert "disable 'hg push' to TS repositories"
by GitHub 30 Mar '16

30 Mar '16

Branch: refs/heads/revert-2033-remove-hg-direct-api Home: https://github.com/galaxyproject/galaxy Commit: a218b6ed2a2ee32b03b2fbbeb22199a6d5adf25e https://github.com/galaxyproject/galaxy/commit/a218b6ed2a2ee32b03b2fbbeb221… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-30 (Wed, 30 Mar 2016) Changed paths: M config/tool_shed.ini.sample M lib/galaxy/webapps/tool_shed/config.py M lib/galaxy/webapps/tool_shed/framework/middleware/hg.py R test/tool_shed/functional/test_0310_hg_clone.py A test/tool_shed/functional/test_0310_hg_push_from_api.py Log Message: ----------- Revert "disable 'hg push' to TS repositories"

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[galaxyproject/galaxy] 4e45e9: disable 'hg push' to TS repositories
by GitHub 30 Mar '16

30 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4e45e993db24c9cadf344c236ec0cd358ff30b0f https://github.com/galaxyproject/galaxy/commit/4e45e993db24c9cadf344c236ec0… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M config/tool_shed.ini.sample M lib/galaxy/webapps/tool_shed/config.py M lib/galaxy/webapps/tool_shed/framework/middleware/hg.py Log Message: ----------- disable 'hg push' to TS repositories deprecated in 15.10 https://docs.galaxyproject.org/en/master/releases/15.10_announce.html#depre… Commit: c866f59915e121adbfaa6d6156857fd1daa05c40 https://github.com/galaxyproject/galaxy/commit/c866f59915e121adbfaa6d615685… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-03-30 (Wed, 30 Mar 2016) Changed paths: M lib/galaxy/webapps/tool_shed/framework/middleware/hg.py Log Message: ----------- Specify default value when getting disable_push Commit: 0fce175aad0504b6a9e47a41060a3f5b9344bd18 https://github.com/galaxyproject/galaxy/commit/0fce175aad0504b6a9e47a41060a… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-03-30 (Wed, 30 Mar 2016) Changed paths: A test/tool_shed/functional/test_0310_hg_clone.py R test/tool_shed/functional/test_0310_hg_push_from_api.py Log Message: ----------- Update Tool Shed tests after disabling 'hg push' Commit: 296b21bf8f60ad943e3abe60ded8395ca8595ea1 https://github.com/galaxyproject/galaxy/commit/296b21bf8f60ad943e3abe60ded8… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-30 (Wed, 30 Mar 2016) Changed paths: M lib/galaxy/webapps/tool_shed/framework/middleware/hg.py A test/tool_shed/functional/test_0310_hg_clone.py R test/tool_shed/functional/test_0310_hg_push_from_api.py Log Message: ----------- Merge pull request #13 from nsoranzo/remove-hg-direct-api Fixes for "Remove hg direct api" Commit: 9a12c14d22cea563c986930359c0ccd7c46c5357 https://github.com/galaxyproject/galaxy/commit/9a12c14d22cea563c986930359c0… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-30 (Wed, 30 Mar 2016) Changed paths: M config/tool_shed.ini.sample M lib/galaxy/webapps/tool_shed/config.py M lib/galaxy/webapps/tool_shed/framework/middleware/hg.py A test/tool_shed/functional/test_0310_hg_clone.py R test/tool_shed/functional/test_0310_hg_push_from_api.py Log Message: ----------- Merge pull request #2033 from martenson/remove-hg-direct-api disable 'hg push' to TS repositories Compare: https://github.com/galaxyproject/galaxy/compare/3ad68fd68eb0...9a12c14d22ce

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[galaxyproject/galaxy] 9c49f5: Use API to initiate repository installation.
by GitHub 30 Mar '16

30 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 9c49f5720d1a25082d59187d70cc7980ea694ba4 https://github.com/galaxyproject/galaxy/commit/9c49f5720d1a25082d59187d70cc… Author: Dave B <dave(a)bx.psu.edu> Date: 2015-08-07 (Fri, 07 Aug 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/buildapp.py M templates/admin/tool_shed_repository/initiate_repository_installation.mako Log Message: ----------- Use API to initiate repository installation. Commit: 849cdab31b3f261d690f8479a87909ed60071941 https://github.com/galaxyproject/galaxy/commit/849cdab31b3f261d690f8479a879… Author: Dave B <dave(a)bx.psu.edu> Date: 2015-08-07 (Fri, 07 Aug 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py Log Message: ----------- Fix imminent import error in travis. Commit: 3f766f5d97a7614fce956bc166544b2834be234b https://github.com/galaxyproject/galaxy/commit/3f766f5d97a7614fce956bc16654… Author: Dave B <dave(a)bx.psu.edu> Date: 2015-08-07 (Fri, 07 Aug 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/buildapp.py M templates/admin/tool_shed_repository/initiate_repository_installation.mako Log Message: ----------- Rename API endpoint. Correct url for API endpoint. Commit: cef6ad81f7ef41d01b85803a3639853722bd2b3e https://github.com/galaxyproject/galaxy/commit/cef6ad81f7ef41d01b85803a3639… Author: Dave B <dave(a)bx.psu.edu> Date: 2015-08-07 (Fri, 07 Aug 2015) Changed paths: M templates/admin/tool_shed_repository/initiate_repository_installation.mako Log Message: ----------- Typo. Commit: ea7ad2486add2357d59fac6c17b48c0bccb0c81d https://github.com/galaxyproject/galaxy/commit/ea7ad2486add2357d59fac6c17b4… Author: Dave B <dave(a)bx.psu.edu> Date: 2015-08-10 (Mon, 10 Aug 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M templates/admin/tool_shed_repository/initiate_repository_installation.mako Log Message: ----------- Additional cleanup. Commit: 6ce5ac58387a6dc38c0eae5c23f7440781d178a3 https://github.com/galaxyproject/galaxy/commit/6ce5ac58387a6dc38c0eae5c23f7… Author: Dave B <dave(a)bx.psu.edu> Date: 2015-08-19 (Wed, 19 Aug 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Add API endpoint to show installation status. This will return a dict of the repository, with the repository_dependencies element containing a list of dicts with the dependency chain descending from that repository. Commit: 992812eb860e58f0c19328bfc6db7ac3e4b26f28 https://github.com/galaxyproject/galaxy/commit/992812eb860e58f0c19328bfc6db… Author: Dave B <dave(a)bx.psu.edu> Date: 2015-11-17 (Tue, 17 Nov 2015) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/tool_shed/api/categories.py A templates/admin/tool_shed_repository/browse_categories.mako Log Message: ----------- Load toolshed categories with API. Commit: 72e8f73858e5177432b51798cc0e229f81297826 https://github.com/galaxyproject/galaxy/commit/72e8f73858e5177432b51798cc0e… Author: Dave B <dave(a)bx.psu.edu> Date: 2015-11-17 (Tue, 17 Nov 2015) Changed paths: M lib/galaxy/webapps/tool_shed/api/categories.py M lib/galaxy/webapps/tool_shed/model/mapping.py M lib/tool_shed/util/shed_util_common.py Log Message: ----------- Update category API endpoint. Optionally show list of repositories in category. Commit: aff62e76c8c8a862166c7e0ac899b2c1a79fea86 https://github.com/galaxyproject/galaxy/commit/aff62e76c8c8a862166c7e0ac899… Author: Dave B <dave(a)bx.psu.edu> Date: 2015-11-17 (Tue, 17 Nov 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/tool_shed/util/repository_util.py M lib/tool_shed/util/shed_util_common.py Log Message: ----------- Add API endpoint to check for updates to installed repositories. Commit: 2dca8f1812a7aaf9f20d3a8baa9f509e7ad8c15a https://github.com/galaxyproject/galaxy/commit/2dca8f1812a7aaf9f20d3a8baa9f… Author: Dave B <dave(a)bx.psu.edu> Date: 2015-11-18 (Wed, 18 Nov 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Fix the update check API method. Commit: a4bf833e219cc571fd87e6e154530449b44519f3 https://github.com/galaxyproject/galaxy/commit/a4bf833e219cc571fd87e6e15453… Author: Dave B <dave(a)bx.psu.edu> Date: 2015-11-18 (Wed, 18 Nov 2015) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/tool_shed/util/shed_util_common.py M templates/admin/tool_shed_repository/browse_categories.mako A templates/admin/tool_shed_repository/browse_category.mako A templates/admin/tool_shed_repository/preview_repository.mako Log Message: ----------- Add rudimentary mako files for the new interface. This is only for development purposes, until the UI designer fixes it. Commit: 83a9c6d440a630ea98b307ad67661c7f2314abef https://github.com/galaxyproject/galaxy/commit/83a9c6d440a630ea98b307ad6766… Author: Dave B <dave(a)bx.psu.edu> Date: 2015-11-25 (Wed, 25 Nov 2015) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/buildapp.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/galaxy/webapps/tool_shed/model/__init__.py M templates/admin/tool_shed_repository/preview_repository.mako Log Message: ----------- Add code to initiate repository installation. Commit: 6e58db947878f542ce51c78956e392afe1515a67 https://github.com/galaxyproject/galaxy/commit/6e58db947878f542ce51c78956e3… Author: Dave B <dave(a)bx.psu.edu> Date: 2015-11-25 (Wed, 25 Nov 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/buildapp.py M templates/admin/tool_shed_repository/initiate_repository_installation.mako Log Message: ----------- Merge in changes from api_install branch. Commit: 099f8eb145cda5064ae587ba171cbd0713cbcaff https://github.com/galaxyproject/galaxy/commit/099f8eb145cda5064ae587ba171c… Author: Dave B <dave(a)bx.psu.edu> Date: 2015-11-25 (Wed, 25 Nov 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/tool_shed/util/common_util.py M templates/admin/tool_shed_repository/browse_category.mako M templates/admin/tool_shed_repository/preview_repository.mako Log Message: ----------- Functional installation of repository. Commit: 2a6712833223507700789440b63eaa6304cbacb5 https://github.com/galaxyproject/galaxy/commit/2a6712833223507700789440b63e… Author: Dave B <dave(a)bx.psu.edu> Date: 2015-11-25 (Wed, 25 Nov 2015) Changed paths: M client/GruntFile.js M client/galaxy/scripts/galaxy-app-base.js M client/galaxy/scripts/galaxy.masthead.js M client/galaxy/scripts/galaxy.menu.js M client/galaxy/scripts/mvc/base-mvc.js M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M client/galaxy/scripts/mvc/collection/pair-collection-creator.js M client/galaxy/scripts/mvc/dataset/dataset-choice.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/history/copy-dialog.js M client/galaxy/scripts/mvc/history/history-panel.js M client/galaxy/scripts/mvc/history/multi-panel.js M client/galaxy/scripts/mvc/job/job-li.js M client/galaxy/scripts/mvc/list/list-panel.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/galaxy/style/less/galaxy_bootstrap/variables.less M client/grunt-tasks/style.js M client/package.json M client/toolshed/scripts/mvc/groups/group-detail-view.js M client/toolshed/scripts/mvc/groups/group-listrow-view.js M config/datatypes_conf.xml.sample A config/plugins/interactive_environments/bam_iobio/config/bam_iobio.ini.sample A config/plugins/interactive_environments/bam_iobio/config/bam_iobio.xml A config/plugins/interactive_environments/bam_iobio/static/js/bam_iobio.js A config/plugins/interactive_environments/bam_iobio/templates/bam_iobio.mako M config/plugins/interactive_environments/common/templates/ie.mako M config/plugins/interactive_environments/ipython/config/ipython.ini.sample M config/plugins/interactive_environments/ipython/static/js/ipython.js M config/plugins/interactive_environments/ipython/templates/ipython.mako M config/plugins/interactive_environments/rstudio/static/js/rstudio.js M config/tool_shed.ini.sample M cron/build_chrom_db.py M doc/source/admin/interactive_environments.rst A doc/source/releases/15.10.rst M doc/source/releases/15.10_announce.rst A doc/source/releases/16.01_announce.rst M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/proteomics.py M lib/galaxy/datatypes/text.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/managers/configuration.py M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/security/__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/parameters/dynamic_options.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/test.py M lib/galaxy/util/xml_macros.py M lib/galaxy/web/base/controller.py M lib/galaxy/web/base/controllers/admin.py M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/webapps/galaxy/api/jobs.py M lib/galaxy/webapps/galaxy/api/remote_files.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/external_service.py M lib/galaxy/webapps/galaxy/controllers/forms.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/library.py M lib/galaxy/webapps/galaxy/controllers/library_admin.py M lib/galaxy/webapps/galaxy/controllers/request_type.py M lib/galaxy/webapps/galaxy/controllers/requests_admin.py M lib/galaxy/webapps/galaxy/controllers/requests_common.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/webapps/reports/controllers/jobs.py M lib/galaxy/webapps/reports/controllers/sample_tracking.py M lib/galaxy/webapps/reports/controllers/workflows.py M lib/galaxy/webapps/tool_shed/config.py M lib/galaxy/workflow/extract.py M lib/galaxy/workflow/modules.py M lib/tool_shed/grids/admin_grids.py M lib/tool_shed/grids/repository_grids.py M lib/tool_shed/grids/repository_review_grids.py M lib/tool_shed/util/shed_util_common.py M scripts/bootstrap_history.py M static/maps/galaxy-app-base.js.map M static/maps/galaxy.masthead.js.map M static/maps/galaxy.menu.js.map M static/maps/mvc/base-mvc.js.map M static/maps/mvc/history/copy-dialog.js.map M static/maps/mvc/list/list-panel.js.map M static/maps/mvc/ui/ui-select-default.js.map M static/scripts/galaxy-app-base.js M static/scripts/galaxy.masthead.js M static/scripts/galaxy.menu.js M static/scripts/mvc/base-mvc.js M static/scripts/mvc/collection/list-collection-creator.js M static/scripts/mvc/collection/list-of-pairs-collection-creator.js M static/scripts/mvc/collection/pair-collection-creator.js M static/scripts/mvc/dataset/dataset-choice.js M static/scripts/mvc/dataset/dataset-li-edit.js M static/scripts/mvc/dataset/dataset-li.js M static/scripts/mvc/history/copy-dialog.js M static/scripts/mvc/history/history-panel.js M static/scripts/mvc/history/multi-panel.js M static/scripts/mvc/job/job-li.js M static/scripts/mvc/list/list-panel.js M static/scripts/mvc/ui/ui-select-default.js M static/style/blue/autocomplete_tagging.css M static/style/blue/base.css M static/style/blue/embed_item.css M static/style/blue/iphone.css M static/style/blue/library.css M static/style/blue/trackster.css M templates/webapps/galaxy/root/index.mako M test/api/helpers.py M test/api/test_jobs.py M test/api/test_libraries.py M test/api/test_workflow_extraction.py M test/api/test_workflows.py M test/api/test_workflows_from_yaml.py A test/api/workflows_format_2/README.txt A test/api/workflows_format_2/__init__.py A test/api/workflows_format_2/converter.py A test/api/workflows_format_2/interface.py A test/api/workflows_format_2/main.py R test/api/yaml_to_workflow.py M test/base/api.py M test/base/interactor.py M test/base/twilltestcase.py A test/functional/tools/cheetah_problem_syntax_error.xml A test/functional/tools/cheetah_problem_unbound_var.xml A test/functional/tools/cheetah_problem_unbound_var_input.xml A test/functional/tools/maxseconds.xml A test/functional/tools/output_format_collection.xml M test/functional/tools/samples_tool_conf.xml M test/functional/tools/simple_constructs.yml M test/qunit/package.json M test/unit/tools/test_actions.py M test/unit/tools/test_parsing.py M test/unit/tools/test_tool_loader.py Log Message: ----------- Merge branch 'dev' of https://github.com/galaxyproject/galaxy into toolshed_decouple Commit: b55ac36a92f9d73406c986fb4b1c637d15065e4d https://github.com/galaxyproject/galaxy/commit/b55ac36a92f9d73406c986fb4b1c… Author: Dave B <dave(a)bx.psu.edu> Date: 2015-11-25 (Wed, 25 Nov 2015) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M templates/webapps/galaxy/admin/index.mako Log Message: ----------- Separate the decoupled and iframed toolshed installations. Commit: 271c8e97f7ddb849f6809a9d8b64a760e88e4efd https://github.com/galaxyproject/galaxy/commit/271c8e97f7ddb849f6809a9d8b64… Author: Dave B <dave(a)bx.psu.edu> Date: 2015-11-30 (Mon, 30 Nov 2015) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M templates/admin/tool_shed_repository/browse_categories.mako M templates/admin/tool_shed_repository/browse_category.mako A templates/webapps/galaxy/admin/toolsheds.mako Log Message: ----------- Some refinements to the beta toolshed browsing. 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static/maps/mvc/ui/ui-select-default.js.map M static/maps/mvc/ui/ui-select-ftp.js.map M static/maps/mvc/ui/ui-select-library.js.map M static/maps/mvc/ui/ui-slider.js.map M static/maps/mvc/upload/upload-ftp.js.map M static/maps/mvc/upload/upload-view.js.map M static/maps/mvc/user/user-model.js.map M static/maps/mvc/visualization/visualization-model.js.map M static/maps/mvc/workflow/workflow-connector.js.map M static/maps/mvc/workflow/workflow-manager.js.map M static/maps/mvc/workflow/workflow-node.js.map M static/maps/mvc/workflow/workflow-view-data.js.map M static/maps/mvc/workflow/workflow-view-node.js.map M static/maps/mvc/workflow/workflow-view.js.map A static/maps/onload.js.map A static/maps/polyfills.js.map R static/maps/rgenetics/checkbox_and_radiobutton.js.map R static/maps/rgenetics/helper_functions.js.map R static/maps/rgenetics/timer.js.map M static/maps/templates/compiled/panel_section.js.map M static/maps/templates/compiled/tool_form.js.map M static/maps/templates/compiled/tool_link.js.map M static/maps/templates/compiled/tool_search.js.map R static/maps/tools/rgenetics/checkbox_and_radiobutton.js.map R static/maps/tools/rgenetics/helper_functions.js.map R static/maps/tools/rgenetics/timer.js.map A static/maps/ui/autocom_tagging.js.map A static/maps/ui/editable-text.js.map A static/maps/ui/popupmenu.js.map A static/maps/ui/scroll-panel.js.map M static/maps/utils/ajax-queue.js.map A static/maps/utils/async-save-text.js.map M static/maps/utils/localization.js.map M static/maps/utils/query-string-parsing.js.map M static/maps/utils/utils.js.map M static/maps/viz/circster.js.map M static/maps/viz/phyloviz.js.map M static/maps/viz/sweepster.js.map M static/maps/viz/trackster.js.map M static/maps/viz/trackster/tracks.js.map M static/maps/viz/trackster/util.js.map M static/maps/viz/visualization.js.map R static/scripts/base.js A static/scripts/bundled/analysis.bundled.js A static/scripts/bundled/analysis.bundled.js.map A static/scripts/bundled/libs.bundled.js A static/scripts/bundled/libs.bundled.js.map A static/scripts/bundled/login.bundled.js A static/scripts/bundled/login.bundled.js.map R static/scripts/galaxy-app-base.js R static/scripts/galaxy.autocom_tagging.js R static/scripts/galaxy.base.js R static/scripts/galaxy.frame.js A static/scripts/galaxy.js M static/scripts/galaxy.library.js R static/scripts/galaxy.masthead.js R static/scripts/galaxy.menu.js M static/scripts/galaxy.pages.js R static/scripts/galaxy.panels.js R static/scripts/galaxy.tools.js R static/scripts/galaxy.ui.scrollPanel.js R static/scripts/galaxy.workflows.js A static/scripts/layout/masthead.js A static/scripts/layout/menu.js A static/scripts/layout/modal.js A static/scripts/layout/page.js A static/scripts/layout/panel.js A static/scripts/layout/scratchbook.js R static/scripts/libs/IE/IE7.js R static/scripts/libs/IE/IE8.js R static/scripts/libs/IE/blank.gif R static/scripts/libs/IE/excanvas.js R static/scripts/libs/IE/ie7-recalc.js A static/scripts/libs/backbone.js A static/scripts/libs/common-libs.js A static/scripts/mvc/annotation.js R static/scripts/mvc/annotations.js R static/scripts/mvc/app/app-analysis.js R static/scripts/mvc/app/app-login.js R static/scripts/mvc/app/app-view.js M static/scripts/mvc/base-mvc.js M static/scripts/mvc/citation/citation-model.js M static/scripts/mvc/collection/collection-model.js R static/scripts/mvc/collection/collection-panel-edit.js R static/scripts/mvc/collection/collection-panel.js A static/scripts/mvc/collection/collection-view-edit.js A static/scripts/mvc/collection/collection-view.js M static/scripts/mvc/collection/list-of-pairs-collection-creator.js R static/scripts/mvc/collection/paired-collection-creator.js R static/scripts/mvc/data.js A static/scripts/mvc/dataset/data.js M static/scripts/mvc/dataset/dataset-li-edit.js M static/scripts/mvc/dataset/dataset-li.js M static/scripts/mvc/dataset/dataset-list.js M static/scripts/mvc/dataset/dataset-model.js M static/scripts/mvc/form/form-data.js M static/scripts/mvc/form/form-input.js M static/scripts/mvc/form/form-parameters.js M static/scripts/mvc/form/form-repeat.js M static/scripts/mvc/form/form-section.js M static/scripts/mvc/form/form-select-content.js M static/scripts/mvc/form/form-view.js M static/scripts/mvc/history/copy-dialog.js M static/scripts/mvc/history/hdca-li-edit.js M static/scripts/mvc/history/hdca-li.js M static/scripts/mvc/history/history-content-model.js M static/scripts/mvc/history/history-contents.js M static/scripts/mvc/history/history-model.js R static/scripts/mvc/history/history-panel-annotated.js R static/scripts/mvc/history/history-panel-edit-current.js R static/scripts/mvc/history/history-panel-edit.js R static/scripts/mvc/history/history-panel.js A static/scripts/mvc/history/history-view-annotated.js A static/scripts/mvc/history/history-view-edit-current.js A static/scripts/mvc/history/history-view-edit.js A static/scripts/mvc/history/history-view.js M static/scripts/mvc/history/multi-panel.js M static/scripts/mvc/history/options-menu.js M static/scripts/mvc/job/job-model.js M static/scripts/mvc/library/library-dataset-view.js M static/scripts/mvc/library/library-folder-view.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-library-view.js M static/scripts/mvc/library/library-librarylist-view.js M static/scripts/mvc/library/library-libraryrow-view.js M static/scripts/mvc/library/library-librarytoolbar-view.js M static/scripts/mvc/library/library-model.js R static/scripts/mvc/list/list-panel.js A static/scripts/mvc/list/list-view.js A static/scripts/mvc/tag.js R static/scripts/mvc/tags.js A static/scripts/mvc/tool/tool-form-base.js A static/scripts/mvc/tool/tool-form-composite.js A static/scripts/mvc/tool/tool-form-workflow.js A static/scripts/mvc/tool/tool-form.js A static/scripts/mvc/tool/tool-template.js A static/scripts/mvc/tool/tools.js R static/scripts/mvc/tools.js R static/scripts/mvc/tools/tools-form-base.js R static/scripts/mvc/tools/tools-form-workflow.js R static/scripts/mvc/tools/tools-form.js R static/scripts/mvc/tools/tools-jobs.js R static/scripts/mvc/tools/tools-template.js M static/scripts/mvc/ui/popup-menu.js M static/scripts/mvc/ui/ui-buttons.js M static/scripts/mvc/ui/ui-drilldown.js M static/scripts/mvc/ui/ui-misc.js M static/scripts/mvc/ui/ui-modal.js M static/scripts/mvc/ui/ui-portlet.js M static/scripts/mvc/ui/ui-select-default.js M static/scripts/mvc/ui/ui-select-ftp.js M static/scripts/mvc/ui/ui-select-library.js M static/scripts/mvc/ui/ui-slider.js M static/scripts/mvc/upload/upload-ftp.js R static/scripts/mvc/upload/upload-row.js M static/scripts/mvc/upload/upload-view.js M static/scripts/mvc/user/user-model.js M static/scripts/mvc/visualization/visualization-model.js M static/scripts/mvc/workflow/workflow-connector.js M static/scripts/mvc/workflow/workflow-manager.js M static/scripts/mvc/workflow/workflow-node.js M static/scripts/mvc/workflow/workflow-view-data.js M static/scripts/mvc/workflow/workflow-view-node.js M static/scripts/mvc/workflow/workflow-view.js R static/scripts/mvc/workflow/workflow.js A static/scripts/onload.js A static/scripts/polyfills.js R static/scripts/rgenetics/checkbox_and_radiobutton.js R static/scripts/rgenetics/helper_functions.js R static/scripts/rgenetics/timer.js M static/scripts/templates/compiled/panel_section.js M static/scripts/templates/compiled/tool_form.js M static/scripts/templates/compiled/tool_link.js M static/scripts/templates/compiled/tool_search.js R static/scripts/tools/rgenetics/checkbox_and_radiobutton.js R static/scripts/tools/rgenetics/helper_functions.js R static/scripts/tools/rgenetics/timer.js A static/scripts/ui/autocom_tagging.js A static/scripts/ui/editable-text.js A static/scripts/ui/popupmenu.js A static/scripts/ui/scroll-panel.js M static/scripts/utils/ajax-queue.js A static/scripts/utils/async-save-text.js M static/scripts/utils/localization.js M static/scripts/utils/query-string-parsing.js M static/scripts/utils/utils.js M static/scripts/viz/circster.js M static/scripts/viz/phyloviz.js M static/scripts/viz/sweepster.js M static/scripts/viz/trackster.js M static/scripts/viz/trackster/tracks.js M static/scripts/viz/trackster/util.js M static/scripts/viz/visualization.js M static/style/blue/base.css R static/style/blue/galaxy.frame.masthead.css M templates/base.mako M templates/base/base_panels.mako M templates/display_base.mako M templates/galaxy_client_app.mako M templates/grid_base.mako M templates/ind_share_base.mako A templates/js-app.mako M templates/refresh_frames.mako M templates/tagging_common.mako M templates/user/logout.mako M templates/webapps/galaxy/dataset/display.mako M templates/webapps/galaxy/dataset/edit_attributes.mako M templates/webapps/galaxy/dataset/tabular_chunked.mako M templates/webapps/galaxy/galaxy.masthead.mako M templates/webapps/galaxy/galaxy.panels.mako R templates/webapps/galaxy/history/copy.mako M templates/webapps/galaxy/history/display.mako M templates/webapps/galaxy/history/embed.mako M templates/webapps/galaxy/history/grid.mako A templates/webapps/galaxy/history/grid_js.mako R templates/webapps/galaxy/history/options.mako M templates/webapps/galaxy/history/share.mako A templates/webapps/galaxy/history/shared_grid.mako M templates/webapps/galaxy/history/view.mako M templates/webapps/galaxy/history/view_multiple.mako M templates/webapps/galaxy/library/common/ldda_edit_info.mako M templates/webapps/galaxy/library/common/move_library_item.mako M templates/webapps/galaxy/library/common/upload.mako M templates/webapps/galaxy/page/editor.mako M templates/webapps/galaxy/requests/common/create_request.mako M templates/webapps/galaxy/requests/common/find_samples.mako R templates/webapps/galaxy/root/index.mako M templates/webapps/galaxy/visualization/display.mako M templates/webapps/galaxy/visualization/display_in_frame.mako M templates/webapps/galaxy/visualization/sweepster.mako M templates/webapps/galaxy/workflow/editor.mako M templates/webapps/galaxy/workflow/editor_generic_form.mako M templates/webapps/galaxy/workflow/editor_tool_form.mako M templates/webapps/galaxy/workflow/run.mako M templates/webapps/tool_shed/common/reset_metadata_on_selected_repositories.mako M test/api/helpers.py M test/api/test_jobs.py M test/api/test_tools.py M test/api/test_workflows.py M test/api/test_workflows_from_yaml.py M test/api/workflows_format_2/converter.py M test/api/workflows_format_2/interface.py M test/api/workflows_format_2/main.py M test/base/interactor.py M test/base/twilltestcase.py M test/casperjs/api-anon-history-permission-tests.js M test/casperjs/api-anon-history-tests.js M test/casperjs/api-history-permission-tests.js R test/casperjs/api-workflow-tests.js M test/casperjs/casperjs_runner.py M test/casperjs/spaceghost.js M test/docker/base/Dockerfile M test/docker/base/run_test_wrapper.sh A test/functional/tools/collection_type_source.xml A test/functional/tools/create_10.xml M test/functional/tools/maxseconds.xml M test/functional/tools/samples_tool_conf.xml M test/qunit/test-app.js M test/qunit/test-common.js M test/qunit/test-data/bootstrapped.js M test/qunit/tests/galaxy-app-base.js M test/qunit/tests/workflow_editor_tests.js M test/tool_shed/functional/test_1460_data_managers.py M test/tool_shed/test_data/1440_files/complex_dependency/tool_dependencies.xml M test/unit/managers/test_HistoryManager.py M test/unit/managers/test_UserManager.py M test/unit/test_galaxy_mapping.py M test/unit/tools/test_actions.py M test/unit/tools/test_collect_primary_datasets.py M test/unit/tools/test_data_parameters.py M test/unit/tools/test_execution.py M test/unit/tools/test_tool_deps.py M test/unit/workflows/test_modules.py M test/unit/workflows/test_render.py M test/unit/workflows/test_run_parameters.py A test/unit/workflows/test_workflow_progress.py M test/unit/workflows/workflow_support.py M tools/data_source/upload.py M tox.ini Log Message: ----------- Merge branch 'dev' of https://github.com/galaxyproject/galaxy into toolshed_decouple Commit: d91fff8f15fdf894b19c67a4328acf8c831c170e https://github.com/galaxyproject/galaxy/commit/d91fff8f15fdf894b19c67a4328a… Author: Dave B <dave(a)bx.psu.edu> Date: 2015-12-18 (Fri, 18 Dec 2015) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/buildapp.py M lib/galaxy/webapps/tool_shed/model/__init__.py M lib/tool_shed/util/shed_util_common.py M lib/tool_shed/util/tool_util.py M templates/admin/tool_shed_repository/browse_categories.mako M templates/admin/tool_shed_repository/browse_category.mako M templates/admin/tool_shed_repository/preview_repository.mako Log Message: ----------- Add some styling, allow selecting revision to install. Commit: 9206e95144c645bd849043055d2ff5f2413d0144 https://github.com/galaxyproject/galaxy/commit/9206e95144c645bd849043055d2f… Author: Dave B <dave(a)bx.psu.edu> Date: 2015-12-22 (Tue, 22 Dec 2015) Changed paths: A .ci/flake8_py3_wrapper.sh A .ci/py3_sources.txt M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/mvc/ui/ui-modal.js M client/galaxy/scripts/mvc/ui/ui-popover.js M client/galaxy/scripts/mvc/upload/default/default-view.js M client/galaxy/scripts/mvc/upload/upload-ftp.js M client/galaxy/scripts/mvc/upload/upload-settings.js M client/galaxy/scripts/utils/uploadbox.js M client/galaxy/style/less/ui.less M lib/galaxy/app.py R lib/galaxy/datatypes/checkers.py M lib/galaxy/datatypes/converters/fastq_to_fqtoc.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/jobs/command_factory.py M lib/galaxy/jobs/metrics/collectl/processes.py M lib/galaxy/jobs/metrics/instrumenters/meminfo.py M lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_paramter_modules.py M lib/galaxy/objectstore/pulsar.py M lib/galaxy/objectstore/s3_multipart_upload.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/execute.py M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/tools/parser/__init__.py M lib/galaxy/tools/parser/output_actions.py A lib/galaxy/tools/parser/output_objects.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/parser/yaml.py A lib/galaxy/tools/special_tools.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/integrated_panel.py M lib/galaxy/tools/toolbox/panel.py M lib/galaxy/util/__init__.py M lib/galaxy/util/aliaspickler.py M lib/galaxy/util/backports/importlib/__init__.py M lib/galaxy/util/biostar.py A lib/galaxy/util/checkers.py M lib/galaxy/util/dictobj.py M lib/galaxy/util/expressions.py M lib/galaxy/util/inflection.py M lib/galaxy/util/json.py M lib/galaxy/util/multi_byte.py M lib/galaxy/util/object_wrapper.py M lib/galaxy/util/odict.py M lib/galaxy/util/pastescript/loadwsgi.py M lib/galaxy/util/pastescript/serve.py M lib/galaxy/util/sanitize_html.py M lib/galaxy/util/topsort.py M lib/galaxy/util/validation.py M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/controllers/upload.py M lib/galaxy/workflow/extract.py M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py M lib/tool_shed/metadata/metadata_generator.py M lib/tool_shed/util/commit_util.py M lib/tool_shed/util/shed_util_common.py M lib/tool_shed/util/tool_util.py M scripts/common_startup.sh M static/maps/layout/menu.js.map M static/maps/layout/page.js.map M static/maps/mvc/ui/ui-modal.js.map M static/maps/mvc/ui/ui-popover.js.map M static/maps/mvc/upload/default/default-view.js.map M static/maps/mvc/upload/upload-ftp.js.map M static/maps/mvc/upload/upload-settings.js.map M static/maps/utils/uploadbox.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/layout/menu.js M static/scripts/layout/page.js M static/scripts/mvc/ui/ui-modal.js M static/scripts/mvc/ui/ui-popover.js M static/scripts/mvc/upload/default/default-view.js M static/scripts/mvc/upload/upload-ftp.js M static/scripts/mvc/upload/upload-settings.js M static/scripts/utils/uploadbox.js M static/style/blue/base.css M test/qunit/test-app.js A test/qunit/tests/modal_tests.html A test/qunit/tests/modal_tests.js A test/qunit/tests/popover_tests.html A test/qunit/tests/popover_tests.js M test/unit/test_objectstore.py M test/unit/tools/test_actions.py M test/unit/tools/test_evaluation.py M tools/data_source/upload.py M tox.ini Log Message: ----------- Merge branch 'dev' of https://github.com/galaxyproject/galaxy into toolshed_decouple Commit: 4fdfc0f47b430a68a90185ebdacd8aa120f60382 https://github.com/galaxyproject/galaxy/commit/4fdfc0f47b430a68a90185ebdacd… Author: Dave B <dave(a)bx.psu.edu> Date: 2015-12-22 (Tue, 22 Dec 2015) Changed paths: M templates/admin/tool_shed_repository/preview_repository.mako Log Message: ----------- Update displayed metadata on changeset change. Commit: 7c357d1d56c98480b076bb7d80f9f1adde97e832 https://github.com/galaxyproject/galaxy/commit/7c357d1d56c98480b076bb7d80f9… Author: Dave B <dave(a)bx.psu.edu> Date: 2015-12-22 (Tue, 22 Dec 2015) Changed paths: M lib/galaxy/web/form_builder.py M lib/tool_shed/util/tool_util.py M templates/admin/tool_shed_repository/preview_repository.mako Log Message: ----------- More dynamic updating. - Repository dependencies reflect the selected changeset - So do tool dependencies - Tool panel select field shows/hides new tool panel section input field Commit: ba9493aed2ff1402097d9e383772e84dceb3f985 https://github.com/galaxyproject/galaxy/commit/ba9493aed2ff1402097d9e383772… Author: Dave B <dave(a)bx.psu.edu> Date: 2015-12-23 (Wed, 23 Dec 2015) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/buildapp.py M lib/tool_shed/util/shed_util_common.py M templates/admin/tool_shed_repository/browse_category.mako Log Message: ----------- Fill in some gaps in the repository listing. Commit: e7072c0aa268d248872540cd56d1e4c054f1fa42 https://github.com/galaxyproject/galaxy/commit/e7072c0aa268d248872540cd56d1… Author: Dave B <dave(a)bx.psu.edu> Date: 2015-12-23 (Wed, 23 Dec 2015) Changed paths: M lib/galaxy/exceptions/error_codes.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/commands.py M lib/galaxy/tools/deps/containers.py M lib/galaxy/tools/lint.py M lib/galaxy/tools/linters/inputs.py M lib/galaxy/tools/linters/stdio.py M lib/galaxy/tools/loader_directory.py M lib/galaxy/tools/parser/factory.py M lib/galaxy/tools/parser/output_objects.py M lib/galaxy/tools/parser/yaml.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/lineages/tool_shed.py M lib/galaxy/tools/toolbox/panel.py M lib/galaxy/util/__init__.py M lib/galaxy/util/heartbeat.py M lib/galaxy/util/json.py M lib/galaxy/util/odict.py M lib/galaxy/util/xml_macros.py M lib/tool_shed/metadata/metadata_generator.py M lib/tool_shed/util/common_util.py Log Message: ----------- Merge branch 'dev' of https://github.com/galaxyproject/galaxy into toolshed_decouple Commit: 68cecc6415054b84016f170c65c79a4460518d76 https://github.com/galaxyproject/galaxy/commit/68cecc6415054b84016f170c65c7… Author: Dave B <dave(a)bx.psu.edu> Date: 2015-12-23 (Wed, 23 Dec 2015) Changed paths: M lib/galaxy/webapps/tool_shed/api/repositories.py Log Message: ----------- Fix typo. Commit: bded6cdfd8f5283f0fc319df714687f374027c1f https://github.com/galaxyproject/galaxy/commit/bded6cdfd8f5283f0fc319df7146… Author: Dave B <dave(a)bx.psu.edu> Date: 2015-12-23 (Wed, 23 Dec 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/tool_shed/api/repositories.py M templates/admin/tool_shed_repository/browse_category.mako Log Message: ----------- Address travis' complaints. Commit: b5a8073d73c15455e89eecc48675cd2fc8bd0622 https://github.com/galaxyproject/galaxy/commit/b5a8073d73c15455e89eecc48675… Author: Dave B <dave(a)bx.psu.edu> Date: 2015-12-23 (Wed, 23 Dec 2015) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/tool_shed/api/categories.py M lib/galaxy/webapps/tool_shed/buildapp.py Log Message: ----------- Add endpoint for repositories in category, per Martin's suggestion. Commit: 86488d9c71e02a49e102e14acb0e8c1f68802989 https://github.com/galaxyproject/galaxy/commit/86488d9c71e02a49e102e14acb0e… Author: Dave B <dave(a)bx.psu.edu> Date: 2015-12-23 (Wed, 23 Dec 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/tool_shed/api/categories.py M lib/galaxy/webapps/tool_shed/api/repositories.py Log Message: ----------- s/trans.app/self.app/g Commit: 78d50994bf1b2091cf0244d99a68356cd8fa34e0 https://github.com/galaxyproject/galaxy/commit/78d50994bf1b2091cf0244d99a68… Author: Dave B <dave(a)bx.psu.edu> Date: 2016-01-04 (Mon, 04 Jan 2016) Changed paths: M client/galaxy/scripts/layout/masthead.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/layout/scratchbook.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/ui/ui-frames.js M client/galaxy/scripts/onload.js M 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test/qunit/tests/masthead_tests.html A test/qunit/tests/masthead_tests.js M test/tool_shed/base/twilltestcase.py M test/unit/jobs/test_command_factory.py M test/unit/jobs/test_job_wrapper.py M test/unit/test_routes.py A test/unit/tools/test_conda_resolution.py M test/unit/tools/test_toolbox.py M test/unit/tools/test_watcher.py M test/unit/workflows/test_run_parameters.py M tox.ini Log Message: ----------- Merge branch 'dev' of https://github.com/galaxyproject/galaxy into toolshed_decouple Commit: cc8175be8ff5c9affd3eb3051739e0ec9071760b https://github.com/galaxyproject/galaxy/commit/cc8175be8ff5c9affd3eb3051739… Author: Dave B <dave(a)bx.psu.edu> Date: 2016-01-05 (Tue, 05 Jan 2016) Changed paths: M client/bower.json M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/scratchbook.js A client/galaxy/scripts/libs/bootstrap-tour.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js A client/galaxy/scripts/mvc/tours.js M client/galaxy/scripts/mvc/ui/ui-frames.js M client/galaxy/scripts/mvc/upload/upload-button.js M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M client/galaxy/scripts/onload.js M client/grunt-tasks/install-libs.js M client/webpack.config.js M config/galaxy.ini.sample A config/plugins/tours/core.galaxy_ui.yaml A config/plugins/tours/core.history.yaml M lib/galaxy/app.py M lib/galaxy/config.py M lib/galaxy/dataset_collections/type_description.py M lib/galaxy/jobs/runners/util/job_script/CLUSTER_SLOTS_STATEMENT.sh M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/history_query.py A lib/galaxy/tours/__init__.py M lib/galaxy/util/__init__.py M lib/galaxy/web/base/pluginframework.py A lib/galaxy/webapps/galaxy/api/tours.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/workflow/modules.py A static/maps/galaxy.menu.js.map M static/maps/layout/menu.js.map M static/maps/layout/scratchbook.js.map A static/maps/libs/bootstrap-tour.js.map A static/maps/mvc/tours.js.map M static/maps/mvc/ui/ui-frames.js.map M static/maps/mvc/upload/upload-button.js.map M static/maps/mvc/workflow/workflow-terminals.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 A static/scripts/galaxy.menu.js M static/scripts/layout/menu.js M static/scripts/layout/scratchbook.js A static/scripts/libs/bootstrap-tour.js A static/scripts/mvc/tours.js M static/scripts/mvc/ui/ui-frames.js M static/scripts/mvc/upload/upload-button.js M static/scripts/mvc/workflow/workflow-terminals.js M static/scripts/onload.js A static/style/blue/bootstrap-tour.css M templates/base.mako M templates/base/base_panels.mako M templates/js-app.mako A test/api/test_tours.py M test/qunit/tests/workflow_editor_tests.js M test/unit/tools/test_parameter_parsing.py M test/unit/workflows/test_modules.py Log Message: ----------- Merge branch 'dev' of https://github.com/galaxyproject/galaxy into toolshed_decouple Commit: 1c6cffd2926d0201d1c3935e228bdab9ca6f426a https://github.com/galaxyproject/galaxy/commit/1c6cffd2926d0201d1c3935e228b… Author: Dave B <dave(a)bx.psu.edu> Date: 2016-01-05 (Tue, 05 Jan 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/tool_shed/util/tool_util.py M templates/admin/tool_shed_repository/preview_repository.mako Log Message: ----------- Implemented selecting or creating a tool panel section. Cleaned up UI a little. Commit: a337118d6bea1623410561c5a164713af4fae38c https://github.com/galaxyproject/galaxy/commit/a337118d6bea1623410561c5a164… Author: Dave B <dave(a)bx.psu.edu> Date: 2016-01-05 (Tue, 05 Jan 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py Log Message: ----------- Revert per Eric's suggestion. Commit: 25c339a2324f13656a1fc3c112d70849fef235ed https://github.com/galaxyproject/galaxy/commit/25c339a2324f13656a1fc3c112d7… Author: Dave B <dave(a)bx.psu.edu> Date: 2016-01-05 (Tue, 05 Jan 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py Log Message: ----------- One more change to revert. Commit: 3840a6290d048195c3d6fc2748ccefbc96b72b13 https://github.com/galaxyproject/galaxy/commit/3840a6290d048195c3d6fc2748cc… Author: Dave B <dave(a)bx.psu.edu> Date: 2016-01-07 (Thu, 07 Jan 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-template.js M client/galaxy/style/less/ui.less M config/datatypes_conf.xml.sample M doc/source/lib/galaxy.datatypes.converters.rst M doc/source/project/issues.rst M lib/galaxy/datatypes/binary.py A lib/galaxy/datatypes/converters/bcf_bgzip_to_bcf_converter.py A lib/galaxy/datatypes/converters/bcf_bgzip_to_bcf_converter.xml A lib/galaxy/datatypes/converters/bcf_to_bcf_bgzip_converter.py A lib/galaxy/datatypes/converters/bcf_to_bcf_bgzip_converter.xml M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/tours/__init__.py M lib/galaxy/util/__init__.py M lib/galaxy/util/multi_byte.py M lib/galaxy/util/pastescript/loadwsgi.py M lib/galaxy/util/properties.py M lib/galaxy/version.py M static/maps/mvc/tool/tool-template.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tool/tool-template.js M static/style/blue/base.css M test/casperjs/api-tool-tests.js M test/casperjs/modules/historyoptions.js M test/casperjs/modules/user.js M test/casperjs/registration-tests.js M test/casperjs/spaceghost.js Log Message: ----------- Merge branch 'dev' of https://github.com/galaxyproject/galaxy into toolshed_decouple Commit: 6d649c1ec3a537bb383f7d25c0bd2a209f8dcb8d https://github.com/galaxyproject/galaxy/commit/6d649c1ec3a537bb383f7d25c0bd… Author: Dave B <dave(a)bx.psu.edu> Date: 2016-01-07 (Thu, 07 Jan 2016) Changed paths: M templates/admin/tool_shed_repository/initiate_repository_installation.mako M templates/admin/tool_shed_repository/preview_repository.mako Log Message: ----------- Un-break traditional repository installations. Commit: 8b29f3ad0d9d9e2c654bf51f56b3587d7158420e https://github.com/galaxyproject/galaxy/commit/8b29f3ad0d9d9e2c654bf51f56b3… Author: Dave B <dave(a)bx.psu.edu> Date: 2016-01-07 (Thu, 07 Jan 2016) Changed paths: M lib/galaxy/webapps/tool_shed/controllers/repository.py M test/tool_shed/functional/test_1040_install_repository_basic_circular_dependencies.py Log Message: ----------- Fix failing tests in jenkins. Commit: d509e8f6028259b8ff055cc67873fcd573fd72de https://github.com/galaxyproject/galaxy/commit/d509e8f6028259b8ff055cc67873… Author: Dave B <dave(a)bx.psu.edu> Date: 2016-01-08 (Fri, 08 Jan 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/buildapp.py M lib/galaxy/webapps/tool_shed/model/__init__.py M lib/tool_shed/util/shed_util_common.py M templates/admin/tool_shed_repository/preview_repository.mako Log Message: ----------- Additional code and style cleanup. Commit: a156f1db1e28efad2a159caef0951261c50ad41f https://github.com/galaxyproject/galaxy/commit/a156f1db1e28efad2a159caef095… Author: Dave B <dave(a)bx.psu.edu> Date: 2016-01-12 (Tue, 12 Jan 2016) Changed paths: M .gitignore M .travis.yml M Makefile M lib/galaxy/tours/__init__.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/tool_shed/dependencies/repository/relation_builder.py M lib/tool_shed/scripts/check_repositories_for_functional_tests.py M lib/tool_shed/util/metadata_util.py M lib/tool_shed/util/shed_util_common.py M templates/grid_base.mako M templates/webapps/galaxy/galaxy.panels.mako M templates/webapps/galaxy/history/embed.mako Log Message: ----------- Merge branch 'dev' of https://github.com/galaxyproject/galaxy into toolshed_decouple Commit: d51c7d2fd4afc9cb31ae34cd0274f03ee2d6a643 https://github.com/galaxyproject/galaxy/commit/d51c7d2fd4afc9cb31ae34cd0274… Author: Dave B <dave(a)bx.psu.edu> Date: 2016-01-14 (Thu, 14 Jan 2016) Changed paths: M .gitignore M 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lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/workflow/extract.py M lib/pulsar/client/amqp_exchange.py M requirements.txt M run.sh M run_tests.sh M scripts/cleanup_datasets/admin_cleanup_datasets.py M scripts/common_startup.sh M static/maps/layout/menu.js.map M static/maps/mvc/collection/list-collection-creator.js.map M static/maps/mvc/form/form-data.js.map M static/maps/mvc/form/form-input.js.map M static/maps/mvc/form/form-parameters.js.map M static/maps/mvc/form/form-repeat.js.map M static/maps/mvc/history/history-view-edit.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/maps/mvc/tool/tool-form-workflow.js.map M static/maps/mvc/upload/default/default-row.js.map M static/maps/mvc/upload/upload-settings.js.map M static/maps/mvc/workflow/workflow-view.js.map M static/maps/utils/utils.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 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test/unit/tools/test_execution.py Log Message: ----------- Merge branch 'dev' of https://github.com/galaxyproject/galaxy into toolshed_decouple Commit: e2776530699e2ba4a6a4780dead63300a7575af3 https://github.com/galaxyproject/galaxy/commit/e2776530699e2ba4a6a4780dead6… Author: Dave B <dave(a)bx.psu.edu> Date: 2016-01-14 (Thu, 14 Jan 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py M templates/admin/tool_shed_repository/preview_repository.mako Log Message: ----------- Enable selecting a tool panel section on a per-tool basis. Commit: 2483f7673a20997cf8ac764bf06e79f253f9b61c https://github.com/galaxyproject/galaxy/commit/2483f7673a20997cf8ac764bf06e… Author: Dave B <dave(a)bx.psu.edu> Date: 2016-01-14 (Thu, 14 Jan 2016) Changed paths: M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py Log Message: ----------- Do not attempt to update the tool panel section if it's not separately mapped. Commit: df722f9c7e192fcfe4fa693d5886d38ac4c3a6bc https://github.com/galaxyproject/galaxy/commit/df722f9c7e192fcfe4fa693d5886… Author: Dave B <dave(a)bx.psu.edu> Date: 2016-01-15 (Fri, 15 Jan 2016) Changed paths: M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/ui/ui-list.js M client/galaxy/scripts/mvc/ui/ui-misc.js M client/galaxy/style/less/ui.less M config/galaxy.ini.sample R config/plugins/visualizations/charts/static/build-app.js M lib/galaxy/config.py M lib/galaxy/web/framework/webapp.py M scripts/binary_compatibility.py M static/maps/mvc/form/form-view.js.map M static/maps/mvc/ui/ui-list.js.map M static/maps/mvc/ui/ui-misc.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/form/form-view.js M static/scripts/mvc/ui/ui-list.js M static/scripts/mvc/ui/ui-misc.js M static/style/blue/base.css A test/qunit/tests/ui_tests.html A test/qunit/tests/ui_tests.js M test/unit/unittest_utils/galaxy_mock.py A test/unit/web/framework/__init__.py A test/unit/web/framework/test_webapp.py Log Message: ----------- Merge branch 'dev' of https://github.com/galaxyproject/galaxy into toolshed_decouple Commit: 6f72b05bd59708eb3b28b17a165f392f6640bf5a https://github.com/galaxyproject/galaxy/commit/6f72b05bd59708eb3b28b17a165f… Author: Dave B <dave(a)bx.psu.edu> Date: 2016-01-15 (Fri, 15 Jan 2016) Changed paths: M lib/galaxy/web/form_builder.py M templates/admin/tool_shed_repository/preview_repository.mako Log Message: ----------- Some tweaks to the repository preview UI. 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Message: ----------- Merge branch 'dev' of https://github.com/galaxyproject/galaxy into toolshed_decouple Commit: 18bc2f39a3a71d4463f211ad4388eb275cff9f19 https://github.com/galaxyproject/galaxy/commit/18bc2f39a3a71d4463f211ad4388… Author: Dave B <dave(a)bx.psu.edu> Date: 2016-01-28 (Thu, 28 Jan 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/buildapp.py M lib/galaxy/webapps/tool_shed/model/__init__.py M lib/galaxy/webapps/tool_shed/model/mapping.py M lib/tool_shed/metadata/metadata_generator.py M lib/tool_shed/metadata/repository_metadata_manager.py M lib/tool_shed/util/metadata_util.py M templates/admin/tool_shed_repository/browse_category.mako M templates/admin/tool_shed_repository/preview_repository.mako Log Message: ----------- Display repository dependencies. Commit: e6247d415c6c5af024e649a09a4d0475cf0ee1da https://github.com/galaxyproject/galaxy/commit/e6247d415c6c5af024e649a09a4d… Author: Dave B <dave(a)bx.psu.edu> Date: 2016-01-28 (Thu, 28 Jan 2016) Changed paths: M .travis.yml M client/galaxy/scripts/mvc/form/form-select-content.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/galaxy/scripts/mvc/visualization/visualization-model.js M client/galaxy/scripts/mvc/workflow/workflow-view.js 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/datatypes/interval.py A lib/galaxy/dependencies/conda-environment.txt M lib/galaxy/jobs/actions/post.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/validation.py M lib/galaxy/tools/special_tools.py M lib/galaxy/webapps/galaxy/controllers/user.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/ui/ui-select-default.js.map M static/maps/mvc/visualization/visualization-model.js.map M static/maps/mvc/workflow/workflow-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 R static/scripts/libs/backbone/backbone.js M static/scripts/mvc/form/form-select-content.js M static/scripts/mvc/ui/ui-select-default.js M static/scripts/mvc/visualization/visualization-model.js M static/scripts/mvc/workflow/workflow-view.js M static/style/blue/base.css 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 M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge branch 'dev' of https://github.com/galaxyproject/galaxy into toolshed_decouple Commit: 3d14626aeb276ecdd9b3f873ffae15d74f6a6b00 https://github.com/galaxyproject/galaxy/commit/3d14626aeb276ecdd9b3f873ffae… Author: Dave B <dave(a)bx.psu.edu> Date: 2016-01-28 (Thu, 28 Jan 2016) Changed paths: M lib/galaxy/webapps/tool_shed/model/__init__.py M lib/tool_shed/util/metadata_util.py Log Message: ----------- Fix some travis errors. Commit: 8d2e17e6d7e276fb3d36f6d49429660d69b031f9 https://github.com/galaxyproject/galaxy/commit/8d2e17e6d7e276fb3d36f6d49429… Author: Dave B <dave(a)bx.psu.edu> Date: 2016-01-28 (Thu, 28 Jan 2016) Changed paths: M lib/tool_shed/util/metadata_util.py Log Message: ----------- Fix more travis errors. Commit: 5937e17c1ab40673904f1914211a6ba02c1f081d https://github.com/galaxyproject/galaxy/commit/5937e17c1ab40673904f1914211a… Author: Dave B <dave(a)bx.psu.edu> Date: 2016-01-28 (Thu, 28 Jan 2016) Changed paths: M lib/galaxy/web/form_builder.py M lib/tool_shed/util/metadata_util.py M templates/admin/tool_shed_repository/preview_repository.mako Log Message: ----------- Code cleanup, fixing even more travis errors. Commit: 210d6e6b8e338a246237fde2bb6818b7d08bf065 https://github.com/galaxyproject/galaxy/commit/210d6e6b8e338a246237fde2bb68… Author: Dave B <dave(a)bx.psu.edu> Date: 2016-01-28 (Thu, 28 Jan 2016) Changed paths: M templates/admin/tool_shed_repository/preview_repository.mako Log Message: ----------- Minor cosmetic cleanup. Commit: aeba386436c3b6741fc3e610a239800149f7bb14 https://github.com/galaxyproject/galaxy/commit/aeba386436c3b6741fc3e610a239… Author: Dave B <dave(a)bx.psu.edu> Date: 2016-01-29 (Fri, 29 Jan 2016) Changed paths: M doc/source/admin/framework_dependencies.rst M doc/source/releases/16.01_announce.rst M lib/galaxy/jobs/runners/condor.py M lib/galaxy/jobs/runners/drmaa.py Log Message: ----------- Merge branch 'dev' of https://github.com/galaxyproject/galaxy into toolshed_decouple Commit: eff4462781c5b8c6c5c776abfee6ab2e3bd27c31 https://github.com/galaxyproject/galaxy/commit/eff4462781c5b8c6c5c776abfee6… Author: Dave B <dave(a)bx.psu.edu> Date: 2016-01-29 (Fri, 29 Jan 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M templates/admin/tool_shed_repository/preview_repository.mako Log Message: ----------- Fix installation of selected repository. Commit: 02c15cbd2530989d454ebaedd3fb595332ac1fc5 https://github.com/galaxyproject/galaxy/commit/02c15cbd2530989d454ebaedd3fb… Author: Dave B <dave(a)bx.psu.edu> Date: 2016-01-29 (Fri, 29 Jan 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/tool_shed/api/repositories.py Log Message: ----------- Remove unused methods and parameters. 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tools/validation/fix_errors.py R tools/validation/fix_errors.xml R tools/validation/fix_errors_code.py R tools/validation/validate.py M tools/visualization/LAJ.py M tools/visualization/LAJ_code.py M tox.ini Log Message: ----------- Resolve merge conflict caused by other merge. Commit: 590115172fe6951ae1c5ac907b0ccc6143d680b2 https://github.com/galaxyproject/galaxy/commit/590115172fe6951ae1c5ac907b0c… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-02-19 (Fri, 19 Feb 2016) Changed paths: M client/galaxy/scripts/galaxy.library.js M client/galaxy/scripts/mvc/library/library-dataset-view.js M client/galaxy/scripts/mvc/library/library-folder-view.js M client/galaxy/style/less/library.less M lib/galaxy/webapps/galaxy/api/lda_datasets.py M static/maps/galaxy.library.js.map M static/maps/mvc/library/library-dataset-view.js.map M static/maps/mvc/library/library-folder-view.js.map M static/scripts/galaxy.library.js M static/scripts/mvc/library/library-dataset-view.js M static/style/blue/base.css M static/style/blue/library.css Log Message: ----------- Merge branch 'dev' of git://github.com/galaxyproject/galaxy into toolshed_decouple Commit: ed5894607dbe1d184d20135a1aa7ba5f9a362c23 https://github.com/galaxyproject/galaxy/commit/ed5894607dbe1d184d20135a1aa7… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-02-19 (Fri, 19 Feb 2016) Changed paths: M lib/galaxy/webapps/tool_shed/model/__init__.py Log Message: ----------- Remove duplicate method definition. Commit: 90d552b05f4727be124fae49767d3f4393e71fd0 https://github.com/galaxyproject/galaxy/commit/90d552b05f4727be124fae49767d… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-02-22 (Mon, 22 Feb 2016) Changed paths: M lib/galaxy/config.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/display_applications/application.py M lib/galaxy/datatypes/sniff.py M lib/galaxy/jobs/__init__.py M lib/galaxy/managers/datasets.py M lib/galaxy/managers/taggable.py M lib/galaxy/managers/tags.py M lib/galaxy/model/__init__.py M lib/galaxy/model/metadata.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/data_manager/manager.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/tools/parameters/sanitize.py M lib/galaxy/tools/parameters/validation.py M lib/galaxy/tools/parser/output_collection_def.py M lib/galaxy/tools/test.py M lib/galaxy/util/__init__.py M lib/galaxy/util/sanitize_html.py M lib/galaxy/visualization/data_providers/registry.py M lib/galaxy/visualization/plugins/config_parser.py M lib/galaxy/web/base/controller.py M lib/galaxy/web/base/controllers/admin.py M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/web/form_builder.py M lib/galaxy/web/framework/base.py M lib/galaxy/web/framework/decorators.py M lib/galaxy/web/framework/helpers/__init__.py M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/web/framework/middleware/translogger.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/webapps/galaxy/api/datasets.py M lib/galaxy/webapps/galaxy/api/jobs.py M lib/galaxy/webapps/galaxy/api/lda_datasets.py M lib/galaxy/webapps/galaxy/api/visualizations.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/data_manager.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/galaxy/webapps/galaxy/controllers/page.py M lib/galaxy/webapps/galaxy/controllers/requests_admin.py M lib/galaxy/webapps/galaxy/controllers/requests_common.py M lib/galaxy/webapps/galaxy/controllers/tag.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/webapps/tool_shed/framework/middleware/hg.py M lib/galaxy_utils/sequence/fasta.py M lib/galaxy_utils/sequence/fastq.py M lib/pulsar/client/interface.py M lib/pulsar/client/manager.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/env_file_builder.py M lib/tool_shed/util/basic_util.py M lib/tool_shed/util/common_util.py M lib/tool_shed/util/tool_util.py M test/unit/tools/test_collect_primary_datasets.py Log Message: ----------- Merge with dev branch. Commit: 7c64277299f576fe84dc1eda86771dc69968fd03 https://github.com/galaxyproject/galaxy/commit/7c64277299f576fe84dc1eda8677… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-02-22 (Mon, 22 Feb 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py Log Message: ----------- Somehow the resolution of the merge conflict didn't get committed. Commit: 9f239a011c2aee197a6539799ef568d65991426b https://github.com/galaxyproject/galaxy/commit/9f239a011c2aee197a6539799ef5… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-02-22 (Mon, 22 Feb 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py Log Message: ----------- Remove unused import. Commit: 5d1e86cfb21675b85248a9e58f3bfd3998643fe5 https://github.com/galaxyproject/galaxy/commit/5d1e86cfb21675b85248a9e58f3b… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-02-23 (Tue, 23 Feb 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M templates/admin/tool_shed_repository/browse_categories.mako Log Message: ----------- Add simple search functionality. Commit: dc7f048c4044bcb36582559526c15314461f608d https://github.com/galaxyproject/galaxy/commit/dc7f048c4044bcb36582559526c1… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-02-23 (Tue, 23 Feb 2016) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M lib/galaxy/visualization/plugins/plugin.py M lib/galaxy/web/base/interactive_environments.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M static/maps/mvc/workflow/workflow-terminals.js.map M static/scripts/mvc/workflow/workflow-terminals.js M test/qunit/tests/workflow_editor_tests.js Log Message: ----------- Merge branch 'dev' of git://github.com/galaxyproject/galaxy into toolshed_decouple Commit: 63d61b11f7bbd16f06bdcf770b987d798caa1680 https://github.com/galaxyproject/galaxy/commit/63d61b11f7bbd16f06bdcf770b98… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-02-23 (Tue, 23 Feb 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/tool_shed/api/repositories.py Log Message: ----------- Do not load recursive metadata in the category browser. Commit: 6b5e1af81807d7d20942767cd3ebbe541379820b https://github.com/galaxyproject/galaxy/commit/6b5e1af81807d7d20942767cd3eb… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-02-25 (Thu, 25 Feb 2016) Changed paths: M .ci/flake8_blacklist.txt M .ci/py3_sources.txt M .travis.yml M Makefile M client/galaxy/style/less/base.less M client/galaxy/style/less/ui/icon-btn.less M config/datatypes_conf.xml.sample M doc/source/releases/16.01.rst M doc/source/releases/16.01_announce.rst M lib/galaxy/datatypes/assembly.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/genetics.py M lib/galaxy/datatypes/images.py M lib/galaxy/datatypes/ngsindex.py M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/text.py M lib/galaxy/exceptions/__init__.py M lib/galaxy/exceptions/error_codes.json M lib/galaxy/model/__init__.py M lib/galaxy/objectstore/__init__.py M lib/galaxy/objectstore/rods.py M lib/galaxy/objectstore/s3.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/imp_exp/__init__.py M 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scripts/api/example_watch_folder.py M scripts/api/form_create_from_xml.py M scripts/api/history_create_history.py M scripts/api/history_delete_history.py M scripts/api/import_library_dataset_to_history.py M scripts/api/import_workflows_from_installed_tool_shed_repository.py M scripts/api/install_tool_shed_repositories.py M scripts/api/library_create_folder.py M scripts/api/library_create_library.py M scripts/api/library_upload_dir.py M scripts/api/library_upload_from_import_dir.py M scripts/api/load_data_with_metadata.py M scripts/api/repair_tool_shed_repository.py M scripts/api/request_type_create_from_xml.py M scripts/api/requests_update_state.py M scripts/api/reset_metadata_on_installed_repositories.py M scripts/api/sample_dataset_update_status.py M scripts/api/sample_update_state.py M scripts/api/search.py M scripts/api/sequencer_configuration_create.py M scripts/api/update.py M scripts/api/upload_to_history.py M scripts/api/workflow_delete.py M scripts/api/workflow_execute.py M 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templates/webapps/galaxy/requests/common/view_sample_datasets.mako M templates/webapps/tool_shed/repository/common.mako M test/functional/tools/output_format.xml M test/unit/test_objectstore.py A test/unit/tools/test_history_imp_exp.py M test/unit/unittest_utils/galaxy_mock.py M tox.ini Log Message: ----------- Merge branch 'dev' of git://github.com/galaxyproject/galaxy into toolshed_decouple Commit: 7df463cdd88776a533aa06d9ae96f04e9bf0d58b https://github.com/galaxyproject/galaxy/commit/7df463cdd88776a533aa06d9ae96… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-02-25 (Thu, 25 Feb 2016) Changed paths: M lib/galaxy/web/form_builder.py Log Message: ----------- Escape values of extra attributes for select fields. Commit: ad101ded626ee44b24d71884fb6fd257c58f1837 https://github.com/galaxyproject/galaxy/commit/ad101ded626ee44b24d71884fb6f… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-02-25 (Thu, 25 Feb 2016) Changed paths: M test/tool_shed/base/twilltestcase.py Log Message: ----------- Apply modified version of fix from #1798. Commit: 4e3ad3c9845c8ee0546fbaaeb4a70b820ecece5b https://github.com/galaxyproject/galaxy/commit/4e3ad3c9845c8ee0546fbaaeb4a7… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-02-29 (Mon, 29 Feb 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M templates/admin/tool_shed_repository/browse_categories.mako M templates/admin/tool_shed_repository/browse_category.mako M templates/admin/tool_shed_repository/preview_repository.mako Log Message: ----------- offer TS searching while browsing a category fix few usability issues Commit: 1b78b86a5ad64a8e91d2309d545a1a6b7ea33503 https://github.com/galaxyproject/galaxy/commit/1b78b86a5ad64a8e91d2309d545a… Author: Dave B <dave(a)bx.psu.edu> Date: 2016-02-29 (Mon, 29 Feb 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M templates/admin/tool_shed_repository/browse_categories.mako M templates/admin/tool_shed_repository/browse_category.mako M templates/admin/tool_shed_repository/preview_repository.mako Log Message: ----------- Merge pull request #3 from martenson/decouple-polish offer TS searching while browsing a category Commit: 3a5584ab1497d16a5c130641515b798a2c7794f5 https://github.com/galaxyproject/galaxy/commit/3a5584ab1497d16a5c130641515b… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-03-03 (Thu, 03 Mar 2016) Changed paths: M Makefile M client/galaxy/scripts/apps/analysis.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/fontawesome/core.less M client/grunt-tasks/style.js M client/package.json M config/galaxy.ini.sample M create_db.sh M lib/galaxy/app.py M lib/galaxy/config.py M lib/galaxy/dependencies/pinned-hashed-requirements.txt M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/command_factory.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/cli.py M lib/galaxy/jobs/runners/condor.py M lib/galaxy/jobs/runners/drmaa.py M lib/galaxy/jobs/runners/pbs.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/jobs/runners/util/job_script/__init__.py M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py M lib/galaxy/objectstore/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/cwl/__init__.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/evaluation.py M lib/galaxy/tools/execute.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/tools/parameters/validation.py M lib/galaxy/tools/parser/cwl.py M lib/galaxy/tools/parser/factory.py M lib/galaxy/tools/parser/interface.py M lib/galaxy/tools/parser/output_collection_def.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/parser/yaml.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/webapps/tool_shed/api/categories.py M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/workflow/extract.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/render.py M lib/tool_shed/util/shed_util_common.py M lib/tool_shed/util/workflow_util.py M manage_db.sh 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/mvc/workflow/workflow-view.js M static/scripts/onload.js M static/style/blue/base.css M templates/webapps/galaxy/workflow/run.mako M test/api/test_tools.py M test/api/test_workflows.py M test/api/test_workflows_from_yaml.py M test/docker/base/Dockerfile M test/docker/base/run_test_wrapper.sh A test/functional/tools/empty_output.xml M test/functional/tools/samples_tool_conf.xml A test/functional/tools/strict_shell.xml A test/functional/tools/strict_shell_default_off.xml A test/functional/tools/validation_empty_dataset.xml M test/tool_shed/base/twilltestcase.py M test/unit/jobs/test_command_factory.py M test/unit/jobs/test_job_wrapper.py M test/unit/test_objectstore.py M test/unit/tools/test_evaluation.py M test/unit/tools/test_parsing.py M test/unit/tools_support.py M test/unit/unittest_utils/galaxy_mock.py M test/unit/workflows/test_render.py Log Message: ----------- Merge branch 'dev' of git://github.com/galaxyproject/galaxy into toolshed_decouple Commit: f44c3ae85ec195d6f59fa8eaf407d56bac4836a6 https://github.com/galaxyproject/galaxy/commit/f44c3ae85ec195d6f59fa8eaf407… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-03-03 (Thu, 03 Mar 2016) Changed paths: M templates/admin/tool_shed_repository/preview_repository.mako Log Message: ----------- Update javascript with Carl's suggestions. Commit: 2a91835da47badd9d2b32cbba0c308aa8907901e https://github.com/galaxyproject/galaxy/commit/2a91835da47badd9d2b32cbba0c3… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-03-03 (Thu, 03 Mar 2016) Changed paths: M templates/admin/tool_shed_repository/preview_repository.mako Log Message: ----------- Do not display the valid tools section if there are none. Commit: 16b179f8a11ca81cc78498d2039ca088b00c0a95 https://github.com/galaxyproject/galaxy/commit/16b179f8a11ca81cc78498d2039c… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-03-08 (Tue, 08 Mar 2016) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/tours.js M client/galaxy/scripts/mvc/workflow/workflow-canvas.js M client/galaxy/scripts/onload.js M config/tool_conf.xml.main M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/external_services/result_handlers/basic.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/actions/post.py M lib/galaxy/jobs/deferred/pacific_biosciences_smrt_portal.py M lib/galaxy/jobs/transfer_manager.py M lib/galaxy/managers/context.py M lib/galaxy/managers/workflows.py M lib/galaxy/model/metadata.py M lib/galaxy/model/search.py M lib/galaxy/queue_worker.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/actions/metadata.py M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/tools/imp_exp/export_history.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/tools/parameters/validation.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/util/__init__.py M lib/galaxy/util/dbkeys.py M lib/galaxy/util/json.py M lib/galaxy/visualization/data_providers/basic.py M lib/galaxy/visualization/data_providers/genome.py M lib/galaxy/visualization/genomes.py M lib/galaxy/visualization/plugins/resource_parser.py M lib/galaxy/web/framework/base.py M lib/galaxy/web/framework/decorators.py M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/webapps/galaxy/api/lda_datasets.py M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/data_manager.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/galaxy/webapps/galaxy/controllers/page.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run_request.py M lib/tool_shed/galaxy_install/repair_repository_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py M lib/tool_shed/galaxy_install/update_repository_manager.py M lib/tool_shed/grids/repository_grids.py M lib/tool_shed/util/readme_util.py M lib/tool_shed/util/shed_util_common.py M lib/tool_shed/util/workflow_util.py M manage_tools.sh M run_reports.sh M run_tool_shed.sh M scripts/check_python.py M scripts/functional_tests.py M scripts/transfer.py M static/maps/layout/menu.js.map M static/maps/mvc/dataset/dataset-li-edit.js.map M static/maps/mvc/tours.js.map M static/maps/mvc/workflow/workflow-canvas.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/layout/menu.js M static/scripts/mvc/dataset/dataset-li-edit.js M static/scripts/mvc/tours.js M static/scripts/mvc/workflow/workflow-canvas.js M static/scripts/onload.js M templates/webapps/galaxy/workflow/editor.mako M templates/webapps/galaxy/workflow/run.mako M templates/webapps/tool_shed/repository/view_repository.mako M test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py M test/tool_shed/base/twilltestcase.py M test/unit/workflows/test_modules.py M tools/data_source/upload.py Log Message: ----------- Merge branch 'dev' of git://github.com/galaxyproject/galaxy into toolshed_decouple Commit: b8fc58523b7a1f324df8572a0293ae27dcfd08b4 https://github.com/galaxyproject/galaxy/commit/b8fc58523b7a1f324df8572a0293… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-03-09 (Wed, 09 Mar 2016) Changed paths: M lib/galaxy/web/framework/middleware/sentry.py M templates/webapps/galaxy/workflow/run.mako Log Message: ----------- Merge branch 'dev' of git://github.com/galaxyproject/galaxy into toolshed_decouple Commit: be2c51d882e0c5cab01bef1f500a61b7d48704cb https://github.com/galaxyproject/galaxy/commit/be2c51d882e0c5cab01bef1f500a… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-03-09 (Wed, 09 Mar 2016) Changed paths: M lib/galaxy/webapps/tool_shed/api/repositories.py Log Message: ----------- Return tools in metadata when repository has no dependencies. Commit: f60edb952a33ce05538fd10018d59c51dc5f656a https://github.com/galaxyproject/galaxy/commit/f60edb952a33ce05538fd10018d5… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-03-09 (Wed, 09 Mar 2016) Changed paths: M lib/galaxy/webapps/tool_shed/api/repositories.py M run_tool_shed.sh M templates/admin/tool_shed_repository/preview_repository.mako Log Message: ----------- Show tool panel selector only when needed. Add the virtualenv to run_tool_shed.sh Commit: 96ca49b7d054b413fa2d939e9dcae470933f441e https://github.com/galaxyproject/galaxy/commit/96ca49b7d054b413fa2d939e9dca… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-03-16 (Wed, 16 Mar 2016) Changed paths: M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/history/history-contents.js M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/history-view.js M client/galaxy/scripts/mvc/history/multi-panel.js M client/galaxy/scripts/mvc/tool/tool-form.js M client/galaxy/style/less/base.less M client/galaxy/style/less/ui.less M client/galaxy/style/less/upload.less M contrib/galaxy.fedora-init A contrib/galaxy_reports.fedora-init M doc/source/admin/framework_dependencies.rst M lib/galaxy/app.py M lib/galaxy/dependencies/conda-environment.txt M lib/galaxy/dependencies/requirements.txt M lib/galaxy/jobs/__init__.py M lib/galaxy/managers/histories.py M lib/galaxy/managers/history_contents.py M lib/galaxy/model/__init__.py M lib/galaxy/model/custom_types.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/visualization/data_providers/genome.py M lib/galaxy/webapps/galaxy/api/quotas.py M lib/galaxy/webapps/galaxy/api/remote_files.py M lib/galaxy/workflow/modules.py M lib/tool_shed/tool_shed_registry.py M run.sh M static/maps/layout/menu.js.map M static/maps/mvc/history/history-contents.js.map M static/maps/mvc/history/history-model.js.map M static/maps/mvc/history/history-view.js.map M static/maps/mvc/history/multi-panel.js.map M static/maps/mvc/tool/tool-form.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/mvc/history/history-contents.js M static/scripts/mvc/history/history-model.js M static/scripts/mvc/history/history-view.js M static/scripts/mvc/history/multi-panel.js M static/scripts/mvc/tool/tool-form.js M static/style/blue/base.css M templates/webapps/galaxy/workflow/display.mako M test/unit/tools/test_column_parameters.py M test/unit/tools/test_data_parameters.py M test/unit/tools/test_select_parameters.py Log Message: ----------- Merge branch 'dev' of git://github.com/galaxyproject/galaxy into toolshed_decouple Commit: ef960a62f788c432b7891fbbf1f8762dfd3dc9e7 https://github.com/galaxyproject/galaxy/commit/ef960a62f788c432b7891fbbf1f8… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-03-30 (Wed, 30 Mar 2016) Changed paths: M Makefile M client/galaxy/scripts/layout/masthead.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-parameters.js R client/galaxy/scripts/mvc/form/form-select-content.js M client/galaxy/scripts/mvc/library/library-dataset-view.js M client/galaxy/scripts/mvc/library/library-folder-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/tool/tool-form-workflow.js A client/galaxy/scripts/mvc/ui/ui-select-content.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/galaxy/scripts/utils/utils.js M client/galaxy/scripts/viz/trackster/tracks.js M client/galaxy/style/less/library.less M client/galaxy/style/less/ui.less M config/datatypes_conf.xml.sample M config/galaxy.ini.sample M config/tool_data_table_conf.xml.sample A display_applications/iobio/bam.xml A display_applications/iobio/vcf.xml M doc/source/releases/index.rst M lib/galaxy/config.py A lib/galaxy/datatypes/converters/cml_to_inchi_converter.xml A lib/galaxy/datatypes/converters/cml_to_mol2_converter.xml A lib/galaxy/datatypes/converters/cml_to_sdf_converter.xml A lib/galaxy/datatypes/converters/cml_to_smi_converter.xml A lib/galaxy/datatypes/converters/inchi_to_cml_converter.xml A lib/galaxy/datatypes/converters/inchi_to_mol2_converter.xml A lib/galaxy/datatypes/converters/inchi_to_mol_converter.xml A lib/galaxy/datatypes/converters/inchi_to_sdf_converter.xml A lib/galaxy/datatypes/converters/inchi_to_smi_converter.xml A lib/galaxy/datatypes/converters/mol2_to_cml_converter.xml A lib/galaxy/datatypes/converters/mol2_to_inchi_converter.xml A lib/galaxy/datatypes/converters/mol2_to_mol_converter.xml A lib/galaxy/datatypes/converters/mol2_to_sdf_converter.xml A lib/galaxy/datatypes/converters/mol2_to_smi_converter.xml A lib/galaxy/datatypes/converters/mol_to_cml_converter.xml A lib/galaxy/datatypes/converters/mol_to_inchi_converter.xml A lib/galaxy/datatypes/converters/mol_to_mol2_converter.xml A lib/galaxy/datatypes/converters/mol_to_smi_converter.xml A lib/galaxy/datatypes/converters/sdf_to_cml_converter.xml A lib/galaxy/datatypes/converters/sdf_to_inchi_converter.xml A lib/galaxy/datatypes/converters/sdf_to_mol2_converter.xml A lib/galaxy/datatypes/converters/sdf_to_smi_converter.xml A lib/galaxy/datatypes/converters/smi_to_cml_converter.xml A lib/galaxy/datatypes/converters/smi_to_inchi_converter.xml A lib/galaxy/datatypes/converters/smi_to_mol2_converter.xml A lib/galaxy/datatypes/converters/smi_to_mol_converter.xml A lib/galaxy/datatypes/converters/smi_to_sdf_converter.xml A lib/galaxy/datatypes/converters/smi_to_smi_converter.xml M lib/galaxy/datatypes/display_applications/application.py A lib/galaxy/datatypes/molecules.py M lib/galaxy/datatypes/sniff.py A lib/galaxy/datatypes/test/5e5z.pdb A lib/galaxy/datatypes/test/drugbank_drugs.cml A lib/galaxy/datatypes/test/drugbank_drugs.inchi A lib/galaxy/datatypes/test/drugbank_drugs.mol2 A lib/galaxy/datatypes/test/drugbank_drugs.sdf A lib/galaxy/datatypes/test/drugbank_drugs.smi A lib/galaxy/datatypes/test/q.fps M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/handler.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/model/__init__.py A lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_parameter_modules.py R lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_paramter_modules.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/deps/containers.py M lib/galaxy/tools/execute.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/wrapped_json.py M lib/galaxy/tools/parser/interface.py M lib/galaxy/util/__init__.py M lib/galaxy/util/log/fluent_log.py M lib/galaxy/web/framework/base.py M lib/galaxy/web/framework/middleware/statsd.py M lib/galaxy/webapps/galaxy/api/datasets.py M lib/galaxy/webapps/galaxy/api/lda_datasets.py M lib/galaxy/webapps/galaxy/api/metrics.py M lib/galaxy/webapps/galaxy/api/remote_files.py M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/config.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/galaxy/webapps/tool_shed/model/__init__.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run.py M lib/galaxy/workflow/scheduling_manager.py M lib/tool_shed/capsule/capsule_manager.py M lib/tool_shed/galaxy_install/dependency_display.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py M lib/tool_shed/galaxy_install/tool_migration_manager.py M lib/tool_shed/galaxy_install/update_repository_manager.py M lib/tool_shed/scripts/api/common.py M lib/tool_shed/scripts/deprecate_repositories_without_metadata.py M lib/tool_shed/tool_shed_registry.py M lib/tool_shed/util/common_util.py M lib/tool_shed/util/readme_util.py M lib/tool_shed/util/shed_util_common.py M run.sh M run_reports.sh M run_tests.sh M run_tool_shed.sh M scripts/bootstrap_history.py M scripts/functional_tests.py M scripts/summarize_timings.py M static/maps/layout/masthead.js.map M static/maps/layout/menu.js.map M static/maps/layout/page.js.map M static/maps/mvc/form/form-input.js.map M static/maps/mvc/form/form-parameters.js.map R static/maps/mvc/form/form-select-content.js.map M static/maps/mvc/library/library-dataset-view.js.map M static/maps/mvc/library/library-folder-view.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/maps/mvc/library/library-librarytoolbar-view.js.map M static/maps/mvc/tool/tool-form-base.js.map A static/maps/mvc/ui/ui-select-content.js.map M static/maps/mvc/ui/ui-select-default.js.map M static/maps/utils/utils.js.map M static/maps/viz/trackster/tracks.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/masthead.js M static/scripts/layout/menu.js M static/scripts/layout/page.js M static/scripts/mvc/form/form-input.js M static/scripts/mvc/form/form-parameters.js R static/scripts/mvc/form/form-select-content.js M static/scripts/mvc/library/library-dataset-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/library/library-librarytoolbar-view.js M static/scripts/mvc/tool/tool-form-base.js M static/scripts/mvc/tool/tool-form-workflow.js A static/scripts/mvc/ui/ui-select-content.js M static/scripts/mvc/ui/ui-select-default.js M static/scripts/utils/utils.js M static/scripts/viz/trackster/tracks.js M static/style/blue/base.css M static/style/blue/library.css M templates/base/base_panels.mako M templates/webapps/galaxy/library/common/library_info.mako A test/base/driver_util.py M test/base/twilltestcase.py R test/functional/test_admin_features.py R test/functional/test_data_security.py R test/functional/test_dataset_features.py R test/functional/test_get_data.py R test/functional/test_library_features.py R test/functional/test_library_security.py R test/functional/test_metadata_editing.py R test/functional/test_sample_tracking.py R test/functional/test_tags.py M test/functional/test_toolbox.py R test/functional/test_ucsc_table_browser.py R test/functional/test_user_info.py M test/functional/tools/collection_creates_list.xml A test/functional/tools/for_workflows/create_input_collection.xml A test/functional/tools/for_workflows/split.xml M test/functional/tools/samples_tool_conf.xml A test/functional/tools/upload_tool_conf.xml M test/functional/workflow.py R test/install_and_test_tool_shed_repositories/__init__.py R test/install_and_test_tool_shed_repositories/base/__init__.py R test/install_and_test_tool_shed_repositories/base/test_db_util.py R test/install_and_test_tool_shed_repositories/base/twilltestcase.py R test/install_and_test_tool_shed_repositories/base/util.py R test/install_and_test_tool_shed_repositories/functional/__init__.py R test/install_and_test_tool_shed_repositories/functional/test_install_repositories.py R test/install_and_test_tool_shed_repositories/repositories_with_tools/__init__.py R test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py R test/install_and_test_tool_shed_repositories/tool_dependency_definitions/__init__.py R test/install_and_test_tool_shed_repositories/tool_dependency_definitions/functional_tests.py A test/manual/launch_and_run.sh A test/manual/workflow_job_conf.xml M test/manual/workflows_scaling.py M test/qunit/test-app.js A test/qunit/tests/form_tests.html A test/qunit/tests/form_tests.js A test/qunit/tests/page_tests.html A test/qunit/tests/page_tests.js M test/qunit/tests/ui_tests.js M test/tool_shed/base/twilltestcase.py M test/tool_shed/functional/test_0490_export_import_repositories.py M test/tool_shed/functional/test_0500_export_repository_simple_dependency.py M test/tool_shed/functional_tests.py M test/unit/jobs/test_runner_local.py M test/unit/test_lazy_process.py A tool-data/bam_iobio.loc.sample A tool-data/vcf_iobio.loc.sample Log Message: ----------- Merge branch 'dev' of git://github.com/galaxyproject/galaxy into toolshed_decouple Commit: 3ad68fd68eb023e0a59d55e2489e896b6ce7aad7 https://github.com/galaxyproject/galaxy/commit/3ad68fd68eb023e0a59d55e2489e… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-03-30 (Wed, 30 Mar 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py M run_tool_shed.sh A templates/admin/tool_shed_repository/browse_categories.mako A templates/admin/tool_shed_repository/browse_category.mako M templates/admin/tool_shed_repository/initiate_repository_installation.mako A templates/admin/tool_shed_repository/preview_repository.mako M templates/webapps/galaxy/admin/index.mako A templates/webapps/galaxy/admin/toolsheds.mako Log Message: ----------- Merge pull request #1392 from davebx/toolshed_decouple Use the API to install repositories instead of loading the toolshed in an iframe. Compare: https://github.com/galaxyproject/galaxy/compare/565f11f142de...3ad68fd68eb0

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