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November 2018
- 1 participants
- 113 discussions
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: a4ce326d8e8bbf812f5573bfe6c14fb566b2be1a
https://github.com/galaxyproject/galaxy/commit/a4ce326d8e8bbf812f5573bfe6c1…
Author: Mason <nerdinacan(a)gmail.com>
Date: 2018-11-10 (Sat, 10 Nov 2018)
Changed paths:
A client/galaxy/scripts/app/galaxy.js
A client/galaxy/scripts/app/index.js
A client/galaxy/scripts/app/monitor.js
A client/galaxy/scripts/app/singleton.js
R client/galaxy/scripts/galaxy.js
R client/galaxy/scripts/galaxy.monitor.js
M client/galaxy/scripts/onload/index.js
M client/galaxy/scripts/utils/add-logging.js
M client/galaxy/scripts/utils/config.js
M client/galaxy/scripts/utils/deferred.js
M client/galaxy/scripts/utils/installMonitor.js
M client/galaxy/scripts/utils/serverPath.js
M client/galaxy/scripts/utils/uploadbox.js
M client/galaxy/scripts/utils/utils.js
M client/webpack.config.js
Log Message:
-----------
added singleton functions
Commit: 4ed27cf13145a77b4f8f1bcd57acbf1bb867886a
https://github.com/galaxyproject/galaxy/commit/4ed27cf13145a77b4f8f1bcd57ac…
Author: Mason <nerdinacan(a)gmail.com>
Date: 2018-11-10 (Sat, 10 Nov 2018)
Changed paths:
M client/galaxy/scripts/qunit/test-app.js
M client/galaxy/scripts/qunit/test-data/bootstrapped.js
M client/galaxy/scripts/qunit/test-data/fakeserver.js
M client/galaxy/scripts/qunit/test-data/job-dag-1.js
A client/galaxy/scripts/qunit/test-data/json/datatypes.json
A client/galaxy/scripts/qunit/test-data/json/datatypes.mapping.json
A client/galaxy/scripts/qunit/test-data/json/tools.test.build.json
M client/galaxy/scripts/qunit/test-data/paired-collection-creator.data.js
M client/galaxy/scripts/qunit/test.js
M client/galaxy/scripts/qunit/tests/form_tests.js
M client/galaxy/scripts/qunit/tests/galaxy_app_base_tests.js
M client/galaxy/scripts/qunit/tests/graph_tests.js
M client/galaxy/scripts/qunit/tests/hda_base_tests.js
M client/galaxy/scripts/qunit/tests/history_contents_model_tests.js
M client/galaxy/scripts/qunit/tests/job_dag_tests.js
A client/galaxy/scripts/qunit/tests/jquery_plugin_tests.js
M client/galaxy/scripts/qunit/tests/list_of_pairs_collection_creator_tests.js
M client/galaxy/scripts/qunit/tests/masthead_tests.js
M client/galaxy/scripts/qunit/tests/metrics_logger_tests.js
M client/galaxy/scripts/qunit/tests/modal_tests.js
M client/galaxy/scripts/qunit/tests/page_tests.js
M client/galaxy/scripts/qunit/tests/ui_tests.js
M client/galaxy/scripts/qunit/tests/upload_dialog_tests.js
M client/galaxy/scripts/qunit/tests/utils_tests.js
M client/galaxy/scripts/qunit/tests/workflow_editor_tests.js
Log Message:
-----------
Added qunit tests
Commit: d4ab893441a5dd8f7a82df902323a5940e1698d7
https://github.com/galaxyproject/galaxy/commit/d4ab893441a5dd8f7a82df902323…
Author: Mason <nerdinacan(a)gmail.com>
Date: 2018-11-10 (Sat, 10 Nov 2018)
Changed paths:
M templates/base.mako
M templates/galaxy_client_app.mako
M templates/js-app.mako
M templates/webapps/galaxy/galaxy.masthead.mako
M templates/webapps/galaxy/galaxy.panels.mako
Log Message:
-----------
Modified python templates
Commit: 969263e94805ff1c2b4568c3bf127d4183515cb4
https://github.com/galaxyproject/galaxy/commit/969263e94805ff1c2b4568c3bf12…
Author: Mason <nerdinacan(a)gmail.com>
Date: 2018-11-10 (Sat, 10 Nov 2018)
Changed paths:
M client/galaxy/scripts/apps/admin.js
M client/galaxy/scripts/apps/analysis.js
M client/galaxy/scripts/apps/extended.js
M client/galaxy/scripts/apps/login.js
M client/galaxy/scripts/apps/panels/admin-panel.js
M client/galaxy/scripts/apps/panels/history-panel.js
M client/galaxy/scripts/apps/panels/tool-panel.js
Log Message:
-----------
Updated entry points to use singleton
Commit: 964875f58a39c36032b7d958d5f3739643ea0dc2
https://github.com/galaxyproject/galaxy/commit/964875f58a39c36032b7d958d5f3…
Author: Mason <nerdinacan(a)gmail.com>
Date: 2018-11-10 (Sat, 10 Nov 2018)
Changed paths:
M client/galaxy/scripts/admin.toolshed.js
M client/galaxy/scripts/components/Citations.vue
M client/galaxy/scripts/components/DataDialog.vue
M client/galaxy/scripts/components/DisplayStructured.vue
M client/galaxy/scripts/components/HistoryImport.vue
M client/galaxy/scripts/components/HistoryView.vue
M client/galaxy/scripts/components/PluginList.vue
M client/galaxy/scripts/components/RuleCollectionBuilder.vue
M client/galaxy/scripts/components/Sharing.vue
M client/galaxy/scripts/components/WorkflowImport.vue
M client/galaxy/scripts/components/admin/DataManager/DataManager.vue
M client/galaxy/scripts/components/admin/DataManager/DataManagerJob.vue
M client/galaxy/scripts/components/admin/DataManager/DataManagerJobs.vue
M client/galaxy/scripts/components/admin/DataManager/DataManagerRouter.vue
M client/galaxy/scripts/components/admin/DataManager/DataManagerTable.vue
M client/galaxy/scripts/components/admin/DataTables.vue
M client/galaxy/scripts/components/admin/DataTypes.vue
M client/galaxy/scripts/galaxy.library.js
M client/galaxy/scripts/layout/communication-server-view.js
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/panel.js
M client/galaxy/scripts/layout/router.js
M client/galaxy/scripts/layout/scratchbook.js
M client/galaxy/scripts/mvc/base/controlled-fetch-collection.js
M client/galaxy/scripts/mvc/collection/collection-model.js
M client/galaxy/scripts/mvc/collection/collection-view-edit.js
M client/galaxy/scripts/mvc/collection/collection-view.js
M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js
M client/galaxy/scripts/mvc/dataset/data.js
M client/galaxy/scripts/mvc/dataset/dataset-edit-attributes.js
M client/galaxy/scripts/mvc/dataset/dataset-error.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/dataset/dataset-model.js
M client/galaxy/scripts/mvc/form/form-parameters.js
M client/galaxy/scripts/mvc/form/form-view.js
M client/galaxy/scripts/mvc/form/form-wrapper.js
M client/galaxy/scripts/mvc/grid/grid-shared.js
M client/galaxy/scripts/mvc/grid/grid-view.js
M client/galaxy/scripts/mvc/history/copy-dialog.js
M client/galaxy/scripts/mvc/history/history-content-model.js
M client/galaxy/scripts/mvc/history/history-contents.js
M client/galaxy/scripts/mvc/history/history-list.js
M client/galaxy/scripts/mvc/history/history-model.js
M client/galaxy/scripts/mvc/history/history-view-edit-current.js
M client/galaxy/scripts/mvc/history/history-view-edit.js
M client/galaxy/scripts/mvc/history/history-view.js
M client/galaxy/scripts/mvc/history/job-states-model.js
M client/galaxy/scripts/mvc/history/multi-panel.js
M client/galaxy/scripts/mvc/history/options-menu.js
M client/galaxy/scripts/mvc/job/job-model.js
M client/galaxy/scripts/mvc/job/job-params.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-folderrow-view.js
M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js
M client/galaxy/scripts/mvc/library/library-library-view.js
M client/galaxy/scripts/mvc/library/library-librarylist-view.js
M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js
M client/galaxy/scripts/mvc/library/library-model.js
M client/galaxy/scripts/mvc/tag.js
M client/galaxy/scripts/mvc/tool/tool-form-base.js
M client/galaxy/scripts/mvc/tool/tool-form-composite.js
M client/galaxy/scripts/mvc/tool/tool-form.js
M client/galaxy/scripts/mvc/tool/tool-genomespace.js
M client/galaxy/scripts/mvc/tool/tools.js
M client/galaxy/scripts/mvc/toolshed/categories-view.js
M client/galaxy/scripts/mvc/toolshed/repositories-view.js
M client/galaxy/scripts/mvc/toolshed/repository-queue-view.js
M client/galaxy/scripts/mvc/toolshed/repository-view.js
M client/galaxy/scripts/mvc/toolshed/toolshed-model.js
M client/galaxy/scripts/mvc/toolshed/util.js
M client/galaxy/scripts/mvc/toolshed/workflows-view.js
M client/galaxy/scripts/mvc/tours.js
M client/galaxy/scripts/mvc/ui/error-modal.js
M client/galaxy/scripts/mvc/ui/ui-frames.js
M client/galaxy/scripts/mvc/ui/ui-rules-edit.js
M client/galaxy/scripts/mvc/ui/ui-select-ftp.js
M client/galaxy/scripts/mvc/ui/ui-select-library.js
M client/galaxy/scripts/mvc/upload/collection/rules-input-view.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-utils.js
M client/galaxy/scripts/mvc/upload/upload-view.js
M client/galaxy/scripts/mvc/user/user-custom-builds.js
M client/galaxy/scripts/mvc/user/user-model.js
M client/galaxy/scripts/mvc/user/user-preferences.js
M client/galaxy/scripts/mvc/visualization/chart/chart-client.js
M client/galaxy/scripts/mvc/visualization/chart/utilities/datasets.js
M client/galaxy/scripts/mvc/visualization/chart/utilities/jobs.js
M client/galaxy/scripts/mvc/visualization/chart/views/description.js
M client/galaxy/scripts/mvc/visualization/chart/views/groups.js
M client/galaxy/scripts/mvc/visualization/visualization-model.js
M client/galaxy/scripts/mvc/webhooks.js
M client/galaxy/scripts/mvc/workflow/workflow-forms.js
M client/galaxy/scripts/mvc/workflow/workflow-manager.js
M client/galaxy/scripts/mvc/workflow/workflow-model.js
M client/galaxy/scripts/mvc/workflow/workflow-node.js
M client/galaxy/scripts/mvc/workflow/workflow-view-data.js
M client/galaxy/scripts/mvc/workflow/workflow-view.js
M client/galaxy/scripts/mvc/workflow/workflow.js
M client/galaxy/scripts/toolshed/groups/group-model.js
M client/galaxy/scripts/viz/bbi-data-manager.js
M client/galaxy/scripts/viz/circster.js
M client/galaxy/scripts/viz/sweepster.js
M client/galaxy/scripts/viz/trackster.js
M client/galaxy/scripts/viz/trackster/tracks.js
M client/galaxy/scripts/viz/visualization.js
M client/karma/karma.config.qunit.js
M client/karma/webpack.config.unittest.js
Log Message:
-----------
Removed global references to Galaxy
Commit: 020bbe92763e98c39c9d345a661dcf5475218d86
https://github.com/galaxyproject/galaxy/commit/020bbe92763e98c39c9d345a661d…
Author: Mason <nerdinacan(a)gmail.com>
Date: 2018-11-12 (Mon, 12 Nov 2018)
Changed paths:
M client/galaxy/scripts/mvc/form/form-data.js
M client/galaxy/scripts/mvc/form/form-input.js
M client/galaxy/scripts/mvc/form/form-section.js
M client/galaxy/scripts/mvc/workflow/workflow-forms.js
M client/galaxy/scripts/mvc/workflow/workflow-icons.js
M client/galaxy/scripts/mvc/workflow/workflow-node.js
M client/galaxy/scripts/mvc/workflow/workflow-terminals.js
M client/galaxy/scripts/mvc/workflow/workflow-view-data.js
M client/galaxy/scripts/mvc/workflow/workflow-view-node.js
M client/galaxy/scripts/mvc/workflow/workflow-view-terminals.js
M client/galaxy/scripts/qunit/tests/workflow_editor_tests.js
M lib/galaxy/datatypes/sequence.py
M lib/galaxy/managers/workflows.py
M lib/galaxy/model/__init__.py
M lib/galaxy/tools/parameters/__init__.py
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/webapps/galaxy/api/workflows.py
M lib/galaxy/workflow/modules.py
M lib/galaxy/workflow/run.py
M lib/galaxy/workflow/run_request.py
M scripts/drmaa_external_runner.py
M test/api/test_workflows.py
M test/galaxy_selenium/navigation.yml
M test/selenium_tests/test_workflow_editor.py
M test/selenium_tests/test_workflow_run.py
Log Message:
-----------
Merged dev, noted unused variables in workflow-node.js but harmless
Commit: 57abad3fa603fdb8325d1eeea61709959eb1dcdb
https://github.com/galaxyproject/galaxy/commit/57abad3fa603fdb8325d1eeea617…
Author: Mason <nerdinacan(a)gmail.com>
Date: 2018-11-12 (Mon, 12 Nov 2018)
Changed paths:
M client/galaxy/scripts/app/singleton.js
Log Message:
-----------
Replaced string-based type comparison with instanceof, fixed production-only build issue where constructor names become uglified
Commit: bdf5c06f04ab4743a5e18872446d4af96f9877db
https://github.com/galaxyproject/galaxy/commit/bdf5c06f04ab4743a5e18872446d…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2018-11-13 (Tue, 13 Nov 2018)
Changed paths:
M client/galaxy/scripts/admin.toolshed.js
M client/galaxy/scripts/app/index.js
M client/galaxy/scripts/app/monitor.js
M client/galaxy/scripts/app/singleton.js
M client/galaxy/scripts/apps/analysis.js
M client/galaxy/scripts/apps/login.js
M client/galaxy/scripts/apps/panels/history-panel.js
M client/galaxy/scripts/layout/data.js
M client/galaxy/scripts/layout/menu.js
M client/galaxy/scripts/layout/scratchbook.js
M client/galaxy/scripts/mvc/dataset/data.js
M client/galaxy/scripts/mvc/dataset/dataset-error.js
M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js
M client/galaxy/scripts/mvc/history/history-content-model.js
M client/galaxy/scripts/mvc/history/history-contents.js
M client/galaxy/scripts/mvc/history/history-list.js
M client/galaxy/scripts/mvc/history/history-model.js
M client/galaxy/scripts/mvc/history/history-view-edit.js
M client/galaxy/scripts/mvc/history/history-view.js
M client/galaxy/scripts/mvc/history/multi-panel.js
M client/galaxy/scripts/mvc/history/options-menu.js
M client/galaxy/scripts/mvc/tool/tool-form-composite.js
M client/galaxy/scripts/mvc/tool/tool-form.js
M client/galaxy/scripts/mvc/tool/tools.js
M client/galaxy/scripts/mvc/toolshed/toolshed-model.js
M client/galaxy/scripts/mvc/tours.js
M client/galaxy/scripts/mvc/ui/error-modal.js
M client/galaxy/scripts/mvc/ui/ui-frames.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/visualization/chart/chart-client.js
M client/galaxy/scripts/mvc/visualization/chart/utilities/jobs.js
M client/galaxy/scripts/mvc/workflow/workflow-node.js
M client/galaxy/scripts/mvc/workflow/workflow-terminals.js
M client/galaxy/scripts/mvc/workflow/workflow-view-data.js
M client/galaxy/scripts/mvc/workflow/workflow-view-terminals.js
M client/galaxy/scripts/mvc/workflow/workflow-view.js
M client/galaxy/scripts/mvc/workflow/workflow.js
M client/galaxy/scripts/onload/index.js
M client/galaxy/scripts/qunit/test-app.js
M client/galaxy/scripts/qunit/test-data/bootstrapped.js
M client/galaxy/scripts/qunit/test-data/fakeserver.js
M client/galaxy/scripts/qunit/test-data/job-dag-1.js
M client/galaxy/scripts/qunit/test-data/paired-collection-creator.data.js
M client/galaxy/scripts/qunit/test.js
M client/galaxy/scripts/qunit/tests/form_tests.js
M client/galaxy/scripts/qunit/tests/galaxy_app_base_tests.js
M client/galaxy/scripts/qunit/tests/list_of_pairs_collection_creator_tests.js
M client/galaxy/scripts/qunit/tests/metrics_logger_tests.js
M client/galaxy/scripts/qunit/tests/ui_tests.js
M client/galaxy/scripts/qunit/tests/workflow_editor_tests.js
M client/galaxy/scripts/utils/installMonitor.js
M client/galaxy/scripts/utils/uploadbox.js
M client/galaxy/scripts/utils/utils.js
M client/galaxy/scripts/viz/circster.js
M client/galaxy/scripts/viz/trackster.js
M client/galaxy/scripts/viz/visualization.js
Log Message:
-----------
Client format.
Commit: c2ac98b9bb48d938fbebc5c70ce563fcb4717ad4
https://github.com/galaxyproject/galaxy/commit/c2ac98b9bb48d938fbebc5c70ce5…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2018-11-13 (Tue, 13 Nov 2018)
Changed paths:
M client/galaxy/scripts/layout/data.js
Log Message:
-----------
Update layout/data to use getGalaxyInstance/etc
Commit: 4ea20bc95915c5a1f4046f31d3b50e11516540d0
https://github.com/galaxyproject/galaxy/commit/4ea20bc95915c5a1f4046f31d3b5…
Author: Dannon <dannon.baker(a)gmail.com>
Date: 2018-11-13 (Tue, 13 Nov 2018)
Changed paths:
M client/galaxy/scripts/admin.toolshed.js
A client/galaxy/scripts/app/galaxy.js
A client/galaxy/scripts/app/index.js
A client/galaxy/scripts/app/monitor.js
A client/galaxy/scripts/app/singleton.js
M client/galaxy/scripts/apps/admin.js
M client/galaxy/scripts/apps/analysis.js
M client/galaxy/scripts/apps/extended.js
M client/galaxy/scripts/apps/login.js
M client/galaxy/scripts/apps/panels/admin-panel.js
M client/galaxy/scripts/apps/panels/history-panel.js
M client/galaxy/scripts/apps/panels/tool-panel.js
M client/galaxy/scripts/components/Citations.vue
M client/galaxy/scripts/components/DataDialog.vue
M client/galaxy/scripts/components/DisplayStructured.vue
M client/galaxy/scripts/components/HistoryImport.vue
M client/galaxy/scripts/components/HistoryView.vue
M client/galaxy/scripts/components/PluginList.vue
M client/galaxy/scripts/components/RuleCollectionBuilder.vue
M client/galaxy/scripts/components/Sharing.vue
M client/galaxy/scripts/components/WorkflowImport.vue
M client/galaxy/scripts/components/admin/DataManager/DataManager.vue
M client/galaxy/scripts/components/admin/DataManager/DataManagerJob.vue
M client/galaxy/scripts/components/admin/DataManager/DataManagerJobs.vue
M client/galaxy/scripts/components/admin/DataManager/DataManagerRouter.vue
M client/galaxy/scripts/components/admin/DataManager/DataManagerTable.vue
M client/galaxy/scripts/components/admin/DataTables.vue
M client/galaxy/scripts/components/admin/DataTypes.vue
R client/galaxy/scripts/galaxy.js
M client/galaxy/scripts/galaxy.library.js
R client/galaxy/scripts/galaxy.monitor.js
M client/galaxy/scripts/layout/communication-server-view.js
M client/galaxy/scripts/layout/data.js
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/panel.js
M client/galaxy/scripts/layout/router.js
M client/galaxy/scripts/layout/scratchbook.js
M client/galaxy/scripts/mvc/base/controlled-fetch-collection.js
M client/galaxy/scripts/mvc/collection/collection-model.js
M client/galaxy/scripts/mvc/collection/collection-view-edit.js
M client/galaxy/scripts/mvc/collection/collection-view.js
M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js
M client/galaxy/scripts/mvc/dataset/data.js
M client/galaxy/scripts/mvc/dataset/dataset-edit-attributes.js
M client/galaxy/scripts/mvc/dataset/dataset-error.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/dataset/dataset-model.js
M client/galaxy/scripts/mvc/form/form-parameters.js
M client/galaxy/scripts/mvc/form/form-view.js
M client/galaxy/scripts/mvc/form/form-wrapper.js
M client/galaxy/scripts/mvc/grid/grid-shared.js
M client/galaxy/scripts/mvc/grid/grid-view.js
M client/galaxy/scripts/mvc/history/copy-dialog.js
M client/galaxy/scripts/mvc/history/history-content-model.js
M client/galaxy/scripts/mvc/history/history-contents.js
M client/galaxy/scripts/mvc/history/history-list.js
M client/galaxy/scripts/mvc/history/history-model.js
M client/galaxy/scripts/mvc/history/history-view-edit-current.js
M client/galaxy/scripts/mvc/history/history-view-edit.js
M client/galaxy/scripts/mvc/history/history-view.js
M client/galaxy/scripts/mvc/history/job-states-model.js
M client/galaxy/scripts/mvc/history/multi-panel.js
M client/galaxy/scripts/mvc/history/options-menu.js
M client/galaxy/scripts/mvc/job/job-model.js
M client/galaxy/scripts/mvc/job/job-params.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-folderrow-view.js
M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js
M client/galaxy/scripts/mvc/library/library-library-view.js
M client/galaxy/scripts/mvc/library/library-librarylist-view.js
M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js
M client/galaxy/scripts/mvc/library/library-model.js
M client/galaxy/scripts/mvc/tag.js
M client/galaxy/scripts/mvc/tool/tool-form-base.js
M client/galaxy/scripts/mvc/tool/tool-form-composite.js
M client/galaxy/scripts/mvc/tool/tool-form.js
M client/galaxy/scripts/mvc/tool/tool-genomespace.js
M client/galaxy/scripts/mvc/tool/tools.js
M client/galaxy/scripts/mvc/toolshed/categories-view.js
M client/galaxy/scripts/mvc/toolshed/repositories-view.js
M client/galaxy/scripts/mvc/toolshed/repository-queue-view.js
M client/galaxy/scripts/mvc/toolshed/repository-view.js
M client/galaxy/scripts/mvc/toolshed/toolshed-model.js
M client/galaxy/scripts/mvc/toolshed/util.js
M client/galaxy/scripts/mvc/toolshed/workflows-view.js
M client/galaxy/scripts/mvc/tours.js
M client/galaxy/scripts/mvc/ui/error-modal.js
M client/galaxy/scripts/mvc/ui/ui-frames.js
M client/galaxy/scripts/mvc/ui/ui-rules-edit.js
M client/galaxy/scripts/mvc/ui/ui-select-ftp.js
M client/galaxy/scripts/mvc/ui/ui-select-library.js
M client/galaxy/scripts/mvc/upload/collection/rules-input-view.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-utils.js
M client/galaxy/scripts/mvc/upload/upload-view.js
M client/galaxy/scripts/mvc/user/user-custom-builds.js
M client/galaxy/scripts/mvc/user/user-model.js
M client/galaxy/scripts/mvc/user/user-preferences.js
M client/galaxy/scripts/mvc/visualization/chart/chart-client.js
M client/galaxy/scripts/mvc/visualization/chart/utilities/datasets.js
M client/galaxy/scripts/mvc/visualization/chart/utilities/jobs.js
M client/galaxy/scripts/mvc/visualization/chart/views/description.js
M client/galaxy/scripts/mvc/visualization/chart/views/groups.js
M client/galaxy/scripts/mvc/visualization/visualization-model.js
M client/galaxy/scripts/mvc/webhooks.js
M client/galaxy/scripts/mvc/workflow/workflow-forms.js
M client/galaxy/scripts/mvc/workflow/workflow-manager.js
M client/galaxy/scripts/mvc/workflow/workflow-model.js
M client/galaxy/scripts/mvc/workflow/workflow-node.js
M client/galaxy/scripts/mvc/workflow/workflow-terminals.js
M client/galaxy/scripts/mvc/workflow/workflow-view-data.js
M client/galaxy/scripts/mvc/workflow/workflow-view-terminals.js
M client/galaxy/scripts/mvc/workflow/workflow-view.js
M client/galaxy/scripts/mvc/workflow/workflow.js
M client/galaxy/scripts/onload/index.js
M client/galaxy/scripts/qunit/test-app.js
M client/galaxy/scripts/qunit/test-data/bootstrapped.js
M client/galaxy/scripts/qunit/test-data/fakeserver.js
M client/galaxy/scripts/qunit/test-data/job-dag-1.js
A client/galaxy/scripts/qunit/test-data/json/datatypes.json
A client/galaxy/scripts/qunit/test-data/json/datatypes.mapping.json
A client/galaxy/scripts/qunit/test-data/json/tools.test.build.json
M client/galaxy/scripts/qunit/test-data/paired-collection-creator.data.js
M client/galaxy/scripts/qunit/test.js
M client/galaxy/scripts/qunit/tests/form_tests.js
M client/galaxy/scripts/qunit/tests/galaxy_app_base_tests.js
M client/galaxy/scripts/qunit/tests/graph_tests.js
M client/galaxy/scripts/qunit/tests/hda_base_tests.js
M client/galaxy/scripts/qunit/tests/history_contents_model_tests.js
M client/galaxy/scripts/qunit/tests/job_dag_tests.js
A client/galaxy/scripts/qunit/tests/jquery_plugin_tests.js
M client/galaxy/scripts/qunit/tests/list_of_pairs_collection_creator_tests.js
M client/galaxy/scripts/qunit/tests/masthead_tests.js
M client/galaxy/scripts/qunit/tests/metrics_logger_tests.js
M client/galaxy/scripts/qunit/tests/modal_tests.js
M client/galaxy/scripts/qunit/tests/page_tests.js
M client/galaxy/scripts/qunit/tests/ui_tests.js
M client/galaxy/scripts/qunit/tests/upload_dialog_tests.js
M client/galaxy/scripts/qunit/tests/utils_tests.js
M client/galaxy/scripts/qunit/tests/workflow_editor_tests.js
M client/galaxy/scripts/toolshed/groups/group-model.js
M client/galaxy/scripts/utils/add-logging.js
M client/galaxy/scripts/utils/config.js
M client/galaxy/scripts/utils/deferred.js
M client/galaxy/scripts/utils/installMonitor.js
M client/galaxy/scripts/utils/serverPath.js
M client/galaxy/scripts/utils/uploadbox.js
M client/galaxy/scripts/utils/utils.js
M client/galaxy/scripts/viz/bbi-data-manager.js
M client/galaxy/scripts/viz/circster.js
M client/galaxy/scripts/viz/sweepster.js
M client/galaxy/scripts/viz/trackster.js
M client/galaxy/scripts/viz/trackster/tracks.js
M client/galaxy/scripts/viz/visualization.js
M client/karma/karma.config.qunit.js
M client/karma/webpack.config.unittest.js
M client/webpack.config.js
M templates/base.mako
M templates/galaxy_client_app.mako
M templates/js-app.mako
M templates/webapps/galaxy/galaxy.masthead.mako
M templates/webapps/galaxy/galaxy.panels.mako
Log Message:
-----------
Merge pull request #7005 from Nerdinacan/app_singleton_cleaned
Replace global Galaxy references with galaxy singleton accessor/setter
Compare: https://github.com/galaxyproject/galaxy/compare/be76d9f8017e...4ea20bc95915
**NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/
Functionality will be removed from GitHub.com on January 31st, 2019.
1
0
13 Nov '18
Branch: refs/heads/master
Home: https://github.com/galaxyproject/usegalaxy-playbook
Commit: a7d0bab3ca7abf4eadb8e7ad5342961560f73fc6
https://github.com/galaxyproject/usegalaxy-playbook/commit/a7d0bab3ca7abf4e…
Author: Dave B <dave(a)bx.psu.edu>
Date: 2018-11-13 (Tue, 13 Nov 2018)
Changed paths:
M env/test/files/galaxy/var/integrated_tool_panel.xml
M env/test/files/galaxy/var/shed_tool_conf.xml
M env/test/files/galaxy/var/shed_tool_data_table_conf.xml
Log Message:
-----------
Installed latest GEMINI tools.
**NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/
Functionality will be removed from GitHub.com on January 31st, 2019.
1
0
11 Nov '18
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 97ba92f3cffd0c17353595c61bd5d22c7a4e8c4e
https://github.com/galaxyproject/galaxy/commit/97ba92f3cffd0c17353595c61bd5…
Author: M Bernt <m.bernt(a)ufz.de>
Date: 2018-11-09 (Fri, 09 Nov 2018)
Changed paths:
M scripts/drmaa_external_runner.py
Log Message:
-----------
external_runner: load json template first
if the JSON is loaded first the cluster_files_directory
does not need to be accessible by the real user (ie all users)
Commit: be76d9f8017efa14f133ee8fb49c0f3b490bdd2a
https://github.com/galaxyproject/galaxy/commit/be76d9f8017efa14f133ee8fb49c…
Author: Marius van den Beek <m.vandenbeek(a)gmail.com>
Date: 2018-11-11 (Sun, 11 Nov 2018)
Changed paths:
M scripts/drmaa_external_runner.py
Log Message:
-----------
Merge pull request #6995 from bernt-matthias/topic/external-runner-json-load-order
external_runner: load json template first
Compare: https://github.com/galaxyproject/galaxy/compare/acfbca32dd7d...be76d9f8017e
**NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/
Functionality will be removed from GitHub.com on January 31st, 2019.
1
0
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 773a9bef892ede8f464a14de5f89469045568ec3
https://github.com/galaxyproject/galaxy/commit/773a9bef892ede8f464a14de5f89…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-11-10 (Sat, 10 Nov 2018)
Changed paths:
M lib/galaxy/datatypes/sequence.py
Log Message:
-----------
Fix fastq set_metadata on python 3
Commit: acfbca32dd7dc381750f6a9362b48ddaa4abd5a5
https://github.com/galaxyproject/galaxy/commit/acfbca32dd7dc381750f6a9362b4…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-11-10 (Sat, 10 Nov 2018)
Changed paths:
M lib/galaxy/datatypes/sequence.py
Log Message:
-----------
Merge pull request #7001 from mvdbeek/fastq_fix
Fix set_peek for fastg datatype
Compare: https://github.com/galaxyproject/galaxy/compare/e98f63caf2d2...acfbca32dd7d
**NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/
Functionality will be removed from GitHub.com on January 31st, 2019.
1
0
10 Nov '18
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 199fe7e0fccbeeb55501bad54f8ae4e44e7c100c
https://github.com/galaxyproject/galaxy/commit/199fe7e0fccbeeb55501bad54f8a…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-11-05 (Mon, 05 Nov 2018)
Changed paths:
M lib/galaxy/managers/workflows.py
Log Message:
-----------
Allow saving workflows with input parameters
Commit: 638b1b7581d38b9044e17937f308c82fd36663ee
https://github.com/galaxyproject/galaxy/commit/638b1b7581d38b9044e17937f308…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-11-05 (Mon, 05 Nov 2018)
Changed paths:
M lib/galaxy/workflow/modules.py
Log Message:
-----------
Allow inserting input parameter into workflow
Commit: c09d1bc150775909f0e2a8f1c48ad0b2b70afea0
https://github.com/galaxyproject/galaxy/commit/c09d1bc150775909f0e2a8f1c48a…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-11-05 (Mon, 05 Nov 2018)
Changed paths:
M client/galaxy/scripts/mvc/workflow/workflow-node.js
M client/galaxy/scripts/mvc/workflow/workflow-terminals.js
M client/galaxy/scripts/mvc/workflow/workflow-view-data.js
M client/galaxy/scripts/mvc/workflow/workflow-view-node.js
M client/galaxy/scripts/mvc/workflow/workflow-view-terminals.js
M lib/galaxy/managers/workflows.py
M lib/galaxy/workflow/modules.py
Log Message:
-----------
WIP: add StepParameter inputs to workflow editor
In the current state when a text, integer, float, boolean or
boolean parameter is set as "Set at Runtime" a new connectable
input appears for the tool node, to which a Parameter can be properly
dragged and connected.
This still needs a little more separation from data inputs/outputs,
and the new connection isn't persisted in a meaningful way.
Commit: 99c270fd77367a813af6202465d5453be78ac4eb
https://github.com/galaxyproject/galaxy/commit/99c270fd77367a813af6202465d5…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-11-05 (Mon, 05 Nov 2018)
Changed paths:
M client/galaxy/scripts/mvc/workflow/workflow-node.js
M lib/galaxy/webapps/galaxy/api/workflows.py
M lib/galaxy/workflow/modules.py
Log Message:
-----------
Fix rebuilding parameter node
Commit: b0d64a8f09e6dc3d29c069edcb2abe77ee9c3662
https://github.com/galaxyproject/galaxy/commit/b0d64a8f09e6dc3d29c069edcb2a…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-11-05 (Mon, 05 Nov 2018)
Changed paths:
M lib/galaxy/workflow/modules.py
Log Message:
-----------
Fix selecting the correct item from select list
select lists don't take a `value` argument.
Commit: c624cc4bce8b7b2bea9eaf61ecbf8bea485c4640
https://github.com/galaxyproject/galaxy/commit/c624cc4bce8b7b2bea9eaf61ecbf…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-11-05 (Mon, 05 Nov 2018)
Changed paths:
M lib/galaxy/workflow/modules.py
Log Message:
-----------
Fix getting correct type
Commit: 83a25c90e66b52890fcd8ad9288059d87b4f4932
https://github.com/galaxyproject/galaxy/commit/83a25c90e66b52890fcd8ad92880…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-11-05 (Mon, 05 Nov 2018)
Changed paths:
M lib/galaxy/managers/workflows.py
M lib/galaxy/model/__init__.py
Log Message:
-----------
Fix restoring saved non-data connections in workflow editor
Commit: 4e3004bb250f86b8c16a1c94c8599f497488e732
https://github.com/galaxyproject/galaxy/commit/4e3004bb250f86b8c16a1c94c859…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-11-05 (Mon, 05 Nov 2018)
Changed paths:
M client/galaxy/scripts/mvc/workflow/workflow-node.js
Log Message:
-----------
Fix node.addOuputParameter
Commit: e135fac159e80549ce611a40f4c66598f51632d2
https://github.com/galaxyproject/galaxy/commit/e135fac159e80549ce611a40f4c6…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-11-05 (Mon, 05 Nov 2018)
Changed paths:
M client/galaxy/scripts/mvc/workflow/workflow-node.js
Log Message:
-----------
Don't render data inputs on parameter_input node
Commit: 0340dcb18a99d9d7984eb7566b3826290fe90025
https://github.com/galaxyproject/galaxy/commit/0340dcb18a99d9d7984eb7566b38…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-11-05 (Mon, 05 Nov 2018)
Changed paths:
M client/galaxy/scripts/mvc/workflow/workflow-node.js
Log Message:
-----------
More defensive runtime check
Commit: 5a5b4abb5bd4b1b142601a94b4498556c4f14946
https://github.com/galaxyproject/galaxy/commit/5a5b4abb5bd4b1b142601a94b449…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-11-05 (Mon, 05 Nov 2018)
Changed paths:
M lib/galaxy/workflow/modules.py
Log Message:
-----------
Allow loading in test-data workfows
Commit: 4812586156b4cf01fe8ee1cb743306cc91ba2c84
https://github.com/galaxyproject/galaxy/commit/4812586156b4cf01fe8ee1cb7433…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-11-05 (Mon, 05 Nov 2018)
Changed paths:
M client/galaxy/scripts/mvc/workflow/workflow-view-data.js
Log Message:
-----------
Add label to input parameters without labels.
Commit: dbe4033abe74035082b510c862c7729212367341
https://github.com/galaxyproject/galaxy/commit/dbe4033abe74035082b510c862c7…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-11-05 (Mon, 05 Nov 2018)
Changed paths:
M client/galaxy/scripts/mvc/workflow/workflow-icons.js
Log Message:
-----------
Give parameter inputs a workflow icon.
Commit: 00b8776db521cab884a107f8b66441690f644f88
https://github.com/galaxyproject/galaxy/commit/00b8776db521cab884a107f8b664…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-11-05 (Mon, 05 Nov 2018)
Changed paths:
M lib/galaxy/workflow/run_request.py
Log Message:
-----------
Convert raw parameters from map into formal parameters when invoking wfs.
Commit: d74b959419a667b2ff3192c9fde07a2cddc5e90d
https://github.com/galaxyproject/galaxy/commit/d74b959419a667b2ff3192c9fde0…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-11-05 (Mon, 05 Nov 2018)
Changed paths:
M lib/galaxy/managers/workflows.py
M lib/galaxy/model/__init__.py
Log Message:
-----------
Revert non-data connection handling, send connections unfiltered to editor.
Commit: 85d777dbe704ccdbf71898853e542c1c2df05303
https://github.com/galaxyproject/galaxy/commit/85d777dbe704ccdbf71898853e54…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-11-05 (Mon, 05 Nov 2018)
Changed paths:
M client/galaxy/scripts/mvc/form/form-data.js
M client/galaxy/scripts/mvc/form/form-input.js
M client/galaxy/scripts/mvc/form/form-section.js
M client/galaxy/scripts/mvc/workflow/workflow-forms.js
M client/galaxy/scripts/mvc/workflow/workflow-node.js
M lib/galaxy/managers/workflows.py
M lib/galaxy/tools/parameters/__init__.py
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/workflow/modules.py
Log Message:
-----------
Separate RuntimeValue into RuntimeValue and ConnectedValue.
Use ConnectedValue values to determine what non-data parameters to display connections for.
Commit: dd8d74f364770a1272555a3753f5d1e1288315e1
https://github.com/galaxyproject/galaxy/commit/dd8d74f364770a1272555a3753f5…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-11-05 (Mon, 05 Nov 2018)
Changed paths:
M client/galaxy/scripts/mvc/workflow/workflow-node.js
M client/galaxy/scripts/mvc/workflow/workflow-view-node.js
M client/galaxy/scripts/qunit/tests/workflow_editor_tests.js
M lib/galaxy/managers/workflows.py
M lib/galaxy/webapps/galaxy/api/workflows.py
M lib/galaxy/workflow/modules.py
M lib/galaxy/workflow/run.py
M test/api/test_workflows.py
Log Message:
-----------
Unify data/non-data input/output handling for workflow editor.
Don't treat data and non-data inputs/outputs different at the API boundary or at the workflow-manager.js level. Keep differences at the level of walking inputs/outputs in the workflow module on the backend and at the terminal definition (models and views) level on the frontend. Make the code and interfaces more consistent in my opinion and is more compatible with future directions I'd like to take things with mix-mode inputs/outputs for CWL.
Commit: 5a99ebd5af9d68f028b86d295846a1c4cefccfb4
https://github.com/galaxyproject/galaxy/commit/5a99ebd5af9d68f028b86d295846…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-11-05 (Mon, 05 Nov 2018)
Changed paths:
M lib/galaxy/managers/workflows.py
Log Message:
-----------
Remove filtering of connections for workflow editor.
Things not matching should be handled there.
Commit: 29950be83f8240acba05685b4a057b38d803b445
https://github.com/galaxyproject/galaxy/commit/29950be83f8240acba05685b4a05…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-11-05 (Mon, 05 Nov 2018)
Changed paths:
M test/galaxy_selenium/navigation.yml
M test/selenium_tests/test_workflow_editor.py
Log Message:
-----------
Workflow editor testing for step parameters/connections.
- Fixes and refactoring for existing input tests (toward reuse).
- Add simple test for non-data input.
Commit: f12e548872b0087b4ba8b5828bc80b6aa10207e4
https://github.com/galaxyproject/galaxy/commit/f12e548872b0087b4ba8b5828bc8…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-11-06 (Tue, 06 Nov 2018)
Changed paths:
M lib/galaxy/workflow/run.py
M test/galaxy_selenium/navigation.yml
M test/selenium_tests/test_workflow_run.py
Log Message:
-----------
Step parameter workflow run test case and fix.
Commit: e98f63caf2d2adfd7857ff9fcba6df0b5923b668
https://github.com/galaxyproject/galaxy/commit/e98f63caf2d2adfd7857ff9fcba6…
Author: Marius van den Beek <m.vandenbeek(a)gmail.com>
Date: 2018-11-10 (Sat, 10 Nov 2018)
Changed paths:
M client/galaxy/scripts/mvc/form/form-data.js
M client/galaxy/scripts/mvc/form/form-input.js
M client/galaxy/scripts/mvc/form/form-section.js
M client/galaxy/scripts/mvc/workflow/workflow-forms.js
M client/galaxy/scripts/mvc/workflow/workflow-icons.js
M client/galaxy/scripts/mvc/workflow/workflow-node.js
M client/galaxy/scripts/mvc/workflow/workflow-terminals.js
M client/galaxy/scripts/mvc/workflow/workflow-view-data.js
M client/galaxy/scripts/mvc/workflow/workflow-view-node.js
M client/galaxy/scripts/mvc/workflow/workflow-view-terminals.js
M client/galaxy/scripts/qunit/tests/workflow_editor_tests.js
M lib/galaxy/managers/workflows.py
M lib/galaxy/model/__init__.py
M lib/galaxy/tools/parameters/__init__.py
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/webapps/galaxy/api/workflows.py
M lib/galaxy/workflow/modules.py
M lib/galaxy/workflow/run.py
M lib/galaxy/workflow/run_request.py
M test/api/test_workflows.py
M test/galaxy_selenium/navigation.yml
M test/selenium_tests/test_workflow_editor.py
M test/selenium_tests/test_workflow_run.py
Log Message:
-----------
Merge pull request #6925 from jmchilton/workflow_step_parameters_3
Add workflow step parameters to workflow editor (try 3)
Compare: https://github.com/galaxyproject/galaxy/compare/b57c25622b74...e98f63caf2d2
**NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/
Functionality will be removed from GitHub.com on January 31st, 2019.
1
0
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 35bc1b387a3371e46b42c16c7b5664c33474d4fd
https://github.com/galaxyproject/galaxy/commit/35bc1b387a3371e46b42c16c7b56…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2018-11-09 (Fri, 09 Nov 2018)
Changed paths:
M doc/source/admin/framework_dependencies.rst
Log Message:
-----------
Typos in admin docs.
Commit: e9ab7add6e8e3ab31cf858e344bd0c568fc5fd83
https://github.com/galaxyproject/galaxy/commit/e9ab7add6e8e3ab31cf858e344bd…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2018-11-09 (Fri, 09 Nov 2018)
Changed paths:
M doc/source/admin/nginx.md
Log Message:
-----------
Another typo in admin/nginx
Commit: b57c25622b74b51b70cfe71d477a86a1f85b05a9
https://github.com/galaxyproject/galaxy/commit/b57c25622b74b51b70cfe71d477a…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2018-11-09 (Fri, 09 Nov 2018)
Changed paths:
M doc/source/admin/framework_dependencies.rst
M doc/source/admin/nginx.md
Log Message:
-----------
Merge pull request #6999 from dannon/typo_fix
Fix several typos in admin docs.
Compare: https://github.com/galaxyproject/galaxy/compare/cfacaae8b50c...b57c25622b74
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[galaxyproject/galaxy] 215993: Merge remote-tracking branch 'galaxyproject/dev' i...
by GitHub 09 Nov '18
by GitHub 09 Nov '18
09 Nov '18
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 21599376501e7a740f8d2700b2463024f02ca58e
https://github.com/galaxyproject/galaxy/commit/21599376501e7a740f8d2700b246…
Author: Jim Johnson <jj(a)umn.edu>
Date: 2018-11-07 (Wed, 07 Nov 2018)
Changed paths:
M .ci/jenkins/selenium-py3/run_tests.sh
M .gitignore
M .travis.yml
M Makefile
M client/.babelrc
R client/GruntFile.js
M client/README.md
A client/galaxy/docs/README.md
M client/galaxy/docs/bootstrap.md
M client/galaxy/docs/galaxy-buttons.md
M client/galaxy/docs/galaxy-forms.md
M client/galaxy/docs/galaxy-masthead.md
M client/galaxy/docs/galaxy-menus.md
M client/galaxy/docs/galaxy-messages.md
M client/galaxy/docs/galaxy-panels.md
M client/galaxy/docs/galaxy-tables.md
M client/galaxy/docs/galaxy-tabs.md
A client/galaxy/images/Armitagep_manhattan.png
A client/galaxy/images/Armitagep_qqplot.png
A client/galaxy/images/add_icon.png
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A client/galaxy/images/aggregate_history1.png
A client/galaxy/images/aggregate_history2.png
A client/galaxy/images/bar_chart.png
A client/galaxy/images/base_bg.png
A client/galaxy/images/bed_warn.png
A client/galaxy/images/button_bar_bg_light.png
A client/galaxy/images/circle.py
A client/galaxy/images/closebox.png
A client/galaxy/images/dat_points_table_brows_1.png
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A client/galaxy/images/delete_tag_icon_white.png
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A client/galaxy/images/footer_title_bg.png
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A client/galaxy/images/fugue/arrow-transition-270-bw.png
A client/galaxy/images/fugue/arrow-transition-bw.png
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A client/galaxy/images/fugue/magnifier-left.png
A client/galaxy/images/fugue/magnifier-zoom-out.png
A client/galaxy/images/fugue/magnifier-zoom.png
A client/galaxy/images/fugue/navigation.png
A client/galaxy/images/fugue/pencil-small.png
A client/galaxy/images/fugue/pencil.png
A client/galaxy/images/fugue/plus-button-bw.png
A client/galaxy/images/fugue/plus-button.png
A client/galaxy/images/fugue/plus-circle.png
A client/galaxy/images/fugue/sticky-note-text.png
A client/galaxy/images/fugue/tag--plus.png
A client/galaxy/images/fugue/tag-label.png
A client/galaxy/images/fugue/tags.png
A client/galaxy/images/fugue/toggle-bw.png
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A client/galaxy/images/fugue/ui-slider-050-bw.png
A client/galaxy/images/fugue/ui-slider-050.png
A client/galaxy/images/galaxy_icons.svg
A client/galaxy/images/galaxy_spinner.fla
A client/galaxy/images/gray_bg.png
A client/galaxy/images/hatch-023858.png
A client/galaxy/images/hgrad.png
A client/galaxy/images/hgrad_over.png
A client/galaxy/images/histogram.png
A client/galaxy/images/histogram2.png
A client/galaxy/images/history-buttons.png
A client/galaxy/images/history-states.png
A client/galaxy/images/info_icon.svg
A client/galaxy/images/info_large.png
A client/galaxy/images/info_message_icon.png
A client/galaxy/images/info_small.png
A client/galaxy/images/jstree/32px.png
A client/galaxy/images/jstree/40px.png
A client/galaxy/images/jstree/throbber.gif
A client/galaxy/images/kendall.png
A client/galaxy/images/largespinner.gif
A client/galaxy/images/layout_callout_top.png
A client/galaxy/images/light_gray_grid.gif
A client/galaxy/images/mag_glass.png
A client/galaxy/images/masthead_bg.png
A client/galaxy/images/menu_bg.png
A client/galaxy/images/mutation_visualization_example.png
A client/galaxy/images/ok_bg.png
A client/galaxy/images/ok_icon.svg
A client/galaxy/images/ok_large.png
A client/galaxy/images/ok_small.png
A client/galaxy/images/overview_arrows.png
A client/galaxy/images/panel_header_bg.png
A client/galaxy/images/pearson.png
A client/galaxy/images/popupmenu_callout_top.png
A client/galaxy/images/question-balloon.png
A client/galaxy/images/question-octagon-frame.png
A client/galaxy/images/resizable.png
A client/galaxy/images/scatter.png
A client/galaxy/images/scatterplot.png
A client/galaxy/images/select2-spinner.gif
A client/galaxy/images/select2.png
A client/galaxy/images/select2x2.png
A client/galaxy/images/silk/add.png
A client/galaxy/images/silk/book.png
A client/galaxy/images/silk/book_open.png
A client/galaxy/images/silk/chart_curve.png
A client/galaxy/images/silk/folder.png
A client/galaxy/images/silk/folder_page.png
A client/galaxy/images/silk/link.png
A client/galaxy/images/silk/link_break.png
A client/galaxy/images/silk/page_white.png
A client/galaxy/images/silk/page_white_compressed.png
A client/galaxy/images/silk/resultset_bottom.png
A client/galaxy/images/silk/resultset_next.png
A client/galaxy/images/silk/resultset_previous.png
A client/galaxy/images/solid_qual.png
A client/galaxy/images/spearman.png
A client/galaxy/images/sprite-fugue.png
A client/galaxy/images/sprite-history-buttons.png
A client/galaxy/images/sprite-history-states.png
A client/galaxy/images/star.gif
A client/galaxy/images/thumbtack_icon.png
A client/galaxy/images/thumbtack_icon_dark.png
A client/galaxy/images/tiny_arrow_left.png
A client/galaxy/images/tiny_arrow_right.png
A client/galaxy/images/tipsy.gif
A client/galaxy/images/tracks/block.png
A client/galaxy/images/tracks/close_btn.gif
A client/galaxy/images/tracks/diag_bg.gif
A client/galaxy/images/tracks/go_btn.gif
A client/galaxy/images/tracks/handle-left.gif
A client/galaxy/images/tracks/handle-right.gif
A client/galaxy/images/tracks/pan_left.gif
A client/galaxy/images/tracks/pan_right.gif
A client/galaxy/images/tracks/show_history.gif
A client/galaxy/images/tracks/zoom_in.gif
A client/galaxy/images/tracks/zoom_in_full.gif
A client/galaxy/images/tracks/zoom_out.gif
A client/galaxy/images/tracks/zoom_out_full.gif
A client/galaxy/images/visualization/draggable_horizontal.png
A client/galaxy/images/visualization/draggable_vertical.png
A client/galaxy/images/visualization/strand_left.png
A client/galaxy/images/visualization/strand_left_inv.png
A client/galaxy/images/visualization/strand_right.png
A client/galaxy/images/visualization/strand_right_inv.png
A client/galaxy/images/wait_icon.svg
A client/galaxy/images/wait_large.png
A client/galaxy/images/wait_small.png
A client/galaxy/images/warn_bg.png
A client/galaxy/images/warn_icon.svg
A client/galaxy/images/warn_large.png
A client/galaxy/images/warn_message_icon.png
A client/galaxy/images/warn_small.png
A client/galaxy/images/workflow_circle_drag.png
A client/galaxy/images/workflow_circle_green.png
A client/galaxy/images/workflow_circle_open.png
A client/galaxy/jsconfig.json
M client/galaxy/scripts/apps/admin.js
M client/galaxy/scripts/apps/analysis.js
M client/galaxy/scripts/apps/chart.js
M client/galaxy/scripts/apps/extended.js
M client/galaxy/scripts/apps/login.js
M client/galaxy/scripts/apps/panels/admin-panel.js
A client/galaxy/scripts/components/Alert.vue
A client/galaxy/scripts/components/admin/DataManager/DataManager.vue
A client/galaxy/scripts/components/admin/DataManager/DataManagerJob.vue
A client/galaxy/scripts/components/admin/DataManager/DataManagerJobs.vue
A client/galaxy/scripts/components/admin/DataManager/DataManagerRouter.vue
A client/galaxy/scripts/components/admin/DataManager/DataManagerTable.vue
A client/galaxy/scripts/components/admin/DataManager/DataManagerView.vue
M client/galaxy/scripts/galaxy.js
A client/galaxy/scripts/galaxy.monitor.js
M client/galaxy/scripts/layout/masthead.js
M client/galaxy/scripts/layout/menu.js
M client/galaxy/scripts/layout/modal.js
M client/galaxy/scripts/layout/panel.js
M client/galaxy/scripts/layout/router.js
M client/galaxy/scripts/layout/scratchbook.js
A client/galaxy/scripts/libs/jquery.custom.js
M client/galaxy/scripts/mvc/base-mvc.js
M client/galaxy/scripts/mvc/base/controlled-fetch-collection.js
M client/galaxy/scripts/mvc/collection/collection-model.js
M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js
M client/galaxy/scripts/mvc/dataset/data.js
M client/galaxy/scripts/mvc/history/history-contents.js
M client/galaxy/scripts/mvc/history/history-list.js
M client/galaxy/scripts/mvc/history/history-model.js
M client/galaxy/scripts/mvc/history/history-view-edit-current.js
M client/galaxy/scripts/mvc/history/history-view.js
M client/galaxy/scripts/mvc/history/job-states-model.js
M client/galaxy/scripts/mvc/history/multi-panel.js
M client/galaxy/scripts/mvc/rules/rule-definitions.js
M client/galaxy/scripts/mvc/tool/tools.js
M client/galaxy/scripts/mvc/tours.js
M client/galaxy/scripts/mvc/ui/ui-rules-edit.js
M client/galaxy/scripts/mvc/ui/ui-slider.js
M client/galaxy/scripts/mvc/user/user-model.js
M client/galaxy/scripts/mvc/workflow/workflow-node.js
M client/galaxy/scripts/mvc/workflow/workflow-view.js
M client/galaxy/scripts/nls/zh/locale.js
R client/galaxy/scripts/onload.js
A client/galaxy/scripts/onload/index.js
A client/galaxy/scripts/onload/loadConfig.js
M client/galaxy/scripts/polyfills.js
M client/galaxy/scripts/qunit/assets/base.css
M client/galaxy/scripts/qunit/tests/galaxy_app_base_tests.js
M client/galaxy/scripts/qunit/tests/page_tests.js
M client/galaxy/scripts/reports/run_stats.js
A client/galaxy/scripts/sample.test.js
A client/galaxy/scripts/style.js
M client/galaxy/scripts/ui/editable-text.js
M client/galaxy/scripts/ui/fa-icon-button.js
A client/galaxy/scripts/unitTestBundle.js
M client/galaxy/scripts/utils/config.js
A client/galaxy/scripts/utils/installMonitor.js
A client/galaxy/scripts/utils/mock.js
A client/galaxy/scripts/utils/serverPath.js
M client/galaxy/scripts/viz/phyloviz.js
M client/galaxy/scripts/viz/sweepster.js
M client/galaxy/scripts/viz/trackster.js
M client/galaxy/scripts/viz/trackster/tracks.js
M client/galaxy/scripts/viz/visualization.js
M client/galaxy/style/scss/autocomplete_tagging.scss
M client/galaxy/style/scss/base.scss
M client/galaxy/style/scss/collection.scss
M client/galaxy/style/scss/history.scss
M client/galaxy/style/scss/iconic_stroke.scss
A client/galaxy/style/scss/jquery.rating.scss
M client/galaxy/style/scss/jstree.scss
M client/galaxy/style/scss/list-item.scss
M client/galaxy/style/scss/select2.scss
A client/galaxy/style/scss/sprite-fugue.scss
A client/galaxy/style/scss/sprite-history-buttons.scss
A client/galaxy/style/scss/sprite-history-states.scss
M client/galaxy/style/scss/trackster.scss
M client/galaxy/style/scss/ui.scss
R client/galaxy/style/source_material/circle.py
R client/galaxy/style/source_material/error_icon.svg
R client/galaxy/style/source_material/galaxy_icons.svg
R client/galaxy/style/source_material/galaxy_spinner.fla
R client/galaxy/style/source_material/info_icon.svg
R client/galaxy/style/source_material/ok_icon.svg
R client/galaxy/style/source_material/wait_icon.svg
R client/galaxy/style/source_material/warn_icon.svg
M client/gulpfile.js
R client/karma.config.js
A client/karma/karma.config.base.js
A client/karma/karma.config.mocha.js
A client/karma/karma.config.qunit.js
A client/karma/webpack.config.qunit.js
A client/karma/webpack.config.unittest.js
M client/package.json
M client/webpack.config.js
M client/yarn.lock
A config/container_resolvers_conf.xml.sample
M config/containers_conf.yml.sample
M config/datatypes_conf.xml.sample
M config/galaxy.yml.sample
M config/migrated_tools_conf.xml.sample
M config/plugins/interactive_environments/bam_iobio/templates/bam_iobio.mako
M config/plugins/interactive_environments/hicbrowser/templates/hicbrowser.mako
M config/plugins/interactive_environments/neo/templates/neo.mako
M config/plugins/visualizations/common/templates/chart_entry_point.mako
M config/plugins/visualizations/scatterplot/package.json
M config/plugins/visualizations/scatterplot/src/scatterplot.js
M config/plugins/visualizations/scatterplot/static/scatterplot.css
M config/plugins/visualizations/scatterplot/static/scatterplot.js
M config/plugins/visualizations/scatterplot/templates/scatterplot.mako
M config/plugins/webhooks/demo/tour_generator/config.yml
A config/plugins/webhooks/demo/tour_generator/package.json
M config/plugins/webhooks/demo/tour_generator/script.js
A config/plugins/webhooks/demo/tour_generator/tour_generator.js
M config/shed_tool_conf.xml.sample
M config/tool_conf.xml.main
M config/tool_conf.xml.sample
M doc/source/admin/conda_faq.rst
M doc/source/admin/dependency_resolvers.rst
M doc/source/admin/framework_dependencies.rst
M doc/source/admin/galaxy_options.rst
M doc/source/admin/jobs.md
M doc/source/admin/scaling.md
M doc/source/admin/special_topics/bug_reports.rst
M doc/source/admin/special_topics/interactive_environments.rst
M doc/source/admin/tool_panel.rst
M doc/source/dev/faq.rst
M doc/source/dev/index.rst
M doc/source/dev/interactive_environments.rst
A doc/source/releases/18.09.rst
A doc/source/releases/18.09_announce.rst
A doc/source/releases/19.01_announce.rst
M doc/source/releases/index.rst
M lib/galaxy/actions/library.py
M lib/galaxy/authnz/managers.py
M lib/galaxy/authnz/psa_authnz.py
M lib/galaxy/config.py
M lib/galaxy/containers/docker.py
M lib/galaxy/containers/docker_model.py
M lib/galaxy/containers/docker_swarm.py
M lib/galaxy/datatypes/assembly.py
M lib/galaxy/datatypes/binary.py
M lib/galaxy/datatypes/blast.py
A lib/galaxy/datatypes/converters/tar_to_directory.xml
M lib/galaxy/datatypes/data.py
M lib/galaxy/datatypes/genetics.py
M lib/galaxy/datatypes/interval.py
A lib/galaxy/datatypes/isa.py
M lib/galaxy/datatypes/molecules.py
M lib/galaxy/datatypes/mothur.py
M lib/galaxy/datatypes/neo4j.py
M lib/galaxy/datatypes/phylip.py
M lib/galaxy/datatypes/proteomics.py
M lib/galaxy/datatypes/registry.py
M lib/galaxy/datatypes/sequence.py
M lib/galaxy/datatypes/sniff.py
M lib/galaxy/datatypes/tabular.py
A lib/galaxy/datatypes/test/0.txt
M lib/galaxy/datatypes/test/1.afg
M lib/galaxy/datatypes/test/1.bcf_uncompressed
A lib/galaxy/datatypes/test/1.excel.xls
M lib/galaxy/datatypes/test/1.fastq
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M lib/galaxy/datatypes/test/1.fastqsanger
M lib/galaxy/datatypes/test/1.fastqsolexa
A lib/galaxy/datatypes/test/1.json
M lib/galaxy/datatypes/test/1.owl
A lib/galaxy/datatypes/test/1.qname_sorted.bam
M lib/galaxy/datatypes/test/1.stockholm
R lib/galaxy/datatypes/test/1.vcf.gz
A lib/galaxy/datatypes/test/1.vcf_bgzip
R lib/galaxy/datatypes/test/1.xls
M lib/galaxy/datatypes/test/2.fastq
R lib/galaxy/datatypes/test/2.fastqsanger
M lib/galaxy/datatypes/test/2.fastqsolexa
R lib/galaxy/datatypes/test/2.shuffled.bam
A lib/galaxy/datatypes/test/2.shuffled.unsorted.bam
M lib/galaxy/datatypes/test/2.txt
A lib/galaxy/datatypes/test/3.fastq
M lib/galaxy/datatypes/test/3.txt
M lib/galaxy/datatypes/test/454Score.pdf
A lib/galaxy/datatypes/test/5e5z.pqr
R lib/galaxy/datatypes/test/Acanium.hmm
A lib/galaxy/datatypes/test/Acanium.snaphmm
M lib/galaxy/datatypes/test/alignment.lav
R lib/galaxy/datatypes/test/biom2_sparse_otu_table_hdf5.biom
A lib/galaxy/datatypes/test/biom2_sparse_otu_table_hdf5.biom2
A lib/galaxy/datatypes/test/diamond.rma6
A lib/galaxy/datatypes/test/gff.gff3
R lib/galaxy/datatypes/test/gff_version_3.gff
A lib/galaxy/datatypes/test/interv1.bed
R lib/galaxy/datatypes/test/interval1.bed
M lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.filter
R lib/galaxy/datatypes/test/sequence.qual
M lib/galaxy/datatypes/test/sequence.qual454
M lib/galaxy/datatypes/test/sequence.qualsolid
A lib/galaxy/datatypes/test/tblastn_four_human_vs_rhodopsin.blastxml
R lib/galaxy/datatypes/test/tblastn_four_human_vs_rhodopsin.xml
R lib/galaxy/datatypes/test/test.CEL
A lib/galaxy/datatypes/test/test.cel
R lib/galaxy/datatypes/test/test.idpDB
A lib/galaxy/datatypes/test/test.idpdb
R lib/galaxy/datatypes/test/test_ensembl.tab
A lib/galaxy/datatypes/test/test_ensembl.tabular
M lib/galaxy/datatypes/test/test_tab.bed
M lib/galaxy/datatypes/test/ucsc.customtrack
M lib/galaxy/datatypes/test/wiggle.wig
M lib/galaxy/datatypes/text.py
M lib/galaxy/datatypes/upload_util.py
M lib/galaxy/datatypes/util/gff_util.py
M lib/galaxy/datatypes/xml.py
M lib/galaxy/dependencies/conda-file.sh
M lib/galaxy/dependencies/pipfiles/default/Pipfile
M lib/galaxy/dependencies/pipfiles/default/pinned-dev-requirements.txt
M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt
M lib/galaxy/dependencies/pipfiles/flake8/pinned-requirements.txt
M lib/galaxy/dependencies/pipfiles/update.sh
M lib/galaxy/exceptions/__init__.py
M lib/galaxy/exceptions/error_codes.json
M lib/galaxy/jobs/__init__.py
M lib/galaxy/jobs/dynamic_tool_destination.py
M lib/galaxy/jobs/handler.py
M lib/galaxy/jobs/metrics/instrumenters/env.py
M lib/galaxy/jobs/runners/__init__.py
M lib/galaxy/jobs/runners/drmaa.py
M lib/galaxy/jobs/runners/kubernetes.py
M lib/galaxy/jobs/runners/util/cli/job/slurm_torque.py
M lib/galaxy/jobs/runners/util/cli/shell/local.py
M lib/galaxy/jobs/runners/util/cli/shell/rsh.py
M lib/galaxy/managers/base.py
M lib/galaxy/managers/cloud.py
M lib/galaxy/managers/collections.py
M lib/galaxy/managers/context.py
M lib/galaxy/managers/datasets.py
M lib/galaxy/managers/folders.py
M lib/galaxy/managers/libraries.py
M lib/galaxy/managers/library_datasets.py
M lib/galaxy/managers/rbac_secured.py
M lib/galaxy/managers/sharable.py
M lib/galaxy/managers/tags.py
M lib/galaxy/managers/users.py
M lib/galaxy/managers/workflows.py
M lib/galaxy/model/__init__.py
M lib/galaxy/model/custom_types.py
M lib/galaxy/model/mapping.py
M lib/galaxy/model/metadata.py
M lib/galaxy/model/migrate/versions/0141_add_oidc_tables.py
M lib/galaxy/model/migrate/versions/0142_change_numeric_metric_precision.py
M lib/galaxy/model/migrate/versions/0143_add_cloudauthz_tables.py
A lib/galaxy/model/migrate/versions/0144_add_cleanup_event_user_table.py
M lib/galaxy/model/search.py
M lib/galaxy/objectstore/cloud.py
M lib/galaxy/security/__init__.py
M lib/galaxy/security/validate_user_input.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/actions/__init__.py
M lib/galaxy/tools/actions/history_imp_exp.py
M lib/galaxy/tools/actions/metadata.py
M lib/galaxy/tools/actions/model_operations.py
M lib/galaxy/tools/actions/upload.py
M lib/galaxy/tools/actions/upload_common.py
M lib/galaxy/tools/cwl/cwltool_deps.py
M lib/galaxy/tools/cwl/parser.py
M lib/galaxy/tools/cwl/schema.py
M lib/galaxy/tools/cwl/util.py
M lib/galaxy/tools/data/__init__.py
M lib/galaxy/tools/deps/brew_exts.py
M lib/galaxy/tools/deps/conda_util.py
M lib/galaxy/tools/deps/containers.py
M lib/galaxy/tools/deps/docker_util.py
M lib/galaxy/tools/deps/mulled/mulled_build.py
M lib/galaxy/tools/deps/mulled/mulled_build_channel.py
M lib/galaxy/tools/deps/resolvers/conda.py
M lib/galaxy/tools/deps/views.py
M lib/galaxy/tools/error_reports/plugins/biostars.py
M lib/galaxy/tools/error_reports/plugins/email.py
M lib/galaxy/tools/error_reports/plugins/github.py
M lib/galaxy/tools/error_reports/plugins/influxdb.py
M lib/galaxy/tools/error_reports/plugins/json.py
M lib/galaxy/tools/error_reports/plugins/sentry.py
M lib/galaxy/tools/execute.py
M lib/galaxy/tools/lint.py
M lib/galaxy/tools/linters/stdio.py
M lib/galaxy/tools/linters/tests.py
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/tools/parameters/dynamic_options.py
M lib/galaxy/tools/parameters/grouping.py
M lib/galaxy/tools/parameters/history_query.py
M lib/galaxy/tools/parser/cwl.py
M lib/galaxy/tools/parser/xml.py
M lib/galaxy/tools/tag_collection_from_file.xml
M lib/galaxy/tools/toolbox/base.py
M lib/galaxy/tools/toolbox/filters/examples.py.sample
M lib/galaxy/tools/verify/asserts/__init__.py
M lib/galaxy/tools/verify/interactor.py
M lib/galaxy/tools/verify/test_data.py
M lib/galaxy/tools/xsd/galaxy.xsd
M lib/galaxy/util/__init__.py
M lib/galaxy/util/checkers.py
M lib/galaxy/util/compression_utils.py
M lib/galaxy/util/inflection.py
M lib/galaxy/util/json.py
M lib/galaxy/util/monitors.py
M lib/galaxy/util/pastescript/serve.py
M lib/galaxy/visualization/data_providers/genome.py
M lib/galaxy/visualization/data_providers/phyloviz/newickparser.py
M lib/galaxy/web/base/controller.py
M lib/galaxy/web/framework/decorators.py
M lib/galaxy/web/framework/middleware/batch.py
M lib/galaxy/webapps/galaxy/api/cloud.py
M lib/galaxy/webapps/galaxy/api/cloudauthz.py
M lib/galaxy/webapps/galaxy/api/configuration.py
M lib/galaxy/webapps/galaxy/api/datasets.py
M lib/galaxy/webapps/galaxy/api/folder_contents.py
M lib/galaxy/webapps/galaxy/api/folders.py
M lib/galaxy/webapps/galaxy/api/forms.py
M lib/galaxy/webapps/galaxy/api/groups.py
M lib/galaxy/webapps/galaxy/api/history_contents.py
M lib/galaxy/webapps/galaxy/api/jobs.py
M lib/galaxy/webapps/galaxy/api/libraries.py
M lib/galaxy/webapps/galaxy/api/library_contents.py
M lib/galaxy/webapps/galaxy/api/library_datasets.py
M lib/galaxy/webapps/galaxy/api/pages.py
M lib/galaxy/webapps/galaxy/api/roles.py
M lib/galaxy/webapps/galaxy/api/search.py
M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py
M lib/galaxy/webapps/galaxy/api/tools.py
M lib/galaxy/webapps/galaxy/api/uploads.py
M lib/galaxy/webapps/galaxy/api/users.py
M lib/galaxy/webapps/galaxy/api/workflows.py
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/galaxy/config_schema.yml
M lib/galaxy/webapps/galaxy/controllers/admin.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/forms.py
M lib/galaxy/webapps/galaxy/controllers/history.py
M lib/galaxy/webapps/galaxy/controllers/page.py
M lib/galaxy/webapps/galaxy/controllers/tool_runner.py
M lib/galaxy/webapps/galaxy/controllers/user.py
M lib/galaxy/webapps/tool_shed/api/categories.py
M lib/galaxy/webapps/tool_shed/api/groups.py
M lib/galaxy/webapps/tool_shed/api/repositories.py
M lib/galaxy/webapps/tool_shed/api/tools.py
M lib/galaxy/webapps/tool_shed/controllers/repository.py
M lib/galaxy/webapps/tool_shed/controllers/repository_review.py
M lib/galaxy/webapps/tool_shed/controllers/upload.py
M lib/galaxy/webapps/tool_shed/controllers/user.py
M lib/galaxy/workflow/modules.py
M lib/galaxy/workflow/resources/example.py.sample
M lib/galaxy/workflow/run.py
M lib/galaxy/workflow/run_request.py
M lib/tool_shed/capsule/capsule_manager.py
M lib/tool_shed/galaxy_install/migrate/check.py
M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py
M lib/tool_shed/galaxy_install/tools/data_manager.py
M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py
M lib/tool_shed/managers/groups.py
M lib/tool_shed/metadata/metadata_generator.py
M lib/tool_shed/tools/tool_validator.py
M lib/tool_shed/util/commit_util.py
M lib/tool_shed/util/common_util.py
M lib/tool_shed/util/hg_util.py
M lib/tool_shed/util/readme_util.py
M lib/tool_shed/util/repository_util.py
M lib/tool_shed/util/workflow_util.py
M lib/tool_shed/util/xml_util.py
M run.sh
M run_tests.sh
M scripts/bootstrap_history.py
M scripts/check_python.py
M scripts/cleanup_datasets/pgcleanup.py
M scripts/get_uwsgi_args.py
M scripts/runtime_stats.py
M scripts/summarize_timings.py
M scripts/tool_shed/api/reset_metadata_on_repositories.py
M scripts/tool_shed/bootstrap_tool_shed/create_user_with_api_key.py
M scripts/transfer.py
M setup.cfg
R static/GruntFile.js
R static/images/Armitagep_manhattan.png
R static/images/Armitagep_qqplot.png
R static/images/add_icon.png
R static/images/add_icon_dark.png
R static/images/aggregate_history1.png
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R static/images/bar_chart.png
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A static/images/fugue
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A static/images/visualization
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M static/style/base.css
A static/style/blue/base.css
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M static/style/blue/trackster.css
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M static/welcome.html.sample
M templates/admin/jobs.mako
M templates/admin/review_tool_migration_stages.mako
M templates/admin/tool_shed_repository/browse_repository.mako
M templates/admin/tool_shed_repository/browse_tool_dependency.mako
M templates/admin/tool_shed_repository/deactivate_or_uninstall_repository.mako
M templates/admin/tool_shed_repository/install_tool_dependencies_with_update.mako
M templates/admin/tool_shed_repository/manage_repository.mako
M templates/admin/tool_shed_repository/manage_repository_tool_dependencies.mako
M templates/admin/tool_shed_repository/monitor_repository_installation.mako
M templates/admin/tool_shed_repository/purge_repository_confirmation.mako
M templates/admin/tool_shed_repository/reselect_tool_panel_section.mako
M templates/admin/tool_shed_repository/reset_metadata_on_selected_repositories.mako
M templates/admin/tool_shed_repository/select_tool_panel_section.mako
M templates/admin/tool_shed_repository/uninstall_tool_dependencies.mako
M templates/admin/tool_shed_repository/view_tool_metadata.mako
M templates/admin/tool_shed_repository/view_workflow.mako
M templates/base.mako
M templates/base/base_panels.mako
M templates/display_base.mako
M templates/galaxy_client_app.mako
M templates/ind_share_base.mako
M templates/js-app.mako
M templates/legacy/grid_base.mako
M templates/message.mako
M templates/show_params.mako
M templates/user/info.mako
M templates/user/register.mako
M templates/webapps/galaxy/admin/manage_dependencies.mako
M templates/webapps/galaxy/admin/sanitize_whitelist.mako
M templates/webapps/galaxy/admin/tool_sheds.mako
M templates/webapps/galaxy/admin/view_display_applications.mako
R templates/webapps/galaxy/data_manager/index.mako
R templates/webapps/galaxy/data_manager/manage_data_manager.mako
R templates/webapps/galaxy/data_manager/manage_data_table.mako
R templates/webapps/galaxy/data_manager/view_job.mako
M templates/webapps/galaxy/galaxy.masthead.mako
M templates/webapps/galaxy/galaxy.panels.mako
M templates/webapps/galaxy/history/display.mako
M templates/webapps/galaxy/history/share.mako
M templates/webapps/galaxy/visualization/display.mako
M templates/webapps/galaxy/visualization/display_in_frame.mako
M templates/webapps/galaxy/visualization/gie.mako
M templates/webapps/galaxy/visualization/sweepster.mako
M templates/webapps/galaxy/workflow/display.mako
M templates/webapps/galaxy/workflow/editor.mako
M templates/webapps/galaxy/workflow/sharing.mako
M templates/webapps/reports/run_stats.mako
M templates/webapps/tool_shed/common/repository_actions_menu.mako
M templates/webapps/tool_shed/common/reset_metadata_on_selected_repositories.mako
M templates/webapps/tool_shed/repository/browse_repository.mako
M templates/webapps/tool_shed/repository/common.mako
M templates/webapps/tool_shed/repository/manage_repository.mako
M templates/webapps/tool_shed/repository/preview_tools_in_changeset.mako
M templates/webapps/tool_shed/repository/rate_repository.mako
M templates/webapps/tool_shed/repository/upload.mako
M templates/webapps/tool_shed/repository/view_changelog.mako
M templates/webapps/tool_shed/repository/view_changeset.mako
M templates/webapps/tool_shed/repository/view_repository.mako
M templates/webapps/tool_shed/repository_review/browse_review.mako
M templates/webapps/tool_shed/repository_review/edit_review.mako
M templates/webapps/tool_shed/repository_review/reviews_of_changeset_revision.mako
M templates/webapps/tool_shed/repository_review/reviews_of_repository.mako
M templates/webapps/tool_shed/repository_review/select_previous_review.mako
M templates/webapps/tool_shed/role/role.mako
M templates/webapps/tool_shed/user/username.mako
A test-data/MTBLS6.zip
A test-data/safetar_with_symlink.tar
A test-data/testdir.tar
A test-data/unsafe.tar
A test-data/unsafe.zip
A test-data/unsafe_relative_symlink.tar
M test/api/test_api_batch.py
M test/api/test_dataset_collections.py
M test/api/test_histories.py
M test/api/test_jobs.py
M test/api/test_pages.py
M test/api/test_tools.py
M test/api/test_tools_upload.py
M test/api/test_workflows.py
M test/api/test_workflows_from_yaml.py
M test/base/driver_util.py
M test/base/populators.py
A test/base/ssh_util.py
M test/base/workflow_fixtures.py
R test/base/workflows_format_2/README.txt
R test/base/workflows_format_2/__init__.py
R test/base/workflows_format_2/converter.py
R test/base/workflows_format_2/interface.py
R test/base/workflows_format_2/main.py
M test/functional/tools/disambiguate_cond.xml
A test/functional/tools/for_workflows/mapper_two.xml
M test/functional/tools/job_environment_default.xml
M test/functional/tools/job_environment_default_legacy.xml
M test/functional/tools/job_environment_explicit_shared_home.xml
M test/functional/tools/output_filter.xml
A test/functional/tools/remove_value.xml
M test/functional/tools/sample_datatypes_conf.xml
M test/functional/tools/samples_tool_conf.xml
M test/functional/webhooks/phdcomics/__init__.py
M test/galaxy_selenium/navigates_galaxy.py
M test/galaxy_selenium/navigation.yml
A test/integration/test_cli_runners.py
A test/integration/test_datatype_upload.py
M test/integration/test_job_environments.py
M test/integration/test_upload_configuration_options.py
M test/manual/workflows_scaling.py
M test/selenium_tests/framework.py
M test/selenium_tests/test_admin_app.py
M test/selenium_tests/test_library_contents.py
M test/selenium_tests/test_uploads.py
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M test/shed_functional/functional/test_1460_data_managers.py
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M test/unit/datatypes/test_vcf.py
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M test/unit/jobs/test_job_wrapper.py
A test/unit/test_compression_util.py
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M test/unit/test_remote_shell.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_evaluation.py
M test/unit/tools/test_toolbox_filters.py
M test/unit/web/framework/test_webapp.py
M test/unit/workflows/test_extract_summary.py
M test/unit/workflows/test_workflow_progress.py
A tools/cloud/send.py
A tools/cloud/send.xml
M tools/data_source/upload.py
M tools/data_source/upload.xml
M tools/extract/extract_genomic_dna.py
M tools/filters/convert_characters.py
M tools/filters/grep.py
M tools/filters/uniq.py
M tools/stats/filtering.py
M tools/stats/gsummary.py
Log Message:
-----------
Merge remote-tracking branch 'galaxyproject/dev' into dev
Commit: d5b46e99d234a615d06b1376bf57e1ada49154c9
https://github.com/galaxyproject/galaxy/commit/d5b46e99d234a615d06b1376bf57…
Author: Jim Johnson <jj(a)umn.edu>
Date: 2018-11-07 (Wed, 07 Nov 2018)
Changed paths:
M config/datatypes_conf.xml.sample
M lib/galaxy/datatypes/sequence.py
A lib/galaxy/datatypes/test/sequence.fastg
Log Message:
-----------
datatype_fastg
FASTG is a format for faithfully representing genome assemblies in the
face of allelic polymorphism and assembly uncertainty.
http://fastg.sourceforge.net/FASTG_Spec_v1.00.pdf
This format can be an output for metagenomics applications metapades
and megahit. It is a required input for Graph2Pro-var application that
generates putative protein sequences for the variant assemblies
described by the FASTG format file.
Commit: a3badf62478f975bb0f9b1ca339d14f74116c4be
https://github.com/galaxyproject/galaxy/commit/a3badf62478f975bb0f9b1ca339d…
Author: Marius van den Beek <m.vandenbeek(a)gmail.com>
Date: 2018-11-08 (Thu, 08 Nov 2018)
Changed paths:
M config/datatypes_conf.xml.sample
Log Message:
-----------
Update config/datatypes_conf.xml.sample
Co-Authored-By: jj-umn <jj(a)umn.edu>
Commit: 8dc824e4831aca566d65e3f488cd8f0e8224c014
https://github.com/galaxyproject/galaxy/commit/8dc824e4831aca566d65e3f488cd…
Author: Jim Johnson <jj(a)umn.edu>
Date: 2018-11-08 (Thu, 08 Nov 2018)
Changed paths:
M lib/galaxy/datatypes/sequence.py
Log Message:
-----------
Update sequence.py
Fix typo for properties.
Commit: 4c71bb43a36ad173718c2f89b4fabaa632e11515
https://github.com/galaxyproject/galaxy/commit/4c71bb43a36ad173718c2f89b4fa…
Author: Jim Johnson <jj(a)umn.edu>
Date: 2018-11-08 (Thu, 08 Nov 2018)
Changed paths:
M lib/galaxy/datatypes/sequence.py
Log Message:
-----------
Update sequence.py
remove extraneous line that was pasted in.
Commit: f21a3dd81572d341ae28e2bd62512fb849e6fecc
https://github.com/galaxyproject/galaxy/commit/f21a3dd81572d341ae28e2bd6251…
Author: Jim Johnson <jj(a)umn.edu>
Date: 2018-11-08 (Thu, 08 Nov 2018)
Changed paths:
M lib/galaxy/datatypes/sequence.py
Log Message:
-----------
Update sequence.py
Line after header must not be empty or start with '>'
Commit: e5c5cd284d6ed927667f330bfd579092f281e5d6
https://github.com/galaxyproject/galaxy/commit/e5c5cd284d6ed927667f330bfd57…
Author: Jim Johnson <jj(a)umn.edu>
Date: 2018-11-09 (Fri, 09 Nov 2018)
Changed paths:
M lib/galaxy/datatypes/sequence.py
Log Message:
-----------
Update sequence.py
Fix a couple of typos.
Commit: cfacaae8b50c9650e4d365063a177fbda9c0895c
https://github.com/galaxyproject/galaxy/commit/cfacaae8b50c9650e4d365063a17…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2018-11-09 (Fri, 09 Nov 2018)
Changed paths:
M config/datatypes_conf.xml.sample
M lib/galaxy/datatypes/sequence.py
A lib/galaxy/datatypes/test/sequence.fastg
Log Message:
-----------
Merge pull request #6987 from jj-umn/dev
datatype_fastg
Compare: https://github.com/galaxyproject/galaxy/compare/3ed0ce862bf9...cfacaae8b50c
**NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/
Functionality will be removed from GitHub.com on January 31st, 2019.
1
0
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 9f8c29520df53ca42e241d69718ddd2e1d37a987
https://github.com/galaxyproject/galaxy/commit/9f8c29520df53ca42e241d69718d…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-11-07 (Wed, 07 Nov 2018)
Changed paths:
M doc/source/admin/framework_dependencies.rst
M scripts/common_startup.sh
Log Message:
-----------
Use virtualenv when conda is on PATH
This uses our proper pinned requirements and is sginificantly easier
to set up and maintain.
Commit: 3ed0ce862bf9397aefa3b3d58552e2013fcd098c
https://github.com/galaxyproject/galaxy/commit/3ed0ce862bf9397aefa3b3d58552…
Author: Dannon <dannon.baker(a)gmail.com>
Date: 2018-11-09 (Fri, 09 Nov 2018)
Changed paths:
M doc/source/admin/framework_dependencies.rst
M scripts/common_startup.sh
Log Message:
-----------
Merge pull request #6975 from mvdbeek/conda_run_sh
Use virtualenv when conda is on PATH
Compare: https://github.com/galaxyproject/galaxy/compare/5f2c785d66f7...3ed0ce862bf9
**NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/
Functionality will be removed from GitHub.com on January 31st, 2019.
1
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[galaxyproject/galaxy] ff4232: Use ``detect_errors="exit_code"`` in ``__SET_METAD...
by GitHub 09 Nov '18
by GitHub 09 Nov '18
09 Nov '18
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: ff4232b8b65b91969ae09f315b2955d44fcc4348
https://github.com/galaxyproject/galaxy/commit/ff4232b8b65b91969ae09f315b29…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2018-11-08 (Thu, 08 Nov 2018)
Changed paths:
M lib/galaxy/datatypes/set_metadata_tool.xml
Log Message:
-----------
Use ``detect_errors="exit_code"`` in ``__SET_METADATA__`` tool
Commit: 5f2c785d66f76467dff23c6cc2edfcf9785e0bdd
https://github.com/galaxyproject/galaxy/commit/5f2c785d66f76467dff23c6cc2ed…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2018-11-09 (Fri, 09 Nov 2018)
Changed paths:
M lib/galaxy/datatypes/set_metadata_tool.xml
Log Message:
-----------
Merge pull request #6989 from nsoranzo/set_metadata_detect_errors
Use ``detect_errors="exit_code"`` in ``__SET_METADATA__`` tool
Compare: https://github.com/galaxyproject/galaxy/compare/4960e08d2ab2...5f2c785d66f7
**NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/
Functionality will be removed from GitHub.com on January 31st, 2019.
1
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09 Nov '18
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 540636a241d61ae504037896b1e8071f83c35431
https://github.com/galaxyproject/galaxy/commit/540636a241d61ae504037896b1e8…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2018-09-12 (Wed, 12 Sep 2018)
Changed paths:
M client/galaxy/scripts/layout/data.js
Log Message:
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Add utility function to create history entries
Commit: fca7bbc903932ed7330a319a2a695fd88e003fca
https://github.com/galaxyproject/galaxy/commit/fca7bbc903932ed7330a319a2a69…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2018-09-18 (Tue, 18 Sep 2018)
Changed paths:
M client/galaxy/scripts/layout/data.js
Log Message:
-----------
Use auto as default extension type
Commit: 8cf85232b489d16fe54de43b33d5b2e2928526ed
https://github.com/galaxyproject/galaxy/commit/8cf85232b489d16fe54de43b33d5…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2018-09-22 (Sat, 22 Sep 2018)
Changed paths:
M client/galaxy/scripts/layout/data.js
Log Message:
-----------
Use ? as default genome
Commit: 4960e08d2ab285e8d02f8498d773a393198a7e01
https://github.com/galaxyproject/galaxy/commit/4960e08d2ab285e8d02f8498d773…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2018-11-09 (Fri, 09 Nov 2018)
Changed paths:
M client/galaxy/scripts/layout/data.js
Log Message:
-----------
Merge pull request #6693 from guerler/create_history_entry
Add utility function to create history entries
Compare: https://github.com/galaxyproject/galaxy/compare/eeca6f37a3b1...4960e08d2ab2
**NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/
Functionality will be removed from GitHub.com on January 31st, 2019.
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