November 2017 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 4c6fdf: Remove invalid user preferences beta (no longer a ...
by GitHub 08 Nov '17

08 Nov '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4c6fdf660cb887ef3fae9e8582f791d0ded82326 https://github.com/galaxyproject/galaxy/commit/4c6fdf660cb887ef3fae9e8582f7… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-11-08 (Wed, 08 Nov 2017) Changed paths: M config/galaxy.ini.sample Log Message: ----------- Remove invalid user preferences beta (no longer a beta, always enabled) Commit: 03dccbae935da2d6a254a59a679ffff3357ec301 https://github.com/galaxyproject/galaxy/commit/03dccbae935da2d6a254a59a679f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-11-08 (Wed, 08 Nov 2017) Changed paths: M config/galaxy.ini.sample Log Message: ----------- Remove no-longer-beta feature toggle for run_workflow_toolform_upgrade Commit: abd9dff404bd82f458f91e13b3f20111daf82914 https://github.com/galaxyproject/galaxy/commit/abd9dff404bd82f458f91e13b3f2… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-11-08 (Wed, 08 Nov 2017) Changed paths: M config/galaxy.ini.sample Log Message: ----------- Remove no-longer-valid feature toggle for enable_sequencer_communication Commit: a50d56e95221c44c47b33136042242a17a27a394 https://github.com/galaxyproject/galaxy/commit/a50d56e95221c44c47b331360422… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-11-08 (Wed, 08 Nov 2017) Changed paths: M config/galaxy.ini.sample Log Message: ----------- Various spelling issues in galaxy.ini.sample. Commit: 98d349332ffdc3a5ec07df2c08ffc5a0f5c972a8 https://github.com/galaxyproject/galaxy/commit/98d349332ffdc3a5ec07df2c08ff… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-11-08 (Wed, 08 Nov 2017) Changed paths: M test/unit/config/1607_root_filters/config/galaxy.ini M test/unit/config/1607_root_samples/config/galaxy.ini Log Message: ----------- Remove from unit test samples, as well. Commit: f50db592ccd055ad46fc2b163b2e8b181e79a914 https://github.com/galaxyproject/galaxy/commit/f50db592ccd055ad46fc2b163b2e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-11-08 (Wed, 08 Nov 2017) Changed paths: M config/galaxy.ini.sample Log Message: ----------- Blank line Commit: 963cfd1a3faabc97c3fa4d916da3277938b68821 https://github.com/galaxyproject/galaxy/commit/963cfd1a3faabc97c3fa4d916da3… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-11-08 (Wed, 08 Nov 2017) Changed paths: M config/galaxy.ini.sample M test/unit/config/1607_root_filters/config/galaxy.ini M test/unit/config/1607_root_samples/config/galaxy.ini Log Message: ----------- Merge pull request #4957 from dannon/inisamplecleanup Remove invalid user preferences beta (no longer a beta, always enabled) Compare: https://github.com/galaxyproject/galaxy/compare/92c6f36e556f...963cfd1a3faa

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[galaxyproject/galaxy] bdc3a0: Fix visualization import link in success message
by GitHub 08 Nov '17

08 Nov '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: bdc3a0be5d1b4aeee3e6fb8437a0219c85515ba1 https://github.com/galaxyproject/galaxy/commit/bdc3a0be5d1b4aeee3e6fb8437a0… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-11-07 (Tue, 07 Nov 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/visualization.py Log Message: ----------- Fix visualization import link in success message Commit: e5463eee8a0dfe7cfbee54d4a1aa7b6dd1e9eb80 https://github.com/galaxyproject/galaxy/commit/e5463eee8a0dfe7cfbee54d4a1aa… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-11-08 (Wed, 08 Nov 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/visualization.py Log Message: ----------- Rewrite route without controller Commit: 92c6f36e556f60bb98ca0eea49b67bdd11f65179 https://github.com/galaxyproject/galaxy/commit/92c6f36e556f60bb98ca0eea49b6… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-11-08 (Wed, 08 Nov 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/visualization.py Log Message: ----------- Merge pull request #4952 from guerler/fix_visualization_link Fix visualization link in import success message Compare: https://github.com/galaxyproject/galaxy/compare/3b4b97a2edd4...92c6f36e556f

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[galaxyproject/galaxy] f3e06c: iqtree and mldist datatypes
by GitHub 08 Nov '17

08 Nov '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f3e06cce9aaa34233d406b17f38cab425a4e0099 https://github.com/galaxyproject/galaxy/commit/f3e06cce9aaa34233d406b17f38c… Author: Mehmet Tekman <m.tekman(a)ucl.ac.uk> Date: 2017-10-27 (Fri, 27 Oct 2017) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/data.py A lib/galaxy/datatypes/test/example.iqtree A lib/galaxy/datatypes/test/example.mldist Log Message: ----------- iqtree and mldist datatypes Commit: b8ce7b516f1a0d66c1ded78b0c93863ad801356c https://github.com/galaxyproject/galaxy/commit/b8ce7b516f1a0d66c1ded78b0c93… Author: Mehmet Tekman <m.tekman(a)ucl.ac.uk> Date: 2017-10-28 (Sat, 28 Oct 2017) Changed paths: M lib/galaxy/datatypes/data.py Log Message: ----------- added binary file checkers and line count limits Commit: f993aceee18a44c262d7b2d93345ced17b93cce6 https://github.com/galaxyproject/galaxy/commit/f993aceee18a44c262d7b2d93345… Author: Mehmet Tekman <m.tekman(a)ucl.ac.uk> Date: 2017-11-02 (Thu, 02 Nov 2017) Changed paths: M .ci/flake8_lint_include_list.txt R .ci/flake8_py3_wrapper.sh M .ci/jenkins/selenium/Dockerfile M .ci/jenkins/selenium/docker-compose.yml M .ci/jenkins/selenium/galaxy.ini M .ci/jenkins/selenium/run_galaxy.bash M .ci/jenkins/selenium/run_tests.sh M .ci/py3_sources.txt M .gitignore M .travis.yml M CITATION M Makefile A client/.babelrc M client/GruntFile.js M client/README.md M client/bower.json M client/galaxy/scripts/admin.toolshed.js M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/analysis.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/galaxy.interactive_environments.js M client/galaxy/scripts/galaxy.js M client/galaxy/scripts/galaxy.library.js M client/galaxy/scripts/galaxy.pages.js M client/galaxy/scripts/i18n.js M client/galaxy/scripts/layout/generic-nav-view.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/page.js M client/galaxy/scripts/layout/panel.js M client/galaxy/scripts/layout/router.js M client/galaxy/scripts/layout/scratchbook.js R client/galaxy/scripts/libs/backbone.js R client/galaxy/scripts/libs/bibtex.js R client/galaxy/scripts/libs/d3.js R client/galaxy/scripts/libs/jquery.complexify.js R client/galaxy/scripts/libs/jquery/jquery.cookie.js R client/galaxy/scripts/libs/jquery/jquery.js R client/galaxy/scripts/libs/jquery/jquery.migrate.js R client/galaxy/scripts/libs/jquery/jquery.mousewheel.js R client/galaxy/scripts/libs/raven.js R client/galaxy/scripts/libs/require.js R client/galaxy/scripts/libs/underscore.js M client/galaxy/scripts/mvc/annotation.js M client/galaxy/scripts/mvc/base-mvc.js M client/galaxy/scripts/mvc/base/controlled-fetch-collection.js M client/galaxy/scripts/mvc/citation/citation-model.js M client/galaxy/scripts/mvc/citation/citation-view.js M client/galaxy/scripts/mvc/collection/base-creator.js M client/galaxy/scripts/mvc/collection/collection-li-edit.js M client/galaxy/scripts/mvc/collection/collection-li.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-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/data.js M client/galaxy/scripts/mvc/dataset/dataset-choice.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-list.js M client/galaxy/scripts/mvc/dataset/dataset-model.js M client/galaxy/scripts/mvc/dataset/states.js 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-parameters.js M client/galaxy/scripts/mvc/form/form-repeat.js M client/galaxy/scripts/mvc/form/form-section.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-model.js M client/galaxy/scripts/mvc/grid/grid-shared.js M client/galaxy/scripts/mvc/grid/grid-template.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/hda-li-edit.js M client/galaxy/scripts/mvc/history/hda-li.js M client/galaxy/scripts/mvc/history/hda-model.js M client/galaxy/scripts/mvc/history/hdca-li-edit.js M client/galaxy/scripts/mvc/history/hdca-li.js M client/galaxy/scripts/mvc/history/hdca-model.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-preferences.js M client/galaxy/scripts/mvc/history/history-structure-view.js M client/galaxy/scripts/mvc/history/history-view-annotated.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-dag.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-li.js M client/galaxy/scripts/mvc/job/job-model.js M client/galaxy/scripts/mvc/job/job-params.js A client/galaxy/scripts/mvc/lazy/lazy-limited.js M 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M client/galaxy/scripts/mvc/tool/tools.js M client/galaxy/scripts/mvc/toolshed/categories-view.js M client/galaxy/scripts/mvc/toolshed/repo-queue-view.js M client/galaxy/scripts/mvc/toolshed/repo-status-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/shed-list-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/icon-button.js M client/galaxy/scripts/mvc/ui/popup-menu.js M client/galaxy/scripts/mvc/ui/ui-buttons.js M client/galaxy/scripts/mvc/ui/ui-color-picker.js M client/galaxy/scripts/mvc/ui/ui-drilldown.js M client/galaxy/scripts/mvc/ui/ui-frames.js M client/galaxy/scripts/mvc/ui/ui-list.js M client/galaxy/scripts/mvc/ui/ui-misc.js M client/galaxy/scripts/mvc/ui/ui-modal.js M client/galaxy/scripts/mvc/ui/ui-options.js M client/galaxy/scripts/mvc/ui/ui-popover.js M client/galaxy/scripts/mvc/ui/ui-portlet.js M client/galaxy/scripts/mvc/ui/ui-select-content.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/galaxy/scripts/mvc/ui/ui-select-ftp.js M client/galaxy/scripts/mvc/ui/ui-select-genomespace.js M client/galaxy/scripts/mvc/ui/ui-select-library.js M client/galaxy/scripts/mvc/ui/ui-select.js M client/galaxy/scripts/mvc/ui/ui-slider.js M client/galaxy/scripts/mvc/ui/ui-table.js M client/galaxy/scripts/mvc/ui/ui-tabs.js M client/galaxy/scripts/mvc/ui/ui-thumbnails.js M client/galaxy/scripts/mvc/upload/collection/collection-row.js M client/galaxy/scripts/mvc/upload/collection/collection-view.js M client/galaxy/scripts/mvc/upload/composite/composite-row.js M client/galaxy/scripts/mvc/upload/composite/composite-view.js M 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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-node.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/nls/de/locale.js M client/galaxy/scripts/nls/es/locale.js M client/galaxy/scripts/nls/fr/locale.js M client/galaxy/scripts/nls/ja/locale.js M client/galaxy/scripts/nls/locale.js M client/galaxy/scripts/nls/zh/locale.js M client/galaxy/scripts/onload.js M client/galaxy/scripts/polyfills.js M client/galaxy/scripts/reports_webapp/run_stats.js M client/galaxy/scripts/ui/autocom_tagging.js M client/galaxy/scripts/ui/editable-text.js M 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templates/webapps/galaxy/visualization/create.mako A test-data/selenium-test-notebook.ipynb M test/api/test_api_batch.py M test/api/test_authenticate.py M test/api/test_dataset_collections.py M test/api/test_datatypes.py M test/api/test_histories.py M test/api/test_history_contents.py M test/api/test_jobs.py M test/api/test_pages.py M test/api/test_tools.py A test/api/test_tools_upload.py M test/api/test_users.py M test/api/test_visualizations.py M test/api/test_workflows.py M test/api/test_workflows_from_yaml.py M test/base/api.py M test/base/api_util.py A test/base/constants.py M test/base/driver_util.py M test/base/integration_util.py M test/base/populators.py M test/base/testcase.py M test/base/workflows_format_2/converter.py M test/base/workflows_format_2/main.py M test/docker/base/Dockerfile M test/docker/base/ansible_vars.yml M test/docker/base/run_test_wrapper.sh A test/docker/base/selenium/LICENSE A test/docker/base/selenium/README A test/docker/base/selenium/entry_point.sh A 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config/datatypes_conf.xml.sample M lib/galaxy/datatypes/data.py Log Message: ----------- vastly simplified iqtree datatypes Commit: 94a77f7524f72375bfef02e6e82f3a30e71924d9 https://github.com/galaxyproject/galaxy/commit/94a77f7524f72375bfef02e6e82f… Author: Mehmet Tekman <m.tekman(a)ucl.ac.uk> Date: 2017-11-03 (Fri, 03 Nov 2017) Changed paths: M config/datatypes_conf.xml.sample R lib/galaxy/datatypes/test/example.mldist Log Message: ----------- removed obsolete sniffer and test data Commit: 97fc49db0ce41b264308b0016f2b7f7633bc4a28 https://github.com/galaxyproject/galaxy/commit/97fc49db0ce41b264308b0016f2b… Author: Mehmet Tekman <m.tekman(a)ucl.ac.uk> Date: 2017-11-03 (Fri, 03 Nov 2017) Changed paths: M lib/galaxy/datatypes/data.py Log Message: ----------- removed unoverriden methods in subclass, empty lines Commit: 00ca4f3cdd1af1845ee3920452680ec2548f902f https://github.com/galaxyproject/galaxy/commit/00ca4f3cdd1af1845ee392045268… Author: Mehmet Tekman <m.tekman(a)ucl.ac.uk> Date: 2017-11-04 (Sat, 04 Nov 2017) Changed paths: M lib/galaxy/datatypes/data.py Log Message: ----------- quickfix to read Commit: d9607ce15659b4b26f377c37e7735c7ffa9ba52d https://github.com/galaxyproject/galaxy/commit/d9607ce15659b4b26f377c37e773… Author: Mehmet Tekman <m.tekman(a)ucl.ac.uk> Date: 2017-11-05 (Sun, 05 Nov 2017) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/data.py R lib/galaxy/datatypes/test/example.mldist Log Message: ----------- vastly simplified iqtree datatypes (squashed) Commit: 77c4ccc655690d4970abe5c0631c1d441d4fd46f https://github.com/galaxyproject/galaxy/commit/77c4ccc655690d4970abe5c0631c… Author: Mehmet Tekman <m.tekman(a)ucl.ac.uk> Date: 2017-11-06 (Mon, 06 Nov 2017) Log Message: ----------- Merge branch 'iqtree' of github.com:mtekman/galaxy into iqtree Commit: 5b594ae255b6615bb2d018c85e2e463c77f9cc46 https://github.com/galaxyproject/galaxy/commit/5b594ae255b6615bb2d018c85e2e… Author: Mehmet Tekman <m.tekman(a)ucl.ac.uk> Date: 2017-11-06 (Mon, 06 Nov 2017) Changed paths: M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/text.py Log Message: ----------- moved from data to text Commit: 4bca1a77cca41cb87b0fe2f758657af0e32a46ce https://github.com/galaxyproject/galaxy/commit/4bca1a77cca41cb87b0fe2f75865… Author: Mehmet Tekman <m.tekman(a)ucl.ac.uk> Date: 2017-11-06 (Mon, 06 Nov 2017) Changed paths: A .ci/jenkins/selenium-compose/Dockerfile A .ci/jenkins/selenium-compose/docker-compose.yml A .ci/jenkins/selenium-compose/galaxy.ini A .ci/jenkins/selenium-compose/run_galaxy.bash A .ci/jenkins/selenium-compose/run_tests.sh R .ci/jenkins/selenium/Dockerfile R .ci/jenkins/selenium/docker-compose.yml R .ci/jenkins/selenium/galaxy.ini R .ci/jenkins/selenium/run_galaxy.bash M .ci/jenkins/selenium/run_tests.sh M Makefile M client/.babelrc M client/galaxy/scripts/admin.toolshed.js M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/apps/login.js M 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static/scripts/ui/loading-indicator.js M static/scripts/ui/mode-button.js M static/scripts/ui/pagination.js M static/scripts/ui/peek-column-selector.js M static/scripts/ui/popupmenu.js M static/scripts/ui/scroll-panel.js M static/scripts/ui/search-input.js M static/scripts/utils/add-logging.js M static/scripts/utils/ajax-queue.js M static/scripts/utils/async-save-text.js M static/scripts/utils/config.js M static/scripts/utils/deferred.js M static/scripts/utils/graph.js M static/scripts/utils/levenshtein.js M static/scripts/utils/localization.js M static/scripts/utils/metrics-logger.js M static/scripts/utils/natural-sort.js M static/scripts/utils/query-string-parsing.js M static/scripts/utils/uploadbox.js M static/scripts/utils/utils.js M static/scripts/viz/bbi-data-manager.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/filters.js M static/scripts/viz/trackster/painters.js M static/scripts/viz/trackster/slotting.js M static/scripts/viz/trackster/tracks.js M static/scripts/viz/trackster/util.js M static/scripts/viz/visualization.js M static/scripts/viz/viz_views.js M templates/galaxy_client_app.mako M templates/grid_base.mako M templates/webapps/galaxy/dataset/display.mako M templates/webapps/galaxy/dataset/tabular_chunked.mako M templates/webapps/galaxy/galaxy.masthead.mako M templates/webapps/galaxy/galaxy.panels.mako M templates/webapps/galaxy/history/citations.mako M templates/webapps/galaxy/history/display.mako M templates/webapps/galaxy/history/display_structured.mako M templates/webapps/galaxy/history/embed.mako M templates/webapps/galaxy/history/structure.mako M templates/webapps/galaxy/history/view.mako M templates/webapps/galaxy/history/view_multiple.mako M templates/webapps/galaxy/page/editor.mako M templates/webapps/galaxy/visualization/display.mako M templates/webapps/galaxy/visualization/phyloviz.mako M templates/webapps/galaxy/visualization/sweepster.mako M templates/webapps/galaxy/workflow/editor.mako M templates/webapps/tool_shed/group/index.mako M test/api/test_dataset_collections.py M test/api/test_tools_upload.py M test/base/populators.py M test/galaxy_selenium/driver_factory.py M test/qunit/test-app.js M test/qunit/tests/form_tests.js M test/qunit/tests/galaxy-app-base.js M test/qunit/tests/graph.js M test/qunit/tests/hda-base.js M test/qunit/tests/history_contents_model_tests.js M test/qunit/tests/job-dag.js M test/qunit/tests/list-of-pairs-collection-creator.js M test/qunit/tests/masthead_tests.js M test/qunit/tests/metrics-logger.js M test/qunit/tests/modal_tests.js M test/qunit/tests/page_tests.js M test/qunit/tests/popover_tests.js M test/qunit/tests/ui_tests.js M test/qunit/tests/upload_dialog_tests.js M test/qunit/tests/utils_test.js M test/qunit/tests/workflow_editor_tests.js M test/selenium_tests/framework.py M test/selenium_tests/test_published_histories_grid.py Log Message: ----------- Merge branch 'dev' of github.com:galaxyproject/galaxy into iqtree Commit: e347aed810f5a67893d4d10b56973ca4a5912962 https://github.com/galaxyproject/galaxy/commit/e347aed810f5a67893d4d10b5697… Author: Mehmet Tekman <m.tekman(a)ucl.ac.uk> Date: 2017-11-07 (Tue, 07 Nov 2017) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- fix to datatype and sniffer Commit: 3b4b97a2edd4e73d6861e9b749ff75f34014d13d https://github.com/galaxyproject/galaxy/commit/3b4b97a2edd4e73d6861e9b749ff… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-08 (Wed, 08 Nov 2017) Changed paths: M config/datatypes_conf.xml.sample A lib/galaxy/datatypes/test/example.iqtree M lib/galaxy/datatypes/text.py Log Message: ----------- Merge pull request #4849 from mtekman/iqtree Add IQtree datatypes Compare: https://github.com/galaxyproject/galaxy/compare/855ea1a6a248...3b4b97a2edd4

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[galaxyproject/galaxy] 2e9bf4: Fix multi operations if grid operations redirects ...
by GitHub 07 Nov '17

07 Nov '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 2e9bf4009591719f43da1f2408a2c090c4df5232 https://github.com/galaxyproject/galaxy/commit/2e9bf4009591719f43da1f2408a2… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-11-07 (Tue, 07 Nov 2017) Changed paths: M client/galaxy/scripts/mvc/grid/grid-view.js M static/maps/mvc/grid/grid-view.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/grid/grid-view.js Log Message: ----------- Fix multi operations if grid operations redirects into center panel Commit: 855ea1a6a24829b5461273ceb1d40450951e84fc https://github.com/galaxyproject/galaxy/commit/855ea1a6a24829b5461273ceb1d4… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2017-11-07 (Tue, 07 Nov 2017) Changed paths: M client/galaxy/scripts/mvc/grid/grid-view.js M static/maps/mvc/grid/grid-view.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/grid/grid-view.js Log Message: ----------- Merge pull request #4951 from guerler/fix_center_multi_operation Fix multiple selections for grid operations redirecting to center panel Compare: https://github.com/galaxyproject/galaxy/compare/74b37a9de905...855ea1a6a248

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[galaxyproject/infrastructure-playbook] c6fd1f: LDAP server role is working. Skipped auditlog/ldap...
by GitHub 06 Nov '17

06 Nov '17

Branch: refs/heads/galaxyenv Home: https://github.com/galaxyproject/infrastructure-playbook Commit: c6fd1ff76b85ec0b92d192fb50314e7158ca076a https://github.com/galaxyproject/infrastructure-playbook/commit/c6fd1ff76b8… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-11-06 (Mon, 06 Nov 2017) Changed paths: M env/galaxy/core.yml A env/galaxy/group_vars/ldapservers/vars.yml A env/galaxy/group_vars/ldapservers/vault.yml M env/galaxy/inventory A roles/ldap_server/defaults/main.yml A roles/ldap_server/files/autofs.ldif A roles/ldap_server/files/dhcp.ldif A roles/ldap_server/files/galaxy.ldif A roles/ldap_server/files/postfix.ldif A roles/ldap_server/files/rfc2307bis.ldif A roles/ldap_server/files/sudo.ldif A roles/ldap_server/handlers/main.yml A roles/ldap_server/meta/required_vars.yml A roles/ldap_server/tasks/debian.yml A roles/ldap_server/tasks/main.yml A roles/ldap_server/tasks/openldap.yml A roles/ldap_server/vars/debian.yml A roles/ldap_server/vars/openldap.yml Log Message: ----------- LDAP server role is working. Skipped auditlog/ldap2pts stuff as I plan to have Ansible create LDAP/AFS users

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[galaxyproject/galaxy] 89c838: Remove unused trackster styles.
by GitHub 06 Nov '17

06 Nov '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 89c83845a173906622bc6b5f0113c4e6bffe499a https://github.com/galaxyproject/galaxy/commit/89c83845a173906622bc6b5f0113… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-11-06 (Mon, 06 Nov 2017) Changed paths: M client/galaxy/style/less/trackster.less M static/style/blue/trackster.css Log Message: ----------- Remove unused trackster styles. Commit: e8c5ea7ad6781acc0729d3190c0978bf726d5062 https://github.com/galaxyproject/galaxy/commit/e8c5ea7ad6781acc0729d3190c09… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-11-06 (Mon, 06 Nov 2017) Changed paths: M client/galaxy/style/less/trackster.less Log Message: ----------- Leave trackster .icon styles in (but commented) since there exists some commented code that may need it as a reference. Commit: 9c47e957c337d21190b10781f2fdcd29cc41b1dc https://github.com/galaxyproject/galaxy/commit/9c47e957c337d21190b10781f2fd… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-11-06 (Mon, 06 Nov 2017) Changed paths: M client/galaxy/scripts/viz/circster.js M client/galaxy/scripts/viz/trackster.js M static/maps/viz/circster.js.map M static/maps/viz/trackster.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/viz/circster.js M static/scripts/viz/trackster.js Log Message: ----------- Bump cssloadfiles to when the views are actually created Commit: 74b37a9de905874da942aa91ca8b6e77dfa60fbf https://github.com/galaxyproject/galaxy/commit/74b37a9de905874da942aa91ca8b… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2017-11-06 (Mon, 06 Nov 2017) Changed paths: M client/galaxy/scripts/viz/circster.js M client/galaxy/scripts/viz/trackster.js M client/galaxy/style/less/trackster.less M static/maps/viz/circster.js.map M static/maps/viz/trackster.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/viz/circster.js M static/scripts/viz/trackster.js M static/style/blue/trackster.css Log Message: ----------- Merge pull request #4948 from dannon/fix_trackster_styles Fix trackster styles bleeding into the app (the slightly offcenter upload .icon buttons) Compare: https://github.com/galaxyproject/galaxy/compare/83eefb6b0413...74b37a9de905

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[galaxyproject/galaxy] 8ef1e5: Remove `requirement` from shell_commands() paramet...
by GitHub 06 Nov '17

06 Nov '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 8ef1e51a4a06a74e2eaa9cd188a7f9194d345c27 https://github.com/galaxyproject/galaxy/commit/8ef1e51a4a06a74e2eaa9cd188a7… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-11-06 (Mon, 06 Nov 2017) Changed paths: M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/resolvers/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/deps/resolvers/galaxy_packages.py M lib/galaxy/tools/deps/resolvers/lmod.py M lib/galaxy/tools/deps/resolvers/modules.py M lib/galaxy/tools/deps/resolvers/resolver_mixins.py M lib/galaxy/tools/deps/resolvers/tool_shed_packages.py M lib/galaxy/tools/deps/resolvers/unlinked_tool_shed_packages.py M test/unit/tools/test_conda_resolution.py M test/unit/tools/test_tool_deps.py Log Message: ----------- Remove `requirement` from shell_commands() parameters Commit: 11a9abbb2d7276208beed66bd153ba0fe7881d2b https://github.com/galaxyproject/galaxy/commit/11a9abbb2d7276208beed66bd153… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-11-06 (Mon, 06 Nov 2017) Changed paths: M lib/galaxy/tools/deps/__init__.py Log Message: ----------- Return an OrderedSet of dependencies instead of a list This avoids activating mulled dependencies multiple times and fixes https://github.com/galaxyproject/galaxy/issues/4821. We use OrderedSet because the order of activation may matter for toolshed dependencies. Commit: 83eefb6b0413b764ef86f755fee65f80d1988170 https://github.com/galaxyproject/galaxy/commit/83eefb6b0413b764ef86f755fee6… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-06 (Mon, 06 Nov 2017) Changed paths: M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/resolvers/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/deps/resolvers/galaxy_packages.py M lib/galaxy/tools/deps/resolvers/lmod.py M lib/galaxy/tools/deps/resolvers/modules.py M lib/galaxy/tools/deps/resolvers/resolver_mixins.py M lib/galaxy/tools/deps/resolvers/tool_shed_packages.py M lib/galaxy/tools/deps/resolvers/unlinked_tool_shed_packages.py M test/unit/tools/test_conda_resolution.py M test/unit/tools/test_tool_deps.py Log Message: ----------- Merge pull request #4945 from nsoranzo/refactor_shell_commands Activate mulled dependencies once per job Compare: https://github.com/galaxyproject/galaxy/compare/363a2e063681...83eefb6b0413

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[galaxyproject/infrastructure-playbook] 372d7f: Don't send memory reports on saturdays
by GitHub 06 Nov '17

06 Nov '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 372d7f4a229681558656375313160a52eddb31b5 https://github.com/galaxyproject/infrastructure-playbook/commit/372d7f4a229… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-11-06 (Mon, 06 Nov 2017) Changed paths: M taccenv/host_vars/galaxy-db-02.tacc.utexas.edu/vars.yml Log Message: ----------- Don't send memory reports on saturdays

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[galaxyproject/infrastructure-playbook] 43cdd8: Move Main reports to galaxy-system mailing list
by GitHub 06 Nov '17

06 Nov '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 43cdd844a66081d84781dff54382d4b525a55e92 https://github.com/galaxyproject/infrastructure-playbook/commit/43cdd844a66… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-11-06 (Mon, 06 Nov 2017) Changed paths: M taccenv/group_vars/galaxyservers.yml M taccenv/host_vars/galaxy-db-02.tacc.utexas.edu/vars.yml Log Message: ----------- Move Main reports to galaxy-system mailing list

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[galaxyproject/galaxy] f927de: Add dataset collectino route without history id
by GitHub 06 Nov '17

06 Nov '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f927ded864250f8f17846dde979263119e2eabb3 https://github.com/galaxyproject/galaxy/commit/f927ded864250f8f17846dde9792… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-11-06 (Mon, 06 Nov 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/history_contents.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Add dataset collectino route without history id Commit: 2faf8577abb1098a15c72a733626ffbf3d74a142 https://github.com/galaxyproject/galaxy/commit/2faf8577abb1098a15c72a733626… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-11-06 (Mon, 06 Nov 2017) Changed paths: M lib/galaxy/managers/collections.py Log Message: ----------- Use a collection's history if trans has no history Commit: 63a3fa483f6c46ef057ba0e3a91300e6c90d7419 https://github.com/galaxyproject/galaxy/commit/63a3fa483f6c46ef057ba0e3a913… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-11-06 (Mon, 06 Nov 2017) Changed paths: M client/galaxy/scripts/mvc/collection/collection-view.js M static/maps/mvc/collection/collection-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.map M static/scripts/mvc/collection/collection-view.js Log Message: ----------- Point download button for collections to api/dataset_collections Commit: 363a2e063681c288dd64bb62728263d736eced86 https://github.com/galaxyproject/galaxy/commit/363a2e063681c288dd64bb627282… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-11-06 (Mon, 06 Nov 2017) Changed paths: M client/galaxy/scripts/mvc/collection/collection-view.js M lib/galaxy/managers/collections.py M lib/galaxy/webapps/galaxy/api/history_contents.py M lib/galaxy/webapps/galaxy/buildapp.py M static/maps/mvc/collection/collection-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.map M static/scripts/mvc/collection/collection-view.js Log Message: ----------- Merge branch 'fix_download_button' into dev Compare: https://github.com/galaxyproject/galaxy/compare/c10da91220a1...363a2e063681

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