- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 5404f7: Small (temporary, mako is going away) layer to sup...
by GitHub 21 Sep '17

21 Sep '17

Branch: refs/heads/release_17.09 Home: https://github.com/galaxyproject/galaxy Commit: 5404f7cda7ca4f3b9a2c423bdd29898fb7d8c911 https://github.com/galaxyproject/galaxy/commit/5404f7cda7ca4f3b9a2c423bdd29… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-09-20 (Wed, 20 Sep 2017) Changed paths: M templates/display_base.mako M templates/display_common.mako Log Message: ----------- Small (temporary, mako is going away) layer to support modern routes in old display_base pages (workflow, history, etc). Commit: c9aead91d75a1e0e636cf08ba725a8c2f8ff300a https://github.com/galaxyproject/galaxy/commit/c9aead91d75a1e0e636cf08ba725… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-21 (Thu, 21 Sep 2017) Changed paths: M templates/display_base.mako M templates/display_common.mako Log Message: ----------- Merge pull request #4656 from dannon/display_link_fixes [17.09] Fix links on workflow, history items. Compare: https://github.com/galaxyproject/galaxy/compare/0e89935460a5...c9aead91d75a

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[galaxyproject/galaxy] fbb678: Remove rss template; unused.
by GitHub 21 Sep '17

21 Sep '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: fbb678bc710acb0fe006867100b313a5f39e6e42 https://github.com/galaxyproject/galaxy/commit/fbb678bc710acb0fe006867100b3… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-09-20 (Wed, 20 Sep 2017) Changed paths: R templates/rss.mako Log Message: ----------- Remove rss template; unused. Commit: 8b24d592447c14da67cadc9b8e686b2ef8737785 https://github.com/galaxyproject/galaxy/commit/8b24d592447c14da67cadc9b8e68… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-09-20 (Wed, 20 Sep 2017) Changed paths: R templates/webapps/galaxy/admin/toolsheds.mako Log Message: ----------- Remove galaxy/admin/toolsheds template; unused. Commit: b86c335c65dd214852b6bc1a106aa333f4cb6bfb https://github.com/galaxyproject/galaxy/commit/b86c335c65dd214852b6bc1a106a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-09-20 (Wed, 20 Sep 2017) Changed paths: R templates/admin/tool_shed_repository/browse_category.mako Log Message: ----------- Remove admin/tool_shed_repository/browse_category template; unused. Commit: e6fc47c495e0e7d6bff6f00eb112dfe6a55356ad https://github.com/galaxyproject/galaxy/commit/e6fc47c495e0e7d6bff6f00eb112… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-09-20 (Wed, 20 Sep 2017) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Minor typo found while grepping around. Commit: 669f944292ecd62a4250d6e409b688e217671ecf https://github.com/galaxyproject/galaxy/commit/669f944292ecd62a4250d6e409b6… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-21 (Thu, 21 Sep 2017) Changed paths: M lib/galaxy/model/__init__.py R templates/admin/tool_shed_repository/browse_category.mako R templates/rss.mako R templates/webapps/galaxy/admin/toolsheds.mako Log Message: ----------- Merge pull request #4664 from dannon/template_cleanup More unused template cleanup Compare: https://github.com/galaxyproject/galaxy/compare/12d9026b99dd...669f944292ec

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[galaxyproject/galaxy] 4711cd: Change routes from 'forms' to 'form' to avoid conf...
by GitHub 21 Sep '17

21 Sep '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4711cd83165cb5113915927283028cff7b666afb https://github.com/galaxyproject/galaxy/commit/4711cd83165cb511391592728302… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-17 (Thu, 17 Aug 2017) Changed paths: M client/galaxy/scripts/apps/admin.js M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin.py M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map Log Message: ----------- Change routes from 'forms' to 'form' to avoid conflicts with forms resources Commit: 2ae500acce205cafba4c32f44ebf44b5207bd02f https://github.com/galaxyproject/galaxy/commit/2ae500acce205cafba4c32f44ebf… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-17 (Thu, 17 Aug 2017) Changed paths: M client/galaxy/scripts/apps/admin.js M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Add to forms list grid to client Commit: c188ccc32ffa50542b878e9cb62836d6d3f88b2d https://github.com/galaxyproject/galaxy/commit/c188ccc32ffa50542b878e9cb628… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-17 (Thu, 17 Aug 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/forms.py R templates/admin/forms/grid.mako Log Message: ----------- Remove grid mako template Commit: ff7ad10eb13947762a57ed6408516fc0428aca93 https://github.com/galaxyproject/galaxy/commit/ff7ad10eb13947762a57ed640851… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-17 (Thu, 17 Aug 2017) Changed paths: M client/galaxy/scripts/apps/panels/admin-panel.js M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/forms.py M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map Log Message: ----------- Fix client routing Commit: 91eda9ef4b3cce266dcd50f8d31318e799c6056f https://github.com/galaxyproject/galaxy/commit/91eda9ef4b3cce266dcd50f8d313… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-17 (Thu, 17 Aug 2017) Changed paths: M client/galaxy/scripts/apps/admin.js M lib/galaxy/webapps/galaxy/controllers/forms.py M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map Log Message: ----------- Show status column for forms grid Commit: 7d2c4f874ffd945be00759e590debace45585cfa https://github.com/galaxyproject/galaxy/commit/7d2c4f874ffd945be00759e590de… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-17 (Thu, 17 Aug 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/forms.py Log Message: ----------- Add async undelete operation for forms grid Commit: 42fe9129591fbe197849e8ec4184f9b8d9ff9f46 https://github.com/galaxyproject/galaxy/commit/42fe9129591fbe197849e8ec4184… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-17 (Thu, 17 Aug 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/forms.py Log Message: ----------- Update redirects, fix operations Commit: ead5882df2e1b890ef1c6b6e4884320c2e7ae4bf https://github.com/galaxyproject/galaxy/commit/ead5882df2e1b890ef1c6b6e4884… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-18 (Fri, 18 Aug 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/forms.py Log Message: ----------- Remove spaces Commit: 3671739657b61d66bee74201501bd48015821aad https://github.com/galaxyproject/galaxy/commit/3671739657b61d66bee74201501b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-18 (Fri, 18 Aug 2017) Changed paths: M client/galaxy/scripts/apps/admin.js M lib/galaxy/webapps/galaxy/controllers/forms.py M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Add form editor Commit: 2c9fe8fc57a0400e3cd23837bad0c95c70516c80 https://github.com/galaxyproject/galaxy/commit/2c9fe8fc57a0400e3cd23837bad0… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-18 (Fri, 18 Aug 2017) Changed paths: M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt M client/galaxy/scripts/mvc/form/form-view.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/workflow/workflow-forms.js M client/galaxy/scripts/mvc/workflow/workflow-manager.js M client/galaxy/scripts/mvc/workflow/workflow-node.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M client/galaxy/style/less/ui.less M lib/galaxy/config.py M lib/galaxy/containers/__init__.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/runners/kubernetes.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/error_reports/plugins/sentry.py M lib/galaxy/tools/execute.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/tools/parser/interface.py M lib/galaxy/tools/parser/output_collection_def.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/util/__init__.py M lib/galaxy/util/pastescript/serve.py M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/webapps/galaxy/api/users.py M lib/galaxy/workflow/modules.py M scripts/cleanup_datasets/admin_cleanup_datasets.py M scripts/cleanup_datasets/cleanup_datasets.py M scripts/communication/communication_server.py M scripts/secret_decoder_ring.py M static/maps/mvc/form/form-view.js.map M static/maps/mvc/tool/tool-form-base.js.map M static/maps/mvc/tool/tool-form-composite.js.map M static/maps/mvc/tool/tool-form.js.map M static/maps/mvc/workflow/workflow-forms.js.map M static/maps/mvc/workflow/workflow-manager.js.map M static/maps/mvc/workflow/workflow-node.js.map M static/maps/mvc/workflow/workflow-view.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/form/form-view.js M static/scripts/mvc/tool/tool-form-base.js M static/scripts/mvc/tool/tool-form-composite.js M static/scripts/mvc/tool/tool-form.js M static/scripts/mvc/workflow/workflow-forms.js M static/scripts/mvc/workflow/workflow-manager.js M static/scripts/mvc/workflow/workflow-node.js M static/scripts/mvc/workflow/workflow-view.js M static/style/blue/base.css A test/functional/tools/collection_creates_dynamic_nested_from_json.xml A test/functional/tools/collection_creates_dynamic_nested_from_json_elements.xml M test/functional/tools/samples_tool_conf.xml M test/functional/tools/tool_provided_metadata_1.xml M test/functional/tools/tool_provided_metadata_2.xml M test/functional/tools/tool_provided_metadata_3.xml A test/functional/tools/tool_provided_metadata_4.xml A test/functional/tools/tool_provided_metadata_5.xml A test/functional/tools/tool_provided_metadata_6.xml A test/functional/tools/tool_provided_metadata_7.xml A test/functional/tools/tool_provided_metadata_8.xml A test/functional/tools/tool_provided_metadata_9.xml M test/unit/tools/test_collect_primary_datasets.py Log Message: ----------- Merge branch 'dev' into admin_grid_formbuilder Commit: 63fe2283a8c27abc9446521b75f5286153c1a90b https://github.com/galaxyproject/galaxy/commit/63fe2283a8c27abc9446521b75f5… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-18 (Fri, 18 Aug 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/forms.py Log Message: ----------- Split form dictionary, prepare adding stored repeats Commit: 097bf705d7681f4ded365d0ce1c8192370a099e8 https://github.com/galaxyproject/galaxy/commit/097bf705d7681f4ded365d0ce1c8… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-18 (Fri, 18 Aug 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/forms.py Log Message: ----------- Display select options as comma-separated string Commit: 76909f2c6713f539127e4f752948b87b7722d685 https://github.com/galaxyproject/galaxy/commit/76909f2c6713f539127e4f752948… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-18 (Fri, 18 Aug 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/forms.py Log Message: ----------- Touchup labels Commit: 604926b2af6ec491c9cebefa87257dd6fa19bd66 https://github.com/galaxyproject/galaxy/commit/604926b2af6ec491c9cebefa8725… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-18 (Fri, 18 Aug 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/forms.py Log Message: ----------- Remove functions which will not be needed or have to be rewritten Commit: d3927b250534ace5f9f98cf38d3842237fe36867 https://github.com/galaxyproject/galaxy/commit/d3927b250534ace5f9f98cf38d38… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-18 (Fri, 18 Aug 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/forms.py Log Message: ----------- Move validation into save function Commit: 7f3eb464f6b0cc750a303a3a6ee5df37719ba141 https://github.com/galaxyproject/galaxy/commit/7f3eb464f6b0cc750a303a3a6ee5… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-19 (Sat, 19 Aug 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/forms.py M templates/admin/forms/edit_form_definition.mako Log Message: ----------- Add save form feature Commit: a914b6f3a85e3de70e8aaeb16d9b1004fecfd5e5 https://github.com/galaxyproject/galaxy/commit/a914b6f3a85e3de70e8aaeb16d9b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-19 (Sat, 19 Aug 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/forms.py Log Message: ----------- Fix selection options Commit: b093e9804e8723354c697e17096a2b6a0b984516 https://github.com/galaxyproject/galaxy/commit/b093e9804e8723354c697e17096a… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-19 (Sat, 19 Aug 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/forms.py Log Message: ----------- Remove unused utility function Commit: 6d5efccc4a02c65283c2580f1acc189eff528ba0 https://github.com/galaxyproject/galaxy/commit/6d5efccc4a02c65283c2580f1acc… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-20 (Sun, 20 Aug 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/forms.py Log Message: ----------- Parse success message Commit: 7fd378dfd85777a1a7ce6118e9dfce1f86b1eaa6 https://github.com/galaxyproject/galaxy/commit/7fd378dfd85777a1a7ce6118e9df… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-21 (Mon, 21 Aug 2017) Changed paths: M client/galaxy/scripts/apps/admin.js M lib/galaxy/webapps/galaxy/controllers/forms.py Log Message: ----------- Changes to csv import Commit: ced3aa0aed555cdf39053484ad0b7222b95dde96 https://github.com/galaxyproject/galaxy/commit/ced3aa0aed555cdf39053484ad0b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-22 (Tue, 22 Aug 2017) Changed paths: M client/galaxy/scripts/apps/admin.js M lib/galaxy/webapps/galaxy/controllers/forms.py M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Add create form, improve messages Commit: cc3a3d5fe22cf428a853fd42e642a7bde9f30e86 https://github.com/galaxyproject/galaxy/commit/cc3a3d5fe22cf428a853fd42e642… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-22 (Tue, 22 Aug 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/forms.py Log Message: ----------- Introduce last updated column Commit: 6719209f96b070a121def35e141a5321f65a53c3 https://github.com/galaxyproject/galaxy/commit/6719209f96b070a121def35e141a… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-22 (Tue, 22 Aug 2017) Changed paths: M client/galaxy/scripts/mvc/form/form-parameters.js A client/galaxy/scripts/mvc/tool/tool-genomespace.js A client/galaxy/scripts/mvc/ui/ui-select-genomespace.js M client/galaxy/style/less/ui.less M config/galaxy.ini.sample M config/tool_conf.xml.main M config/tool_conf.xml.sample M lib/galaxy/config.py M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/managers/configuration.py M lib/galaxy/managers/workflows.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/web/form_builder.py M lib/galaxy/webapps/galaxy/api/quotas.py M lib/galaxy/webapps/galaxy/controllers/history.py M static/maps/mvc/form/form-parameters.js.map A static/maps/mvc/tool/tool-genomespace.js.map A static/maps/mvc/ui/ui-select-genomespace.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/form/form-parameters.js A static/scripts/mvc/tool/tool-genomespace.js A static/scripts/mvc/ui/ui-select-genomespace.js M static/style/blue/base.css M templates/tagging_common.mako M test/api/test_workflows.py M test/unit/workflows/workflow_support.py M tools/genomespace/genomespace_exporter.py M tools/genomespace/genomespace_exporter.xml M tools/genomespace/genomespace_file_browser.py R tools/genomespace/genomespace_file_browser_dev.xml R tools/genomespace/genomespace_file_browser_prod.xml R tools/genomespace/genomespace_file_browser_test.xml M tools/genomespace/genomespace_importer.py M tools/genomespace/genomespace_importer.xml A tools/genomespace/genomespace_push.xml Log Message: ----------- Merge branch 'dev' into admin_grid_formbuilder Commit: 64e4d43c6d5f0d3231c727ce0e36c9fb674e82c4 https://github.com/galaxyproject/galaxy/commit/64e4d43c6d5f0d3231c727ce0e36… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-22 (Tue, 22 Aug 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/forms.py Log Message: ----------- Revise message Commit: 2c5266a70fb1d980e1302e7f47967d35f7821882 https://github.com/galaxyproject/galaxy/commit/2c5266a70fb1d980e1302e7f4796… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-22 (Tue, 22 Aug 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/forms.py Log Message: ----------- Lint Commit: d99d6cef5c37ee0f498d4665b706a6dbef6ab1fd https://github.com/galaxyproject/galaxy/commit/d99d6cef5c37ee0f498d4665b706… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-23 (Wed, 23 Aug 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/forms.py Log Message: ----------- Remove unused libraries Commit: 376916a32cc5c0f2f0b918c4ab0a937641e4d4a2 https://github.com/galaxyproject/galaxy/commit/376916a32cc5c0f2f0b918c4ab0a… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-24 (Thu, 24 Aug 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/forms.py Log Message: ----------- Remove preview mako, link edit form with item button Commit: 9b71ba9d88f7ca72ec968350c65cc750d7ea34ff https://github.com/galaxyproject/galaxy/commit/9b71ba9d88f7ca72ec968350c65c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-24 (Thu, 24 Aug 2017) Changed paths: R templates/admin/forms/create_form.mako R templates/admin/forms/edit_form_definition.mako R templates/admin/forms/view_form_definition.mako Log Message: ----------- Remove form makos Commit: 792727bb30420356516f971566a0bbaa34d96ee2 https://github.com/galaxyproject/galaxy/commit/792727bb30420356516f971566a0… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-24 (Thu, 24 Aug 2017) Changed paths: M client/galaxy/style/less/dataset.less M lib/galaxy/tools/verify/__init__.py M lib/galaxy/web/base/interactive_environments.py M static/style/blue/base.css Log Message: ----------- Merge branch 'dev' into admin_grid_formbuilder Commit: 9eabb2a49004d3ef19c5df86f097f7152267d094 https://github.com/galaxyproject/galaxy/commit/9eabb2a49004d3ef19c5df86f097… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-30 (Wed, 30 Aug 2017) Changed paths: M client/bower.json R client/galaxy/scripts/libs/jquery/jqtouch.js M client/galaxy/scripts/mvc/tool/tools.js M client/galaxy/scripts/mvc/ui/ui-select-content.js M client/galaxy/style/less/base.less M client/galaxy/style/less/galaxy_bootstrap/variables.less M client/galaxy/style/less/galaxy_variables.less R client/galaxy/style/less/iphone.less A client/galaxy/style/less/theme/plain.less M client/grunt-tasks/install-libs.js M client/grunt-tasks/style.js M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py R lib/galaxy/datatypes/converters/bcf_bgzip_to_bcf_converter.py R lib/galaxy/datatypes/converters/bcf_bgzip_to_bcf_converter.xml R lib/galaxy/datatypes/converters/bcf_to_bcf_bgzip_converter.py R lib/galaxy/datatypes/converters/bcf_to_bcf_bgzip_converter.xml A lib/galaxy/datatypes/converters/bcf_to_bcf_uncompressed_converter.xml A lib/galaxy/datatypes/converters/bcf_uncompressed_to_bcf_converter.xml M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/set_metadata_tool.xml M lib/galaxy/datatypes/tabular.py A lib/galaxy/datatypes/test/1.bcf A lib/galaxy/datatypes/test/1.bcf_uncompressed M lib/galaxy/web/framework/base.py R lib/galaxy/webapps/galaxy/controllers/mobile.py M lib/galaxy/webapps/reports/config.py M lib/galaxy/workflow/modules.py R static/jqtouch/img/backButton.png R static/jqtouch/img/back_button.png R static/jqtouch/img/back_button_clicked.png R static/jqtouch/img/bg_row.gif R static/jqtouch/img/bg_row_select.gif R static/jqtouch/img/blueButton.png R static/jqtouch/img/button.png R static/jqtouch/img/button_clicked.png R static/jqtouch/img/cancel.png R static/jqtouch/img/chevron.png R static/jqtouch/img/chevron_select.png R static/jqtouch/img/grayButton.png R static/jqtouch/img/header.gif R static/jqtouch/img/listGroup.png R static/jqtouch/img/loading.gif R static/jqtouch/img/pinstripes.png R static/jqtouch/img/selection.png R static/jqtouch/img/thumb.png R static/jqtouch/img/toggle.png R static/jqtouch/img/toggleOn.png R static/jqtouch/img/toolButton.png R static/jqtouch/img/toolbar.gif R static/jqtouch/img/toolbar.png R static/jqtouch/img/whiteButton.png R static/jqtouch/jqtouch.css M static/maps/mvc/tool/tools.js.map M static/maps/mvc/ui/ui-select-content.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tool/tools.js M static/scripts/mvc/ui/ui-select-content.js M static/style/blue/base.css R static/style/blue/iphone.css M templates/webapps/galaxy/dataset/copy_view.mako R templates/webapps/galaxy/mobile/dataset/detail.mako R templates/webapps/galaxy/mobile/dataset/peek.mako R templates/webapps/galaxy/mobile/form.mako R templates/webapps/galaxy/mobile/history/detail.mako R templates/webapps/galaxy/mobile/history/list.mako R templates/webapps/galaxy/mobile/index.mako R templates/webapps/galaxy/mobile/manage_library.mako R templates/webapps/galaxy/mobile/settings.mako M test/api/test_jobs.py M test/functional/tools/sample_datatypes_conf.xml A test/selenium_tests/test_published_histories_grid.py Log Message: ----------- Merge branch 'dev' into admin_grid_formbuilder Commit: 87f2ad191f9bb97b58cfe64b7076e7ab7890d62c https://github.com/galaxyproject/galaxy/commit/87f2ad191f9bb97b58cfe64b7076… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-30 (Wed, 30 Aug 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/forms.py Log Message: ----------- Remove unused library Commit: 809cabdfd40ea1eb810f8639834c6ed9a1c5b840 https://github.com/galaxyproject/galaxy/commit/809cabdfd40ea1eb810f8639834c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-09-13 (Wed, 13 Sep 2017) Changed paths: M .ci/flake8_lint_include_list.txt M .ci/jenkins/selenium/docker-compose.yml M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.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/history-list.js M client/galaxy/scripts/mvc/history/history-view-edit.js M client/galaxy/scripts/mvc/history/options-menu.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-folderlist-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-librarytoolbar-view.js M client/galaxy/scripts/mvc/tag.js M client/galaxy/scripts/mvc/tours.js M client/galaxy/scripts/mvc/user/user-preferences.js A client/galaxy/scripts/mvc/workflow/workflow-model.js M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M client/galaxy/scripts/mvc/workflow/workflow-view-terminals.js M client/galaxy/scripts/mvc/workflow/workflow.js M client/galaxy/scripts/utils/uploadbox.js M client/galaxy/scripts/utils/utils.js M client/galaxy/style/less/base.less M client/galaxy/style/less/library.less M config/datatypes_conf.xml.sample M config/dependency_resolvers_conf.xml.sample M config/error_report.yml.sample M config/galaxy.ini.sample A config/lmod_modules_mapping.yml.sample A config/plugins/interactive_environments/hicbrowser/config/allowed_images.yml.sample A config/plugins/interactive_environments/hicbrowser/config/hicbrowser.ini.sample A config/plugins/interactive_environments/hicbrowser/config/hicbrowser.xml A config/plugins/interactive_environments/hicbrowser/static/js/hicbrowser.js A config/plugins/interactive_environments/hicbrowser/templates/hicbrowser.mako M doc/source/admin/special_topics/bug_reports.rst A doc/source/dev/finding_and_improving_slow_code.rst M lib/galaxy/config.py M lib/galaxy/datatypes/binary.py R lib/galaxy/datatypes/converters/bam_to_bai.xml A lib/galaxy/datatypes/converters/biom1_to_biom2.xml A 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lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/work/context.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run.py M lib/tool_shed/galaxy_install/installed_repository_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py M lib/tool_shed/grids/repository_grids.py M lib/tool_shed/util/commit_util.py M lib/tool_shed/util/xml_util.py M scripts/tool_shed/build_ts_whoosh_index.py M static/maps/layout/page.js.map M static/maps/mvc/grid/grid-shared.js.map M static/maps/mvc/grid/grid-view.js.map M static/maps/mvc/history/history-list.js.map M static/maps/mvc/history/history-view-edit.js.map M static/maps/mvc/history/options-menu.js.map M static/maps/mvc/library/library-dataset-view.js.map M static/maps/mvc/library/library-folder-view.js.map M static/maps/mvc/library/library-folderlist-view.js.map M 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static/scripts/mvc/collection/list-of-pairs-collection-creator.js M static/scripts/mvc/grid/grid-shared.js M static/scripts/mvc/grid/grid-view.js M static/scripts/mvc/history/history-list.js M static/scripts/mvc/history/history-view-edit.js M static/scripts/mvc/history/options-menu.js M static/scripts/mvc/library/library-dataset-view.js M static/scripts/mvc/library/library-folder-view.js M static/scripts/mvc/library/library-folderlist-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/library/library-library-view.js M static/scripts/mvc/library/library-librarytoolbar-view.js M static/scripts/mvc/tag.js M static/scripts/mvc/tours.js M static/scripts/mvc/user/user-preferences.js A static/scripts/mvc/workflow/workflow-model.js M static/scripts/mvc/workflow/workflow-terminals.js M static/scripts/mvc/workflow/workflow-view-terminals.js M static/scripts/mvc/workflow/workflow.js M static/scripts/utils/uploadbox.js M static/scripts/utils/utils.js M static/style/blue/base.css M static/style/blue/library.css M templates/webapps/galaxy/workflow/editor.mako A test-data/joiner_header_in1.tab A test-data/joiner_header_in2.tab A test-data/joiner_out1.bed A test-data/joiner_out2.bed A test-data/joiner_out3.bed A test-data/joiner_out4.bed A test-data/joiner_out5.tab A test-data/joiner_out6.tab A test-data/joiner_out7.tab M test/api/test_histories.py M test/api/test_libraries.py M test/api/test_tools.py M test/api/test_workflows.py M test/base/api.py M test/base/driver_util.py M test/base/interactor.py M test/base/populators.py R test/base/test_db_util.py A test/base/testcase.py M test/base/tool_shed_util.py R test/base/twilltestcase.py R test/functional/database_contexts.py R test/functional/test_library_templates.py M test/functional/test_toolbox.py M test/functional/tools/composite.xml M test/functional/tools/composite_output.xml M test/functional/tools/composite_output_tests.xml M test/functional/tools/metadata.xml A test/functional/twilltestcase.py M test/galaxy_selenium/driver_factory.py M test/galaxy_selenium/has_driver.py M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/sizzle.py M test/integration/test_upload_configuration_options.py M test/selenium_tests/framework.py M test/selenium_tests/test_history_panel.py M test/selenium_tests/test_history_sharing.py M test/selenium_tests/test_login.py M test/selenium_tests/test_published_histories_grid.py A test/selenium_tests/test_saved_histories.py A test/selenium_tests/test_sizzle_loading.py M test/selenium_tests/test_workflow_editor.py M test/selenium_tests/test_workflow_management.py M test/selenium_tests/test_workflow_run.py M test/shed_functional/base/test_db_util.py M test/shed_functional/base/twilltestcase.py M test/unit/tools/test_tool_deps.py M tools/data_source/upload.py M tools/filters/join.py M tools/filters/joiner.xml M tools/sr_assembly/velvetg.xml Log Message: ----------- Merge branch 'dev' into admin_grid_formbuilder Commit: 9a348167ff77b66013eefe23e7e222cb13055843 https://github.com/galaxyproject/galaxy/commit/9a348167ff77b66013eefe23e7e2… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-09-14 (Thu, 14 Sep 2017) Changed paths: M client/galaxy/scripts/mvc/library/library-dataset-view.js M client/galaxy/scripts/mvc/library/library-folder-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/library/library-library-view.js M client/galaxy/scripts/mvc/library/library-librarylist-view.js M client/toolshed/scripts/mvc/groups/group-list-view.js M lib/galaxy/app.py M lib/galaxy/datatypes/registry.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/command_factory.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/tools/actions/metadata.py M lib/galaxy/tools/evaluation.py M lib/galaxy_ext/metadata/set_metadata.py M static/maps/mvc/library/library-dataset-view.js.map M static/maps/mvc/library/library-folder-view.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/maps/mvc/library/library-library-view.js.map M static/maps/mvc/library/library-librarylist-view.js.map M static/scripts/mvc/library/library-dataset-view.js M static/scripts/mvc/library/library-folder-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/library/library-library-view.js M static/scripts/mvc/library/library-librarylist-view.js Log Message: ----------- Merge branch 'dev' into admin_grid_formbuilder Commit: c9db5f8dfeb05f8cab5484ef877e187c3b425742 https://github.com/galaxyproject/galaxy/commit/c9db5f8dfeb05f8cab5484ef877e… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-09-18 (Mon, 18 Sep 2017) Changed paths: M .travis.yml M client/galaxy/scripts/mvc/base/controlled-fetch-collection.js M client/galaxy/scripts/mvc/history/history-model.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-folderlist-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/user/user-custom-builds.js M client/toolshed/scripts/mvc/groups/group-detail-view.js M client/toolshed/scripts/mvc/groups/group-list-view.js M create_db.sh M extract_dataset_parts.sh M lib/galaxy/jobs/__init__.py M lib/galaxy/model/__init__.py M lib/galaxy/objectstore/__init__.py M lib/galaxy/security/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/actions/metadata.py M lib/galaxy/tools/loader_directory.py M lib/galaxy/tools/parser/yaml.py M lib/galaxy/tools/util/maf_utilities.py M lib/galaxy/webapps/galaxy/api/library_datasets.py M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/galaxy/webhooks/__init__.py M manage_db.sh M manage_tools.sh M static/maps/mvc/base/controlled-fetch-collection.js.map M static/maps/mvc/history/history-model.js.map M static/maps/mvc/library/library-dataset-view.js.map M static/maps/mvc/library/library-folder-view.js.map M static/maps/mvc/library/library-folderlist-view.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/maps/mvc/library/library-library-view.js.map M static/maps/mvc/library/library-librarylist-view.js.map M static/maps/mvc/user/user-custom-builds.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/base/controlled-fetch-collection.js M static/scripts/mvc/library/library-dataset-view.js M static/scripts/mvc/library/library-folder-view.js M static/scripts/mvc/library/library-folderlist-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/library/library-library-view.js M static/scripts/mvc/library/library-librarylist-view.js M static/scripts/mvc/user/user-custom-builds.js M static/toolshed/scripts/mvc/groups/group-detail-view.js M static/toolshed/scripts/mvc/groups/group-list-view.js M templates/webapps/galaxy/admin/sanitize_whitelist.mako Log Message: ----------- Merge branch 'dev' into admin_grid_formbuilder Commit: 12d9026b99dd7282b509823ce3e9ffef4181b9e5 https://github.com/galaxyproject/galaxy/commit/12d9026b99dd7282b509823ce3e9… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-09-21 (Thu, 21 Sep 2017) Changed paths: M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/panels/admin-panel.js M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/galaxy/webapps/galaxy/controllers/forms.py M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map R templates/admin/forms/create_form.mako R templates/admin/forms/edit_form_definition.mako R templates/admin/forms/grid.mako R templates/admin/forms/view_form_definition.mako Log Message: ----------- Merge branch 'admin_grid_formbuilder' into dev Compare: https://github.com/galaxyproject/galaxy/compare/71c5398f4860...12d9026b99dd

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[galaxyproject/galaxy] cf9e19: Move wait for dataset_collection to populators.py
by GitHub 21 Sep '17

21 Sep '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: cf9e191e276cd008b3af8d7ed42adb03b18a0ca2 https://github.com/galaxyproject/galaxy/commit/cf9e191e276cd008b3af8d7ed42a… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-09-20 (Wed, 20 Sep 2017) Changed paths: M test/api/test_dataset_collections.py M test/base/populators.py Log Message: ----------- Move wait for dataset_collection to populators.py Commit: 71c5398f4860bd90aebc820b2478cccab9913671 https://github.com/galaxyproject/galaxy/commit/71c5398f4860bd90aebc820b2478… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-09-21 (Thu, 21 Sep 2017) Changed paths: M test/api/test_dataset_collections.py M test/base/populators.py Log Message: ----------- Merge pull request #4658 from mvdbeek/wait_for_collectino_test Move wait_for_dataset_collection to populators Compare: https://github.com/galaxyproject/galaxy/compare/a25a76ab6a7f...71c5398f4860

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[galaxyproject/usegalaxy-playbook] 0740d8: Update Pulsar on other pulsar servers
by GitHub 21 Sep '17

21 Sep '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 0740d81f653ff6f37f7f308b3a81a173249281ce https://github.com/galaxyproject/usegalaxy-playbook/commit/0740d81f653ff6f3… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-09-21 (Thu, 21 Sep 2017) Changed paths: M env/test/group_vars/pulsarservers/vars.yml M env/test/host_vars/br005.bridges.psc.edu.yml Log Message: ----------- Update Pulsar on other pulsar servers Commit: 996b99d22617962e48ff00ad07461d15d18ffd41 https://github.com/galaxyproject/usegalaxy-playbook/commit/996b99d22617962e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-09-21 (Thu, 21 Sep 2017) Changed paths: M env/main/templates/galaxy/config/job_conf.xml.j2 Log Message: ----------- Macro-ize Main's job conf Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/f3a1a4748053...…

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[galaxyproject/usegalaxy-playbook] f3a1a4: A few more test job conf changes
by GitHub 21 Sep '17

21 Sep '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: f3a1a474805352f6551a735c6c5c68ca4fdb9630 https://github.com/galaxyproject/usegalaxy-playbook/commit/f3a1a474805352f6… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-09-21 (Thu, 21 Sep 2017) Changed paths: M env/common/files/galaxy/dynamic_rules/multi_dynamic_walltime.py M env/test/templates/galaxy/config/job_conf.xml.j2 Log Message: ----------- A few more test job conf changes

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[galaxyproject/usegalaxy-playbook] 899d7d: Convert Test job_conf.xml to use macros.
by GitHub 21 Sep '17

21 Sep '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 899d7d6e59e3592c0de322460b0364195bfe6b09 https://github.com/galaxyproject/usegalaxy-playbook/commit/899d7d6e59e3592c… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-09-21 (Thu, 21 Sep 2017) Changed paths: M env/common/files/galaxy/dynamic_rules/bridges_select.py M env/common/files/galaxy/dynamic_rules/multi_dynamic_walltime.py M env/common/files/galaxy/dynamic_rules/reserved.py M env/test/files/galaxy/config/job_resource_params_conf.xml M env/test/group_vars/all.yml M env/test/group_vars/galaxyservers/vars.yml M env/test/templates/galaxy/config/job_conf.xml.j2 Log Message: ----------- Convert Test job_conf.xml to use macros.

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[galaxyproject/usegalaxy-playbook] 9107dd: Fix version fact handling and update Test
by GitHub 20 Sep '17

20 Sep '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 9107dd7da5f37f0eff09ef8d74242336287f808a https://github.com/galaxyproject/usegalaxy-playbook/commit/9107dd7da5f37f0e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-09-20 (Wed, 20 Sep 2017) Changed paths: M env/test/files/galaxy/galaxy_version.yml M roles/usegalaxy_cvmfs/tasks/update.yml Log Message: ----------- Fix version fact handling and update Test

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[galaxyproject/usegalaxy-playbook] a1ffe3: Set $GALAXY_VIRTUAL_ENV on Bridges
by GitHub 20 Sep '17

20 Sep '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: a1ffe39ec0801b596661dd0a465bc23fdc02659e https://github.com/galaxyproject/usegalaxy-playbook/commit/a1ffe39ec0801b59… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-09-20 (Wed, 20 Sep 2017) Changed paths: M env/test/templates/galaxy/config/job_conf.xml.j2 Log Message: ----------- Set $GALAXY_VIRTUAL_ENV on Bridges

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[galaxyproject/usegalaxy-playbook] a4fa5e: usegalaxy CVMFS role enhancements:
by GitHub 20 Sep '17

20 Sep '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: a4fa5ea2962d0722ad99e5342fc17abae7ef7743 https://github.com/galaxyproject/usegalaxy-playbook/commit/a4fa5ea2962d0722… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-09-20 (Wed, 20 Sep 2017) Changed paths: A roles/usegalaxy_cvmfs/defaults/main.yml M roles/usegalaxy_cvmfs/tasks/update.yml Log Message: ----------- usegalaxy CVMFS role enhancements: - Check for running docker containers, fail if there are any - Get latest branch HEAD version from Github so we don't have to transaction/pull/abort if there are no changes - Use Ansible blocks to abort the transaction on failure Commit: 9a817b65c1a21d39be2bb593809efade760a3d89 https://github.com/galaxyproject/usegalaxy-playbook/commit/9a817b65c1a21d39… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-09-20 (Wed, 20 Sep 2017) Changed paths: M env/test/files/galaxy/galaxy_version.yml M env/test/group_vars/all.yml M env/test/host_vars/br005.bridges.psc.edu.yml Log Message: ----------- Update Test to a branch of mine for testing pending Pulsar changes in a production environment. Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/d004b3540989...…

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