March 2018 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/usegalaxy-playbook] f377a8: Update Test
by GitHub 20 Mar '18

20 Mar '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: f377a81fe74b5190f3182a0aa8a34e163d0b8ecb https://github.com/galaxyproject/usegalaxy-playbook/commit/f377a81fe74b5190… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-03-20 (Tue, 20 Mar 2018) Changed paths: M env/test/files/galaxy/galaxy_version.yml Log Message: ----------- Update Test

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[galaxyproject/galaxy] ade672: Add script to propagate hashtags in history
by GitHub 20 Mar '18

20 Mar '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ade6727fda1b7ff05303a8ce727d1dceee0d61ab https://github.com/galaxyproject/galaxy/commit/ade6727fda1b7ff05303a8ce727d… Author: anup kumar <anup.rulez(a)gmail.com> Date: 2018-03-08 (Thu, 08 Mar 2018) Changed paths: A scripts/apply_tags.py Log Message: ----------- Add script to propagate hashtags in history Commit: 3b6f6b803e5affb292ef485742094739afc4023a https://github.com/galaxyproject/galaxy/commit/3b6f6b803e5affb292ef48574209… Author: anup kumar <anup.rulez(a)gmail.com> Date: 2018-03-08 (Thu, 08 Mar 2018) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/apps/extended.js A client/galaxy/scripts/components/DisplayStructured.vue A client/galaxy/scripts/components/HistoryView.vue M client/galaxy/scripts/mvc/grid/grid-template.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/ui/ui-select-genomespace.js M client/galaxy/style/less/ui.less M config/datatypes_conf.xml.sample M config/galaxy.yml.sample M config/plugins/webhooks/demo/tour_generator/__init__.py M doc/source/admin/galaxy_options.rst M lib/galaxy/app.py M lib/galaxy/config.py M lib/galaxy/datatypes/binary.py R lib/galaxy/datatypes/converters/bam_native_to_bam_converter.xml M lib/galaxy/datatypes/converters/sam_to_bam_native.xml A lib/galaxy/datatypes/converters/to_coordinate_sorted_bam.xml A lib/galaxy/datatypes/converters/to_qname_sorted_bam.xml M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/qualityscore.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt M lib/galaxy/exceptions/__init__.py M lib/galaxy/jobs/dynamic_tool_destination.py M lib/galaxy/jobs/handler.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/managers/containers.py M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/model/item_attrs.py M lib/galaxy/security/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/data/__init__.py M lib/galaxy/tools/deps/container_resolvers/__init__.py M lib/galaxy/tools/deps/containers.py M lib/galaxy/tools/deps/mulled/mulled_build.py M lib/galaxy/tools/deps/mulled/util.py M lib/galaxy/tools/deps/resolvers/__init__.py M lib/galaxy/tools/deps/resolvers/brewed_tool_shed_packages.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/deps/resolvers/galaxy_packages.py M lib/galaxy/tools/deps/resolvers/homebrew.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 lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/tools/parser/interface.py M lib/galaxy/tools/parser/output_objects.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/parser/yaml.py M lib/galaxy/tools/test.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/integrated_panel.py M lib/galaxy/tools/toolbox/lineages/interface.py M lib/galaxy/tools/toolbox/panel.py M lib/galaxy/tools/verify/asserts/__init__.py A lib/galaxy/tools/verify/interactor.py A lib/galaxy/tools/verify/script.py M lib/galaxy/tools/verify/test_data.py M lib/galaxy/tools/wrappers.py M lib/galaxy/tools/xsd/galaxy.xsd A lib/galaxy/util/create_history_template.py M lib/galaxy/util/inflection.py M lib/galaxy/util/monitors.py M lib/galaxy/util/none_like.py M lib/galaxy/util/path/__init__.py M lib/galaxy/util/sanitize_html.py M lib/galaxy/util/validation.py M lib/galaxy/visualization/data_providers/genome.py M lib/galaxy/visualization/plugins/resource_parser.py M lib/galaxy/web/base/controller.py M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/webapps/galaxy/api/annotations.py M lib/galaxy/webapps/galaxy/api/folder_contents.py M lib/galaxy/webapps/galaxy/api/page_revisions.py M lib/galaxy/webapps/galaxy/api/pages.py M lib/galaxy/webapps/galaxy/api/remote_files.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/api/visualizations.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/config_schema.yml M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/page.py M lib/galaxy/webapps/galaxy/controllers/tag.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/webapps/reports/controllers/query.py M lib/galaxy/webapps/tool_shed/security/__init__.py M lib/galaxy/workflow/scheduling_manager.py M lib/tool_shed/util/workflow_util.py R scripts/microbes/BeautifulSoup.py M scripts/microbes/harvest_bacteria.py M scripts/migrate_tools/migrate_tools.py M static/style/blue/base.css R templates/webapps/galaxy/history/display_structured.mako R templates/webapps/galaxy/history/view.mako A test-data/qname_sorted.bam M test/api/test_tools.py M test/base/api.py M test/base/driver_util.py M test/base/interactor.py M test/base/testcase.py R test/base/tool_shed_util.py M test/functional/test_data_managers.py M test/functional/test_toolbox.py M test/functional/tools/multi_output_recurse.xml M test/functional/tools/sam_to_bam_native.xml M test/functional/tools/sample_datatypes_conf.xml M test/functional/twilltestcase.py M test/integration/test_data_manager_table_reload.py A test/integration/test_shed_tool_tests.py A test/integration/uses_shed.py M test/shed_functional/base/twilltestcase.py M test/unit/tools/test_parsing.py M test/unit/tools/test_toolbox.py M tools/genomespace/genomespace_exporter.xml M tools/genomespace/genomespace_importer.xml M tools/genomespace/genomespace_push.xml Log Message: ----------- Merge branch 'dev' of https://github.com/bgruening/galaxy into propagate_tags_script Commit: 81e971af1d4e8e39d7b9aae311c1036b3f737c51 https://github.com/galaxyproject/galaxy/commit/81e971af1d4e8e39d7b9aae311c1… Author: anup kumar <anup.rulez(a)gmail.com> Date: 2018-03-09 (Fri, 09 Mar 2018) Changed paths: M scripts/apply_tags.py Log Message: ----------- Fix python lint errors Commit: 122384f33eff5e576e1092a99e9cfdcbcfda2bb7 https://github.com/galaxyproject/galaxy/commit/122384f33eff5e576e1092a99e9c… Author: anup kumar <anup.rulez(a)gmail.com> Date: 2018-03-09 (Fri, 09 Mar 2018) Changed paths: M scripts/apply_tags.py Log Message: ----------- Add print statements with brackets Commit: 6422955a22d9a81359279bacd2ceacc079aff6ed https://github.com/galaxyproject/galaxy/commit/6422955a22d9a81359279bacd2ce… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-20 (Tue, 20 Mar 2018) Changed paths: A scripts/apply_tags.py Log Message: ----------- Merge pull request #5669 from bgruening/propagate_tags_script Add script for propagating hashtags in a Galaxy history Compare: https://github.com/galaxyproject/galaxy/compare/9e2b277fc7d6...6422955a22d9

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[galaxyproject/galaxy] df471d: Add buffer-size to galaxy.yml.sample
by GitHub 20 Mar '18

20 Mar '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: df471d4bbc575c51c59a3b24a59f38cf6828e429 https://github.com/galaxyproject/galaxy/commit/df471d4bbc575c51c59a3b24a59f… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2018-03-07 (Wed, 07 Mar 2018) Changed paths: M config/galaxy.yml.sample Log Message: ----------- Add buffer-size to galaxy.yml.sample Commit: 53e6156ddfc5f5fd1f37542de8f859a5e8beaaad https://github.com/galaxyproject/galaxy/commit/53e6156ddfc5f5fd1f37542de8f8… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2018-03-07 (Wed, 07 Mar 2018) Changed paths: M config/galaxy.yml.sample Log Message: ----------- ASCII Commit: e65f23e1a326dfe1707a0df055f024e94aadb95e https://github.com/galaxyproject/galaxy/commit/e65f23e1a326dfe1707a0df055f0… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2018-03-07 (Wed, 07 Mar 2018) Changed paths: M config/galaxy.yml.sample M config/reports.yml.sample M config/tool_shed.yml.sample M lib/galaxy/webapps/config_manage.py Log Message: ----------- add to config_manage.py and rebuild Commit: df718aee172edc5387c4c91c317ebc478cb37bc0 https://github.com/galaxyproject/galaxy/commit/df718aee172edc5387c4c91c317e… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2018-03-07 (Wed, 07 Mar 2018) Changed paths: M config/galaxy.yml.sample M config/reports.yml.sample M config/tool_shed.yml.sample M lib/galaxy/webapps/config_manage.py Log Message: ----------- typo Commit: 9e2b277fc7d614f5227629ff487b021be361219e https://github.com/galaxyproject/galaxy/commit/9e2b277fc7d614f5227629ff487b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-20 (Tue, 20 Mar 2018) Changed paths: M config/galaxy.yml.sample M config/reports.yml.sample M config/tool_shed.yml.sample M lib/galaxy/webapps/config_manage.py Log Message: ----------- Merge pull request #5658 from blankenberg/uwsg-buffer-size Add buffer-size to galaxy.yml.sample Compare: https://github.com/galaxyproject/galaxy/compare/fbec6ddc3246...9e2b277fc7d6

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[galaxyproject/galaxy] 0fa4ef: allow registration without mail
by GitHub 20 Mar '18

20 Mar '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 0fa4ef24657a711492a0fadcfdb4da58d35d2710 https://github.com/galaxyproject/galaxy/commit/0fa4ef24657a711492a0fadcfdb4… Author: Matthias Bernt <m.bernt(a)ufz.de> Date: 2018-01-17 (Wed, 17 Jan 2018) Changed paths: M lib/galaxy/security/validate_user_input.py M lib/galaxy/webapps/galaxy/controllers/user.py Log Message: ----------- allow registration without mail Commit: 145bba0ad6a8000461006b33b3d35b17604e58a6 https://github.com/galaxyproject/galaxy/commit/145bba0ad6a8000461006b33b3d3… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-20 (Tue, 20 Mar 2018) Changed paths: M .ci/check_py3_compatibility.sh M .ci/flake8_blacklist.txt M .ci/flake8_wrapper.sh M .ci/flake8_wrapper_docstrings.sh M .ci/jenkins/api/run_tests.sh M .ci/jenkins/selenium-compose/run_tests.sh M .ci/jenkins/selenium/run_tests.sh M .gitignore M .travis.yml M Makefile M client/galaxy/scripts/apps/analysis.js A client/galaxy/scripts/apps/chart.js M client/galaxy/scripts/apps/extended.js M client/galaxy/scripts/apps/panels/tool-panel.js A client/galaxy/scripts/components/DisplayStructured.vue A client/galaxy/scripts/components/HistoryView.vue M client/galaxy/scripts/galaxy.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/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/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-data.js M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/form/form-view.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/hdca-li-edit.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/list/list-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/tool/tool-genomespace.js M client/galaxy/scripts/mvc/tours.js M client/galaxy/scripts/mvc/ui/ui-select-genomespace.js M client/galaxy/scripts/mvc/ui/ui-thumbnails.js M client/galaxy/scripts/mvc/upload/collection/collection-view.js M 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static/scripts/utils/add-logging.js R static/scripts/utils/ajax-queue.js R static/scripts/utils/async-save-text.js R static/scripts/utils/config.js R static/scripts/utils/deferred.js R static/scripts/utils/graph.js R static/scripts/utils/levenshtein.js R static/scripts/utils/localization.js R static/scripts/utils/metrics-logger.js R static/scripts/utils/natural-sort.js R static/scripts/utils/query-string-parsing.js R static/scripts/utils/uploadbox.js R static/scripts/utils/utils.js R static/scripts/viz/bbi-data-manager.js R static/scripts/viz/circster.js R static/scripts/viz/phyloviz.js R static/scripts/viz/sweepster.js R static/scripts/viz/trackster.js R static/scripts/viz/trackster/filters.js R static/scripts/viz/trackster/painters.js R static/scripts/viz/trackster/slotting.js R static/scripts/viz/trackster/tracks.js R static/scripts/viz/trackster/util.js R static/scripts/viz/visualization.js R static/scripts/viz/viz_views.js M static/style/blue/base.css M templates/admin/tool_shed_repository/deactivate_or_uninstall_repository.mako M templates/admin/tool_shed_repository/manage_repository_tool_dependencies.mako M templates/admin/tool_shed_repository/reset_metadata_on_selected_repositories.mako M templates/galaxy_client_app.mako M templates/js-app.mako M templates/user/register.mako M templates/webapps/galaxy/dataset/security_common.mako M templates/webapps/galaxy/galaxy.masthead.mako R templates/webapps/galaxy/history/display_structured.mako R templates/webapps/galaxy/history/view.mako M templates/webapps/galaxy/workflow/sharing.mako M templates/webapps/tool_shed/common/reset_metadata_on_selected_repositories.mako M templates/webapps/tool_shed/repository/tool_form.mako A test-data/1.csv A test-data/bam_native_from_sam.bam A test-data/example-bag.zip A test-data/new_tags_1.txt A test-data/qname_sorted.bam M test-data/sam_with_header.sam A test-data/testdir1.zip M test/api/test_dataset_collections.py M test/api/test_libraries.py M test/api/test_tools.py M test/api/test_tools_upload.py M test/api/test_visualizations.py M test/api/test_webhooks.py M test/api/test_workflows.py M test/base/api.py M test/base/driver_util.py M test/base/integration_util.py M test/base/interactor.py M test/base/populators.py M test/base/testcase.py R test/base/tool_shed_util.py M test/base/workflows_format_2/converter.py R test/casperjs/README.txt R test/casperjs/api-anon-history-permission-tests.js R test/casperjs/api-anon-history-tests.js R test/casperjs/api-hda-tests.js R test/casperjs/api-history-permission-tests.js R test/casperjs/casperjs_runner.py R test/casperjs/modules/api.js R test/casperjs/modules/historyoptions.js R test/casperjs/modules/historypanel.js R test/casperjs/modules/tools.js R test/casperjs/modules/user.js R test/casperjs/page-data/selectors.json R test/casperjs/server_env.py R test/casperjs/spaceghost.js R test/casperjs/test-data/simple_test.ga R test/casperjs/utils/simple-galaxy.js M test/docker/base/run_test_wrapper.sh M test/functional/test_data_managers.py M test/functional/test_toolbox.py M test/functional/tools/collection_creates_dynamic_list_of_pairs.xml A test/functional/tools/fail_writing_work_dir_file.xml A test/functional/tools/job_environment_default.xml A test/functional/tools/job_environment_default_legacy.xml A test/functional/tools/job_environment_explicit_shared_home.xml A test/functional/tools/mulled_example_explicit.xml A test/functional/tools/mulled_example_simple.xml A test/functional/tools/multi_output_recurse.xml A test/functional/tools/sam_to_unsorted_bam.xml M test/functional/tools/sample_datatypes_conf.xml M test/functional/tools/samples_tool_conf.xml M test/functional/twilltestcase.py A test/functional/webhooks/history_test1/config.yml R test/functional/webhooks/history_test1/config/history_test1.yml A test/functional/webhooks/history_test2/config.yml R test/functional/webhooks/history_test2/config/history_test2.yml A test/functional/webhooks/masthead_test/config.yml R test/functional/webhooks/masthead_test/config/masthead_test.yml A test/functional/webhooks/phdcomics/__init__.py A test/functional/webhooks/phdcomics/config.yaml R test/functional/webhooks/phdcomics/config/phdcomics.yaml R test/functional/webhooks/phdcomics/helper/__init__.py A test/functional/webhooks/phdcomics/script.js R test/functional/webhooks/phdcomics/static/script.js R test/functional/webhooks/phdcomics/static/styles.css A test/functional/webhooks/phdcomics/styles.css A test/functional/webhooks/trans_object/__init__.py A test/functional/webhooks/trans_object/config.yaml R test/functional/webhooks/trans_object/config/trans_object.yaml R test/functional/webhooks/trans_object/helper/__init__.py A test/functional/webhooks/xkcd/config.yml R test/functional/webhooks/xkcd/config/xkcd.yml A test/functional/webhooks/xkcd/script.js R test/functional/webhooks/xkcd/static/script.js R test/functional/webhooks/xkcd/static/styles.css A test/functional/webhooks/xkcd/styles.css M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/navigation.yml A test/integration/dockerized_job_conf.xml A test/integration/sets_tmp_dir_expression_job_conf.xml A test/integration/sets_tmp_dir_to_true_job_conf.xml A test/integration/simple_job_conf.xml M test/integration/test_data_manager_table_reload.py A test/integration/test_dockerized_jobs.py A test/integration/test_job_environments.py A test/integration/test_shed_tool_tests.py M test/integration/test_upload_configuration_options.py A test/integration/uses_shed.py M test/manual/launch_and_run.sh M test/selenium_tests/framework.py M test/selenium_tests/test_collection_builders.py M test/selenium_tests/test_jupyter.py M test/selenium_tests/test_library_to_collections.py M test/selenium_tests/test_saved_histories.py M test/selenium_tests/test_tool_describing_tours.py M test/selenium_tests/test_tool_form.py M test/shed_functional/base/twilltestcase.py M test/shed_functional/test_data/emboss/datatypes/datatypes_conf.xml A test/unit/config/1705_allow_path_paste/config/galaxy.ini A test/unit/config/__init__.py M test/unit/config/test_config_manage.py M test/unit/jobs/test_mapper.py M test/unit/jobs/test_runner_local.py M test/unit/managers/test_HistoryManager.py M test/unit/tools/test_collect_primary_datasets.py M test/unit/tools/test_evaluation.py M test/unit/tools/test_parsing.py M test/unit/tools/test_tool_validation.py M test/unit/tools/test_toolbox.py M tools/data_source/microbial_import_code.py M tools/data_source/upload.py M tools/data_source/upload.xml M tools/genomespace/genomespace_exporter.xml M tools/genomespace/genomespace_importer.xml M tools/genomespace/genomespace_push.xml M tox.ini Log Message: ----------- Merge remote-tracking branch 'jmchilton/dev' into topic/allow_empty_mail Commit: fbec6ddc3246996291e2baa947aa8b7eb3c82bdc https://github.com/galaxyproject/galaxy/commit/fbec6ddc3246996291e2baa947aa… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-20 (Tue, 20 Mar 2018) Changed paths: M lib/galaxy/security/validate_user_input.py M lib/galaxy/webapps/galaxy/controllers/user.py Log Message: ----------- Merge pull request #5320 from bernt-matthias/topic/allow_empty_mail allow registration with empty email Compare: https://github.com/galaxyproject/galaxy/compare/d95b3dbfd5fe...fbec6ddc3246

1 0

[galaxyproject/galaxy] e66a09: Workflow-to-Job Scheduling Parameters
by GitHub 20 Mar '18

20 Mar '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: e66a091be0fa0cb1e0b9b646331cc4113dc1dfa9 https://github.com/galaxyproject/galaxy/commit/e66a091be0fa0cb1e0b9b646331c… Author: Jeffrey Thiessen <jeffthiessen(a)corefacility.ca> Date: 2017-10-19 (Thu, 19 Oct 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M lib/galaxy/jobs/dynamic_tool_destination.py M lib/galaxy/jobs/mapper.py M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py A lib/galaxy/model/migrate/versions/0136_add_workflow_request_input_parameter_job_options.py M lib/galaxy/tools/execute.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run_request.py M static/maps/mvc/tool/tool-form-composite.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tool/tool-form-composite.js Log Message: ----------- Workflow-to-Job Scheduling Parameters Commit: e46156a073d0987d8a743a8ca92b1ae9f33d337e https://github.com/galaxyproject/galaxy/commit/e46156a073d0987d8a743a8ca92b… Author: Jeffrey Thiessen <jeffthiessen(a)corefacility.ca> Date: 2017-10-19 (Thu, 19 Oct 2017) Changed paths: M lib/galaxy/managers/workflows.py M lib/galaxy/model/migrate/versions/0136_add_workflow_request_input_parameter_job_options.py M lib/galaxy/workflow/modules.py Log Message: ----------- PEP8 fixes Commit: ddb423b29ae3ad5803451255bb0be2b6b991c75c https://github.com/galaxyproject/galaxy/commit/ddb423b29ae3ad5803451255bb0b… Author: Jeffrey Thiessen <jeffthiessen(a)corefacility.ca> Date: 2017-10-19 (Thu, 19 Oct 2017) Changed paths: M lib/galaxy/model/migrate/versions/0136_add_workflow_request_input_parameter_job_options.py M test/unit/jobs/dynamic_tool_destination/mockGalaxy.py Log Message: ----------- Update DTD test object Commit: 0a28b4927cf1e727a22761dc9ad1d59af584c2c1 https://github.com/galaxyproject/galaxy/commit/0a28b4927cf1e727a22761dc9ad1… Author: Jeffrey Thiessen <jeffthiessen(a)corefacility.ca> Date: 2017-10-27 (Fri, 27 Oct 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js A config/workflow_resource_params_conf.xml.sample M lib/galaxy/config.py M lib/galaxy/managers/workflows.py Log Message: ----------- xml parsing Commit: 6157ce757743ec09ab905303222f3cb8597a072e https://github.com/galaxyproject/galaxy/commit/6157ce757743ec09ab905303222f… Author: Jeffrey Thiessen <jeffthiessen(a)corefacility.ca> Date: 2017-10-27 (Fri, 27 Oct 2017) Changed paths: M .ci/flake8_lint_include_list.txt M .travis.yml M Makefile M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/panels/admin-panel.js M client/galaxy/scripts/galaxy.interactive_environments.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/mvc/grid/grid-view.js M client/galaxy/scripts/mvc/library/library-dataset-view.js M client/galaxy/scripts/mvc/library/library-folderlist-view.js M client/galaxy/scripts/mvc/library/library-folderrow-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/library/library-libraryrow-view.js M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js M client/galaxy/scripts/mvc/tours.js M client/galaxy/scripts/utils/utils.js M client/galaxy/style/less/base.less M client/galaxy/style/less/library.less M client/gulpfile.js M client/package.json M client/yarn.lock M config/datatypes_conf.xml.sample M config/galaxy.ini.sample M config/plugins/interactive_environments/jupyter/static/js/jupyter.js M config/plugins/tours/core.galaxy_ui.yaml M config/plugins/tours/core.history.yaml M config/plugins/tours/core.scratchbook.yaml M config/plugins/webhooks/demo/tour_generator/helper/__init__.py M cron/add_manual_builds.py M cron/build_chrom_db.py M cron/parse_builds.py M cron/parse_builds_3_sites.py M doc/schema_template.md A doc/source/releases/17.09.rst M doc/source/releases/17.09_announce.rst A doc/source/releases/18.01_announce.rst M doc/source/releases/index.rst M lib/galaxy/auth/providers/ldap_ad.py M lib/galaxy/config.py M lib/galaxy/containers/docker_model.py M lib/galaxy/datatypes/annotation.py M lib/galaxy/datatypes/assembly.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/constructive_solid_geometry.py M lib/galaxy/datatypes/converters/bed_to_gff_converter.py M lib/galaxy/datatypes/converters/fastqsolexa_to_qual_converter.py M lib/galaxy/datatypes/converters/gff_to_bed_converter.py M lib/galaxy/datatypes/converters/interval_to_bed_converter.py M lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.py M lib/galaxy/datatypes/converters/interval_to_coverage.py M lib/galaxy/datatypes/converters/interval_to_fli.py M lib/galaxy/datatypes/converters/lped_to_fped_converter.py M 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M lib/galaxy/webapps/galaxy/api/requests.py M lib/galaxy/webapps/galaxy/api/roles.py M lib/galaxy/webapps/galaxy/api/samples.py M lib/galaxy/webapps/galaxy/api/tool_data.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/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/dataset.py R lib/galaxy/webapps/galaxy/controllers/external_service.py R lib/galaxy/webapps/galaxy/controllers/external_services.py M lib/galaxy/webapps/galaxy/controllers/library.py M lib/galaxy/webapps/galaxy/controllers/library_common.py R lib/galaxy/webapps/galaxy/controllers/request_type.py R lib/galaxy/webapps/galaxy/controllers/requests.py R lib/galaxy/webapps/galaxy/controllers/requests_admin.py R lib/galaxy/webapps/galaxy/controllers/requests_common.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/galaxy/webapps/galaxy/controllers/tool_runner.py M 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tools/filters/bed_to_gff_converter.py M tools/filters/catWrapper.py M tools/filters/convert_characters.py M tools/filters/gff/extract_GFF_Features.py M tools/filters/gff/gff_filter_by_attribute.py M tools/filters/gff/gff_filter_by_feature_count.py M tools/filters/gff_to_bed_converter.py M tools/filters/gtf_to_bedgraph_converter.py M tools/filters/join.py M tools/filters/lav_to_bed_code.py M tools/filters/mergeCols.py M tools/filters/sff_extract.py M tools/filters/ucsc_gene_bed_to_exon_bed.py M tools/filters/ucsc_gene_bed_to_intron_bed.py M tools/filters/ucsc_gene_table_to_intervals.py M tools/genomespace/genomespace_importer.py M tools/maf/maf_by_block_number.py M tools/maf/maf_filter.py M tools/maf/maf_limit_size.py M tools/maf/maf_limit_to_species.py M tools/maf/maf_reverse_complement.py M tools/maf/maf_stats.py M tools/maf/maf_thread_for_species.py M tools/maf/maf_to_bed.py M tools/maf/vcf_to_maf_customtrack.py M tools/metag_tools/blat_wrapper.py M tools/metag_tools/shrimp_color_wrapper.py M tools/metag_tools/shrimp_wrapper.py M tools/next_gen_conversion/solid2fastq.py M tools/plotting/bar_chart.py M tools/solid_tools/maq_cs_wrapper.py M tools/solid_tools/solid_qual_stats.py M tools/sr_mapping/bfast_wrapper.py M tools/stats/aggregate_scores_in_intervals.py M tools/stats/filtering.py M tools/stats/grouping.py M tools/stats/gsummary.py M tox.ini Log Message: ----------- update dev branch Commit: 78f64de4a555e2db7ab720d9df5e973de25e3c00 https://github.com/galaxyproject/galaxy/commit/78f64de4a555e2db7ab720d9df5e… Author: Jeffrey Thiessen <jeffthiessen(a)corefacility.ca> Date: 2017-10-27 (Fri, 27 Oct 2017) Changed paths: M .ci/flake8_lint_include_list.txt M .travis.yml M Makefile M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/panels/admin-panel.js M client/galaxy/scripts/galaxy.interactive_environments.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/page.js M 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aa4a1560a70763883e59c001b459400cd1f34ea9 https://github.com/galaxyproject/galaxy/commit/aa4a1560a70763883e59c001b459… Author: Jeffrey Thiessen <jeffthiessen(a)corefacility.ca> Date: 2017-10-27 (Fri, 27 Oct 2017) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- pep8 Commit: f8313a3428545cdc89bcfb8b9338a59d9e4ae0f3 https://github.com/galaxyproject/galaxy/commit/f8313a3428545cdc89bcfb8b9338… Author: Jeffrey Thiessen <jeffthiessen(a)corefacility.ca> Date: 2017-10-30 (Mon, 30 Oct 2017) Changed paths: M lib/galaxy/jobs/dynamic_tool_destination.py M lib/galaxy/managers/workflows.py Log Message: ----------- small fix and refactor Commit: 3bc9506c547778574f1a5f2f7cfd8f7119f48522 https://github.com/galaxyproject/galaxy/commit/3bc9506c547778574f1a5f2f7cfd… Author: Jeffrey Thiessen <jeffthiessen(a)corefacility.ca> Date: 2017-10-30 (Mon, 30 Oct 2017) Changed paths: M lib/galaxy/jobs/dynamic_tool_destination.py M lib/galaxy/managers/workflows.py M lib/galaxy/util/__init__.py Log Message: ----------- Validate users allowed priorities before running job from DTD, + Refactoring Commit: c67523c27e9550b90e3de77a7f759443990d0022 https://github.com/galaxyproject/galaxy/commit/c67523c27e9550b90e3de77a7f75… Author: Jeffrey Thiessen <jeffthiessen(a)corefacility.ca> Date: 2017-10-30 (Mon, 30 Oct 2017) Changed paths: M config/workflow_resource_params_conf.xml.sample Log Message: ----------- fix sample file Commit: 6a7522b3a4afe573f2533eae7541a8cc521d6ddd https://github.com/galaxyproject/galaxy/commit/6a7522b3a4afe573f2533eae7541… Author: Jeffrey Thiessen <jeffthiessen(a)corefacility.ca> Date: 2017-11-02 (Thu, 02 Nov 2017) Changed paths: M lib/galaxy/jobs/mapper.py M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py R lib/galaxy/model/migrate/versions/0136_add_workflow_request_input_parameter_job_options.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run_request.py Log Message: ----------- Fixed use of 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test/unit/datatypes/dataproviders/test_base_dataproviders.py M test/unit/datatypes/dataproviders/test_line_dataproviders.py M test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py M test/unit/jobs/test_job_wrapper.py M test/unit/jobs/test_mapper.py M test/unit/jobs/test_runner_local.py M test/unit/managers/base.py M test/unit/managers/test_CollectionManager.py M test/unit/managers/test_DatasetManager.py M test/unit/managers/test_HDAManager.py M test/unit/managers/test_HDCAManager.py M test/unit/managers/test_HistoryContentsManager.py M test/unit/managers/test_HistoryManager.py M test/unit/managers/test_UserManager.py M test/unit/shed_unit/test_installed_repository_manager.py M test/unit/shed_unit/test_tool_panel_manager.py M test/unit/test_objectstore.py M test/unit/tools/test_actions.py M test/unit/tools/test_collect_primary_datasets.py M test/unit/tools/test_column_parameters.py M test/unit/tools/test_conda_resolution.py M test/unit/tools/test_data_parameters.py M test/unit/tools/test_dataset_matcher.py M test/unit/tools/test_evaluation.py M test/unit/tools/test_execution.py M test/unit/tools/test_history_imp_exp.py M test/unit/tools/test_parameter_parsing.py M test/unit/tools/test_parsing.py M test/unit/tools/test_select_parameters.py M test/unit/tools/test_tool_deps.py M test/unit/tools/test_tool_loader.py M test/unit/tools/test_toolbox.py M test/unit/tools/test_watcher.py M test/unit/tools_support.py M test/unit/visualizations/plugins/test_VisualizationPlugin.py M test/unit/visualizations/plugins/test_VisualizationsRegistry.py M test/unit/web/framework/test_webapp.py M test/unit/workflows/test_modules.py M test/unit/workflows/test_run_parameters.py M test/unit/workflows/test_workflow_progress.py M tools/data_source/microbial_import.xml M tools/filters/gff/gff_filter_by_attribute.py M tools/filters/gff/gff_filter_by_feature_count.py M tools/phenotype_association/senatag.py M tox.ini Log Message: ----------- merge conflicts Commit: 784431b9819f1b04664431c53f8b6816055015ca https://github.com/galaxyproject/galaxy/commit/784431b9819f1b04664431c53f8b… Author: Jeffrey Thiessen <jeffreylthiessen(a)gmail.com> Date: 2017-11-20 (Mon, 20 Nov 2017) Changed paths: M static/maps/mvc/tool/tool-form-composite.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tool/tool-form-composite.js Log Message: ----------- update static files after merge confict fix Commit: 497df0d4a8728a2741533e4f3bc7e3637b04303b https://github.com/galaxyproject/galaxy/commit/497df0d4a8728a2741533e4f3bc7… Author: Jeffrey Thiessen <jeffreylthiessen(a)gmail.com> Date: 2017-11-21 (Tue, 21 Nov 2017) Changed paths: M lib/galaxy/jobs/dynamic_tool_destination.py Log Message: ----------- fix import order Commit: b7b55ad0a4f20087f0196d6828c6ec9daaf25e11 https://github.com/galaxyproject/galaxy/commit/b7b55ad0a4f20087f0196d6828c6… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M config/galaxy.ini.sample A config/workflow_resource_mapper_conf.yml.sample M config/workflow_resource_params_conf.xml.sample M lib/galaxy/config.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/dynamic_tool_destination.py M lib/galaxy/jobs/mapper.py M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/execute.py M lib/galaxy/util/__init__.py M lib/galaxy/workflow/modules.py A lib/galaxy/workflow/resources/__init__.py A lib/galaxy/workflow/resources/example.py.sample M lib/galaxy/workflow/run_request.py Log Message: ----------- Refactor workflow resource parameters. This refactoring is untested and definitely broken in a couple places - but it illustrates broad directions I'd like the work to move in. - On the input side of things - it serializes the individual parameters to the database each as its own instance of a WorkflowRequestInputParameter. In a couple places I've retried to refactor away from the terminology of "workflow_options" toward resource parameters - there are already other kinds of workflow options. - On the backend - I've moved a lot of the logic into galaxy.workflow.resources and tried to make it more extensible. The goal is to allow the admin to specify any kind of function to define the parameters as they want for a given workflow and user - but to implement the existing "group based" variant desired by phac-nml as just one potential variant of that with a convient YAML description. - This moves the priority validation for workflow priorities out of the plugin and handles it up when the request is being handled. This is kind of a hack - but it results in cleaner separation between the DTD and code for defining workflow priorities so that the DTD would work with any potential workflow parameter mapping XML format or dynamic mapping Python function. - This exposes the workflow parameters to traditional dynamic job destinations (the DTD framework re-computes it from the "job" object and that is fine). Commit: 5c44ed54b66271d412b87b97f29e88241e491c98 https://github.com/galaxyproject/galaxy/commit/5c44ed54b66271d412b87b97f29e… Author: Jeffrey Thiessen <jeffreylthiessen(a)gmail.com> Date: 2017-12-12 (Tue, 12 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M config/workflow_resource_mapper_conf.yml.sample M lib/galaxy/jobs/dynamic_tool_destination.py M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/resources/__init__.py M lib/galaxy/workflow/resources/example.py.sample M lib/galaxy/workflow/run_request.py M static/maps/mvc/tool/tool-form-composite.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tool/tool-form-composite.js Log Message: ----------- Added and fixed changes from 'Refactor workflow resource parameters.' by jmchilton Commit: f1879bee2e4e352a68f70ed223149cf5721dcccd https://github.com/galaxyproject/galaxy/commit/f1879bee2e4e352a68f70ed22314… Author: Jeffrey Thiessen <jeffreylthiessen(a)gmail.com> Date: 2017-12-12 (Tue, 12 Dec 2017) Changed paths: M .gitignore M .travis.yml M Makefile M client/README.md M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/analysis.js A client/galaxy/scripts/apps/extended.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 A client/galaxy/scripts/components/Citations.vue A client/galaxy/scripts/components/HistoryImport.vue A client/galaxy/scripts/components/UserAPIKeys.vue M client/galaxy/scripts/galaxy.library.js M client/galaxy/scripts/galaxy.pages.js M client/galaxy/scripts/layout/generic-nav-view.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/panel.js M client/galaxy/scripts/layout/scratchbook.js R 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static/scripts/viz/viz_views.js Log Message: ----------- fix static files Commit: bac40dcb21e37292062a02bcb5b7df54a2c6a66e https://github.com/galaxyproject/galaxy/commit/bac40dcb21e37292062a02bcb5b7… Author: Jeffrey Thiessen <jeffreylthiessen(a)gmail.com> Date: 2017-12-13 (Wed, 13 Dec 2017) Changed paths: M lib/galaxy/jobs/dynamic_tool_destination.py M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/workflow/resources/__init__.py M lib/galaxy/workflow/resources/example.py M test/unit/jobs/test_mapper.py Log Message: ----------- pep8 + tests Commit: cb45e57367a9383d192dc49335ea0ee3524342de https://github.com/galaxyproject/galaxy/commit/cb45e57367a9383d192dc49335ea… Author: Jeffrey Thiessen <jeffreylthiessen(a)gmail.com> Date: 2017-12-13 (Wed, 13 Dec 2017) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/workflow/resources/__init__.py M test/unit/jobs/test_mapper.py Log Message: ----------- undo test case change Commit: a9912296f768e3fc2acab2cc34c044dc25880df9 https://github.com/galaxyproject/galaxy/commit/a9912296f768e3fc2acab2cc34c0… Author: Jeffrey Thiessen <jeffreylthiessen(a)gmail.com> Date: 2017-12-13 (Wed, 13 Dec 2017) Changed paths: M lib/galaxy/workflow/resources/__init__.py Log Message: ----------- flake8 Commit: fef1208a1049a453e6c3249f179ded4e3cc7a394 https://github.com/galaxyproject/galaxy/commit/fef1208a1049a453e6c3249f179d… Author: Jeffrey Thiessen <jeffreylthiessen(a)gmail.com> Date: 2017-12-13 (Wed, 13 Dec 2017) Changed paths: M lib/galaxy/workflow/resources/__init__.py Log Message: ----------- fixed pep8 Commit: 2d35acafd1806f35f25ba76e0c22f07a24f1356c https://github.com/galaxyproject/galaxy/commit/2d35acafd1806f35f25ba76e0c22… Author: Jeffrey Thiessen <jeffreylthiessen(a)gmail.com> Date: 2017-12-13 (Wed, 13 Dec 2017) Changed paths: M lib/galaxy/tools/execute.py Log Message: ----------- fix unit test cases Commit: 7c3c984242161378bcbe626369755b58dc8e6131 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test/integration/test_upload_configuration_options.py M test/selenium_tests/test_library_contents.py A test/selenium_tests/test_library_to_collections.py M test/selenium_tests/test_tool_form.py M test/unit/jobs/test_job_output_checker.py M test/unit/jobs/test_runner_local.py M test/unit/tools/test_collect_primary_datasets.py M test/unit/tools/test_parsing.py M tools/data_source/microbial_import_code.py M tools/data_source/upload.py M tools/genomespace/genomespace_importer.py M tox.ini Log Message: ----------- Merge dev into branch + merge conflict fixes Commit: 33c01aba6fb5dcdf4c2e33c1756eec1cbf2cfb90 https://github.com/galaxyproject/galaxy/commit/33c01aba6fb5dcdf4c2e33c1756e… Author: Jeffrey Thiessen <jeffreylthiessen(a)gmail.com> Date: 2018-01-18 (Thu, 18 Jan 2018) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- fixed missing comma Commit: af3a69b1afa6637308ca4f667a745b2e02859ae2 https://github.com/galaxyproject/galaxy/commit/af3a69b1afa6637308ca4f667a74… Author: Jeffrey Thiessen <jeffreylthiessen(a)gmail.com> Date: 2018-02-06 (Tue, 06 Feb 2018) Changed paths: M lib/galaxy/jobs/dynamic_tool_destination.py M lib/galaxy/model/__init__.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/resources/__init__.py R lib/galaxy/workflow/resources/example.py Log Message: ----------- remove/fix todo's Commit: 8cd6df15828d69739915d7c1bf6d6e0f0116fe10 https://github.com/galaxyproject/galaxy/commit/8cd6df15828d69739915d7c1bf6d… Author: Jeffrey Thiessen <jeffreylthiessen(a)gmail.com> Date: 2018-02-06 (Tue, 06 Feb 2018) Changed paths: M .ci/check_py3_compatibility.sh M .ci/flake8_blacklist.txt M .ci/flake8_wrapper.sh M .ci/flake8_wrapper_docstrings.sh M .ci/jenkins/api/run_tests.sh M .ci/jenkins/selenium-compose/run_tests.sh M .ci/jenkins/selenium/run_tests.sh M .gitignore M .travis.yml M Makefile M client/galaxy/scripts/apps/extended.js M client/galaxy/scripts/layout/masthead.js M client/galaxy/scripts/layout/menu.js M 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test/integration/sets_tmp_dir_expression_job_conf.xml A test/integration/sets_tmp_dir_to_true_job_conf.xml A test/integration/simple_job_conf.xml A test/integration/test_dockerized_jobs.py A test/integration/test_job_environments.py M test/manual/launch_and_run.sh M test/selenium_tests/test_tool_describing_tours.py M test/shed_functional/base/twilltestcase.py A test/unit/config/1705_allow_path_paste/config/galaxy.ini A test/unit/config/__init__.py M test/unit/config/test_config_manage.py M test/unit/jobs/test_mapper.py M test/unit/jobs/test_runner_local.py M test/unit/managers/test_HistoryManager.py M test/unit/tools/test_evaluation.py M tox.ini Log Message: ----------- merge conflicts Commit: 7d8cddb40087fa1186dc16350f485d1e863fa30e https://github.com/galaxyproject/galaxy/commit/7d8cddb40087fa1186dc16350f48… Author: Jeffrey Thiessen <jeffreylthiessen(a)gmail.com> Date: 2018-02-08 (Thu, 08 Feb 2018) Changed paths: M config/galaxy.yml.sample M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- move vars from galaxy.ini to galaxy.yml Commit: 3bcb80386300c17db33d51397f71d120693d9306 https://github.com/galaxyproject/galaxy/commit/3bcb80386300c17db33d51397f71… Author: Jeffrey Thiessen <jeffreylthiessen(a)gmail.com> Date: 2018-02-08 (Thu, 08 Feb 2018) Changed paths: M client/galaxy/scripts/galaxy.js M client/galaxy/scripts/utils/localization.js M client/package.json M config/datatypes_conf.xml.sample M config/galaxy.yml.sample M config/user_preferences_extra_conf.yml.sample M doc/source/admin/galaxy_options.rst M lib/galaxy/config.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/genetics.py M lib/galaxy/jobs/actions/post.py M lib/galaxy/managers/configuration.py M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/views.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/web/framework/middleware/sentry.py M lib/galaxy/web/security/__init__.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/config_schema.yml M scripts/common_startup.sh M static/style/blue/base.css M templates/webapps/galaxy/galaxy.masthead.mako M test/functional/twilltestcase.py Log Message: ----------- merge in dev Commit: 182bfbe50d9277f7bda6a2deb9fc83060160e14f https://github.com/galaxyproject/galaxy/commit/182bfbe50d9277f7bda6a2deb9fc… Author: Jeffrey Thiessen <jeffreylthiessen(a)gmail.com> Date: 2018-02-13 (Tue, 13 Feb 2018) Changed paths: M Makefile M config/datatypes_conf.xml.sample M config/reports.yml.sample M config/tool_conf.xml.sample M doc/source/admin/reports_options.rst M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/interval.py M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt M lib/galaxy/managers/taggable.py M lib/galaxy/managers/tags.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/basic.py A lib/galaxy/tools/tag_collection_from_file.xml M lib/galaxy/web/framework/middleware/sentry.py M lib/tool_shed/tools/tool_validator.py M templates/webapps/galaxy/workflow/sharing.mako A test-data/new_tags_1.txt M test/base/interactor.py M test/functional/tools/samples_tool_conf.xml M test/unit/tools/test_tool_validation.py Log Message: ----------- merge dev into branch Commit: 1a66a8d2e6f33aed07e9e50d34d7d561eb5b3274 https://github.com/galaxyproject/galaxy/commit/1a66a8d2e6f33aed07e9e50d34d7… Author: Jeffrey Thiessen <jeffreylthiessen(a)gmail.com> Date: 2018-02-13 (Tue, 13 Feb 2018) Changed paths: M lib/galaxy/workflow/resources/__init__.py Log Message: ----------- fix by group validation Commit: 9c4494490944d64915240a5b45909e09eab401bc https://github.com/galaxyproject/galaxy/commit/9c4494490944d64915240a5b4590… Author: Jeffrey Thiessen <jeffreylthiessen(a)gmail.com> Date: 2018-02-13 (Tue, 13 Feb 2018) Changed paths: R static/maps/mvc/tool/tool-form-composite.js.map R static/scripts/bundled/analysis.bundled.js.map R static/scripts/bundled/libs.bundled.js.map R static/scripts/libs/bibtex.js Log Message: ----------- 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lib/galaxy/datatypes/converters/bam_native_to_bam_converter.xml M lib/galaxy/datatypes/converters/sam_to_bam_native.xml M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/model/mapping.py M lib/galaxy/util/xml_macros.py M lib/galaxy/visualization/plugins/config_parser.py M lib/galaxy/visualization/plugins/plugin.py M lib/galaxy/visualization/plugins/registry.py M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/webapps/galaxy/api/visualizations.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/page.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M lib/galaxy/webapps/galaxy/controllers/workflow.py R static/scripts/packed M static/style/blue/base.css M templates/js-app.mako M test/api/test_visualizations.py Log Message: ----------- merge from dev Commit: 451342ed9ea0f60d674b04256c67abdf441d1189 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----------- fix merge conflict Commit: d95b3dbfd5fecb776aa95337c6405d8dd5093e39 https://github.com/galaxyproject/galaxy/commit/d95b3dbfd5fecb776aa95337c640… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-20 (Tue, 20 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M config/galaxy.yml.sample A config/workflow_resource_mapper_conf.yml.sample A config/workflow_resource_params_conf.xml.sample M lib/galaxy/config.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/dynamic_tool_destination.py M lib/galaxy/jobs/mapper.py M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/execute.py M lib/galaxy/util/__init__.py M lib/galaxy/webapps/galaxy/config_schema.yml M lib/galaxy/workflow/modules.py A lib/galaxy/workflow/resources/__init__.py A lib/galaxy/workflow/resources/example.py.sample M lib/galaxy/workflow/run_request.py M test/unit/jobs/dynamic_tool_destination/mockGalaxy.py Log Message: ----------- Merge pull request #4830 from phac-nml/dev Workflow-to-Job Scheduling Parameters Compare: https://github.com/galaxyproject/galaxy/compare/2f41ccc13d04...d95b3dbfd5fe

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[galaxyproject/galaxy] 313aa0: Change initial bind for slow query logging -- this...
by GitHub 20 Mar '18

20 Mar '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 313aa0a6c9d4470c7da16aba24f983ebf73401ff https://github.com/galaxyproject/galaxy/commit/313aa0a6c9d4470c7da16aba24f9… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-01-26 (Fri, 26 Jan 2018) Changed paths: M lib/galaxy/model/orm/engine_factory.py Log Message: ----------- Change initial bind for slow query logging -- this should allow multiple cursor start/stops, timing the whole transaction start->finish. Commit: dcdc38107d46574dbdbc31be76e10af087a52ef7 https://github.com/galaxyproject/galaxy/commit/dcdc38107d46574dbdbc31be76e1… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-20 (Tue, 20 Mar 2018) Changed paths: M .ci/check_py3_compatibility.sh M .ci/flake8_blacklist.txt M .ci/flake8_wrapper.sh M .ci/flake8_wrapper_docstrings.sh M .gitignore M .travis.yml M Makefile M client/galaxy/scripts/apps/analysis.js A client/galaxy/scripts/apps/chart.js M client/galaxy/scripts/apps/extended.js M client/galaxy/scripts/apps/panels/tool-panel.js A client/galaxy/scripts/components/DisplayStructured.vue A client/galaxy/scripts/components/HistoryView.vue M client/galaxy/scripts/galaxy.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/scratchbook.js M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/collection/collection-view.js M 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static/scripts/mvc/ui/ui-select-ftp.js R static/scripts/mvc/ui/ui-select-genomespace.js R static/scripts/mvc/ui/ui-select-library.js R static/scripts/mvc/ui/ui-select.js R static/scripts/mvc/ui/ui-slider.js R static/scripts/mvc/ui/ui-table.js R static/scripts/mvc/ui/ui-tabs.js R static/scripts/mvc/ui/ui-thumbnails.js R static/scripts/mvc/upload/collection/collection-row.js R static/scripts/mvc/upload/collection/collection-view.js R static/scripts/mvc/upload/composite/composite-row.js R static/scripts/mvc/upload/composite/composite-view.js R static/scripts/mvc/upload/default/default-row.js R static/scripts/mvc/upload/default/default-view.js R static/scripts/mvc/upload/upload-button.js R static/scripts/mvc/upload/upload-extension.js R static/scripts/mvc/upload/upload-ftp.js R static/scripts/mvc/upload/upload-model.js R static/scripts/mvc/upload/upload-settings.js R static/scripts/mvc/upload/upload-view.js R static/scripts/mvc/user/user-custom-builds.js R static/scripts/mvc/user/user-model.js R static/scripts/mvc/user/user-preferences.js R static/scripts/mvc/user/user-quotameter.js R static/scripts/mvc/visualization/visualization-model.js R static/scripts/mvc/webhooks.js R static/scripts/mvc/workflow/workflow-canvas.js R static/scripts/mvc/workflow/workflow-connector.js R static/scripts/mvc/workflow/workflow-forms.js R static/scripts/mvc/workflow/workflow-icons.js R static/scripts/mvc/workflow/workflow-manager.js R static/scripts/mvc/workflow/workflow-model.js R static/scripts/mvc/workflow/workflow-node.js R static/scripts/mvc/workflow/workflow-terminals.js R static/scripts/mvc/workflow/workflow-view-data.js R static/scripts/mvc/workflow/workflow-view-node.js R static/scripts/mvc/workflow/workflow-view-terminals.js R static/scripts/mvc/workflow/workflow-view.js R static/scripts/mvc/workflow/workflow.js R static/scripts/nls/de/locale.js R static/scripts/nls/es/locale.js R static/scripts/nls/fr/locale.js R static/scripts/nls/ja/locale.js R static/scripts/nls/locale.js R static/scripts/nls/zh/locale.js R static/scripts/onload.js R static/scripts/packed R static/scripts/polyfills.js R static/scripts/reports/run_stats.js R static/scripts/toolshed/groups/group-detail-view.js R static/scripts/toolshed/groups/group-list-view.js R static/scripts/toolshed/groups/group-listrow-view.js R static/scripts/toolshed/groups/group-model.js R static/scripts/toolshed/toolshed.groups.js R static/scripts/ui/autocom_tagging.js R static/scripts/ui/editable-text.js R static/scripts/ui/fa-icon-button.js R static/scripts/ui/filter-control.js R static/scripts/ui/hoverhighlight.js R static/scripts/ui/loading-indicator.js R static/scripts/ui/mode-button.js R static/scripts/ui/pagination.js R static/scripts/ui/peek-column-selector.js R static/scripts/ui/popupmenu.js R static/scripts/ui/scroll-panel.js R static/scripts/ui/search-input.js R static/scripts/utils/add-logging.js R static/scripts/utils/ajax-queue.js R static/scripts/utils/async-save-text.js R static/scripts/utils/config.js R static/scripts/utils/deferred.js R static/scripts/utils/graph.js R static/scripts/utils/levenshtein.js R static/scripts/utils/localization.js R static/scripts/utils/metrics-logger.js R static/scripts/utils/natural-sort.js R static/scripts/utils/query-string-parsing.js R static/scripts/utils/uploadbox.js R static/scripts/utils/utils.js R static/scripts/viz/bbi-data-manager.js R static/scripts/viz/circster.js R static/scripts/viz/phyloviz.js R static/scripts/viz/sweepster.js R static/scripts/viz/trackster.js R static/scripts/viz/trackster/filters.js R static/scripts/viz/trackster/painters.js R static/scripts/viz/trackster/slotting.js R static/scripts/viz/trackster/tracks.js R static/scripts/viz/trackster/util.js R static/scripts/viz/visualization.js R static/scripts/viz/viz_views.js M static/style/blue/base.css M templates/galaxy_client_app.mako M templates/js-app.mako M templates/webapps/galaxy/dataset/security_common.mako M templates/webapps/galaxy/galaxy.masthead.mako R templates/webapps/galaxy/history/display_structured.mako R templates/webapps/galaxy/history/view.mako M templates/webapps/galaxy/workflow/sharing.mako M templates/webapps/tool_shed/repository/tool_form.mako A test-data/1.csv A test-data/example-bag.zip A test-data/new_tags_1.txt A test-data/qname_sorted.bam A test-data/testdir1.zip M test/api/test_dataset_collections.py M test/api/test_libraries.py M test/api/test_tools.py M test/api/test_tools_upload.py M test/api/test_visualizations.py M test/api/test_webhooks.py M test/api/test_workflows.py M test/base/api.py M test/base/driver_util.py M test/base/integration_util.py M test/base/interactor.py M test/base/populators.py M test/base/testcase.py R test/base/tool_shed_util.py M test/base/workflows_format_2/converter.py R test/casperjs/README.txt R test/casperjs/api-anon-history-permission-tests.js R test/casperjs/api-anon-history-tests.js R test/casperjs/api-hda-tests.js R test/casperjs/api-history-permission-tests.js R test/casperjs/casperjs_runner.py R test/casperjs/modules/api.js R test/casperjs/modules/historyoptions.js R test/casperjs/modules/historypanel.js R test/casperjs/modules/tools.js R test/casperjs/modules/user.js R test/casperjs/page-data/selectors.json R test/casperjs/server_env.py R test/casperjs/spaceghost.js R test/casperjs/test-data/simple_test.ga R test/casperjs/utils/simple-galaxy.js M test/functional/test_data_managers.py M test/functional/test_toolbox.py M test/functional/tools/collection_creates_dynamic_list_of_pairs.xml A test/functional/tools/fail_writing_work_dir_file.xml M test/functional/tools/multi_output_recurse.xml R test/functional/tools/sam_to_bam_native.xml A test/functional/tools/sam_to_unsorted_bam.xml M test/functional/tools/sample_datatypes_conf.xml M test/functional/tools/samples_tool_conf.xml M test/functional/twilltestcase.py A test/functional/webhooks/history_test1/config.yml R test/functional/webhooks/history_test1/config/history_test1.yml A test/functional/webhooks/history_test2/config.yml R test/functional/webhooks/history_test2/config/history_test2.yml A test/functional/webhooks/masthead_test/config.yml R test/functional/webhooks/masthead_test/config/masthead_test.yml A test/functional/webhooks/phdcomics/__init__.py A test/functional/webhooks/phdcomics/config.yaml R test/functional/webhooks/phdcomics/config/phdcomics.yaml R test/functional/webhooks/phdcomics/helper/__init__.py A test/functional/webhooks/phdcomics/script.js R test/functional/webhooks/phdcomics/static/script.js R test/functional/webhooks/phdcomics/static/styles.css A test/functional/webhooks/phdcomics/styles.css A test/functional/webhooks/trans_object/__init__.py A test/functional/webhooks/trans_object/config.yaml R test/functional/webhooks/trans_object/config/trans_object.yaml R test/functional/webhooks/trans_object/helper/__init__.py A test/functional/webhooks/xkcd/config.yml R test/functional/webhooks/xkcd/config/xkcd.yml A test/functional/webhooks/xkcd/script.js R test/functional/webhooks/xkcd/static/script.js R test/functional/webhooks/xkcd/static/styles.css A test/functional/webhooks/xkcd/styles.css M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/navigation.yml M test/integration/test_data_manager_table_reload.py A test/integration/test_shed_tool_tests.py M test/integration/test_upload_configuration_options.py A test/integration/uses_shed.py M test/selenium_tests/framework.py M test/selenium_tests/test_collection_builders.py M test/selenium_tests/test_jupyter.py M test/selenium_tests/test_library_to_collections.py M test/selenium_tests/test_saved_histories.py M test/selenium_tests/test_tool_describing_tours.py M test/selenium_tests/test_tool_form.py M test/shed_functional/base/twilltestcase.py M test/shed_functional/test_data/emboss/datatypes/datatypes_conf.xml M test/unit/tools/test_parsing.py M test/unit/tools/test_tool_validation.py M test/unit/tools/test_toolbox.py M tools/data_source/upload.py M tools/data_source/upload.xml M tools/genomespace/genomespace_exporter.xml M tools/genomespace/genomespace_importer.xml M tools/genomespace/genomespace_push.xml M tox.ini Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into slow_query_logging_tweaks Commit: 2f41ccc13d0447aaa0a566b37fc317be2ab5cbf5 https://github.com/galaxyproject/galaxy/commit/2f41ccc13d0447aaa0a566b37fc3… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-20 (Tue, 20 Mar 2018) Changed paths: M lib/galaxy/model/orm/engine_factory.py Log Message: ----------- Merge pull request #5401 from dannon/slow_query_logging_tweaks Change initial bind for slow query logging Compare: https://github.com/galaxyproject/galaxy/compare/b0761de45438...2f41ccc13d04

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[galaxyproject/galaxy] 8330bb: Drop old charts building from makefile/package scr...
by GitHub 20 Mar '18

20 Mar '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 8330bbfe996d92fc937c851497b097dc0746279a https://github.com/galaxyproject/galaxy/commit/8330bbfe996d92fc937c851497b0… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-20 (Tue, 20 Mar 2018) Changed paths: M Makefile M client/package.json Log Message: ----------- Drop old charts building from makefile/package scripts -- this is no longer necessary and charts are individually packed. Commit: 3e10656e1abbdb9505e2abdb3ce50bc897c909d0 https://github.com/galaxyproject/galaxy/commit/3e10656e1abbdb9505e2abdb3ce5… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-20 (Tue, 20 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/collection/collection-model.js Log Message: ----------- Make client-format (minor, unrelated to charts cleanup in this branch) Commit: b0761de4543851ed1282887c9afb5e088177fa3a https://github.com/galaxyproject/galaxy/commit/b0761de4543851ed1282887c9afb… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-03-20 (Tue, 20 Mar 2018) Changed paths: M Makefile M client/galaxy/scripts/mvc/collection/collection-model.js M client/package.json Log Message: ----------- Merge pull request #5737 from dannon/charts-build-cleanup Drop old charts building from makefile/package scripts Compare: https://github.com/galaxyproject/galaxy/compare/2b8eb1ea7783...b0761de45438

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[galaxyproject/galaxy] 17e2bd: fixed tab highlighting issue for user->preferences
by GitHub 20 Mar '18

20 Mar '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 17e2bd38ad69870fabfe3e5e5a2dc05305265539 https://github.com/galaxyproject/galaxy/commit/17e2bd38ad69870fabfe3e5e5a2d… Author: qiagu <guqiang01(a)gmail.com> Date: 2018-03-12 (Mon, 12 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/user/user-preferences.js Log Message: ----------- fixed tab highlighting issue for user->preferences Commit: 6bcbc54e6fbc25d832c776d3004cffb41b05c67f https://github.com/galaxyproject/galaxy/commit/6bcbc54e6fbc25d832c776d3004c… Author: qiagu <guqiang01(a)gmail.com> Date: 2018-03-12 (Mon, 12 Mar 2018) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/mvc/form/form-wrapper.js Log Message: ----------- fixed tab highlighting issue for user->preferences->forms Commit: e72b9aa6d0b66a2aa0c8eba904ac8bc7aa67f46a https://github.com/galaxyproject/galaxy/commit/e72b9aa6d0b66a2aa0c8eba904ac… Author: qiagu <guqiang01(a)gmail.com> Date: 2018-03-12 (Mon, 12 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/user/user-custom-builds.js Log Message: ----------- fixed tab highlighting issue for user->custom builds Commit: 94404aa4ebe30c90c08cb555e66c993c91a1503c https://github.com/galaxyproject/galaxy/commit/94404aa4ebe30c90c08cb555e66c… Author: qiagu <guqiang01(a)gmail.com> Date: 2018-03-12 (Mon, 12 Mar 2018) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/mvc/grid/grid-shared.js Log Message: ----------- linked /visualizations/(:action_id) to tab visualization Commit: f7f3698757d8b597d2da1bb917414ca4ee1b103f https://github.com/galaxyproject/galaxy/commit/f7f3698757d8b597d2da1bb91741… Author: qiagu <guqiang01(a)gmail.com> Date: 2018-03-12 (Mon, 12 Mar 2018) Changed paths: M client/galaxy/scripts/apps/analysis.js Log Message: ----------- linked /pages/create, /pages/edit/, /pages/(:action_id) to tab user Commit: 00bf7f666ec863df2434eb056a4c436b33d125e6 https://github.com/galaxyproject/galaxy/commit/00bf7f666ec863df2434eb056a4c… Author: qiagu <guqiang01(a)gmail.com> Date: 2018-03-12 (Mon, 12 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-edit-attributes.js Log Message: ----------- linked /datasets/edit to tab user Commit: 6202475532bc1e91f98e250fff9c32dab0f78493 https://github.com/galaxyproject/galaxy/commit/6202475532bc1e91f98e250fff9c… Author: qiagu <guqiang01(a)gmail.com> Date: 2018-03-12 (Mon, 12 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-error.js Log Message: ----------- linked /datasets/error to tab user Commit: 8bac244d26ce403ddfa45cf8aa618a1cc9f9cb9c https://github.com/galaxyproject/galaxy/commit/8bac244d26ce403ddfa45cf8aa61… Author: qiagu <guqiang01(a)gmail.com> Date: 2018-03-12 (Mon, 12 Mar 2018) Changed paths: M client/galaxy/scripts/apps/analysis.js Log Message: ----------- linked /visualizations/edit to tab visualization Commit: b8b0af37436e9a62111bf1085f671133df570176 https://github.com/galaxyproject/galaxy/commit/b8b0af37436e9a62111bf1085f67… Author: qiagu <guqiang01(a)gmail.com> Date: 2018-03-12 (Mon, 12 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/visualization/visualization-view.js Log Message: ----------- linked /visualizations/dataset_id=(:dataset_id) to tab visualization Commit: e21c3709f1479c10cf953c4f977dc6130f259e78 https://github.com/galaxyproject/galaxy/commit/e21c3709f1479c10cf953c4f977d… Author: qiagu <guqiang01(a)gmail.com> Date: 2018-03-12 (Mon, 12 Mar 2018) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/mvc/workflow/workflow.js Log Message: ----------- linked /workflows/create/, /workflows/import_workflow to tab workflow Commit: 79db9f51943663b69d4aa3eba58858b5e08893a2 https://github.com/galaxyproject/galaxy/commit/79db9f51943663b69d4aa3eba588… Author: qiagu <guqiang01(a)gmail.com> Date: 2018-03-12 (Mon, 12 Mar 2018) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/ui/ui-misc.js Log Message: ----------- linked /workflows/run/ to tab workflow Commit: 7067c6c2f9633c08c64020247d7e185ff4b900c8 https://github.com/galaxyproject/galaxy/commit/7067c6c2f9633c08c64020247d7e… Author: qiagu <guqiang01(a)gmail.com> Date: 2018-03-12 (Mon, 12 Mar 2018) Changed paths: M client/galaxy/scripts/apps/analysis.js Log Message: ----------- split /visualizations/(:action_id), make /list_published/ link to tab shared Commit: bbd51345eb2c3ab7d2daa4b19944b5d112a1aefa https://github.com/galaxyproject/galaxy/commit/bbd51345eb2c3ab7d2daa4b19944… Author: qiagu <guqiang01(a)gmail.com> Date: 2018-03-12 (Mon, 12 Mar 2018) Changed paths: M client/galaxy/scripts/apps/analysis.js Log Message: ----------- changed to concise code for /visualizations/(:action_id) Commit: e9c60896a6e5e547695cc07d0dc34e0744127ba4 https://github.com/galaxyproject/galaxy/commit/e9c60896a6e5e547695cc07d0dc3… Author: qiagu <guqiang01(a)gmail.com> Date: 2018-03-12 (Mon, 12 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/history/history-list.js Log Message: ----------- split /histories/(:action_id), link 'list_published' to tab 'shared' and 'list' to 'user' Commit: b7da6c5d25fef83b3f7af6f9bfe48ae85f44c70d https://github.com/galaxyproject/galaxy/commit/b7da6c5d25fef83b3f7af6f9bfe4… Author: qiagu <guqiang01(a)gmail.com> Date: 2018-03-12 (Mon, 12 Mar 2018) Changed paths: M client/galaxy/scripts/apps/analysis.js Log Message: ----------- split /pages/(:action_id): link 'list_published' to tab 'shared' and others to 'user' Commit: abc1aa91e7dac993a0611f7e0fda06851b0b4301 https://github.com/galaxyproject/galaxy/commit/abc1aa91e7dac993a0611f7e0fda… Author: qiagu <guqiang01(a)gmail.com> Date: 2018-03-12 (Mon, 12 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/form/form-wrapper.js M client/galaxy/scripts/mvc/grid/grid-shared.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/ui/ui-misc.js Log Message: ----------- fixed the active_tab undefined issue Commit: 28877c55cf3e5b66124809f00eb8a06c261832ce https://github.com/galaxyproject/galaxy/commit/28877c55cf3e5b66124809f00eb8… Author: qiagu <guqiang01(a)gmail.com> Date: 2018-03-16 (Fri, 16 Mar 2018) Changed paths: M client/galaxy/scripts/layout/menu.js Log Message: ----------- fix highlighting dropoff issue when clicking menu Commit: 2b8eb1ea778316e40584258558b8c284a080bb49 https://github.com/galaxyproject/galaxy/commit/2b8eb1ea778316e40584258558b8… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-20 (Tue, 20 Mar 2018) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/layout/menu.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/form/form-wrapper.js M client/galaxy/scripts/mvc/grid/grid-shared.js M client/galaxy/scripts/mvc/history/history-list.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/ui/ui-misc.js M client/galaxy/scripts/mvc/user/user-custom-builds.js M client/galaxy/scripts/mvc/user/user-preferences.js M client/galaxy/scripts/mvc/visualization/visualization-view.js M client/galaxy/scripts/mvc/workflow/workflow.js Log Message: ----------- Merge pull request #5675 from qiagu/iss4846 Fix active tab highlighting Compare: https://github.com/galaxyproject/galaxy/compare/a684ddc400f9...2b8eb1ea7783

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[galaxyproject/galaxy] 043403: bring samples on par with what Main uses
by GitHub 20 Mar '18

20 Mar '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 04340384cc6b18dad02f6e4195cb73e9eb87a171 https://github.com/galaxyproject/galaxy/commit/04340384cc6b18dad02f6e4195cb… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-03-02 (Fri, 02 Mar 2018) Changed paths: M config/tool_conf.xml.main M config/tool_conf.xml.sample Log Message: ----------- bring samples on par with what Main uses Commit: 464c581ec13fc711f2f10aef2921c62f41ac9bd2 https://github.com/galaxyproject/galaxy/commit/464c581ec13fc711f2f10aef2921… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-03-02 (Fri, 02 Mar 2018) Changed paths: M config/tool_conf.xml.sample Log Message: ----------- re-enable hvar, remove nonresponding datasources Commit: a684ddc400f9b1717913bb2e21b52c13bd0dee1d https://github.com/galaxyproject/galaxy/commit/a684ddc400f9b1717913bb2e21b5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-20 (Tue, 20 Mar 2018) Changed paths: M config/tool_conf.xml.main M config/tool_conf.xml.sample Log Message: ----------- Merge pull request #5637 from martenson/update-conf-samples Update tool conf samples Compare: https://github.com/galaxyproject/galaxy/compare/5f23f5da7251...a684ddc400f9

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[galaxyproject/galaxy] 1534d9: Merge remote-tracking branch 'upstream/master' int...
by GitHub 20 Mar '18

20 Mar '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 1534d9d8b40c468ee0fa70342be4a83ff50bb2c8 https://github.com/galaxyproject/galaxy/commit/1534d9d8b40c468ee0fa70342be4… Author: Matthias Bernt <bernt.matthias(a)gmail.com> Date: 2017-09-01 (Fri, 01 Sep 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/style/less/ui.less M lib/galaxy/datatypes/registry.py M lib/galaxy/jobs/actions/post.py M lib/galaxy/managers/tags.py M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/wrappers.py M static/maps/mvc/tool/tool-form-base.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 M static/scripts/mvc/tool/tool-form-base.js M static/style/blue/base.css M test/functional/tools/sample_datatypes_conf.xml Log Message: ----------- Merge remote-tracking branch 'upstream/master' into dev Commit: 4de7f0efd136f355395a741c9a865df71967f676 https://github.com/galaxyproject/galaxy/commit/4de7f0efd136f355395a741c9a86… Author: Matthias Bernt <bernt.matthias(a)gmail.com> Date: 2017-09-07 (Thu, 07 Sep 2017) Changed paths: A .ci/autopep8.sh M .ci/flake8_lint_include_list.txt M .ci/jenkins/selenium/docker-compose.yml M .ci/py3_sources.txt M .gitignore M CONTRIBUTING.md M Makefile A SECURITY_POLICY.md M client/bower.json M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/apps/panels/admin-panel.js M client/galaxy/scripts/apps/panels/tool-panel.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/layout/menu.js M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/layout/panel.js A client/galaxy/scripts/layout/router.js M client/galaxy/scripts/layout/scratchbook.js R client/galaxy/scripts/libs/jquery/jqtouch.js M client/galaxy/scripts/mvc/collection/collection-model.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/dataset/data.js A client/galaxy/scripts/mvc/dataset/dataset-edit-attributes.js A client/galaxy/scripts/mvc/dataset/dataset-error.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.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-view.js A client/galaxy/scripts/mvc/form/form-wrapper.js M client/galaxy/scripts/mvc/grid/grid-model.js A 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 A client/galaxy/scripts/mvc/history/history-list.js M client/galaxy/scripts/mvc/history/history-view-edit-current.js M client/galaxy/scripts/mvc/history/options-menu.js A 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-folderlist-view.js M client/galaxy/scripts/mvc/library/library-folderrow-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/library/library-library-view.js M client/galaxy/scripts/mvc/library/library-librarylist-view.js M client/galaxy/scripts/mvc/library/library-libraryrow-view.js M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js M client/galaxy/scripts/mvc/library/library-model.js R client/galaxy/scripts/mvc/page/page-list.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 A 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/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/util.js M client/galaxy/scripts/mvc/toolshed/workflows-view.js M client/galaxy/scripts/mvc/ui/ui-buttons.js M client/galaxy/scripts/mvc/ui/ui-drilldown.js M client/galaxy/scripts/mvc/ui/ui-list.js M client/galaxy/scripts/mvc/ui/ui-popover.js M client/galaxy/scripts/mvc/ui/ui-select-content.js M client/galaxy/scripts/mvc/ui/ui-select-default.js A client/galaxy/scripts/mvc/ui/ui-select-genomespace.js M client/galaxy/scripts/mvc/upload/upload-ftp.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-preferences.js R client/galaxy/scripts/mvc/workflow/workflow-configure-menu.js M client/galaxy/scripts/mvc/workflow/workflow-forms.js M client/galaxy/scripts/mvc/workflow/workflow-manager.js A 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-terminals.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M client/galaxy/scripts/mvc/workflow/workflow.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/reports_webapp/run_stats.js M client/galaxy/scripts/ui/scroll-panel.js M client/galaxy/scripts/utils/graph.js M client/galaxy/scripts/utils/query-string-parsing.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/phyloviz.js M client/galaxy/scripts/viz/trackster.js M client/galaxy/scripts/viz/trackster/painters.js M client/galaxy/scripts/viz/trackster/tracks.js M client/galaxy/scripts/viz/visualization.js M client/galaxy/style/less/base.less M client/galaxy/style/less/dataset.less M client/galaxy/style/less/galaxy_bootstrap/overrides.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/galaxy/style/less/ui.less M client/galaxy/style/source_material/circle.py M client/grunt-tasks/install-libs.js M client/grunt-tasks/style.js A client/package-lock.json M client/toolshed/scripts/mvc/groups/group-list-view.js M config/datatypes_conf.xml.sample M config/dependency_resolvers_conf.xml.sample A config/error_report.yml.sample M 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doc/source/admin/special_topics/index.rst A doc/source/dev/finding_and_improving_slow_code.rst M doc/source/project/organization.rst M lib/galaxy/__init__.py M lib/galaxy/actions/admin.py M lib/galaxy/app.py M lib/galaxy/auth/__init__.py M lib/galaxy/config.py M lib/galaxy/containers/__init__.py M lib/galaxy/dataset_collections/builder.py M lib/galaxy/dataset_collections/matching.py M lib/galaxy/dataset_collections/registry.py M lib/galaxy/dataset_collections/structure.py M lib/galaxy/dataset_collections/subcollections.py M lib/galaxy/dataset_collections/type_description.py M lib/galaxy/dataset_collections/types/__init__.py M lib/galaxy/dataset_collections/types/list.py M lib/galaxy/dataset_collections/types/paired.py M lib/galaxy/datatypes/assembly.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/blast.py M lib/galaxy/datatypes/chrominfo.py R lib/galaxy/datatypes/converters/bcf_bgzip_to_bcf_converter.py R lib/galaxy/datatypes/converters/bcf_bgzip_to_bcf_converter.xml R 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M lib/galaxy/datatypes/converters/wiggle_to_array_tree_converter.py M lib/galaxy/datatypes/converters/wiggle_to_simple_converter.py M lib/galaxy/datatypes/coverage.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/dataproviders/base.py M lib/galaxy/datatypes/dataproviders/chunk.py M lib/galaxy/datatypes/dataproviders/column.py M lib/galaxy/datatypes/dataproviders/dataset.py M lib/galaxy/datatypes/dataproviders/decorators.py M lib/galaxy/datatypes/dataproviders/exceptions.py M lib/galaxy/datatypes/dataproviders/external.py M lib/galaxy/datatypes/dataproviders/hierarchy.py M lib/galaxy/datatypes/dataproviders/line.py M lib/galaxy/datatypes/display_applications/application.py M lib/galaxy/datatypes/display_applications/parameters.py M lib/galaxy/datatypes/display_applications/util.py M lib/galaxy/datatypes/genetics.py M lib/galaxy/datatypes/graph.py M lib/galaxy/datatypes/images.py M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/molecules.py M 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test/unit/tools/test_collect_primary_datasets.py M test/unit/tools/test_column_parameters.py M test/unit/tools/test_data_parameters.py M test/unit/tools/test_dataset_matcher.py M test/unit/tools/test_evaluation.py M test/unit/tools/test_execution.py M test/unit/tools/test_history_imp_exp.py M test/unit/tools/test_parameter_parsing.py M test/unit/tools/test_parsing.py M test/unit/tools/test_select_parameters.py M test/unit/tools/test_tool_deps.py M test/unit/tools/test_tool_panel.py M test/unit/tools/test_toolbox.py M test/unit/tools/test_toolbox_filters.py M test/unit/tools/test_watcher.py M test/unit/tools/test_wrappers.py M test/unit/tools_support.py M test/unit/unittest_utils/galaxy_mock.py M test/unit/unittest_utils/tempfilecache.py M test/unit/unittest_utils/utility.py M test/unit/visualizations/plugins/test_VisualizationPlugin.py M test/unit/visualizations/plugins/test_VisualizationsRegistry.py M test/unit/web/base/test_HookPluginManager.py M test/unit/web/base/test_PageServingPluginManager.py M test/unit/web/base/test_PluginManager.py M test/unit/web/framework/test_webapp.py M test/unit/workflows/test_extract_summary.py M test/unit/workflows/test_modules.py M test/unit/workflows/test_run_parameters.py M test/unit/workflows/test_workflow_progress.py M test/unit/workflows/workflow_support.py M tool_list.py M tools/data_source/data_source.py M tools/data_source/fetch.py M tools/data_source/genbank.py M tools/data_source/hbvar_filter.py M tools/data_source/import.py M tools/data_source/microbial_import.py M tools/data_source/microbial_import_code.py M tools/data_source/upload.py M tools/data_source/upload.xml M tools/evolution/add_scores.py M tools/evolution/codingSnps_filter.py M tools/extract/extract_genomic_dna.py M tools/extract/liftOver_wrapper.py M tools/filters/axt_to_lav.py M tools/filters/axt_to_lav_code.py M tools/filters/bed_to_gff_converter.py M tools/filters/gff/extract_GFF_Features.py M 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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 M tools/maf/interval2maf.py M tools/maf/interval_maf_to_merged_fasta.py M tools/maf/maf_by_block_number.py M tools/maf/maf_filter.py M tools/maf/maf_limit_size.py M tools/maf/maf_limit_to_species.py M tools/maf/maf_reverse_complement.py M tools/maf/maf_split_by_species.py M tools/maf/maf_stats.py M tools/maf/maf_thread_for_species.py M tools/maf/maf_to_bed.py M tools/maf/maf_to_bed_code.py M tools/maf/maf_to_fasta_concat.py M tools/maf/maf_to_fasta_multiple_sets.py M tools/maf/maf_to_interval.py M tools/maf/vcf_to_maf_customtrack.py M tools/meme/fimo_wrapper.py M tools/metag_tools/blat_wrapper.py M tools/metag_tools/shrimp_color_wrapper.py M tools/metag_tools/shrimp_wrapper.py M tools/next_gen_conversion/fastq_conversions.py M tools/next_gen_conversion/fastq_gen_conv.py M tools/next_gen_conversion/solid2fastq.py M tools/next_gen_conversion/solid_to_fastq.py M tools/ngs_simulation/ngs_simulation.py M tools/plotting/bar_chart.py M tools/solid_tools/maq_cs_wrapper.py M tools/solid_tools/solid_qual_stats.py M tools/sr_assembly/velvetg.xml M tools/sr_assembly/velvetg_wrapper.py M tools/sr_assembly/velveth_wrapper.py M tools/sr_mapping/bfast_wrapper.py M tools/sr_mapping/srma_wrapper.py M tools/stats/aggregate_scores_in_intervals.py M tools/stats/filtering.py M tools/stats/grouping.py M tools/stats/gsummary.py M tools/visualization/LAJ.py M tools/visualization/LAJ_code.py M tox.ini Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into dev Commit: 5a3ada59615d81907baad36699597a7d855d9d5c https://github.com/galaxyproject/galaxy/commit/5a3ada59615d81907baad3669959… Author: Matthias Bernt <bernt.matthias(a)gmail.com> Date: 2017-10-23 (Mon, 23 Oct 2017) Changed paths: M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/mvc/base/controlled-fetch-collection.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-model.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-librarylist-view.js M client/galaxy/scripts/mvc/tours.js M client/galaxy/scripts/mvc/user/user-preferences.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/library.less M client/toolshed/scripts/mvc/groups/group-list-view.js M config/datatypes_conf.xml.sample M config/galaxy.ini.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 lib/galaxy/app.py 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 lib/galaxy/datatypes/converters/biom2_to_biom1.xml M lib/galaxy/datatypes/dataproviders/base.py M lib/galaxy/datatypes/dataproviders/dataset.py M 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lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/galaxy/workflow/run.py M lib/galaxy_ext/metadata/set_metadata.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py M lib/tool_shed/grids/repository_grids.py M static/maps/layout/page.js.map M static/maps/mvc/base/controlled-fetch-collection.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-model.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 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/tours.js.map M 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static/scripts/mvc/library/library-library-view.js M static/scripts/mvc/library/library-librarylist-view.js M static/scripts/mvc/tours.js M static/scripts/mvc/user/user-preferences.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 M test/api/test_workflows.py M test/galaxy_selenium/has_driver.py M test/galaxy_selenium/navigates_galaxy.py M test/integration/test_upload_configuration_options.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 M test/selenium_tests/test_workflow_editor.py M tools/data_source/upload.py Log Message: ----------- Merge branch 'dev' of https://github.com/bernt-matthias/galaxy into dev Commit: 496a10f0c1d0394f960f4a7405b2742609f6ad74 https://github.com/galaxyproject/galaxy/commit/496a10f0c1d0394f960f4a7405b2… Author: Matthias Bernt <bernt.matthias(a)gmail.com> Date: 2017-10-23 (Mon, 23 Oct 2017) Changed paths: M create_db.sh M extract_dataset_parts.sh 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/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 Log Message: ----------- Merge remote-tracking branch 'upstream/master' into dev Commit: 095a797548dab55b3af70c6be2c135de9f373aca https://github.com/galaxyproject/galaxy/commit/095a797548dab55b3af70c6be2c1… Author: Matthias Bernt <m.bernt(a)ufz.de> Date: 2017-10-24 (Tue, 24 Oct 2017) Changed paths: M .ci/flake8_lint_include_list.txt R .ci/flake8_py3_wrapper.sh M .ci/jenkins/selenium/Dockerfile M 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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 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tools/metag_tools/shrimp_wrapper.py M tools/sr_assembly/velvetg_wrapper.py M tox.ini Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into dev Commit: c3911038a3c24e19544cf0f1f9f339ddcfcb954b https://github.com/galaxyproject/galaxy/commit/c3911038a3c24e19544cf0f1f9f3… Author: Matthias Bernt <m.bernt(a)ufz.de> Date: 2017-11-15 (Wed, 15 Nov 2017) Changed paths: R .ci/flake8_lint_include_list.txt R .ci/flake8_wrapper_imports.sh 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 .travis.yml M Makefile M README.rst M client/.babelrc M client/galaxy/scripts/admin.toolshed.js M client/galaxy/scripts/apps/admin.js M 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test/selenium_tests/test_history_copy_elements.py A test/selenium_tests/test_history_multi_view.py A test/selenium_tests/test_history_panel_collections.py A test/selenium_tests/test_history_panel_pagination.py M test/selenium_tests/test_library_contents.py A test/selenium_tests/test_library_to_collections.py M test/selenium_tests/test_tool_form.py M test/selenium_tests/test_workflow_editor.py M test/shed_functional/base/test_db_util.py M test/shed_functional/base/twilltestcase.py M test/shed_functional/functional_tests.py A test/shed_functional/test_data/bowtie2_loc_sample/bowtie2_indices.loc.sample M test/unit/dataset_collections/test_matching.py A test/unit/datatypes/converters/__init__.py A test/unit/datatypes/converters/test_interval_to_tabix.py A test/unit/datatypes/test_bam.py A test/unit/datatypes/test_bcf.py A test/unit/datatypes/test_cram.py A test/unit/datatypes/test_vcf.py A test/unit/datatypes/util.py M test/unit/jobs/test_job_configuration.py M test/unit/jobs/test_job_output_checker.py M test/unit/jobs/test_runner_local.py M test/unit/tools/test_parsing.py A test/unit/tools/test_tool_validation.py M test/unit/unittest_utils/galaxy_mock.py M test/unit/workflows/test_workflow_progress.py M tools/data_source/data_source.py M tools/data_source/upload.py M tools/data_source/upload.xml M tools/genomespace/genomespace_importer.py M tools/stats/aggregate_scores_in_intervals.py M tools/stats/gsummary.py M tox.ini Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into dev Commit: c0983880cca3134666e34d3b758581a0451ea99d https://github.com/galaxyproject/galaxy/commit/c0983880cca3134666e34d3b7585… Author: Matthias Bernt <m.bernt(a)ufz.de> Date: 2018-01-03 (Wed, 03 Jan 2018) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/tool/tool-form.js M config/datatypes_conf.xml.sample M config/user_preferences_extra_conf.yml.sample A 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test/casperjs/modules/user.js R test/casperjs/page-data/selectors.json R test/casperjs/server_env.py R test/casperjs/spaceghost.js R test/casperjs/test-data/simple_test.ga R test/casperjs/utils/simple-galaxy.js M test/galaxy_selenium/navigation.yml M test/selenium_tests/test_jupyter.py Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into dev Commit: c5f597f35345a1bdcf4f0633052b3cdc67a3556b https://github.com/galaxyproject/galaxy/commit/c5f597f35345a1bdcf4f0633052b… Author: Matthias Bernt <m.bernt(a)ufz.de> Date: 2018-02-28 (Wed, 28 Feb 2018) Changed paths: 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/list/list-view.js M client/galaxy/scripts/mvc/workflow/workflow.js M client/galaxy/scripts/ui/loading-indicator.js M lib/galaxy/actions/library.py M lib/galaxy/datatypes/binary.py M lib/galaxy/model/migrate/versions/0137_add_copied_from_job_id_column.py M lib/galaxy/tools/actions/upload.py M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/tools/cwl/__init__.py M lib/galaxy/tools/cwl/parser.py M lib/galaxy/tools/cwl/representation.py M lib/galaxy/tools/cwl/runtime_actions.py M lib/galaxy/tools/cwl/schema.py A lib/galaxy/tools/cwl/util.py M lib/galaxy/tools/deps/commands.py M lib/galaxy/tools/deps/mulled/invfile.lua M lib/galaxy/tools/deps/mulled/mulled_build.py M lib/galaxy/tools/deps/mulled/mulled_build_files.py M lib/galaxy/tools/deps/mulled/util.py M lib/galaxy/tools/deps/requirements.py M lib/galaxy/tools/linters/command.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/util/__init__.py M lib/galaxy/util/checkers.py M lib/galaxy/util/compression_utils.py M lib/galaxy/util/path/__init__.py M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M test/base/populators.py M test/integration/test_upload_configuration_options.py M tools/data_source/upload.py M tools/data_source/upload.xml Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into dev Commit: ee76c06da486e47c87fb4b8c236fa2191a403980 https://github.com/galaxyproject/galaxy/commit/ee76c06da486e47c87fb4b8c236f… Author: Matthias Bernt <m.bernt(a)ufz.de> Date: 2018-03-01 (Thu, 01 Mar 2018) Changed paths: M lib/galaxy/jobs/runners/util/job_script/MEMORY_STATEMENT.sh Log Message: ----------- added GALAXY_MEMORY_MB_PERSLOT Commit: c6c47be0cbb7d29cefe3e1c0657f4b188286abb6 https://github.com/galaxyproject/galaxy/commit/c6c47be0cbb7d29cefe3e1c0657f… Author: Matthias Bernt <m.bernt(a)ufz.de> Date: 2018-03-01 (Thu, 01 Mar 2018) Changed paths: M lib/galaxy/jobs/runners/util/job_script/MEMORY_STATEMENT.sh Log Message: ----------- added GALAXY_MEMORY_MB_PERSLOT Commit: 27a93fe8f463803e4d918a2f83e409bef8d404d8 https://github.com/galaxyproject/galaxy/commit/27a93fe8f463803e4d918a2f83e4… Author: Matthias Bernt <m.bernt(a)ufz.de> Date: 2018-03-01 (Thu, 01 Mar 2018) Log Message: ----------- Merge branch 'topic/memperslot' of https://github.com/bernt-matthias/galaxy into topic/memperslot Commit: 7316302ba385c329f458aa333994e6eeb6d5b97d https://github.com/galaxyproject/galaxy/commit/7316302ba385c329f458aa333994… Author: Matthias Bernt <m.bernt(a)ufz.de> Date: 2018-03-05 (Mon, 05 Mar 2018) Changed paths: M lib/galaxy/jobs/runners/util/job_script/MEMORY_STATEMENT.sh Log Message: ----------- renamed variable to GALAXY_MEMORY_MB_PER_SLOT Commit: f54f3aa9e47141fa4b564ec56d37a97a129bea12 https://github.com/galaxyproject/galaxy/commit/f54f3aa9e47141fa4b564ec56d37… Author: Matthias Bernt <m.bernt(a)ufz.de> Date: 2018-03-06 (Tue, 06 Mar 2018) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- added a bit of documentation Commit: 4a59f30209c9a9bee4e2ae70b56ff02f5248716c https://github.com/galaxyproject/galaxy/commit/4a59f30209c9a9bee4e2ae70b56f… Author: Matthias Bernt <m.bernt(a)ufz.de> Date: 2018-03-13 (Tue, 13 Mar 2018) Changed paths: M doc/source/admin/cluster.md Log Message: ----------- added cluster admin docs for the new variables Commit: b92a5e1b470cbe3848e251c8c844cc652782d43d https://github.com/galaxyproject/galaxy/commit/b92a5e1b470cbe3848e251c8c844… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2018-03-13 (Tue, 13 Mar 2018) Changed paths: M doc/source/admin/cluster.md Log Message: ----------- Small doc fixes Commit: 5f23f5da725199204950d89bb6b4b0af9e1d2f82 https://github.com/galaxyproject/galaxy/commit/5f23f5da725199204950d89bb6b4… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-20 (Tue, 20 Mar 2018) Changed paths: M doc/source/admin/cluster.md M lib/galaxy/jobs/runners/util/job_script/MEMORY_STATEMENT.sh M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- Merge pull request #5625 from bernt-matthias/topic/memperslot added GALAXY_MEMORY_MB_PER_SLOT variable Compare: https://github.com/galaxyproject/galaxy/compare/11b32f38f46c...5f23f5da7251

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