galaxy-commits March 2018

galaxy-commits@lists.galaxyproject.org

1 participants
194 discussions

[galaxyproject/galaxy] c47516: Remove show history structure mako
by GitHub 02 Mar '18

02 Mar '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c47516a1cb3f1e66fb24fcd78e078fd04d77f9a6 https://github.com/galaxyproject/galaxy/commit/c47516a1cb3f1e66fb24fcd78e07… Author: anup kumar <anup.rulez(a)gmail.com> Date: 2018-01-08 (Mon, 08 Jan 2018) Changed paths: A client/galaxy/scripts/components/DisplayStructured.vue M client/galaxy/scripts/mvc/history/options-menu.js A lib/galaxy/util/create_history_template.py M lib/galaxy/webapps/galaxy/controllers/history.py M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/extended.bundled.js M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/login.bundled.js M static/scripts/mvc/history/options-menu.js R templates/webapps/galaxy/history/display_structured.mako Log Message: ----------- Remove show history structure mako Commit: 9c8fb8f9d97ba0d5ab6eaec74ea62706483a9148 https://github.com/galaxyproject/galaxy/commit/9c8fb8f9d97ba0d5ab6eaec74ea6… Author: anup kumar <anup.rulez(a)gmail.com> Date: 2018-01-13 (Sat, 13 Jan 2018) Changed paths: M client/galaxy/scripts/components/DisplayStructured.vue M lib/galaxy/util/create_history_template.py M static/scripts/bundled/analysis.bundled.js Log Message: ----------- Update the styling Commit: c1ec73aa58467d255dd3aa8ca43bb20721b5f4e3 https://github.com/galaxyproject/galaxy/commit/c1ec73aa58467d255dd3aa8ca43b… Author: anup kumar <anup.rulez(a)gmail.com> Date: 2018-01-13 (Sat, 13 Jan 2018) Changed paths: M client/galaxy/scripts/components/Citations.vue M client/galaxy/scripts/components/HistoryImport.vue M client/galaxy/scripts/components/Message.vue M client/galaxy/scripts/components/admin/BaseGrid.vue M client/galaxy/scripts/components/admin/DataManagerGrid.vue M client/galaxy/scripts/components/admin/DataTables.vue M client/galaxy/scripts/components/admin/DataTablesGrid.vue M client/galaxy/scripts/mvc/dataset/dataset-error.js M client/galaxy/scripts/nls/zh/locale.js M client/package.json M client/webpack.config.js M client/yarn.lock M config/datatypes_conf.xml.sample M config/galaxy.ini.sample M doc/source/admin/production.md M lib/galaxy/datatypes/msa.py A lib/galaxy/datatypes/test/infernal_model.cm M lib/galaxy/model/migrate/check.py M lib/galaxy/workflow/modules.py M scripts/common_startup.sh M scripts/db_shell.py M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/libs.bundled.js M static/scripts/mvc/dataset/dataset-error.js M static/scripts/nls/zh/locale.js M test/api/test_workflows.py Log Message: ----------- Merging with dev Commit: e9755e111ac6f3e3d8412d539ecd91fb6a98cc31 https://github.com/galaxyproject/galaxy/commit/e9755e111ac6f3e3d8412d539ecd… Author: anup kumar <anup.rulez(a)gmail.com> Date: 2018-01-13 (Sat, 13 Jan 2018) Changed paths: M lib/galaxy/util/create_history_template.py M lib/galaxy/webapps/galaxy/controllers/history.py Log Message: ----------- Remove extra spacings around the braces Commit: 5d5260260b3f44cbc9aac5018f41166006380c12 https://github.com/galaxyproject/galaxy/commit/5d5260260b3f44cbc9aac5018f41… Author: anup kumar <anup.rulez(a)gmail.com> Date: 2018-01-14 (Sun, 14 Jan 2018) Changed paths: M client/galaxy/scripts/components/DisplayStructured.vue Log Message: ----------- Remove unused variables Commit: 30a3ebee184de55755141b5baa1f495b2cf2b2ec https://github.com/galaxyproject/galaxy/commit/30a3ebee184de55755141b5baa1f… Author: anup kumar <anup.rulez(a)gmail.com> Date: 2018-01-14 (Sun, 14 Jan 2018) Changed paths: M client/galaxy/scripts/apps/analysis.js A client/galaxy/scripts/components/HistoryView.vue M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/history.py M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/extended.bundled.js M static/scripts/bundled/libs.bundled.js Log Message: ----------- Update structure to replace history/view mako file Commit: 394ae3340c52d632d2cc58929448352eae42dbdb https://github.com/galaxyproject/galaxy/commit/394ae3340c52d632d2cc58929448… Author: anup kumar <anup.rulez(a)gmail.com> Date: 2018-01-14 (Sun, 14 Jan 2018) Changed paths: M client/galaxy/scripts/components/DisplayStructured.vue M client/galaxy/scripts/components/HistoryView.vue M lib/galaxy/util/create_history_template.py M lib/galaxy/webapps/galaxy/controllers/history.py M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/extended.bundled.js M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/login.bundled.js Log Message: ----------- Add view feature for a history in the list of histories Commit: 92c7900356842fce23504bca607d4712b8adc8c8 https://github.com/galaxyproject/galaxy/commit/92c7900356842fce23504bca607d… Author: anup kumar <anup.rulez(a)gmail.com> Date: 2018-01-14 (Sun, 14 Jan 2018) Changed paths: R templates/webapps/galaxy/history/view.mako Log Message: ----------- Remove history/view.mako file Commit: 2e8ce77fc099481ec29bc5f65390640260073ec3 https://github.com/galaxyproject/galaxy/commit/2e8ce77fc099481ec29bc5f65390… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2018-01-16 (Tue, 16 Jan 2018) Changed paths: M client/galaxy/scripts/mvc/library/library-dataset-view.js M lib/galaxy/managers/library_datasets.py M lib/galaxy/tools/__init__.py M scripts/common_startup.sh Log Message: ----------- Merge branch 'dev' of https://github.com/bgruening/galaxy into history_structure Commit: 523bccdef829e03cbe84144d7139c5a9b163ba1b https://github.com/galaxyproject/galaxy/commit/523bccdef829e03cbe84144d7139… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2018-01-16 (Tue, 16 Jan 2018) Changed paths: M lib/galaxy/util/create_history_template.py Log Message: ----------- Update the dataset url Commit: f2b0a3936e33081999103023f52397ecef492512 https://github.com/galaxyproject/galaxy/commit/f2b0a3936e33081999103023f523… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2018-01-16 (Tue, 16 Jan 2018) Changed paths: M client/galaxy/scripts/components/DisplayStructured.vue M client/galaxy/scripts/components/HistoryView.vue M client/galaxy/scripts/mvc/history/options-menu.js M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/analysis.bundled.js M static/scripts/mvc/history/options-menu.js Log Message: ----------- Update styling Commit: dab7248c4e2bc6975052136a28f614321574dc78 https://github.com/galaxyproject/galaxy/commit/dab7248c4e2bc6975052136a28f6… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2018-01-16 (Tue, 16 Jan 2018) Changed paths: M client/galaxy/scripts/components/DisplayStructured.vue Log Message: ----------- Remove console.log statement from vue Commit: 99f744f8353b37fd4d0a43b2ed9fe1493846c844 https://github.com/galaxyproject/galaxy/commit/99f744f8353b37fd4d0a43b2ed9f… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2018-01-16 (Tue, 16 Jan 2018) Changed paths: M client/galaxy/scripts/components/HistoryView.vue M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/extended.bundled.js M static/scripts/bundled/libs.bundled.js M static/scripts/mvc/library/library-dataset-view.js Log Message: ----------- Update json structure and add static files Commit: 29695ecf52ba1ce1ea07d2e1158e1f7fe5432678 https://github.com/galaxyproject/galaxy/commit/29695ecf52ba1ce1ea07d2e1158e… Author: anup kumar <anup.rulez(a)gmail.com> Date: 2018-01-16 (Tue, 16 Jan 2018) Changed paths: M lib/galaxy/util/create_history_template.py M lib/galaxy/webapps/galaxy/controllers/history.py Log Message: ----------- Fix build fail issues Commit: e619faefe405fe30c1d2a06b4d337e275f06ee5f https://github.com/galaxyproject/galaxy/commit/e619faefe405fe30c1d2a06b4d33… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2018-01-17 (Wed, 17 Jan 2018) Changed paths: M lib/galaxy/util/create_history_template.py M lib/galaxy/webapps/galaxy/controllers/history.py Log Message: ----------- Fix scripts Commit: 3f8b38f4cb90e26cb13533a44c41e3756af68db0 https://github.com/galaxyproject/galaxy/commit/3f8b38f4cb90e26cb13533a44c41… Author: anup kumar <anup.rulez(a)gmail.com> Date: 2018-01-28 (Sun, 28 Jan 2018) Changed paths: 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/mvc/base/controlled-fetch-collection.js M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/multi-panel.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/tool/tool-form.js M client/galaxy/scripts/mvc/tours.js M client/galaxy/style/less/base.less M client/galaxy/style/less/dataset.less M client/galaxy/style/less/history.less M config/auth_conf.xml.sample M config/datatypes_conf.xml.sample R config/galaxy.ini.sample A config/galaxy.yml.sample M config/job_conf.xml.sample_advanced M config/tool_shed.yml.sample M doc/Makefile A doc/source/admin/_inc_proxy_prereq.rst A doc/source/admin/_inc_proxy_serving_root.rst A doc/source/admin/_inc_proxy_ssl.rst A doc/source/admin/apache.md M doc/source/admin/authentication.md M doc/source/admin/cluster.md M doc/source/admin/conda_faq.rst A doc/source/admin/config.rst A doc/source/admin/config_logging.rst M doc/source/admin/dependency_resolvers.rst A doc/source/admin/galaxy_options.rst M doc/source/admin/index.rst M doc/source/admin/jobs.md A doc/source/admin/nginx.md A doc/source/admin/options.rst M doc/source/admin/production.md A doc/source/admin/proxy_package_layout.rst M doc/source/admin/reports.md M doc/source/admin/reports.rst M doc/source/admin/scaling.md R doc/source/admin/special_topics/apache.md M doc/source/admin/special_topics/bug_reports.rst M doc/source/admin/special_topics/chat.rst M doc/source/admin/special_topics/ftp.md M doc/source/admin/special_topics/index.rst M doc/source/admin/special_topics/interactive_environments.rst R doc/source/admin/special_topics/nginx.md M doc/source/admin/special_topics/performance_tracking.rst M doc/source/admin/special_topics/webhooks.rst M doc/source/admin/tool_panel.rst M doc/source/conf.py M lib/galaxy/app.py M lib/galaxy/auth/__init__.py M lib/galaxy/auth/providers/ldap_ad.py A lib/galaxy/auth/util.py M lib/galaxy/config.py M lib/galaxy/datatypes/binary.py A lib/galaxy/datatypes/converters/bam_native_to_bam_converter.xml M lib/galaxy/datatypes/converters/bam_to_bigwig_converter.xml A lib/galaxy/datatypes/converters/sam_to_bam_native.xml A lib/galaxy/datatypes/phylip.py M lib/galaxy/datatypes/sniff.py A lib/galaxy/datatypes/test/test.phylip M lib/galaxy/dependencies/conda-environment.txt M lib/galaxy/dependencies/conditional-requirements.txt M lib/galaxy/dependencies/pinned-hashed-requirements.txt M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/pipfiles/develop/Pipfile M lib/galaxy/dependencies/pipfiles/develop/Pipfile.lock M lib/galaxy/dependencies/pipfiles/develop/pinned-hashed-requirements.txt M lib/galaxy/dependencies/pipfiles/develop/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/rule_helper.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh M lib/galaxy/jobs/runners/util/job_script/__init__.py M lib/galaxy/managers/configuration.py M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py M lib/galaxy/model/tool_shed_install/__init__.py M lib/galaxy/objectstore/__init__.py M lib/galaxy/security/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/data/__init__.py M lib/galaxy/tools/data_manager/manager.py M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/containers.py M lib/galaxy/tools/deps/docker_util.py M lib/galaxy/tools/deps/views.py M lib/galaxy/tools/error_reports/plugins/sentry.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/tools/parser/interface.py M lib/galaxy/tools/parser/output_collection_def.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/filters/__init__.py M lib/galaxy/tools/toolbox/integrated_panel.py M lib/galaxy/tools/toolbox/watcher.py M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/util/dictifiable.py M lib/galaxy/util/handlers.py M lib/galaxy/util/path/__init__.py M lib/galaxy/version.py M lib/galaxy/web/framework/helpers/__init__.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/web/security/__init__.py M lib/galaxy/web/stack/__init__.py M lib/galaxy/webapps/config_manage.py M lib/galaxy/webapps/galaxy/api/configuration.py M lib/galaxy/webapps/galaxy/api/histories.py M lib/galaxy/webapps/galaxy/api/jobs.py A lib/galaxy/webapps/galaxy/config_schema.yml M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/user.py A lib/galaxy/webapps/galaxy/uwsgi_schema.yml M lib/galaxy/webapps/reports/config.py M lib/galaxy/webapps/tool_shed/config.py M lib/galaxy/webapps/tool_shed/config_schema.yml M lib/galaxy/webapps/tool_shed/model/__init__.py M lib/galaxy/workflow/scheduling_manager.py M lib/tool_shed/galaxy_install/migrate/common.py M lib/tool_shed/util/admin_util.py M run_tests.sh M scripts/cleanup_datasets/cleanup_datasets.py M scripts/common_startup.sh M scripts/common_startup_functions.sh A scripts/common_startup_variables.sh M scripts/db_shell.py M scripts/functional_tests.py M scripts/galaxy-main M scripts/get_uwsgi_args.py A scripts/maintenance.sh M scripts/tool_shed/bootstrap_tool_shed/bootstrap_tool_shed.sh M scripts/tool_shed/bootstrap_tool_shed/bootstrap_util.py 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/user/register.mako M templates/webapps/tool_shed/common/reset_metadata_on_selected_repositories.mako A test-data/bam_native_from_sam.bam M test-data/sam_with_header.sam M test/base/driver_util.py M test/base/integration_util.py M test/docker/base/run_test_wrapper.sh 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_bam_native.xml M test/functional/tools/sample_datatypes_conf.xml M test/functional/tools/samples_tool_conf.xml 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 A test/integration/test_dockerized_jobs.py A test/integration/test_job_environments.py M test/manual/launch_and_run.sh 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 tools/data_source/microbial_import_code.py Log Message: ----------- Merging with dev Commit: dc3fcadda12a71c0eb8e508b88538ca09741d529 https://github.com/galaxyproject/galaxy/commit/dc3fcadda12a71c0eb8e508b8853… Author: anup kumar <anup.rulez(a)gmail.com> Date: 2018-01-28 (Sun, 28 Jan 2018) Changed paths: M lib/galaxy/util/create_history_template.py M lib/galaxy/webapps/galaxy/controllers/history.py Log Message: ----------- Merge branch 'history_structure' of https://github.com/bgruening/galaxy into history_structure Commit: da23ed2ec60a851b011902acd6498ccddcb03f64 https://github.com/galaxyproject/galaxy/commit/da23ed2ec60a851b011902acd649… Author: anuprulez <anup.rulez(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 client/galaxy/scripts/layout/page.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.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-model.js M client/galaxy/scripts/mvc/history/multi-panel.js M client/galaxy/scripts/mvc/history/options-menu.js M client/galaxy/scripts/mvc/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/tours.js M client/galaxy/scripts/mvc/webhooks.js M client/galaxy/scripts/mvc/workflow/workflow-node.js M client/galaxy/scripts/onload.js M client/galaxy/scripts/qunit/test-app.js M client/galaxy/scripts/qunit/tests/page_tests.js M client/galaxy/style/less/base.less M client/galaxy/style/less/dataset.less M client/galaxy/style/less/history.less M client/galaxy/style/less/ui/icon-btn.less M config/auth_conf.xml.sample M config/datatypes_conf.xml.sample R config/galaxy.ini.sample A config/galaxy.yml.sample M config/job_conf.xml.sample_advanced A config/plugins/webhooks/demo/search/config.yml R config/plugins/webhooks/demo/search/config/searchover.yaml A config/plugins/webhooks/demo/search/script.js R config/plugins/webhooks/demo/search/static/script.js R config/plugins/webhooks/demo/search/static/styles.css A config/plugins/webhooks/demo/search/styles.css A config/plugins/webhooks/demo/tool_list/__init__.py A config/plugins/webhooks/demo/tool_list/config.yml R config/plugins/webhooks/demo/tool_list/config/tool_list.yml R config/plugins/webhooks/demo/tool_list/helper/__init__.py A config/plugins/webhooks/demo/tour_generator/__init__.py A config/plugins/webhooks/demo/tour_generator/config.yml R config/plugins/webhooks/demo/tour_generator/config/tour_generator.yml R config/plugins/webhooks/demo/tour_generator/helper/__init__.py A config/plugins/webhooks/demo/tour_generator/script.js R config/plugins/webhooks/demo/tour_generator/static/script.js R config/plugins/webhooks/demo/tour_generator/static/styles.css A config/plugins/webhooks/demo/tour_generator/styles.css M config/tool_shed.yml.sample M doc/Makefile A doc/source/admin/_inc_proxy_prereq.rst A doc/source/admin/_inc_proxy_serving_root.rst A doc/source/admin/_inc_proxy_ssl.rst A doc/source/admin/apache.md M doc/source/admin/authentication.md M doc/source/admin/cluster.md M doc/source/admin/conda_faq.rst A doc/source/admin/config.rst A doc/source/admin/config_logging.rst M doc/source/admin/dependency_resolvers.rst M doc/source/admin/framework_dependencies.rst A doc/source/admin/galaxy_options.rst M doc/source/admin/index.rst M doc/source/admin/jobs.md A doc/source/admin/nginx.md A doc/source/admin/options.rst M doc/source/admin/production.md A doc/source/admin/proxy_package_layout.rst M doc/source/admin/reports.md M doc/source/admin/reports.rst M doc/source/admin/scaling.md R doc/source/admin/special_topics/apache.md M doc/source/admin/special_topics/bug_reports.rst M doc/source/admin/special_topics/chat.rst M doc/source/admin/special_topics/ftp.md M doc/source/admin/special_topics/index.rst M doc/source/admin/special_topics/interactive_environments.rst R doc/source/admin/special_topics/nginx.md M doc/source/admin/special_topics/performance_tracking.rst M doc/source/admin/special_topics/webhooks.rst M doc/source/admin/tool_panel.rst M doc/source/conf.py M lib/galaxy/app.py M lib/galaxy/auth/__init__.py M lib/galaxy/auth/providers/ldap_ad.py A lib/galaxy/auth/util.py M lib/galaxy/config.py M lib/galaxy/dataset_collections/structure.py M lib/galaxy/datatypes/binary.py A lib/galaxy/datatypes/converters/bam_native_to_bam_converter.xml M lib/galaxy/datatypes/converters/bam_to_bigwig_converter.xml M lib/galaxy/datatypes/converters/sam_to_bam.py A lib/galaxy/datatypes/converters/sam_to_bam_native.xml A lib/galaxy/datatypes/phylip.py M lib/galaxy/datatypes/sniff.py A lib/galaxy/datatypes/test/test.phylip R lib/galaxy/dependencies/conda-environment.txt A lib/galaxy/dependencies/conda-file.sh M lib/galaxy/dependencies/conditional-requirements.txt M lib/galaxy/dependencies/pinned-hashed-requirements.txt M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/pipfiles/develop/Pipfile M lib/galaxy/dependencies/pipfiles/develop/Pipfile.lock M lib/galaxy/dependencies/pipfiles/develop/pinned-hashed-requirements.txt M lib/galaxy/dependencies/pipfiles/develop/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/actions/post.py M lib/galaxy/jobs/rule_helper.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh M lib/galaxy/jobs/runners/util/job_script/__init__.py M lib/galaxy/managers/collections.py M lib/galaxy/managers/configuration.py M lib/galaxy/model/__init__.py M lib/galaxy/model/custom_types.py M lib/galaxy/model/mapping.py M lib/galaxy/model/tool_shed_install/__init__.py M lib/galaxy/objectstore/__init__.py M lib/galaxy/security/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/actions/model_operations.py M lib/galaxy/tools/data/__init__.py M lib/galaxy/tools/data_manager/manager.py M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/commands.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/containers.py M lib/galaxy/tools/deps/docker_util.py M lib/galaxy/tools/deps/mulled/mulled_build.py M lib/galaxy/tools/deps/mulled/util.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/deps/views.py M lib/galaxy/tools/error_reports/plugins/sentry.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/execute.py M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/tools/merge_collection.xml M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/tools/parameters/sanitize.py M lib/galaxy/tools/parser/interface.py M lib/galaxy/tools/parser/output_collection_def.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/filters/__init__.py M lib/galaxy/tools/toolbox/integrated_panel.py M lib/galaxy/tools/toolbox/lineages/interface.py M lib/galaxy/tools/toolbox/watcher.py M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/util/dictifiable.py M lib/galaxy/util/facts.py M lib/galaxy/util/handlers.py M lib/galaxy/util/logging/__init__.py M lib/galaxy/util/path/__init__.py M lib/galaxy/version.py M lib/galaxy/visualization/data_providers/genome.py M lib/galaxy/web/framework/base.py M lib/galaxy/web/framework/helpers/__init__.py A lib/galaxy/web/framework/helpers/tags.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/web/security/__init__.py M lib/galaxy/web/stack/__init__.py M lib/galaxy/web/stack/message.py M lib/galaxy/webapps/config_manage.py M lib/galaxy/webapps/galaxy/api/configuration.py M lib/galaxy/webapps/galaxy/api/histories.py M lib/galaxy/webapps/galaxy/api/history_contents.py M lib/galaxy/webapps/galaxy/api/jobs.py M lib/galaxy/webapps/galaxy/api/webhooks.py M lib/galaxy/webapps/galaxy/buildapp.py A lib/galaxy/webapps/galaxy/config_schema.yml M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/user.py A lib/galaxy/webapps/galaxy/uwsgi_schema.yml M lib/galaxy/webapps/reports/config.py M lib/galaxy/webapps/tool_shed/config.py M lib/galaxy/webapps/tool_shed/config_schema.yml M lib/galaxy/webapps/tool_shed/model/__init__.py M lib/galaxy/webhooks/__init__.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/scheduling_manager.py M lib/tool_shed/galaxy_install/migrate/common.py M lib/tool_shed/util/admin_util.py M lib/tool_shed/util/repository_util.py M lib/tool_shed/util/xml_util.py M run_tests.sh M scripts/cleanup_datasets/cleanup_datasets.py M scripts/common_startup.sh M scripts/common_startup_functions.sh A scripts/common_startup_variables.sh M scripts/db_shell.py A scripts/dump_library_paths.py M scripts/functional_tests.py M scripts/galaxy-main M scripts/get_uwsgi_args.py A scripts/maintenance.sh M scripts/tool_shed/bootstrap_tool_shed/bootstrap_tool_shed.sh M scripts/tool_shed/bootstrap_tool_shed/bootstrap_util.py R static/scripts/admin.toolshed.js R static/scripts/bundled/admin.bundled.js R static/scripts/bundled/analysis.bundled.js R static/scripts/bundled/extended.bundled.js R static/scripts/bundled/libs.bundled.js R static/scripts/bundled/login.bundled.js R static/scripts/galaxy.interactive_environments.js R static/scripts/galaxy.js R static/scripts/galaxy.library.js R static/scripts/galaxy.pages.js R static/scripts/i18n.js R static/scripts/layout/generic-nav-view.js R static/scripts/layout/masthead.js R static/scripts/layout/menu.js R static/scripts/layout/modal.js R static/scripts/layout/page.js R static/scripts/layout/panel.js R static/scripts/layout/router.js R static/scripts/layout/scratchbook.js R static/scripts/legacy/grid/grid-model.js R static/scripts/legacy/grid/grid-template.js R static/scripts/legacy/grid/grid-view.js R static/scripts/libs/backbone.js R static/scripts/libs/bbi/bigwig.js R static/scripts/libs/bbi/jquery-ajax-native.js R static/scripts/libs/bbi/jszlib.js R static/scripts/libs/bbi/spans.js R static/scripts/libs/bibtexParse.js R static/scripts/libs/bootstrap-tour.js R static/scripts/libs/bootstrap.js R static/scripts/libs/d3.js R static/scripts/libs/farbtastic.js R static/scripts/libs/jquery.sparklines.js R static/scripts/libs/jquery/jquery-ui.js R static/scripts/libs/jquery/jquery.autocomplete.js R static/scripts/libs/jquery/jquery.complexify.js R static/scripts/libs/jquery/jquery.cookie.js R static/scripts/libs/jquery/jquery.dynatree.js R static/scripts/libs/jquery/jquery.event.drag.js R static/scripts/libs/jquery/jquery.event.drop.js R static/scripts/libs/jquery/jquery.event.hover.js R static/scripts/libs/jquery/jquery.form.js R static/scripts/libs/jquery/jquery.js R static/scripts/libs/jquery/jquery.migrate.js R static/scripts/libs/jquery/jquery.mousewheel.js R static/scripts/libs/jquery/jquery.rating.js R static/scripts/libs/jquery/jquery.wymeditor.js R static/scripts/libs/jquery/jstorage.js R static/scripts/libs/jquery/jstree.js R static/scripts/libs/jquery/select2.js R static/scripts/libs/raven.js R static/scripts/libs/require.js R static/scripts/libs/toastr.js R static/scripts/libs/underscore.js R static/scripts/mvc/annotation.js R static/scripts/mvc/base-mvc.js R static/scripts/mvc/base/controlled-fetch-collection.js R static/scripts/mvc/collection/base-creator.js R static/scripts/mvc/collection/collection-li-edit.js R static/scripts/mvc/collection/collection-li.js R static/scripts/mvc/collection/collection-model.js R static/scripts/mvc/collection/collection-view-edit.js R static/scripts/mvc/collection/collection-view.js R static/scripts/mvc/collection/list-collection-creator.js R static/scripts/mvc/collection/list-of-pairs-collection-creator.js R static/scripts/mvc/collection/pair-collection-creator.js R static/scripts/mvc/dataset/data.js R static/scripts/mvc/dataset/dataset-choice.js R static/scripts/mvc/dataset/dataset-edit-attributes.js R static/scripts/mvc/dataset/dataset-error.js R static/scripts/mvc/dataset/dataset-li-edit.js R static/scripts/mvc/dataset/dataset-li.js R static/scripts/mvc/dataset/dataset-list.js R static/scripts/mvc/dataset/dataset-model.js R static/scripts/mvc/dataset/states.js R static/scripts/mvc/form/form-data.js R static/scripts/mvc/form/form-input.js R static/scripts/mvc/form/form-parameters.js R static/scripts/mvc/form/form-repeat.js R static/scripts/mvc/form/form-section.js R static/scripts/mvc/form/form-view.js R static/scripts/mvc/form/form-wrapper.js R static/scripts/mvc/grid/grid-model.js R static/scripts/mvc/grid/grid-shared.js R static/scripts/mvc/grid/grid-template.js R static/scripts/mvc/grid/grid-view.js R static/scripts/mvc/history/copy-dialog.js R static/scripts/mvc/history/hda-li-edit.js R static/scripts/mvc/history/hda-li.js R static/scripts/mvc/history/hda-model.js R static/scripts/mvc/history/hdca-li-edit.js R static/scripts/mvc/history/hdca-li.js R static/scripts/mvc/history/hdca-model.js R static/scripts/mvc/history/history-content-model.js R static/scripts/mvc/history/history-contents.js R static/scripts/mvc/history/history-item-li.js R static/scripts/mvc/history/history-list.js R static/scripts/mvc/history/history-model.js R static/scripts/mvc/history/history-preferences.js R static/scripts/mvc/history/history-structure-view.js R static/scripts/mvc/history/history-view-annotated.js R static/scripts/mvc/history/history-view-edit-current.js R static/scripts/mvc/history/history-view-edit.js R static/scripts/mvc/history/history-view.js R static/scripts/mvc/history/job-dag.js R static/scripts/mvc/history/job-states-model.js R static/scripts/mvc/history/multi-panel.js R static/scripts/mvc/history/options-menu.js R static/scripts/mvc/job/job-li.js R static/scripts/mvc/job/job-model.js R static/scripts/mvc/job/job-params.js R static/scripts/mvc/lazy/lazy-limited.js R static/scripts/mvc/library/library-dataset-view.js R static/scripts/mvc/library/library-folder-view.js R static/scripts/mvc/library/library-folderlist-view.js R static/scripts/mvc/library/library-folderrow-view.js R static/scripts/mvc/library/library-foldertoolbar-view.js R static/scripts/mvc/library/library-library-view.js R static/scripts/mvc/library/library-librarylist-view.js R static/scripts/mvc/library/library-libraryrow-view.js R static/scripts/mvc/library/library-librarytoolbar-view.js R static/scripts/mvc/library/library-model.js R static/scripts/mvc/library/library-util.js R static/scripts/mvc/list/list-item.js R static/scripts/mvc/list/list-view.js R static/scripts/mvc/tag.js R static/scripts/mvc/tool/tool-form-base.js R static/scripts/mvc/tool/tool-form-composite.js R static/scripts/mvc/tool/tool-form.js R static/scripts/mvc/tool/tool-genomespace.js R static/scripts/mvc/tool/tools.js R static/scripts/mvc/toolshed/categories-view.js R static/scripts/mvc/toolshed/repo-queue-view.js R static/scripts/mvc/toolshed/repo-status-view.js R static/scripts/mvc/toolshed/repositories-view.js R static/scripts/mvc/toolshed/repository-queue-view.js R static/scripts/mvc/toolshed/repository-view.js R static/scripts/mvc/toolshed/shed-list-view.js R static/scripts/mvc/toolshed/toolshed-model.js R static/scripts/mvc/toolshed/util.js R static/scripts/mvc/toolshed/workflows-view.js R static/scripts/mvc/tours.js R static/scripts/mvc/ui/error-modal.js R static/scripts/mvc/ui/icon-button.js R static/scripts/mvc/ui/popup-menu.js R static/scripts/mvc/ui/ui-buttons.js R static/scripts/mvc/ui/ui-color-picker.js R static/scripts/mvc/ui/ui-drilldown.js R static/scripts/mvc/ui/ui-frames.js R static/scripts/mvc/ui/ui-list.js R static/scripts/mvc/ui/ui-misc.js R static/scripts/mvc/ui/ui-modal.js R static/scripts/mvc/ui/ui-options.js R static/scripts/mvc/ui/ui-popover.js R static/scripts/mvc/ui/ui-portlet.js R static/scripts/mvc/ui/ui-select-content.js R static/scripts/mvc/ui/ui-select-default.js R 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/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 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/user/register.mako M templates/webapps/galaxy/dataset/security_common.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/bam_native_from_sam.bam M test-data/sam_with_header.sam M test/api/test_tools.py M test/api/test_webhooks.py M test/api/test_workflows.py M test/base/driver_util.py M test/base/integration_util.py M test/base/workflows_format_2/converter.py M test/docker/base/run_test_wrapper.sh M test/functional/tools/collection_creates_dynamic_list_of_pairs.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_bam_native.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 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 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_collect_primary_datasets.py M test/unit/tools/test_evaluation.py M tools/data_source/microbial_import_code.py M tox.ini Log Message: ----------- Merge with dev Commit: 8772dbbb38664edfb6b6d472553ad7e421b35b0b https://github.com/galaxyproject/galaxy/commit/8772dbbb38664edfb6b6d472553a… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2018-02-06 (Tue, 06 Feb 2018) Log Message: ----------- Merge branch 'history_structure' of https://github.com/bgruening/galaxy into history_structure Commit: 73db0a5e80fa6cc528ec9170bd443971c001b32c https://github.com/galaxyproject/galaxy/commit/73db0a5e80fa6cc528ec9170bd44… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-02-19 (Mon, 19 Feb 2018) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/mvc/history/options-menu.js M lib/galaxy/webapps/galaxy/buildapp.py M static/style/blue/base.css Log Message: ----------- Move show_structure to first class client route enabling direct nav, linking, etc. Minor cleanup Commit: 3c0344bf15fe40f662586ac212e34bf5963c3345 https://github.com/galaxyproject/galaxy/commit/3c0344bf15fe40f662586ac212e3… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-02-19 (Mon, 19 Feb 2018) Changed paths: M client/galaxy/scripts/components/DisplayStructured.vue M client/galaxy/scripts/components/HistoryView.vue Log Message: ----------- Vue formatting via prettier. Commit: baeb99e54720767066e8a1e96c9f237c2fcce890 https://github.com/galaxyproject/galaxy/commit/baeb99e54720767066e8a1e96c9f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-02-19 (Mon, 19 Feb 2018) Changed paths: M client/galaxy/scripts/components/DisplayStructured.vue Log Message: ----------- Use explicit imports instead of relying on bundleEntries. Kill toastr for axios error -- unnecessary. Commit: 3c25883d5522c9763a16b977343a50a84cc28ddc https://github.com/galaxyproject/galaxy/commit/3c25883d5522c9763a16b977343a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-02-19 (Mon, 19 Feb 2018) Changed paths: M client/galaxy/scripts/components/HistoryView.vue Log Message: ----------- Remove another toastr error -- this sort of thing should be console; reporting http errors in the main UI isn't great UX Commit: 433472a315ced57e033583ef0569d95e36d13bc3 https://github.com/galaxyproject/galaxy/commit/433472a315ced57e033583ef0569… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-02-19 (Mon, 19 Feb 2018) Changed paths: M client/galaxy/scripts/apps/extended.js M client/galaxy/scripts/components/HistoryView.vue M client/galaxy/scripts/mvc/history/history-view.js M client/galaxy/scripts/mvc/history/multi-panel.js Log Message: ----------- refactor history view entrypoint out of extended bundle into history-view; swap HistoryView.vue to use new points. Minor import refactoring/cleanup, too. Commit: ee3b25c68f7ceb7fb3022d4002362806eabb38c0 https://github.com/galaxyproject/galaxy/commit/ee3b25c68f7ceb7fb3022d400236… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-02-19 (Mon, 19 Feb 2018) Changed paths: M client/galaxy/scripts/components/DisplayStructured.vue M client/galaxy/scripts/components/HistoryView.vue Log Message: ----------- V-cloak hides uncompiled templates -- we precompile everything (and intend to, always) so this isn't necessary Commit: 97fac3983d894df0b6c75a9c2f0ea3b54421a774 https://github.com/galaxyproject/galaxy/commit/97fac3983d894df0b6c75a9c2f0e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-02-19 (Mon, 19 Feb 2018) Changed paths: M client/galaxy/scripts/components/DisplayStructured.vue M client/galaxy/scripts/components/HistoryView.vue Log Message: ----------- Slightly better temporary error handling for new vue components. Commit: 6b72952e953c118234357585cb6d3a50c3df4837 https://github.com/galaxyproject/galaxy/commit/6b72952e953c118234357585cb6d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-02-19 (Mon, 19 Feb 2018) Changed paths: M Makefile M client/galaxy/scripts/apps/analysis.js A client/galaxy/scripts/apps/chart.js M client/galaxy/scripts/galaxy.js M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/layout/scratchbook.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/history/history-list.js M client/galaxy/scripts/mvc/tool/tool-genomespace.js M client/galaxy/scripts/mvc/ui/ui-select-genomespace.js M client/galaxy/scripts/mvc/ui/ui-thumbnails.js A client/galaxy/scripts/mvc/visualization/chart/chart-client.js A client/galaxy/scripts/mvc/visualization/chart/components/model.js A client/galaxy/scripts/mvc/visualization/chart/components/screenshot.js A client/galaxy/scripts/mvc/visualization/chart/utilities/datasets.js A client/galaxy/scripts/mvc/visualization/chart/utilities/jobs.js A client/galaxy/scripts/mvc/visualization/chart/utilities/series.js A client/galaxy/scripts/mvc/visualization/chart/views/description.js A client/galaxy/scripts/mvc/visualization/chart/views/editor.js A client/galaxy/scripts/mvc/visualization/chart/views/groups.js A client/galaxy/scripts/mvc/visualization/chart/views/menu.js A client/galaxy/scripts/mvc/visualization/chart/views/settings.js A client/galaxy/scripts/mvc/visualization/chart/views/viewer.js A client/galaxy/scripts/mvc/visualization/visualization-view.js M client/galaxy/scripts/onload.js M client/galaxy/scripts/qunit/tests/ui_tests.js M client/galaxy/scripts/utils/localization.js M client/galaxy/style/less/base.less A client/galaxy/style/less/charts.less M client/galaxy/style/less/galaxy_variables.less M client/galaxy/style/less/ui.less M client/package.json M client/webpack.config.js M config/datatypes_conf.xml.sample M config/galaxy.yml.sample R config/plugins/visualizations/charts/config/charts.xml R config/plugins/visualizations/charts/package.json R config/plugins/visualizations/charts/static/client/app.css R config/plugins/visualizations/charts/static/client/app.js R config/plugins/visualizations/charts/static/client/components/model.js R config/plugins/visualizations/charts/static/client/components/screenshot.js R config/plugins/visualizations/charts/static/client/views/description.js R config/plugins/visualizations/charts/static/client/views/editor.js R config/plugins/visualizations/charts/static/client/views/groups.js R config/plugins/visualizations/charts/static/client/views/settings.js R config/plugins/visualizations/charts/static/client/views/viewer.js R config/plugins/visualizations/charts/static/client/views/viewport.js R config/plugins/visualizations/charts/static/repository/build/benfred_venn.js R config/plugins/visualizations/charts/static/repository/build/benfred_venn.js.map R config/plugins/visualizations/charts/static/repository/build/biojs_drawrnajs.js R config/plugins/visualizations/charts/static/repository/build/biojs_drawrnajs.js.map R config/plugins/visualizations/charts/static/repository/build/biojs_msa.js R config/plugins/visualizations/charts/static/repository/build/biojs_msa.js.map R config/plugins/visualizations/charts/static/repository/build/biojs_phylocanvas.js R config/plugins/visualizations/charts/static/repository/build/biojs_phylocanvas.js.map R config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js R config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js.map R config/plugins/visualizations/charts/static/repository/build/jqplot_bar.js R config/plugins/visualizations/charts/static/repository/build/jqplot_bar.js.map R config/plugins/visualizations/charts/static/repository/build/jqplot_boxplot.js R config/plugins/visualizations/charts/static/repository/build/jqplot_boxplot.js.map R config/plugins/visualizations/charts/static/repository/build/jqplot_histogram_discrete.js R config/plugins/visualizations/charts/static/repository/build/jqplot_histogram_discrete.js.map R config/plugins/visualizations/charts/static/repository/build/jqplot_line.js R config/plugins/visualizations/charts/static/repository/build/jqplot_line.js.map R config/plugins/visualizations/charts/static/repository/build/jqplot_scatter.js R config/plugins/visualizations/charts/static/repository/build/jqplot_scatter.js.map R config/plugins/visualizations/charts/static/repository/build/ngl_viewer.js R config/plugins/visualizations/charts/static/repository/build/ngl_viewer.js.map R config/plugins/visualizations/charts/static/repository/build/nvd3_bar.js R config/plugins/visualizations/charts/static/repository/build/nvd3_bar.js.map R config/plugins/visualizations/charts/static/repository/build/nvd3_bar_horizontal.js R config/plugins/visualizations/charts/static/repository/build/nvd3_bar_horizontal.js.map R config/plugins/visualizations/charts/static/repository/build/nvd3_bar_horizontal_stacked.js R config/plugins/visualizations/charts/static/repository/build/nvd3_bar_horizontal_stacked.js.map R config/plugins/visualizations/charts/static/repository/build/nvd3_bar_stacked.js R config/plugins/visualizations/charts/static/repository/build/nvd3_bar_stacked.js.map R config/plugins/visualizations/charts/static/repository/build/nvd3_histogram.js R config/plugins/visualizations/charts/static/repository/build/nvd3_histogram.js.map R config/plugins/visualizations/charts/static/repository/build/nvd3_histogram_discrete.js R config/plugins/visualizations/charts/static/repository/build/nvd3_histogram_discrete.js.map R config/plugins/visualizations/charts/static/repository/build/nvd3_line.js R config/plugins/visualizations/charts/static/repository/build/nvd3_line.js.map R config/plugins/visualizations/charts/static/repository/build/nvd3_line_focus.js R config/plugins/visualizations/charts/static/repository/build/nvd3_line_focus.js.map R config/plugins/visualizations/charts/static/repository/build/nvd3_pie.js R config/plugins/visualizations/charts/static/repository/build/nvd3_pie.js.map R config/plugins/visualizations/charts/static/repository/build/nvd3_scatter.js R config/plugins/visualizations/charts/static/repository/build/nvd3_scatter.js.map R config/plugins/visualizations/charts/static/repository/build/nvd3_stackedarea.js R config/plugins/visualizations/charts/static/repository/build/nvd3_stackedarea.js.map R config/plugins/visualizations/charts/static/repository/build/nvd3_stackedarea_full.js R config/plugins/visualizations/charts/static/repository/build/nvd3_stackedarea_full.js.map R config/plugins/visualizations/charts/static/repository/build/nvd3_stackedarea_stream.js R config/plugins/visualizations/charts/static/repository/build/nvd3_stackedarea_stream.js.map R config/plugins/visualizations/charts/static/repository/build/others_example.js R config/plugins/visualizations/charts/static/repository/build/others_example.js.map R config/plugins/visualizations/charts/static/repository/build/others_heatmap.js R config/plugins/visualizations/charts/static/repository/build/others_heatmap.js.map R config/plugins/visualizations/charts/static/repository/build/others_heatmap_cluster.js R config/plugins/visualizations/charts/static/repository/build/others_heatmap_cluster.js.map R config/plugins/visualizations/charts/static/repository/build/pv_viewer.js R config/plugins/visualizations/charts/static/repository/build/pv_viewer.js.map R config/plugins/visualizations/charts/static/repository/build/registry.js R config/plugins/visualizations/charts/static/repository/build/registry.js.map R config/plugins/visualizations/charts/static/repository/build/registry.tmp.js R config/plugins/visualizations/charts/static/repository/plugins/benfred/venn.css R config/plugins/visualizations/charts/static/repository/plugins/benfred/venn.js R config/plugins/visualizations/charts/static/repository/plugins/biojs/biojs.msa.js R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/drawrna.js R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/layouts/layout.js R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/layouts/naview/base.js R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/layouts/naview/connection.js R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/layouts/naview/getnaview.js R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/layouts/naview/loop.js R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/layouts/naview/naview.js R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/layouts/naview/radloop.js R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/layouts/naview/region.js R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/layouts/radiate/getradiate.js R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/models/link.js R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/models/linkcol.js R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/models/ncanno.js R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/models/residue.js R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/models/residuecol.js R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/models/structure.js R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/utils/.Rhistory R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/utils/lasso.js R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/utils/parsedbr.js R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/utils/spectrum.js R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/utils/style.js R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/views/annoview.js R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/views/optspanel.js R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/views/seqpanel.js R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/views/vispanel.js R config/plugins/visualizations/charts/static/repository/plugins/biojs/phylocanvas/phylocanvas.js R config/plugins/visualizations/charts/static/repository/plugins/cytoscape/cytoscape.js R config/plugins/visualizations/charts/static/repository/plugins/jqplot/jquery.jqplot.css R config/plugins/visualizations/charts/static/repository/plugins/jqplot/jquery.jqplot.js R config/plugins/visualizations/charts/static/repository/plugins/jqplot/jquery.jqplot.plugins.js R config/plugins/visualizations/charts/static/repository/plugins/ngl/viewer.js R config/plugins/visualizations/charts/static/repository/plugins/nvd3/nv.d3.css R config/plugins/visualizations/charts/static/repository/plugins/nvd3/nv.d3.js R config/plugins/visualizations/charts/static/repository/plugins/pv/viewer.js R config/plugins/visualizations/charts/static/repository/registry.json R config/plugins/visualizations/charts/static/repository/utilities/jobs.js R config/plugins/visualizations/charts/static/repository/utilities/sifjson.js R config/plugins/visualizations/charts/static/repository/utilities/utils.js R config/plugins/visualizations/charts/static/repository/visualizations/benfred/venn/config.js R config/plugins/visualizations/charts/static/repository/visualizations/benfred/venn/logo.png R config/plugins/visualizations/charts/static/repository/visualizations/benfred/venn/wrapper.js R config/plugins/visualizations/charts/static/repository/visualizations/biojs/drawrnajs/config.js R config/plugins/visualizations/charts/static/repository/visualizations/biojs/drawrnajs/logo.png R config/plugins/visualizations/charts/static/repository/visualizations/biojs/drawrnajs/wrapper.js R config/plugins/visualizations/charts/static/repository/visualizations/biojs/msa/config.js R config/plugins/visualizations/charts/static/repository/visualizations/biojs/msa/logo.png R config/plugins/visualizations/charts/static/repository/visualizations/biojs/msa/wrapper.js R config/plugins/visualizations/charts/static/repository/visualizations/biojs/phylocanvas/config.js R config/plugins/visualizations/charts/static/repository/visualizations/biojs/phylocanvas/logo.png R config/plugins/visualizations/charts/static/repository/visualizations/biojs/phylocanvas/wrapper.js R config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/config.js R config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/logo.png R config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/wrapper.js R config/plugins/visualizations/charts/static/repository/visualizations/jqplot/bar/config.js R config/plugins/visualizations/charts/static/repository/visualizations/jqplot/bar/logo.png R config/plugins/visualizations/charts/static/repository/visualizations/jqplot/bar/wrapper.js R config/plugins/visualizations/charts/static/repository/visualizations/jqplot/boxplot/config.js R config/plugins/visualizations/charts/static/repository/visualizations/jqplot/boxplot/logo.png R config/plugins/visualizations/charts/static/repository/visualizations/jqplot/boxplot/wrapper.js R config/plugins/visualizations/charts/static/repository/visualizations/jqplot/common/config.js R config/plugins/visualizations/charts/static/repository/visualizations/jqplot/common/plot-config.js R config/plugins/visualizations/charts/static/repository/visualizations/jqplot/common/wrapper.js R config/plugins/visualizations/charts/static/repository/visualizations/jqplot/histogram_discrete/config.js R config/plugins/visualizations/charts/static/repository/visualizations/jqplot/histogram_discrete/logo.png R config/plugins/visualizations/charts/static/repository/visualizations/jqplot/histogram_discrete/wrapper.js R config/plugins/visualizations/charts/static/repository/visualizations/jqplot/line/config.js R config/plugins/visualizations/charts/static/repository/visualizations/jqplot/line/logo.png R config/plugins/visualizations/charts/static/repository/visualizations/jqplot/line/wrapper.js R config/plugins/visualizations/charts/static/repository/visualizations/jqplot/scatter/config.js R config/plugins/visualizations/charts/static/repository/visualizations/jqplot/scatter/logo.png R config/plugins/visualizations/charts/static/repository/visualizations/jqplot/scatter/wrapper.js R config/plugins/visualizations/charts/static/repository/visualizations/ngl/viewer/config.js R config/plugins/visualizations/charts/static/repository/visualizations/ngl/viewer/logo.png R config/plugins/visualizations/charts/static/repository/visualizations/ngl/viewer/wrapper.js R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar/config.js R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar/logo.png R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar/wrapper.js R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar_horizontal/config.js R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar_horizontal/logo.png R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar_horizontal/wrapper.js R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar_horizontal_stacked/config.js R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar_horizontal_stacked/logo.png R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar_horizontal_stacked/wrapper.js R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar_stacked/config.js R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar_stacked/logo.png R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar_stacked/wrapper.js R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/common/config.js R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/common/wrapper.js R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/histogram/config.js R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/histogram/logo.png R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/histogram/wrapper.js R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/histogram_discrete/config.js R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/histogram_discrete/logo.png R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/histogram_discrete/wrapper.js R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/line/config.js R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/line/logo.png R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/line/wrapper.js R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/line_focus/config.js R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/line_focus/logo.png R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/line_focus/wrapper.js R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/pie/config.js R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/pie/logo.png R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/pie/wrapper.js R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/scatter/config.js R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/scatter/logo.png R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/scatter/wrapper.js R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/stackedarea/config.js R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/stackedarea/logo.png R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/stackedarea/wrapper.js R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/stackedarea_full/config.js R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/stackedarea_full/logo.png R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/stackedarea_full/wrapper.js R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/stackedarea_stream/config.js R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/stackedarea_stream/logo.png R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/stackedarea_stream/wrapper.js R config/plugins/visualizations/charts/static/repository/visualizations/others/example/config.js R config/plugins/visualizations/charts/static/repository/visualizations/others/example/logo.png R config/plugins/visualizations/charts/static/repository/visualizations/others/example/wrapper.js R config/plugins/visualizations/charts/static/repository/visualizations/others/heatmap/config.js R config/plugins/visualizations/charts/static/repository/visualizations/others/heatmap/heatmap-parameters.js R config/plugins/visualizations/charts/static/repository/visualizations/others/heatmap/heatmap-plugin.js R config/plugins/visualizations/charts/static/repository/visualizations/others/heatmap/logo.png R config/plugins/visualizations/charts/static/repository/visualizations/others/heatmap/wrapper.js R config/plugins/visualizations/charts/static/repository/visualizations/others/heatmap_cluster/config.js R config/plugins/visualizations/charts/static/repository/visualizations/others/heatmap_cluster/logo.png R config/plugins/visualizations/charts/static/repository/visualizations/others/heatmap_cluster/wrapper.js R config/plugins/visualizations/charts/static/repository/visualizations/pv/viewer/config.js R config/plugins/visualizations/charts/static/repository/visualizations/pv/viewer/logo.png R config/plugins/visualizations/charts/static/repository/visualizations/pv/viewer/wrapper.js R config/plugins/visualizations/charts/static/repository/visualizations/utilities/tabular-datasets.js R config/plugins/visualizations/charts/static/repository/visualizations/utilities/tabular-form.js R config/plugins/visualizations/charts/static/repository/visualizations/utilities/tabular-utilities.js R config/plugins/visualizations/charts/templates/charts.mako R config/plugins/visualizations/charts/webpack.config.js A config/plugins/visualizations/common/templates/chart_entry_point.mako M config/plugins/visualizations/common/templates/script_entry_point.mako A config/plugins/visualizations/cytoscape/config/cytoscape.xml A config/plugins/visualizations/cytoscape/package.json A config/plugins/visualizations/cytoscape/src/script.js A config/plugins/visualizations/cytoscape/static/logo.png A config/plugins/visualizations/cytoscape/static/script.js A config/plugins/visualizations/drawrna/config/drawrna.xml A config/plugins/visualizations/drawrna/package.json A config/plugins/visualizations/drawrna/src/drawrnajs/drawrna.js A config/plugins/visualizations/drawrna/src/drawrnajs/layouts/layout.js A config/plugins/visualizations/drawrna/src/drawrnajs/layouts/naview/base.js A config/plugins/visualizations/drawrna/src/drawrnajs/layouts/naview/connection.js A config/plugins/visualizations/drawrna/src/drawrnajs/layouts/naview/getnaview.js A config/plugins/visualizations/drawrna/src/drawrnajs/layouts/naview/loop.js A config/plugins/visualizations/drawrna/src/drawrnajs/layouts/naview/naview.js A config/plugins/visualizations/drawrna/src/drawrnajs/layouts/naview/radloop.js A config/plugins/visualizations/drawrna/src/drawrnajs/layouts/naview/region.js A config/plugins/visualizations/drawrna/src/drawrnajs/layouts/radiate/getradiate.js A config/plugins/visualizations/drawrna/src/drawrnajs/models/link.js A config/plugins/visualizations/drawrna/src/drawrnajs/models/linkcol.js A config/plugins/visualizations/drawrna/src/drawrnajs/models/ncanno.js A config/plugins/visualizations/drawrna/src/drawrnajs/models/residue.js A config/plugins/visualizations/drawrna/src/drawrnajs/models/residuecol.js A config/plugins/visualizations/drawrna/src/drawrnajs/models/structure.js A config/plugins/visualizations/drawrna/src/drawrnajs/utils/.Rhistory A config/plugins/visualizations/drawrna/src/drawrnajs/utils/lasso.js A config/plugins/visualizations/drawrna/src/drawrnajs/utils/parsedbr.js A config/plugins/visualizations/drawrna/src/drawrnajs/utils/spectrum.js A config/plugins/visualizations/drawrna/src/drawrnajs/utils/style.js A config/plugins/visualizations/drawrna/src/drawrnajs/views/annoview.js A config/plugins/visualizations/drawrna/src/drawrnajs/views/optspanel.js A config/plugins/visualizations/drawrna/src/drawrnajs/views/seqpanel.js A config/plugins/visualizations/drawrna/src/drawrnajs/views/vispanel.js A config/plugins/visualizations/drawrna/src/script.js A config/plugins/visualizations/drawrna/static/logo.png A config/plugins/visualizations/drawrna/static/script.js A config/plugins/visualizations/example/config/example.xml A config/plugins/visualizations/example/package.json A config/plugins/visualizations/example/src/script.js A config/plugins/visualizations/example/static/logo.png A config/plugins/visualizations/example/static/script.js R config/plugins/visualizations/graphviz/static/js/jquery.qtip.js R config/plugins/visualizations/graphviz/static/js/tip_centerwindow.js R config/plugins/visualizations/graphviz/static/js/tip_followscroll.js M config/plugins/visualizations/graphviz/templates/graphviz.mako A config/plugins/visualizations/heatmap/heatmap_cluster/config/heatmap_cluster.xml A config/plugins/visualizations/heatmap/heatmap_cluster/static/logo.png A config/plugins/visualizations/heatmap/heatmap_default/config/heatmap_default.xml A config/plugins/visualizations/heatmap/heatmap_default/config/heatmap_shared.xml A config/plugins/visualizations/heatmap/heatmap_default/package.json A config/plugins/visualizations/heatmap/heatmap_default/src/colorsets.js A config/plugins/visualizations/heatmap/heatmap_default/src/script.js A config/plugins/visualizations/heatmap/heatmap_default/static/logo.png A config/plugins/visualizations/heatmap/heatmap_default/static/script.js A config/plugins/visualizations/jqplot/jqplot_bar/config/jqplot_bar.xml A config/plugins/visualizations/jqplot/jqplot_bar/config/jqplot_shared.xml A config/plugins/visualizations/jqplot/jqplot_bar/package.json A config/plugins/visualizations/jqplot/jqplot_bar/src/script.js A config/plugins/visualizations/jqplot/jqplot_bar/static/logo.png A config/plugins/visualizations/jqplot/jqplot_bar/static/script.css A config/plugins/visualizations/jqplot/jqplot_bar/static/script.js A config/plugins/visualizations/jqplot/jqplot_box/config/jqplot_box.xml A config/plugins/visualizations/jqplot/jqplot_box/static/logo.png A config/plugins/visualizations/jqplot/jqplot_histogram/config/jqplot_histogram.xml A config/plugins/visualizations/jqplot/jqplot_histogram/static/logo.png A config/plugins/visualizations/jqplot/jqplot_line/config/jqplot_line.xml A config/plugins/visualizations/jqplot/jqplot_line/static/logo.png A config/plugins/visualizations/jqplot/jqplot_scatter/config/jqplot_scatter.xml A config/plugins/visualizations/jqplot/jqplot_scatter/static/logo.png A config/plugins/visualizations/msa/config/msa.xml A config/plugins/visualizations/msa/package.json A config/plugins/visualizations/msa/src/msa.js A config/plugins/visualizations/msa/static/logo.png A config/plugins/visualizations/msa/static/script.js A config/plugins/visualizations/ngl/config/ngl.xml A config/plugins/visualizations/ngl/package.json A config/plugins/visualizations/ngl/src/ngl.js A config/plugins/visualizations/ngl/src/viewer.js A config/plugins/visualizations/ngl/static/logo.png A config/plugins/visualizations/ngl/static/ngl.js A config/plugins/visualizations/nvd3/nvd3_bar/.babelrc A config/plugins/visualizations/nvd3/nvd3_bar/config/nvd3_bar.xml A config/plugins/visualizations/nvd3/nvd3_bar/config/nvd3_shared.xml A config/plugins/visualizations/nvd3/nvd3_bar/package.json A config/plugins/visualizations/nvd3/nvd3_bar/src/nvd3.js A config/plugins/visualizations/nvd3/nvd3_bar/static/logo.png A config/plugins/visualizations/nvd3/nvd3_bar/static/nvd3.css A config/plugins/visualizations/nvd3/nvd3_bar/static/nvd3.js A config/plugins/visualizations/nvd3/nvd3_bar_stacked/config/nvd3_bar_stacked.xml A config/plugins/visualizations/nvd3/nvd3_bar_stacked/static/logo.png A config/plugins/visualizations/nvd3/nvd3_histogram/config/nvd3_histogram.xml A config/plugins/visualizations/nvd3/nvd3_histogram/static/logo.png A config/plugins/visualizations/nvd3/nvd3_histogram_discrete/config/nvd3_histogram_discrete.xml A config/plugins/visualizations/nvd3/nvd3_histogram_discrete/static/logo.png A config/plugins/visualizations/nvd3/nvd3_horizontal/config/nvd3_horizontal.xml A config/plugins/visualizations/nvd3/nvd3_horizontal/static/logo.png A config/plugins/visualizations/nvd3/nvd3_horizontal_stacked/config/nvd3_horizontal_stacked.xml A config/plugins/visualizations/nvd3/nvd3_horizontal_stacked/static/logo.png A config/plugins/visualizations/nvd3/nvd3_line/config/nvd3_line.xml A config/plugins/visualizations/nvd3/nvd3_line/static/logo.png A config/plugins/visualizations/nvd3/nvd3_line_focus/config/nvd3_line_focus.xml A config/plugins/visualizations/nvd3/nvd3_line_focus/static/logo.png A config/plugins/visualizations/nvd3/nvd3_pie/config/nvd3_pie.xml A config/plugins/visualizations/nvd3/nvd3_pie/static/logo.png A config/plugins/visualizations/nvd3/nvd3_scatter/config/nvd3_scatter.xml A config/plugins/visualizations/nvd3/nvd3_scatter/static/logo.png A config/plugins/visualizations/nvd3/nvd3_stackedarea/config/nvd3_stackedarea.xml A config/plugins/visualizations/nvd3/nvd3_stackedarea/static/logo.png A config/plugins/visualizations/nvd3/nvd3_stackedarea_full/config/nvd3_stackedarea_full.xml A config/plugins/visualizations/nvd3/nvd3_stackedarea_full/static/logo.png A config/plugins/visualizations/nvd3/nvd3_stackedarea_stream/config/nvd3_stackedarea_stream.xml A config/plugins/visualizations/nvd3/nvd3_stackedarea_stream/static/logo.png A config/plugins/visualizations/phylocanvas/config/phylocanvas.xml A config/plugins/visualizations/phylocanvas/package.json A config/plugins/visualizations/phylocanvas/src/script.js A config/plugins/visualizations/phylocanvas/static/logo.png A config/plugins/visualizations/phylocanvas/static/script.js A config/plugins/visualizations/pv/config/pv.xml A config/plugins/visualizations/pv/package.json A config/plugins/visualizations/pv/src/pv.js A config/plugins/visualizations/pv/static/logo.png A config/plugins/visualizations/pv/static/pv.js M config/plugins/visualizations/scatterplot/config/scatterplot.xml M config/plugins/visualizations/scatterplot/package.json A config/plugins/visualizations/scatterplot/src/numeric-column-stats.js M config/plugins/visualizations/scatterplot/src/scatterplot.js A config/plugins/visualizations/scatterplot/src/worker-stats.js A config/plugins/visualizations/scatterplot/static/8850628034555be072a0e4f882d4d8e5.js R config/plugins/visualizations/scatterplot/static/numeric-column-stats.js R config/plugins/visualizations/scatterplot/static/scatterplot.bundle.js A config/plugins/visualizations/scatterplot/static/scatterplot.js R config/plugins/visualizations/scatterplot/static/worker-stats.js M config/plugins/visualizations/scatterplot/templates/scatterplot.mako R config/plugins/visualizations/scatterplot/webpack.config.js A config/plugins/visualizations/venn/config/venn.xml A config/plugins/visualizations/venn/package.json A config/plugins/visualizations/venn/src/script.js A config/plugins/visualizations/venn/src/venn.js A config/plugins/visualizations/venn/static/logo.png A config/plugins/visualizations/venn/static/script.css A config/plugins/visualizations/venn/static/script.js M config/plugins/webhooks/demo/search/script.js M config/reports.yml.sample M config/tool_conf.xml.sample M config/user_preferences_extra_conf.yml.sample M doc/source/admin/galaxy_options.rst M doc/source/admin/reports_options.rst M doc/source/conf.py A doc/source/conf.versioning.py M lib/galaxy/config.py M lib/galaxy/dataset_collections/structure.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/converters/bam_native_to_bam_converter.xml M lib/galaxy/datatypes/converters/sam_to_bam_native.xml M lib/galaxy/datatypes/genetics.py M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/text.py M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt M lib/galaxy/jobs/actions/post.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/managers/configuration.py M lib/galaxy/managers/libraries.py M lib/galaxy/managers/taggable.py M lib/galaxy/managers/tags.py M lib/galaxy/model/mapping.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/views.py M lib/galaxy/tools/execute.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/repositories.py A lib/galaxy/tools/tag_collection_from_file.xml M lib/galaxy/tools/toolbox/filters/__init__.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/web/framework/middleware/sentry.py M lib/galaxy/web/security/__init__.py M lib/galaxy/webapps/galaxy/api/libraries.py M lib/galaxy/webapps/galaxy/api/users.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/config_schema.yml 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 M lib/tool_shed/tools/tool_validator.py M scripts/common_startup.sh R static/scripts/packed M static/style/blue/base.css M templates/js-app.mako M templates/webapps/galaxy/galaxy.masthead.mako M templates/webapps/galaxy/workflow/sharing.mako A test-data/new_tags_1.txt M test/api/test_visualizations.py M test/base/interactor.py A test/functional/tools/fail_writing_work_dir_file.xml M test/functional/tools/samples_tool_conf.xml M test/functional/twilltestcase.py M test/selenium_tests/test_saved_histories.py M test/unit/tools/test_tool_validation.py Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into history_structure Commit: a847ce20965ecb6418b48616effb049c56568c01 https://github.com/galaxyproject/galaxy/commit/a847ce20965ecb6418b48616effb… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2018-03-02 (Fri, 02 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/history/history-view.js M client/galaxy/scripts/mvc/history/multi-panel.js M client/galaxy/scripts/mvc/history/options-menu.js A lib/galaxy/util/create_history_template.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/history.py M static/style/blue/base.css R templates/webapps/galaxy/history/display_structured.mako R templates/webapps/galaxy/history/view.mako Log Message: ----------- Merge pull request #5317 from bgruening/history_structure History structure Compare: https://github.com/galaxyproject/galaxy/compare/de2bfa2ccacf...a847ce20965e

1 0

[galaxyproject/galaxy] bb19c7: Add queryname sorted and input sorted datatypes
by GitHub 01 Mar '18

01 Mar '18

Branch: refs/heads/usegalaxy Home: https://github.com/galaxyproject/galaxy Commit: bb19c7e44844bd724ba2ad3920abd078aae083a0 https://github.com/galaxyproject/galaxy/commit/bb19c7e44844bd724ba2ad3920ab… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-02-22 (Thu, 22 Feb 2018) Changed paths: M config/datatypes_conf.xml.sample 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 A test-data/qname_sorted.bam M test/functional/tools/sam_to_bam_native.xml M test/functional/tools/sample_datatypes_conf.xml Log Message: ----------- Add queryname sorted and input sorted datatypes The queryname sorted datatype (BamQuerynameSorted) ensures that the file is queryname ordered. The BamInputSorted datatype can be used to describe the output of aligners, which usually keep mate pairs adjacent. The BamInputSorted datatype allows using tools that require mates to be adjacent, without requiring an explicit sorting step. This can reduce the time and space required for duplicate marking tools, HiC tools and structural variant detection tools that require mates to be grouped together in an alignment file. The BamQuerynameSorted has a converter that works for all datatypes that can be consumed by samtools. There is no converter for BamInputSorted, since BamQuerynameSorted is valid input for tools requiring BamInputSorted input. I'm targeting 18.01 since I think it would be very unfortunate if we start annotating aligners with the very loose BamNative datatype, since this datatype does not make any promises about sort order at all. This closes https://github.com/galaxyproject/galaxy/issues/5497, goes a long way towards the problems mentioned in https://github.com/galaxyproject/galaxy/issues/5496 and would make https://github.com/galaxyproject/tools-iuc/pull/1732 and https://github.com/galaxyproject/tools-iuc/pull/1591 better Commit: 3dec3bdd21176d0fb66d7606a1e513ef244e4e86 https://github.com/galaxyproject/galaxy/commit/3dec3bdd21176d0fb66d7606a1e5… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-03-01 (Thu, 01 Mar 2018) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Move `Extract genomic DNA 1` to list of version galaxy lib tools Commit: 2d132a45d9af112a9d96e6a1d58646aff1a72910 https://github.com/galaxyproject/galaxy/commit/2d132a45d9af112a9d96e6a1d586… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2018-03-01 (Thu, 01 Mar 2018) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Merge pull request #5626 from mvdbeek/limit_extract_dna_legacy_versions [17.09] Move `Extract genomic DNA 1` to list of versioned galaxy tools requiring galaxy to be importable Commit: 87c70d844747b6d99880e495be0102fe386ccdb0 https://github.com/galaxyproject/galaxy/commit/87c70d844747b6d99880e495be01… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-03-01 (Thu, 01 Mar 2018) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Merge branch 'release_17.09' into release_18.01 Conflicts: lib/galaxy/tools/__init__.py Commit: d648e22080ac97b3940799d35e3be304d1a0aed7 https://github.com/galaxyproject/galaxy/commit/d648e22080ac97b3940799d35e3b… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-03-01 (Thu, 01 Mar 2018) Changed paths: M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/panel.py Log Message: ----------- fix for cases where panel elements have to_dict with different signature we want to only cache Tools anyways, so this fixes other possible bug where section/label etc would have same id as a Tool change the detection of Tool object to avoid circular import errors Also use cache for dictifying sections, we should gain more speed from that. Commit: 5406a7153bd6a51174145d04eda26b6796211154 https://github.com/galaxyproject/galaxy/commit/5406a7153bd6a51174145d04eda2… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-03-01 (Thu, 01 Mar 2018) Changed paths: M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/panel.py Log Message: ----------- pass the toolbox obj to make sure cache is available Commit: b96fd2c74010009a7dc85c09e77f87a9d4eff271 https://github.com/galaxyproject/galaxy/commit/b96fd2c74010009a7dc85c09e77f… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-03-01 (Thu, 01 Mar 2018) Changed paths: M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/panel.py Log Message: ----------- enable cache for tools that inherit from Tool Commit: 77d085a40f5d5d2e131dc2fc8073e0c030599988 https://github.com/galaxyproject/galaxy/commit/77d085a40f5d5d2e131dc2fc8073… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-01 (Thu, 01 Mar 2018) Changed paths: M config/datatypes_conf.xml.sample 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 A test-data/qname_sorted.bam M test/functional/tools/sam_to_bam_native.xml M test/functional/tools/sample_datatypes_conf.xml Log Message: ----------- Merge pull request #5589 from mvdbeek/samtools_queryname_and_input_order_datatypes [18.01] Add queryname sorted and input sorted datatypes Commit: 41910f824ea311e8ce7d93e4dc03a44c75c8132b https://github.com/galaxyproject/galaxy/commit/41910f824ea311e8ce7d93e4dc03… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-03-01 (Thu, 01 Mar 2018) Changed paths: M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/panel.py Log Message: ----------- Merge pull request #5615 from martenson/distinct-elts [18.01] fix for cases where panel elements have to_dict with different signature Commit: 56b8ecd3d50340c366aa22d5327fd635a3485ff0 https://github.com/galaxyproject/galaxy/commit/56b8ecd3d50340c366aa22d5327f… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-03-01 (Thu, 01 Mar 2018) Changed paths: M config/datatypes_conf.xml.sample 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/tools/__init__.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/panel.py A test-data/qname_sorted.bam M test/functional/tools/sam_to_bam_native.xml M test/functional/tools/sample_datatypes_conf.xml Log Message: ----------- Merge branch 'release_18.01' into usegalaxy Compare: https://github.com/galaxyproject/galaxy/compare/ab928fe55ed1...56b8ecd3d503

1 0

[galaxyproject/galaxy] d648e2: fix for cases where panel elements have to_dict wi...
by GitHub 01 Mar '18

01 Mar '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: d648e22080ac97b3940799d35e3be304d1a0aed7 https://github.com/galaxyproject/galaxy/commit/d648e22080ac97b3940799d35e3b… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-03-01 (Thu, 01 Mar 2018) Changed paths: M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/panel.py Log Message: ----------- fix for cases where panel elements have to_dict with different signature we want to only cache Tools anyways, so this fixes other possible bug where section/label etc would have same id as a Tool change the detection of Tool object to avoid circular import errors Also use cache for dictifying sections, we should gain more speed from that. Commit: 5406a7153bd6a51174145d04eda26b6796211154 https://github.com/galaxyproject/galaxy/commit/5406a7153bd6a51174145d04eda2… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-03-01 (Thu, 01 Mar 2018) Changed paths: M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/panel.py Log Message: ----------- pass the toolbox obj to make sure cache is available Commit: b96fd2c74010009a7dc85c09e77f87a9d4eff271 https://github.com/galaxyproject/galaxy/commit/b96fd2c74010009a7dc85c09e77f… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-03-01 (Thu, 01 Mar 2018) Changed paths: M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/panel.py Log Message: ----------- enable cache for tools that inherit from Tool Commit: 41910f824ea311e8ce7d93e4dc03a44c75c8132b https://github.com/galaxyproject/galaxy/commit/41910f824ea311e8ce7d93e4dc03… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-03-01 (Thu, 01 Mar 2018) Changed paths: M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/panel.py Log Message: ----------- Merge pull request #5615 from martenson/distinct-elts [18.01] fix for cases where panel elements have to_dict with different signature Compare: https://github.com/galaxyproject/galaxy/compare/77d085a40f5d...41910f824ea3

1 0

[galaxyproject/galaxy] a90b88: Client-format
by GitHub 01 Mar '18

01 Mar '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a90b889c11dbd7eb2362325cc777b71a43b0d022 https://github.com/galaxyproject/galaxy/commit/a90b889c11dbd7eb2362325cc777… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-01 (Thu, 01 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/history/history-view-edit.js M client/galaxy/scripts/mvc/tool/tool-genomespace.js Log Message: ----------- Client-format Commit: 05b6d87239f1b975f823c2a00c31923f310544fe https://github.com/galaxyproject/galaxy/commit/05b6d87239f1b975f823c2a00c31… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-01 (Thu, 01 Mar 2018) Changed paths: M client/galaxy/scripts/utils/utils.js Log Message: ----------- Minor cleanup of imports, explicit conditionals in utils/utils.js Commit: 841bc4d1fa5d8c17579f5a9aaea77feef5c1a766 https://github.com/galaxyproject/galaxy/commit/841bc4d1fa5d8c17579f5a9aaea7… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-01 (Thu, 01 Mar 2018) Changed paths: M client/galaxy/scripts/utils/utils.js Log Message: ----------- Minor tweak to active dropdown toggle to only search within the masthead for dropping active class; just to avoid this accidentally manipulating other areas on the page. The following line is fine, since it selects by the (assumed) unique id. Commit: de2bfa2ccacf809342b63280e5af99db98ecb18f https://github.com/galaxyproject/galaxy/commit/de2bfa2ccacf809342b63280e5af… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-01 (Thu, 01 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/history/history-view-edit.js M client/galaxy/scripts/mvc/tool/tool-genomespace.js M client/galaxy/scripts/utils/utils.js Log Message: ----------- Merge pull request #5630 from dannon/minor_tweaks_active_tab Minor tweak to active tab wrangling Compare: https://github.com/galaxyproject/galaxy/compare/3c7dd7f104b8...de2bfa2ccacf

1 0

[galaxyproject/galaxy] bb19c7: Add queryname sorted and input sorted datatypes
by GitHub 01 Mar '18

01 Mar '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: bb19c7e44844bd724ba2ad3920abd078aae083a0 https://github.com/galaxyproject/galaxy/commit/bb19c7e44844bd724ba2ad3920ab… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-02-22 (Thu, 22 Feb 2018) Changed paths: M config/datatypes_conf.xml.sample 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 A test-data/qname_sorted.bam M test/functional/tools/sam_to_bam_native.xml M test/functional/tools/sample_datatypes_conf.xml Log Message: ----------- Add queryname sorted and input sorted datatypes The queryname sorted datatype (BamQuerynameSorted) ensures that the file is queryname ordered. The BamInputSorted datatype can be used to describe the output of aligners, which usually keep mate pairs adjacent. The BamInputSorted datatype allows using tools that require mates to be adjacent, without requiring an explicit sorting step. This can reduce the time and space required for duplicate marking tools, HiC tools and structural variant detection tools that require mates to be grouped together in an alignment file. The BamQuerynameSorted has a converter that works for all datatypes that can be consumed by samtools. There is no converter for BamInputSorted, since BamQuerynameSorted is valid input for tools requiring BamInputSorted input. I'm targeting 18.01 since I think it would be very unfortunate if we start annotating aligners with the very loose BamNative datatype, since this datatype does not make any promises about sort order at all. This closes https://github.com/galaxyproject/galaxy/issues/5497, goes a long way towards the problems mentioned in https://github.com/galaxyproject/galaxy/issues/5496 and would make https://github.com/galaxyproject/tools-iuc/pull/1732 and https://github.com/galaxyproject/tools-iuc/pull/1591 better Commit: 77d085a40f5d5d2e131dc2fc8073e0c030599988 https://github.com/galaxyproject/galaxy/commit/77d085a40f5d5d2e131dc2fc8073… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-01 (Thu, 01 Mar 2018) Changed paths: M config/datatypes_conf.xml.sample 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 A test-data/qname_sorted.bam M test/functional/tools/sam_to_bam_native.xml M test/functional/tools/sample_datatypes_conf.xml Log Message: ----------- Merge pull request #5589 from mvdbeek/samtools_queryname_and_input_order_datatypes [18.01] Add queryname sorted and input sorted datatypes Compare: https://github.com/galaxyproject/galaxy/compare/87c70d844747...77d085a40f5d

1 0

[galaxyproject/galaxy] fcfa3c: fix highlighted workflow tab issue #4846
by GitHub 01 Mar '18

01 Mar '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: fcfa3cad89a6ed3476837f945da2e9f6c3aa3ba8 https://github.com/galaxyproject/galaxy/commit/fcfa3cad89a6ed3476837f945da2… Author: qiagu <guqiang01(a)gmail.com> Date: 2018-02-22 (Thu, 22 Feb 2018) Changed paths: M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/mvc/workflow/workflow.js M client/galaxy/scripts/utils/utils.js Log Message: ----------- fix highlighted workflow tab issue #4846 Commit: cf65c73c9d0a34420fa1bdcaf02cd00e810c7308 https://github.com/galaxyproject/galaxy/commit/cf65c73c9d0a34420fa1bdcaf02c… Author: Qiang.Gu <36086881+qiagu(a)users.noreply.github.com> Date: 2018-02-22 (Thu, 22 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow.js Log Message: ----------- Update workflow.js Commit: 0c3ee287cc90abe59e5e74ea0e3d76e245082700 https://github.com/galaxyproject/galaxy/commit/0c3ee287cc90abe59e5e74ea0e3d… Author: Qiang.Gu <36086881+qiagu(a)users.noreply.github.com> Date: 2018-02-23 (Fri, 23 Feb 2018) Changed paths: M client/galaxy/scripts/layout/page.js Log Message: ----------- Update page.js Commit: c76227524c0875dcca617876c9c09534807e641a https://github.com/galaxyproject/galaxy/commit/c76227524c0875dcca617876c9c0… Author: qiagu <guqiang01(a)gmail.com> Date: 2018-02-23 (Fri, 23 Feb 2018) Changed paths: M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/mvc/workflow/workflow.js M client/galaxy/scripts/utils/utils.js Log Message: ----------- fix workflow tab hightlight issue #4846 Commit: bc9d73c03b25b335e176dc5826d206d36ac57157 https://github.com/galaxyproject/galaxy/commit/bc9d73c03b25b335e176dc5826d2… Author: qiagu <guqiang01(a)gmail.com> Date: 2018-02-28 (Wed, 28 Feb 2018) Changed paths: M client/galaxy/scripts/layout/page.js Log Message: ----------- change to if statement Commit: 15111e5265afb62b357f302752d8e2747d25acf0 https://github.com/galaxyproject/galaxy/commit/15111e5265afb62b357f302752d8… Author: qiagu <guqiang01(a)gmail.com> Date: 2018-02-28 (Wed, 28 Feb 2018) Changed paths: M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/mvc/workflow/workflow.js M lib/galaxy/auth/__init__.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/util/gff_util.py M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt M lib/galaxy/jobs/__init__.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/web/proxy/js/package.json M lib/galaxy/webapps/galaxy/controllers/workflow.py M run_tests.sh M test/base/populators.py M test/galaxy_selenium/navigation.yml M test/integration/test_upload_configuration_options.py M test/selenium_tests/test_jupyter.py M tools/data_source/upload.py Log Message: ----------- update Commit: 9bc7be300c8ac982a8bd73e8c624944f605c6caa https://github.com/galaxyproject/galaxy/commit/9bc7be300c8ac982a8bd73e8c624… Author: qiagu <guqiang01(a)gmail.com> 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/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/conda_util.py M lib/galaxy/tools/deps/containers.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/tools/verify/test_data.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 tools/data_source/upload.xml Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into iss4846 update to dev Commit: 03656eeeb8df7b1c5614c6a98aeab58b1d523ee1 https://github.com/galaxyproject/galaxy/commit/03656eeeb8df7b1c5614c6a98aea… Author: qiagu <guqiang01(a)gmail.com> Date: 2018-02-28 (Wed, 28 Feb 2018) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/mvc/grid/grid-view.js Log Message: ----------- fix more tabs with issue #4846 Commit: 3c7dd7f104b8438beaa03aeb4d27f4c8f1d26efb https://github.com/galaxyproject/galaxy/commit/3c7dd7f104b8438beaa03aeb4d27… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-01 (Thu, 01 Mar 2018) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/mvc/grid/grid-view.js M client/galaxy/scripts/mvc/workflow/workflow.js M client/galaxy/scripts/utils/utils.js Log Message: ----------- Merge pull request #5593 from qiagu/iss4846 Fix active tab highlighting issue #4846 Compare: https://github.com/galaxyproject/galaxy/compare/c5affb92f901...3c7dd7f104b8

1 0

[galaxyproject/galaxy] 86f993: Remove broken write_from_stream() and set_raw_data...
by GitHub 01 Mar '18

01 Mar '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 86f993b8d831b0e6ce86d425cf673bcde278f652 https://github.com/galaxyproject/galaxy/commit/86f993b8d831b0e6ce86d425cf67… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-02-28 (Wed, 28 Feb 2018) Changed paths: M lib/galaxy/datatypes/data.py M lib/galaxy/model/__init__.py M lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py Log Message: ----------- Remove broken write_from_stream() and set_raw_data() methods They use `os.close()` on file handles open with `open()`. It seems they have never been used. Commit: 319454f216e6bdd24fc5e1eb7d576e5d8c769493 https://github.com/galaxyproject/galaxy/commit/319454f216e6bdd24fc5e1eb7d57… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-03-01 (Thu, 01 Mar 2018) Changed paths: M lib/galaxy/datatypes/assembly.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/blast.py M lib/galaxy/datatypes/converters/bed_to_gff_converter.py M lib/galaxy/datatypes/converters/fasta_to_len.py M lib/galaxy/datatypes/converters/fastqsolexa_to_fasta_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 lib/galaxy/datatypes/converters/maf_to_fasta_converter.py M lib/galaxy/datatypes/converters/maf_to_interval_converter.py M lib/galaxy/datatypes/converters/picard_interval_list_to_bed6_converter.py M lib/galaxy/datatypes/converters/ref_to_seq_taxonomy_converter.py M lib/galaxy/datatypes/converters/sam_to_bam.py M lib/galaxy/datatypes/converters/wiggle_to_simple_converter.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/images.py M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/molecules.py M lib/galaxy/datatypes/msa.py M lib/galaxy/datatypes/qualityscore.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/text.py M lib/galaxy/datatypes/xml.py Log Message: ----------- Use with statement in lib/galaxy/datatypes/ Commit: c5affb92f901d470e8c562f64ad402b3c1d8b076 https://github.com/galaxyproject/galaxy/commit/c5affb92f901d470e8c562f64ad4… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-01 (Thu, 01 Mar 2018) Changed paths: M lib/galaxy/datatypes/assembly.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/blast.py M lib/galaxy/datatypes/converters/bed_to_gff_converter.py M lib/galaxy/datatypes/converters/fasta_to_len.py M lib/galaxy/datatypes/converters/fastqsolexa_to_fasta_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 lib/galaxy/datatypes/converters/maf_to_fasta_converter.py M lib/galaxy/datatypes/converters/maf_to_interval_converter.py M lib/galaxy/datatypes/converters/picard_interval_list_to_bed6_converter.py M lib/galaxy/datatypes/converters/ref_to_seq_taxonomy_converter.py M lib/galaxy/datatypes/converters/sam_to_bam.py M lib/galaxy/datatypes/converters/wiggle_to_simple_converter.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/images.py M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/molecules.py M lib/galaxy/datatypes/msa.py M lib/galaxy/datatypes/qualityscore.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/text.py M lib/galaxy/datatypes/xml.py M lib/galaxy/model/__init__.py M lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py Log Message: ----------- Merge pull request #5623 from nsoranzo/use_with_statement Use with statement in lib/galaxy/datatypes/ Compare: https://github.com/galaxyproject/galaxy/compare/e53e90895d2e...c5affb92f901

1 0

[galaxyproject/usegalaxy-playbook] 1b50a6: Correct Pulsar stream size (it's in bytes not MB)
by GitHub 01 Mar '18

01 Mar '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 1b50a6b42fb0fb083d2e0eec729fef205603c3d6 https://github.com/galaxyproject/usegalaxy-playbook/commit/1b50a6b42fb0fb08… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-03-01 (Thu, 01 Mar 2018) Changed paths: M env/main/host_vars/br005.bridges.psc.edu.yml M env/main/host_vars/jetstream-iu0.galaxyproject.org.yml M env/main/host_vars/jetstream-tacc0.galaxyproject.org.yml M env/main/host_vars/login5.stampede.tacc.utexas.edu.yml M env/test/host_vars/jetstream-iu0.galaxyproject.org.yml M env/test/host_vars/jetstream-tacc0.galaxyproject.org.yml M env/test/host_vars/login5.stampede.tacc.utexas.edu.yml Log Message: ----------- Correct Pulsar stream size (it's in bytes not MB)

1 0

[galaxyproject/usegalaxy-playbook] dd343c: Move Bridges Pulsar from /pylon2 to /home
by GitHub 01 Mar '18

01 Mar '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: dd343c05db70e5ae1b1e836418bc5ec955956921 https://github.com/galaxyproject/usegalaxy-playbook/commit/dd343c05db70e5ae… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-03-01 (Thu, 01 Mar 2018) Changed paths: M CHANGELOG.md M env/main/host_vars/br005.bridges.psc.edu.yml M env/main/templates/galaxy/config/job_conf.xml.j2 M env/test/host_vars/br005.bridges.psc.edu.yml M env/test/templates/galaxy/config/job_conf.xml.j2 Log Message: ----------- Move Bridges Pulsar from /pylon2 to /home

1 0

[galaxyproject/usegalaxy-playbook] 2fae8f: Bug fix for Galaxy update ref feature recently add...
by GitHub 01 Mar '18

01 Mar '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 2fae8f3ab058bba8f353967f3e758455489f4cb0 https://github.com/galaxyproject/usegalaxy-playbook/commit/2fae8f3ab058bba8… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-03-01 (Thu, 01 Mar 2018) Changed paths: A roles/usegalaxy_cvmfs/files/makepyc.py A roles/usegalaxy_cvmfs/files/update_galaxy.sh M roles/usegalaxy_cvmfs/tasks/update.yml Log Message: ----------- Bug fix for Galaxy update ref feature recently added, plus move the update and makepyc scripts in to Ansible so they are version controlled and I don't have to make manual transactions to change them. Commit: bebea945a4f64a582de4ceacc2a3077f038aa6d4 https://github.com/galaxyproject/usegalaxy-playbook/commit/bebea945a4f64a58… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-03-01 (Thu, 01 Mar 2018) Changed paths: M env/test/files/galaxy/galaxy_version.yml Log Message: ----------- Update Test Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/038df8395fb5...…

1 0

Jump to page:

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

galaxy-commits March 2018