- galaxy-commits - lists.galaxyproject.org

[galaxyproject/usegalaxy-playbook] a461bf: unhide cut and cat
by GitHub 02 Mar '18

02 Mar '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: a461bf5adf0e0eea3aa50f0c44977101a00f38be https://github.com/galaxyproject/usegalaxy-playbook/commit/a461bf5adf0e0eea… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-03-02 (Fri, 02 Mar 2018) Changed paths: M env/main/files/galaxy/config/tool_conf.xml Log Message: ----------- unhide cut and cat

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[galaxyproject/usegalaxy-playbook] 9520ae: hide tools from Main
by GitHub 02 Mar '18

02 Mar '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 9520aeab701220229f7b5c57a45b9364f91883b7 https://github.com/galaxyproject/usegalaxy-playbook/commit/9520aeab70122022… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-03-02 (Fri, 02 Mar 2018) Changed paths: M env/main/files/galaxy/config/tool_conf.xml Log Message: ----------- hide tools from Main that are no longer wanted

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[galaxyproject/galaxy] 7254d5: Remove href from grid sorting links
by GitHub 02 Mar '18

02 Mar '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: 7254d55e8b192ff4387ef6a276e202db5821ca60 https://github.com/galaxyproject/galaxy/commit/7254d55e8b192ff4387ef6a276e2… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-02 (Fri, 02 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/grid/grid-template.js M lib/galaxy/web/framework/helpers/grids.py Log Message: ----------- Remove href from grid sorting links Commit: 7ffabb1df3f6feb11a3746c2f27bc762b1af29c7 https://github.com/galaxyproject/galaxy/commit/7ffabb1df3f6feb11a3746c2f27b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-02 (Fri, 02 Mar 2018) Changed paths: M lib/galaxy/web/framework/helpers/grids.py Log Message: ----------- Remove unused variable Commit: e01f9fa1b89e6a5fd12f9ef98ddb005959e1b761 https://github.com/galaxyproject/galaxy/commit/e01f9fa1b89e6a5fd12f9ef98ddb… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-03-02 (Fri, 02 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/grid/grid-template.js M lib/galaxy/web/framework/helpers/grids.py Log Message: ----------- Merge pull request #5634 from guerler/fix_async_grid_links [18.01] Remove href from grid sorting links Compare: https://github.com/galaxyproject/galaxy/compare/41910f824ea3...e01f9fa1b89e

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[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 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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 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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 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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 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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 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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

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[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

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[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

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[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

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[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

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[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

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[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

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[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)

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[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

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[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...…

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[galaxyproject/galaxy] 3dec3b: Move `Extract genomic DNA 1` to list of version ga...
by GitHub 01 Mar '18

01 Mar '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy 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: e53e90895d2e195322af65364b0fb55049ea728b https://github.com/galaxyproject/galaxy/commit/e53e90895d2e195322af65364b0f… 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_18.01' into dev Compare: https://github.com/galaxyproject/galaxy/compare/740c78c734f1...e53e90895d2e

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[galaxyproject/galaxy] 3dec3b: Move `Extract genomic DNA 1` to list of version ga...
by GitHub 01 Mar '18

01 Mar '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy 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 Compare: https://github.com/galaxyproject/galaxy/compare/a90c3a1d3f2c...87c70d844747

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[galaxyproject/galaxy] 3dec3b: Move `Extract genomic DNA 1` to list of version ga...
by GitHub 01 Mar '18

01 Mar '18

Branch: refs/heads/release_17.09 Home: https://github.com/galaxyproject/galaxy 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 Compare: https://github.com/galaxyproject/galaxy/compare/13e72e84c523...2d132a45d9af

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[galaxyproject/galaxy] e594b2: fix for cases where panel elements have to_dict wi...
by GitHub 01 Mar '18

01 Mar '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: e594b2b257e62622f686a7f5244a342e416ceb8e https://github.com/galaxyproject/galaxy/commit/e594b2b257e62622f686a7f5244a… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-02-27 (Tue, 27 Feb 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: e9aad5ea965edb2853631971634493bd82679c75 https://github.com/galaxyproject/galaxy/commit/e9aad5ea965edb28536319716344… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-02-28 (Wed, 28 Feb 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: 713bf6fa8e0274bd55571a91842ba593c68fe03e https://github.com/galaxyproject/galaxy/commit/713bf6fa8e0274bd55571a91842b… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-02-28 (Wed, 28 Feb 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: 740c78c734f14f0679c975057fa9fd414dfa4e87 https://github.com/galaxyproject/galaxy/commit/740c78c734f14f0679c975057fa9… Author: John Chilton <jmchilton(a)gmail.com> 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 #5616 from martenson/improve-tb-caching toolbox to_dict cache fix and improvements Compare: https://github.com/galaxyproject/galaxy/compare/cbade98a233d...740c78c734f1

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[galaxyproject/galaxy] 49a001: Conda fixes for 18.01 - stdout redirection.
by GitHub 28 Feb '18

28 Feb '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 49a001cf7c4bbca1dd866a0a97082d343b3ea349 https://github.com/galaxyproject/galaxy/commit/49a001cf7c4bbca1dd866a0a9708… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-02-28 (Wed, 28 Feb 2018) Changed paths: M lib/galaxy/tools/deps/conda_util.py Log Message: ----------- Conda fixes for 18.01 - stdout redirection. Broken in #5397 I think. Commit: 79a5acaaec6d4b6e4ee36998977d85a8dc769612 https://github.com/galaxyproject/galaxy/commit/79a5acaaec6d4b6e4ee36998977d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-02-28 (Wed, 28 Feb 2018) Changed paths: M lib/galaxy/tools/cwl/util.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/containers.py M lib/galaxy/tools/verify/test_data.py Log Message: ----------- Conda fixes for dev - mostly Python 3. Commit: 0dbbfc7afcbde64a068c0bb321184b219b8c51af https://github.com/galaxyproject/galaxy/commit/0dbbfc7afcbde64a068c0bb32118… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-02-28 (Wed, 28 Feb 2018) Changed paths: M lib/galaxy/tools/cwl/util.py M lib/galaxy/tools/verify/test_data.py Log Message: ----------- Prettier imports Commit: 77537ad55398b004cf0c4de3e7aaa11ce15a7a60 https://github.com/galaxyproject/galaxy/commit/77537ad55398b004cf0c4de3e7aa… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-02-28 (Wed, 28 Feb 2018) Changed paths: M lib/galaxy/tools/cwl/util.py Log Message: ----------- Tweak to Python 3 fix as suggested by @nsoranzo. Commit: cbade98a233db9f7a4c8ae28ccff2bc1258d5802 https://github.com/galaxyproject/galaxy/commit/cbade98a233db9f7a4c8ae28ccff… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2018-02-28 (Wed, 28 Feb 2018) Changed paths: M lib/galaxy/tools/cwl/util.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/containers.py M lib/galaxy/tools/verify/test_data.py Log Message: ----------- Merge pull request #5621 from jmchilton/galaxy_lib_update Fixes from galaxy-lib Compare: https://github.com/galaxyproject/galaxy/compare/4caaa70006ce...cbade98a233d

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[galaxyproject/usegalaxy-playbook] 038df8: Updated Diffbind
by GitHub 27 Feb '18

27 Feb '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 038df8395fb5e039500b016d60460cb2187b67f7 https://github.com/galaxyproject/usegalaxy-playbook/commit/038df8395fb5e039… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-02-27 (Tue, 27 Feb 2018) Changed paths: M env/main/files/galaxy/var/integrated_tool_panel.xml M env/main/files/galaxy/var/shed_tool_conf.xml Log Message: ----------- Updated Diffbind

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[galaxyproject/usegalaxy-playbook] 829ec6: Test mutable configs for installation of Diffbind ...
by GitHub 27 Feb '18

27 Feb '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 829ec671430825b19f440d056bfaf7d78694d885 https://github.com/galaxyproject/usegalaxy-playbook/commit/829ec671430825b1… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-02-27 (Tue, 27 Feb 2018) Changed paths: M env/test/files/galaxy/var/integrated_tool_panel.xml M env/test/files/galaxy/var/shed_tool_conf.xml Log Message: ----------- Test mutable configs for installation of Diffbind and format-BIOM tools

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[galaxyproject/usegalaxy-playbook] afab2f: Add support for reverting Galaxy and revert.
by GitHub 27 Feb '18

27 Feb '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: afab2f57674523e6ae8be9ae5347f3ebd57807e7 https://github.com/galaxyproject/usegalaxy-playbook/commit/afab2f57674523e6… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-02-27 (Tue, 27 Feb 2018) Changed paths: M env/main/files/galaxy/galaxy_version.yml M env/main/group_vars/all.yml M roles/usegalaxy_cvmfs/tasks/update.yml Log Message: ----------- Add support for reverting Galaxy and revert.

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[galaxyproject/usegalaxy-playbook] 789919: Update Main
by GitHub 27 Feb '18

27 Feb '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 78991922b95abbf073699f86078f7fba53d70053 https://github.com/galaxyproject/usegalaxy-playbook/commit/78991922b95abbf0… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-02-27 (Tue, 27 Feb 2018) Changed paths: M env/main/files/galaxy/galaxy_version.yml Log Message: ----------- Update Main

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[galaxyproject/galaxy] f6ac13: Don't fail rest of multi-action queue when attempt...
by GitHub 27 Feb '18

27 Feb '18

Branch: refs/heads/usegalaxy Home: https://github.com/galaxyproject/galaxy Commit: f6ac13568f62731fb785e3aafafbf3aacf21a7a2 https://github.com/galaxyproject/galaxy/commit/f6ac13568f62731fb785e3aafafb… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-02-18 (Sun, 18 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/history/history-view-edit.js Log Message: ----------- Don't fail rest of multi-action queue when attempting to purge a collection. Fixes https://github.com/galaxyproject/galaxy/issues/5117. Commit: 31e31e692311ba2e9f11d3eabe5253628f8e39c9 https://github.com/galaxyproject/galaxy/commit/31e31e692311ba2e9f11d3eabe52… Author: nekrut <anton(a)nekrut.org> Date: 2018-02-19 (Mon, 19 Feb 2018) Changed paths: M config/datatypes_conf.xml.sample A lib/galaxy/datatypes/converters/fastagz_to_fasta.xml M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py Log Message: ----------- added fasta.gz Commit: d79717b86e0b6ecf5e540eb939888066b88081de https://github.com/galaxyproject/galaxy/commit/d79717b86e0b6ecf5e540eb93988… Author: nekrut <anton(a)nekrut.org> Date: 2018-02-19 (Mon, 19 Feb 2018) Changed paths: M lib/galaxy/datatypes/sequence.py Log Message: ----------- fixed flake8 errors Commit: 8cec1fd592a354be9b055fbb8b7f3ce72df39990 https://github.com/galaxyproject/galaxy/commit/8cec1fd592a354be9b055fbb8b7f… Author: nekrut <anton(a)nekrut.org> Date: 2018-02-19 (Mon, 19 Feb 2018) Changed paths: M lib/galaxy/datatypes/sequence.py Log Message: ----------- removing stray whitespace Commit: d34524ff8adc694e41f0e582a57f705f2ed0dd7d https://github.com/galaxyproject/galaxy/commit/d34524ff8adc694e41f0e582a57f… Author: nekrut <anton(a)nekrut.org> Date: 2018-02-19 (Mon, 19 Feb 2018) Changed paths: M lib/galaxy/datatypes/converters/fastagz_to_fasta.xml Log Message: ----------- fixed name of fastagz->fasta converter Commit: c4ce9695bbb577a0e9514c5cb71069156d33a943 https://github.com/galaxyproject/galaxy/commit/c4ce9695bbb577a0e9514c5cb710… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-02-19 (Mon, 19 Feb 2018) Changed paths: M lib/galaxy/datatypes/converters/fastagz_to_fasta.xml Log Message: ----------- fix copypasta Commit: 9feaf85585a30820dd71762431e1ed7d5b5c3b5e https://github.com/galaxyproject/galaxy/commit/9feaf85585a30820dd71762431e1… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-02-19 (Mon, 19 Feb 2018) Changed paths: M lib/galaxy/datatypes/sequence.py Log Message: ----------- fix more fasta copypasta Commit: 17a5d20278f7306e69e77054f92d976020e048ee https://github.com/galaxyproject/galaxy/commit/17a5d20278f7306e69e77054f92d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-02-19 (Mon, 19 Feb 2018) Changed paths: M run_tests.sh Log Message: ----------- In test framework only build client if running Selenium tests. These shouldn't be required for any other test types I believe and it slows things down. Commit: 6a3ce34c09bd516a18bd7d8f04851e1155d6d174 https://github.com/galaxyproject/galaxy/commit/6a3ce34c09bd516a18bd7d8f0485… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-02-19 (Mon, 19 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/history/history-view-edit.js Log Message: ----------- Merge pull request #5443 from jmchilton/fix5117 [18.01] Don't silently fail rest of multi-action queue when attempting to purge a collection. Commit: 2ca339d2b7cfdde817097837033e317a19b4a801 https://github.com/galaxyproject/galaxy/commit/2ca339d2b7cfdde817097837033e… Author: Jelle Scholtalbers <j.scholtalbers(a)gmail.com> Date: 2018-02-20 (Tue, 20 Feb 2018) Changed paths: M lib/galaxy/auth/__init__.py Log Message: ----------- fix broken admin 'create new user' when registration =='challenge' Commit: 01776c617b691c467e423c7a5f60c17be9b71503 https://github.com/galaxyproject/galaxy/commit/01776c617b691c467e423c7a5f60… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-02-20 (Tue, 20 Feb 2018) Changed paths: M lib/galaxy/auth/__init__.py Log Message: ----------- Merge pull request #5569 from scholtalbers/fix/broken_create_new_user_challenge [18.01] fix broken admin 'create new user' when registration =='challenge' Commit: 99f7de456ce953f36e6122270209083fe443654b https://github.com/galaxyproject/galaxy/commit/99f7de456ce953f36e6122270209… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-02-20 (Tue, 20 Feb 2018) Changed paths: M run_tests.sh Log Message: ----------- Merge pull request #5566 from jmchilton/optimize_tests_0 [18.01] In test framework only build client if running Selenium tests. Commit: 7715838dbbbcad980a47d1a96619b6e91fa7a623 https://github.com/galaxyproject/galaxy/commit/7715838dbbbcad980a47d1a96619… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-02-20 (Tue, 20 Feb 2018) Changed paths: M config/datatypes_conf.xml.sample A lib/galaxy/datatypes/converters/fastagz_to_fasta.xml M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py Log Message: ----------- Merge pull request #5561 from martenson/backport-fastgz [18.01] add fasta.gz support Commit: 93d5c54946e992112841df3461512bbeb6f5c7e9 https://github.com/galaxyproject/galaxy/commit/93d5c54946e992112841df346151… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-02-21 (Wed, 21 Feb 2018) Changed paths: M lib/galaxy/web/framework/helpers/grids.py Log Message: ----------- Optimize count query in grids (part 1). Many grid operations execute a complex query twice - once to produce the total number of rows and once to iterate through the selected parts of the data. This can be more optimal in many ways - this starts us down the path to addressing that by doing two things. The first thing it does is eliminates the query all together if paging is enabled but the user has opted to see "all" the rows. There was never a reason to execute the query in that case I don't think. The second thing it does is move the calculation of the count query until after the data has been generated - this isn't more optimal by itself but it allows us to potentially calculate the count as part of the main query. I've implemented this in a broken way @ https://github.com/galaxyproject/galaxy/commit/ea404721585b5f78da1b91e57e31… but I realized it was too broad an approach and doesn't work if certain kinds of joins are used in the initial query - but a more targetted approach on a per-grid basis could work I think and moving this code after allow us to potentially do that more easily in subsequent commits. Additionally I added a note - that I think it would be best to just return None as the number of pages and issue a second query to the same endpoint with the same arguments but with count_only=true added as a query request parameter so we can render the main grid faster and then render the paging elements after the second query finishes. This would feel more responsive I think. Commit: 1a782eb4eb29158a203df9e02b0195ecfe496e37 https://github.com/galaxyproject/galaxy/commit/1a782eb4eb29158a203df9e02b01… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-02-21 (Wed, 21 Feb 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- Paginate published workflow grid. @martenson mentioned he prefers the look and feel of the published history grid so this replicates that and very likely will result in quicker rendering on usegalaxy.org - though we should verify this after it is deployed since the paginated grid do result in two big join queries instead of one big query - but I suspect rendering details on fewer objects (which includes fetching tag information from the db) will saved more than enough to make up for that. Commit: af0b40ea95c5244c58fbaa545b81ef4c4eff7cf0 https://github.com/galaxyproject/galaxy/commit/af0b40ea95c5244c58fbaa545b81… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-02-21 (Wed, 21 Feb 2018) Changed paths: M lib/galaxy/web/proxy/js/package.json Log Message: ----------- Bump sqlite3 dependency for web proxy Commit: 5d422898582446575dfe30d13805c9e13a3f8104 https://github.com/galaxyproject/galaxy/commit/5d422898582446575dfe30d13805… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-02-21 (Wed, 21 Feb 2018) Changed paths: M lib/galaxy/web/proxy/js/package.json Log Message: ----------- Minor updates to commander, http-proxy. eventemitter3 is several major versions behind, needs testing before upgrade. Commit: 1656c7b429854323efda82accc4c190a965be8a3 https://github.com/galaxyproject/galaxy/commit/1656c7b429854323efda82accc4c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-02-21 (Wed, 21 Feb 2018) Changed paths: M lib/galaxy/tools/parameters/output_collect.py Log Message: ----------- Fix repeated fetching dataset permissions in dynamic output collection. Commit: b5b41d6172bd7e2894efcc3b423b11a37fb92823 https://github.com/galaxyproject/galaxy/commit/b5b41d6172bd7e2894efcc3b423b… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2018-02-21 (Wed, 21 Feb 2018) Changed paths: M lib/galaxy/web/proxy/js/package.json Log Message: ----------- Merge pull request #5575 from dannon/web_proxy_fixes [18.01] Bump sqlite3 dependency for web proxy Commit: ff73cf2e6f8e1143e82681a9cfa97d769610f2c2 https://github.com/galaxyproject/galaxy/commit/ff73cf2e6f8e1143e82681a9cfa9… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-02-21 (Wed, 21 Feb 2018) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- Handle header-only bam files correctly indicating there is no more data to fetch when chunking Commit: 34c5a1a1f39e4805b4b6e46d86e9db721c98199a https://github.com/galaxyproject/galaxy/commit/34c5a1a1f39e4805b4b6e46d86e9… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-02-21 (Wed, 21 Feb 2018) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- Two minor linting issues (deprecated e.message, unused var) Commit: 75b06187053de95f07fdbbb6caeaf3e52265238e https://github.com/galaxyproject/galaxy/commit/75b06187053de95f07fdbbb6caea… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-02-21 (Wed, 21 Feb 2018) Changed paths: M tools/data_source/upload.py Log Message: ----------- Do not remove external path files during library uploads xref. https://github.com/galaxyproject/galaxy/pull/5264#issuecomment-367172820 Commit: f7f9c120eda7f9d735257eecaeb759ad50473f57 https://github.com/galaxyproject/galaxy/commit/f7f9c120eda7f9d735257eecaeb7… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-02-21 (Wed, 21 Feb 2018) Changed paths: M test/integration/test_upload_configuration_options.py Log Message: ----------- Refactor BaseFtpUploadConfigurationTestCase._write_ftp_file() method Commit: f41230034689448abc6059d8e2771001961bafb9 https://github.com/galaxyproject/galaxy/commit/f41230034689448abc6059d8e277… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-02-21 (Wed, 21 Feb 2018) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- No need to str() it; %s does this -- thanks @nsoranzo Commit: 117b4dcd6c503c51fb376c98ae8ba38d462d0301 https://github.com/galaxyproject/galaxy/commit/117b4dcd6c503c51fb376c98ae8b… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-02-21 (Wed, 21 Feb 2018) Changed paths: M test/base/populators.py M test/integration/test_upload_configuration_options.py Log Message: ----------- Update integration test to check external path files are not deleted after library upload This test would have failed before commit 75b06187053de95f07fdbbb6caeaf3e52265238e. Commit: c00e772159f6a121bc4f7759fa57f48e79c48f32 https://github.com/galaxyproject/galaxy/commit/c00e772159f6a121bc4f7759fa57… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-02-21 (Wed, 21 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 Log Message: ----------- Fix lack of feedback when slow grids are loading data from the server. Fixes #5473 (after numerous other backend optimizations also). Commit: 8afeffe95cc63832a6208e119cbfea4671a49a47 https://github.com/galaxyproject/galaxy/commit/8afeffe95cc63832a6208e119cbf… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-02-21 (Wed, 21 Feb 2018) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- Merge pull request #5579 from dannon/fix_bam_nodata [18.01] Fix small bam (header-only) infinite fetching Commit: b861b9ad4d693000ba8cf492ce6b1ff057db3d34 https://github.com/galaxyproject/galaxy/commit/b861b9ad4d693000ba8cf492ce6b… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-02-21 (Wed, 21 Feb 2018) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- implement basic cache on toolbox to_dict objects base the cache on absence of filters allow cache for users that don't opt in for filters Commit: 8cc675eedd8bb895cf26cfc1fa5cbcc97e75f638 https://github.com/galaxyproject/galaxy/commit/8cc675eedd8bb895cf26cfc1fa5c… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-02-21 (Wed, 21 Feb 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- Merge pull request #5576 from jmchilton/workflow_paginate [18.01] Paginate published workflows grid. Commit: d9372739376f5d289740faae40e8790391d8d843 https://github.com/galaxyproject/galaxy/commit/d9372739376f5d289740faae40e8… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-02-22 (Thu, 22 Feb 2018) Changed paths: M test/base/populators.py M test/integration/test_upload_configuration_options.py M tools/data_source/upload.py Log Message: ----------- Merge pull request #5573 from nsoranzo/release_18.01_fix_filesystem_library_uploads [18.01] Do not remove external path files during library uploads Commit: 8806030f53c2b9d0002505bf5193be88d7cff8f9 https://github.com/galaxyproject/galaxy/commit/8806030f53c2b9d0002505bf5193… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-02-22 (Thu, 22 Feb 2018) Changed paths: M lib/galaxy/datatypes/converters/sam_to_bam.py M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/mulled/util.py M lib/galaxy/tools/toolbox/lineages/interface.py M lib/galaxy/visualization/data_providers/genome.py Log Message: ----------- Replace distutils.version with packaging.version distutils under Python3 has this bug: https://bugs.python.org/issue14894 which causes this traceback: ``` Traceback (most recent call last): File "lib/galaxy/webapps/galaxy/buildapp.py", line 49, in app_factory app = galaxy.app.UniverseApplication(global_conf=global_conf, **kwargs) File "lib/galaxy/app.py", line 125, in __init__ self._configure_toolbox() File "lib/galaxy/config.py", line 930, in _configure_toolbox self.toolbox = tools.ToolBox(tool_configs, self.config.tool_path, self) File "lib/galaxy/tools/__init__.py", line 232, in __init__ app=app, File "lib/galaxy/tools/toolbox/base.py", line 1056, in __init__ super(BaseGalaxyToolBox, self).__init__(config_filenames, tool_root_dir, app) File "lib/galaxy/tools/toolbox/base.py", line 84, in __init__ self._load_tool_panel() File "lib/galaxy/tools/toolbox/base.py", line 358, in _load_tool_panel self.__add_tool_to_tool_panel(section_val, section, section=True) File "lib/galaxy/tools/toolbox/base.py", line 278, in __add_tool_to_tool_panel related_tool = self._lineage_in_panel(panel_dict, tool=tool) File "lib/galaxy/tools/toolbox/base.py", line 961, in _lineage_in_panel lineage_tool_versions = reversed(tool_lineage.get_versions()) File "lib/galaxy/tools/toolbox/lineages/interface.py", line 77, in get_versions return [ToolLineageVersion(tool_id, tool_version) for tool_id, tool_version in zip(self.tool_ids, self.tool_versions)] File "lib/galaxy/tools/toolbox/lineages/interface.py", line 55, in tool_ids return ["%s/%s" % (tool_id, version) for version in self.tool_versions] File "lib/galaxy/tools/toolbox/lineages/interface.py", line 49, in tool_versions return sorted(self._tool_versions, key=LooseVersion) File "/usr/lib/python3.4/distutils/version.py", line 58, in __lt__ c = self._cmp(other) File "/usr/lib/python3.4/distutils/version.py", line 343, in _cmp if self.version < other.version: TypeError: unorderable types: str() < int() ``` when a tool version contains a letter in the "wrong" place (e.g. in the first position). Fix https://github.com/galaxyproject/galaxy/issues/5408 . Commit: ce3b40cfc10e134d5acc477757404eba40ea6553 https://github.com/galaxyproject/galaxy/commit/ce3b40cfc10e134d5acc47775740… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-02-22 (Thu, 22 Feb 2018) Changed paths: M lib/galaxy/tools/parameters/output_collect.py Log Message: ----------- Merge pull request #5578 from jmchilton/opt_dyn_collect [18.01] Fix repeated fetching dataset permissions in dynamic output collection. Commit: fc52fe5c62700b4f8527e4edead0fba4e7cfe33f https://github.com/galaxyproject/galaxy/commit/fc52fe5c62700b4f8527e4edead0… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-02-22 (Thu, 22 Feb 2018) Changed paths: M lib/galaxy/datatypes/converters/sam_to_bam.py M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/mulled/util.py M lib/galaxy/tools/toolbox/lineages/interface.py M lib/galaxy/visualization/data_providers/genome.py Log Message: ----------- Merge pull request #5588 from jmchilton/backport_packaging [18.01] Replace distutils.version with packaging.version Commit: 8a88cb9827b68e6795cf00496008e1aa189185ad https://github.com/galaxyproject/galaxy/commit/8a88cb9827b68e6795cf00496008… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-02-26 (Mon, 26 Feb 2018) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- move the cache from toolbox level to tool level the cache remains toolbox-specific so it is stored within the toolbox object includes refactor thanks to eagle eyes Commit: e3ced2c669485f76eae7fcfb3b32aa048730964d https://github.com/galaxyproject/galaxy/commit/e3ced2c669485f76eae7fcfb3b32… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-02-26 (Mon, 26 Feb 2018) Changed paths: M lib/galaxy/model/migrate/versions/0137_add_copied_from_job_id_column.py Log Message: ----------- Fix migration 0137's downgrade -- previously failed to select the correct column to drop Commit: c8407786f25c98c87f441f15222f72eeea4edc72 https://github.com/galaxyproject/galaxy/commit/c8407786f25c98c87f441f15222f… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-02-26 (Mon, 26 Feb 2018) Changed paths: M lib/galaxy/model/migrate/versions/0137_add_copied_from_job_id_column.py Log Message: ----------- Merge pull request #5605 from dannon/migrate_fix [18.01] Fix migration 0137's downgrade Commit: d8585f6a6f87735d072635495bd49047da746624 https://github.com/galaxyproject/galaxy/commit/d8585f6a6f87735d072635495bd4… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-02-27 (Tue, 27 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 Log Message: ----------- Merge pull request #5582 from jmchilton/indicators [18.01] Fix lack of feedback when slow grids are loading data from the server. Commit: 50cd159d4c212a36b8d3861295125ef055a296d9 https://github.com/galaxyproject/galaxy/commit/50cd159d4c212a36b8d386129512… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-02-27 (Tue, 27 Feb 2018) Changed paths: M lib/galaxy/web/framework/helpers/grids.py Log Message: ----------- Merge pull request #5574 from jmchilton/optimize_count_query_1 [18.01] Optimize count query in grids (Part 1). Commit: a90c3a1d3f2c2a12f285f3c21e91ca364f81853e https://github.com/galaxyproject/galaxy/commit/a90c3a1d3f2c2a12f285f3c21e91… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-02-27 (Tue, 27 Feb 2018) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Merge pull request #5583 from martenson/backport-toolbox-cache [18.01] Backport toolbox cache Commit: ab928fe55ed1f871dbe6221e95af199579f312e1 https://github.com/galaxyproject/galaxy/commit/ab928fe55ed1f871dbe6221e95af… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-02-27 (Tue, 27 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/history/history-view-edit.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/auth/__init__.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/converters/sam_to_bam.py M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/model/migrate/versions/0137_add_copied_from_job_id_column.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/mulled/util.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/lineages/interface.py M lib/galaxy/visualization/data_providers/genome.py M lib/galaxy/web/framework/helpers/grids.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/integration/test_upload_configuration_options.py M tools/data_source/upload.py Log Message: ----------- Merge branch 'release_18.01' into usegalaxy Compare: https://github.com/galaxyproject/galaxy/compare/fa283b525f44...ab928fe55ed1

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[galaxyproject/usegalaxy-playbook] a68841: Update Test
by GitHub 27 Feb '18

27 Feb '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: a68841098821f3a5a2fde4afca042a724556e78f https://github.com/galaxyproject/usegalaxy-playbook/commit/a68841098821f3a5… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-02-27 (Tue, 27 Feb 2018) Changed paths: M env/test/files/galaxy/galaxy_version.yml Log Message: ----------- Update Test

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[galaxyproject/galaxy] 93d5c5: Optimize count query in grids (part 1).
by GitHub 27 Feb '18

27 Feb '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 93d5c54946e992112841df3461512bbeb6f5c7e9 https://github.com/galaxyproject/galaxy/commit/93d5c54946e992112841df346151… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-02-21 (Wed, 21 Feb 2018) Changed paths: M lib/galaxy/web/framework/helpers/grids.py Log Message: ----------- Optimize count query in grids (part 1). Many grid operations execute a complex query twice - once to produce the total number of rows and once to iterate through the selected parts of the data. This can be more optimal in many ways - this starts us down the path to addressing that by doing two things. The first thing it does is eliminates the query all together if paging is enabled but the user has opted to see "all" the rows. There was never a reason to execute the query in that case I don't think. The second thing it does is move the calculation of the count query until after the data has been generated - this isn't more optimal by itself but it allows us to potentially calculate the count as part of the main query. I've implemented this in a broken way @ https://github.com/galaxyproject/galaxy/commit/ea404721585b5f78da1b91e57e31… but I realized it was too broad an approach and doesn't work if certain kinds of joins are used in the initial query - but a more targetted approach on a per-grid basis could work I think and moving this code after allow us to potentially do that more easily in subsequent commits. Additionally I added a note - that I think it would be best to just return None as the number of pages and issue a second query to the same endpoint with the same arguments but with count_only=true added as a query request parameter so we can render the main grid faster and then render the paging elements after the second query finishes. This would feel more responsive I think. Commit: 1656c7b429854323efda82accc4c190a965be8a3 https://github.com/galaxyproject/galaxy/commit/1656c7b429854323efda82accc4c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-02-21 (Wed, 21 Feb 2018) Changed paths: M lib/galaxy/tools/parameters/output_collect.py Log Message: ----------- Fix repeated fetching dataset permissions in dynamic output collection. Commit: c00e772159f6a121bc4f7759fa57f48e79c48f32 https://github.com/galaxyproject/galaxy/commit/c00e772159f6a121bc4f7759fa57… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-02-21 (Wed, 21 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 Log Message: ----------- Fix lack of feedback when slow grids are loading data from the server. Fixes #5473 (after numerous other backend optimizations also). Commit: b861b9ad4d693000ba8cf492ce6b1ff057db3d34 https://github.com/galaxyproject/galaxy/commit/b861b9ad4d693000ba8cf492ce6b… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-02-21 (Wed, 21 Feb 2018) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- implement basic cache on toolbox to_dict objects base the cache on absence of filters allow cache for users that don't opt in for filters Commit: 8806030f53c2b9d0002505bf5193be88d7cff8f9 https://github.com/galaxyproject/galaxy/commit/8806030f53c2b9d0002505bf5193… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-02-22 (Thu, 22 Feb 2018) Changed paths: M lib/galaxy/datatypes/converters/sam_to_bam.py M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/mulled/util.py M lib/galaxy/tools/toolbox/lineages/interface.py M lib/galaxy/visualization/data_providers/genome.py Log Message: ----------- Replace distutils.version with packaging.version distutils under Python3 has this bug: https://bugs.python.org/issue14894 which causes this traceback: ``` Traceback (most recent call last): File "lib/galaxy/webapps/galaxy/buildapp.py", line 49, in app_factory app = galaxy.app.UniverseApplication(global_conf=global_conf, **kwargs) File "lib/galaxy/app.py", line 125, in __init__ self._configure_toolbox() File "lib/galaxy/config.py", line 930, in _configure_toolbox self.toolbox = tools.ToolBox(tool_configs, self.config.tool_path, self) File "lib/galaxy/tools/__init__.py", line 232, in __init__ app=app, File "lib/galaxy/tools/toolbox/base.py", line 1056, in __init__ super(BaseGalaxyToolBox, self).__init__(config_filenames, tool_root_dir, app) File "lib/galaxy/tools/toolbox/base.py", line 84, in __init__ self._load_tool_panel() File "lib/galaxy/tools/toolbox/base.py", line 358, in _load_tool_panel self.__add_tool_to_tool_panel(section_val, section, section=True) File "lib/galaxy/tools/toolbox/base.py", line 278, in __add_tool_to_tool_panel related_tool = self._lineage_in_panel(panel_dict, tool=tool) File "lib/galaxy/tools/toolbox/base.py", line 961, in _lineage_in_panel lineage_tool_versions = reversed(tool_lineage.get_versions()) File "lib/galaxy/tools/toolbox/lineages/interface.py", line 77, in get_versions return [ToolLineageVersion(tool_id, tool_version) for tool_id, tool_version in zip(self.tool_ids, self.tool_versions)] File "lib/galaxy/tools/toolbox/lineages/interface.py", line 55, in tool_ids return ["%s/%s" % (tool_id, version) for version in self.tool_versions] File "lib/galaxy/tools/toolbox/lineages/interface.py", line 49, in tool_versions return sorted(self._tool_versions, key=LooseVersion) File "/usr/lib/python3.4/distutils/version.py", line 58, in __lt__ c = self._cmp(other) File "/usr/lib/python3.4/distutils/version.py", line 343, in _cmp if self.version < other.version: TypeError: unorderable types: str() < int() ``` when a tool version contains a letter in the "wrong" place (e.g. in the first position). Fix https://github.com/galaxyproject/galaxy/issues/5408 . Commit: ce3b40cfc10e134d5acc477757404eba40ea6553 https://github.com/galaxyproject/galaxy/commit/ce3b40cfc10e134d5acc47775740… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-02-22 (Thu, 22 Feb 2018) Changed paths: M lib/galaxy/tools/parameters/output_collect.py Log Message: ----------- Merge pull request #5578 from jmchilton/opt_dyn_collect [18.01] Fix repeated fetching dataset permissions in dynamic output collection. Commit: fc52fe5c62700b4f8527e4edead0fba4e7cfe33f https://github.com/galaxyproject/galaxy/commit/fc52fe5c62700b4f8527e4edead0… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-02-22 (Thu, 22 Feb 2018) Changed paths: M lib/galaxy/datatypes/converters/sam_to_bam.py M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/mulled/util.py M lib/galaxy/tools/toolbox/lineages/interface.py M lib/galaxy/visualization/data_providers/genome.py Log Message: ----------- Merge pull request #5588 from jmchilton/backport_packaging [18.01] Replace distutils.version with packaging.version Commit: 8a88cb9827b68e6795cf00496008e1aa189185ad https://github.com/galaxyproject/galaxy/commit/8a88cb9827b68e6795cf00496008… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-02-26 (Mon, 26 Feb 2018) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- move the cache from toolbox level to tool level the cache remains toolbox-specific so it is stored within the toolbox object includes refactor thanks to eagle eyes Commit: e3ced2c669485f76eae7fcfb3b32aa048730964d https://github.com/galaxyproject/galaxy/commit/e3ced2c669485f76eae7fcfb3b32… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-02-26 (Mon, 26 Feb 2018) Changed paths: M lib/galaxy/model/migrate/versions/0137_add_copied_from_job_id_column.py Log Message: ----------- Fix migration 0137's downgrade -- previously failed to select the correct column to drop Commit: c8407786f25c98c87f441f15222f72eeea4edc72 https://github.com/galaxyproject/galaxy/commit/c8407786f25c98c87f441f15222f… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-02-26 (Mon, 26 Feb 2018) Changed paths: M lib/galaxy/model/migrate/versions/0137_add_copied_from_job_id_column.py Log Message: ----------- Merge pull request #5605 from dannon/migrate_fix [18.01] Fix migration 0137's downgrade Commit: d8585f6a6f87735d072635495bd49047da746624 https://github.com/galaxyproject/galaxy/commit/d8585f6a6f87735d072635495bd4… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-02-27 (Tue, 27 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 Log Message: ----------- Merge pull request #5582 from jmchilton/indicators [18.01] Fix lack of feedback when slow grids are loading data from the server. Commit: 50cd159d4c212a36b8d3861295125ef055a296d9 https://github.com/galaxyproject/galaxy/commit/50cd159d4c212a36b8d386129512… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-02-27 (Tue, 27 Feb 2018) Changed paths: M lib/galaxy/web/framework/helpers/grids.py Log Message: ----------- Merge pull request #5574 from jmchilton/optimize_count_query_1 [18.01] Optimize count query in grids (Part 1). Commit: a90c3a1d3f2c2a12f285f3c21e91ca364f81853e https://github.com/galaxyproject/galaxy/commit/a90c3a1d3f2c2a12f285f3c21e91… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-02-27 (Tue, 27 Feb 2018) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Merge pull request #5583 from martenson/backport-toolbox-cache [18.01] Backport toolbox cache Commit: 4caaa70006cead1c286c1bbf5f036860a3fd8a85 https://github.com/galaxyproject/galaxy/commit/4caaa70006cead1c286c1bbf5f03… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-02-27 (Tue, 27 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/model/migrate/versions/0137_add_copied_from_job_id_column.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/web/framework/helpers/grids.py Log Message: ----------- Merge branch 'release_18.01' into dev Compare: https://github.com/galaxyproject/galaxy/compare/73a0d72e0c98...4caaa70006ce

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