Branch: refs/heads/master Home: https://github.com/galaxyproject/galaxy Commit: 3ce2a3564799595fef08e5692a951757e853bf72 https://github.com/galaxyproject/galaxy/commit/3ce2a3564799595fef08e5692a951... Author: vahid jalili.vahid@gmail.com Date: 2018-10-15 (Mon, 15 Oct 2018)

Changed paths: M tools/cloud/download.py

Log Message: ----------- Update print func syntax in cloud download tool to adhere with py3 req.

Commit: e943ec2bb48c6cbd693e0981d6134c4443f5ed70 https://github.com/galaxyproject/galaxy/commit/e943ec2bb48c6cbd693e0981d6134... Author: vahid jalili.vahid@gmail.com Date: 2018-10-15 (Mon, 15 Oct 2018)

Changed paths: M tools/cloud/download.xml

Log Message: ----------- Rename cloud download tool log dataset.

Commit: 4e3ef50cb202ab43d7fb0ce3f9932f4da1666378 https://github.com/galaxyproject/galaxy/commit/4e3ef50cb202ab43d7fb0ce3f9932... Author: guerler aysam.guerler@gmail.com Date: 2018-10-15 (Mon, 15 Oct 2018)

Changed paths: M templates/message.mako

Log Message: ----------- Fix custom message status

Commit: cf4fca4b6a66488325dbc94edb67784b78ad9bb9 https://github.com/galaxyproject/galaxy/commit/cf4fca4b6a66488325dbc94edb677... Author: guerler aysam.guerler@gmail.com Date: 2018-10-15 (Mon, 15 Oct 2018)

Changed paths: M templates/admin/tool_shed_repository/browse_repository.mako M templates/admin/tool_shed_repository/browse_tool_dependency.mako M templates/admin/tool_shed_repository/deactivate_or_uninstall_repository.mako M templates/admin/tool_shed_repository/install_tool_dependencies_with_update.mako M templates/admin/tool_shed_repository/manage_repository.mako M templates/admin/tool_shed_repository/manage_repository_tool_dependencies.mako M templates/admin/tool_shed_repository/purge_repository_confirmation.mako M templates/admin/tool_shed_repository/reselect_tool_panel_section.mako M templates/admin/tool_shed_repository/select_tool_panel_section.mako M templates/admin/tool_shed_repository/uninstall_tool_dependencies.mako M templates/admin/tool_shed_repository/view_tool_metadata.mako M templates/admin/tool_shed_repository/view_workflow.mako

Log Message: ----------- Add fixes for toolshed related makos

Commit: 6a94b18a7b0866a3b12b4d3f0d80e4b4efb35a8b https://github.com/galaxyproject/galaxy/commit/6a94b18a7b0866a3b12b4d3f0d80e... Author: guerler aysam.guerler@gmail.com Date: 2018-10-15 (Mon, 15 Oct 2018)

Changed paths: M client/galaxy/scripts/mvc/ui/ui-slider.js

Log Message: ----------- Use fluid container for slider to get full width

Commit: db67cd2f56fd831251ee3b2d713e9e883c7edde1 https://github.com/galaxyproject/galaxy/commit/db67cd2f56fd831251ee3b2d713e9... Author: Dannon Baker dannon.baker@gmail.com Date: 2018-10-15 (Mon, 15 Oct 2018)

Changed paths: M .ci/jenkins/api-py3/run_tests.sh M .ci/jenkins/api/run_tests.sh M .ci/jenkins/framework-py3/run_tests.sh M .ci/jenkins/framework/run_tests.sh A .ci/jenkins/main-tools-py3/run_tests.sh A .ci/jenkins/main-tools/run_tests.sh M .ci/jenkins/selenium-py3/run_tests.sh M .ci/jenkins/selenium/run_tests.sh M .ci/jenkins/toolshed/run_tests.sh M .coveragerc M .gitignore M client/README.md M client/galaxy/docs/bootstrap.md M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/apps/panels/admin-panel.js M client/galaxy/scripts/components/DisplayStructured.vue M client/galaxy/scripts/components/PluginList.vue M client/galaxy/scripts/components/RuleCollectionBuilder.vue M client/galaxy/scripts/components/Sharing.vue M client/galaxy/scripts/components/admin/BaseGrid.vue M client/galaxy/scripts/galaxy.pages.js M client/galaxy/scripts/layout/scratchbook.js M client/galaxy/scripts/mvc/dataset/dataset-edit-attributes.js M client/galaxy/scripts/mvc/dataset/dataset-error.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-repeat.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/form/form-wrapper.js M client/galaxy/scripts/mvc/history/history-view-edit-current.js M client/galaxy/scripts/mvc/history/history-view.js M client/galaxy/scripts/mvc/lazy/lazy-limited.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/rules/rule-definitions.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/tool/tool-form.js M client/galaxy/scripts/mvc/tool/tools.js M client/galaxy/scripts/mvc/toolshed/repository-view.js M client/galaxy/scripts/mvc/ui/ui-buttons.js M client/galaxy/scripts/mvc/ui/ui-list.js M client/galaxy/scripts/mvc/ui/ui-misc.js M client/galaxy/scripts/mvc/ui/ui-options.js M client/galaxy/scripts/mvc/ui/ui-popover.js M client/galaxy/scripts/mvc/ui/ui-portlet.js M client/galaxy/scripts/mvc/ui/ui-rules-edit.js M client/galaxy/scripts/mvc/ui/ui-select-content.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/galaxy/scripts/mvc/ui/ui-select-genomespace.js M client/galaxy/scripts/mvc/ui/ui-select-library.js M client/galaxy/scripts/mvc/ui/ui-slider.js M client/galaxy/scripts/mvc/ui/ui-table.js M client/galaxy/scripts/mvc/ui/ui-tabs.js M client/galaxy/scripts/mvc/upload/collection/collection-row.js M client/galaxy/scripts/mvc/upload/collection/collection-view.js M client/galaxy/scripts/mvc/upload/composite/composite-row.js M client/galaxy/scripts/mvc/upload/composite/composite-view.js M client/galaxy/scripts/mvc/upload/default/default-row.js M client/galaxy/scripts/mvc/upload/default/default-view.js M client/galaxy/scripts/mvc/upload/upload-extension.js M client/galaxy/scripts/mvc/upload/upload-ftp.js M client/galaxy/scripts/mvc/upload/upload-settings.js M client/galaxy/scripts/mvc/user/user-custom-builds.js M client/galaxy/scripts/mvc/user/user-preferences.js M client/galaxy/scripts/mvc/visualization/chart/views/description.js M client/galaxy/scripts/mvc/visualization/chart/views/editor.js M client/galaxy/scripts/mvc/visualization/chart/views/groups.js M client/galaxy/scripts/mvc/visualization/chart/views/menu.js M client/galaxy/scripts/mvc/visualization/chart/views/settings.js M client/galaxy/scripts/mvc/workflow/workflow-connector.js M client/galaxy/scripts/mvc/workflow/workflow-forms.js M client/galaxy/scripts/mvc/workflow/workflow-manager.js M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M client/galaxy/scripts/mvc/workflow/workflow-view-data.js M client/galaxy/scripts/mvc/workflow/workflow-view-terminals.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M client/galaxy/scripts/qunit/test.js M client/galaxy/scripts/qunit/tests/form_tests.js R 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doc/source/admin/framework_dependencies.rst M doc/source/admin/galaxy_options.rst M doc/source/admin/jobs.md M doc/source/admin/special_topics/interactive_environments.rst M doc/source/dev/index.rst M doc/source/dev/interactive_environments.rst A doc/source/releases/18.09.rst A doc/source/releases/18.09_announce.rst A doc/source/releases/19.01_announce.rst M lib/galaxy/actions/library.py M lib/galaxy/authnz/managers.py M lib/galaxy/authnz/psa_authnz.py M lib/galaxy/config.py M lib/galaxy/dataset_collections/matching.py M lib/galaxy/datatypes/binary.py A lib/galaxy/datatypes/test/test.loom M lib/galaxy/datatypes/util/gff_util.py M lib/galaxy/dependencies/conda-file.sh M lib/galaxy/dependencies/conditional-requirements.txt M lib/galaxy/dependencies/pipfiles/default/Pipfile M lib/galaxy/dependencies/pipfiles/default/pinned-dev-requirements.txt M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt M lib/galaxy/dependencies/pipfiles/update.sh R 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lib/galaxy/objectstore/__init__.py M lib/galaxy/objectstore/cloud.py M lib/galaxy/security/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/actions/history_imp_exp.py M lib/galaxy/tools/actions/metadata.py M lib/galaxy/tools/actions/model_operations.py M lib/galaxy/tools/actions/upload.py M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/tools/cache.py M lib/galaxy/tools/cwl/cwltool_deps.py M lib/galaxy/tools/cwl/parser.py M lib/galaxy/tools/cwl/schema.py M lib/galaxy/tools/cwl/util.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/docker_util.py M lib/galaxy/tools/deps/mulled/mulled_build.py M lib/galaxy/tools/deps/mulled/mulled_build_channel.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/execute.py M lib/galaxy/tools/extract_dataset.xml M lib/galaxy/tools/lint.py M lib/galaxy/tools/linters/stdio.py M lib/galaxy/tools/linters/tests.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/tools/parameters/wrapped.py M lib/galaxy/tools/parser/cwl.py M lib/galaxy/tools/search/__init__.py M lib/galaxy/tools/tag_collection_from_file.xml M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/filters/examples.py.sample M lib/galaxy/tools/util/maf_utilities.py M lib/galaxy/tools/verify/interactor.py M lib/galaxy/tools/wrappers.py M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/util/__init__.py M lib/galaxy/util/compression_utils.py M lib/galaxy/util/create_history_template.py M lib/galaxy/util/monitors.py M lib/galaxy/util/rules_dsl.py M lib/galaxy/util/streamball.py M lib/galaxy/util/ucsc.py M lib/galaxy/util/xml_macros.py M lib/galaxy/version.py M lib/galaxy/web/base/controller.py M lib/galaxy/web/form_builder.py M lib/galaxy/web/framework/base.py M lib/galaxy/web/framework/decorators.py M lib/galaxy/web/framework/helpers/__init__.py M lib/galaxy/webapps/config_manage.py M lib/galaxy/webapps/galaxy/api/cloud.py A lib/galaxy/webapps/galaxy/api/cloudauthz.py M lib/galaxy/webapps/galaxy/api/configuration.py M lib/galaxy/webapps/galaxy/api/folder_contents.py M lib/galaxy/webapps/galaxy/api/folders.py M lib/galaxy/webapps/galaxy/api/forms.py M lib/galaxy/webapps/galaxy/api/groups.py M lib/galaxy/webapps/galaxy/api/history_contents.py M lib/galaxy/webapps/galaxy/api/jobs.py M lib/galaxy/webapps/galaxy/api/libraries.py M lib/galaxy/webapps/galaxy/api/library_contents.py M lib/galaxy/webapps/galaxy/api/library_datasets.py M lib/galaxy/webapps/galaxy/api/pages.py M lib/galaxy/webapps/galaxy/api/roles.py M lib/galaxy/webapps/galaxy/api/search.py M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/api/users.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/config_schema.yml M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/galaxy/webapps/galaxy/controllers/data_manager.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/page.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/galaxy/webapps/galaxy/controllers/tool_runner.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/webapps/tool_shed/api/categories.py M lib/galaxy/webapps/tool_shed/api/groups.py M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/galaxy/webapps/tool_shed/controllers/repository_review.py M lib/galaxy/webapps/tool_shed/controllers/user.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/resources/example.py.sample M lib/galaxy/workflow/run.py M lib/galaxy/workflow/run_request.py M lib/tool_shed/managers/groups.py M lib/tool_shed/util/repository_util.py M pytest.ini M run_tests.sh M scripts/api/library_upload_dir.py M scripts/apply_tags.py M scripts/bootstrap_history.py M scripts/check_galaxy.py M scripts/cleanup_datasets/pgcleanup.py M scripts/common_startup.sh M scripts/common_startup_functions.sh M scripts/galaxy-main M scripts/get_uwsgi_args.py M scripts/grt/export.py M scripts/loc_files/create_all_fasta_loc.py M scripts/microbes/util.py A scripts/pages_identifier_conversion.py M scripts/plugin_staging.py A static/style/blue/base.css M static/style/blue/library.css M templates/display_base.mako M templates/galaxy_client_app.mako M templates/ind_share_base.mako M templates/show_params.mako M templates/user/info.mako M templates/user/register.mako M templates/webapps/galaxy/galaxy.masthead.mako M templates/webapps/galaxy/history/display.mako M templates/webapps/galaxy/history/share.mako M templates/webapps/galaxy/page/editor.mako M templates/webapps/galaxy/visualization/display.mako M templates/webapps/galaxy/visualization/display_in_frame.mako M templates/webapps/galaxy/workflow/display.mako M templates/webapps/galaxy/workflow/editor.mako M templates/webapps/tool_shed/common/repository_actions_menu.mako M templates/webapps/tool_shed/common/reset_metadata_on_selected_repositories.mako M templates/webapps/tool_shed/repository/manage_repository.mako M templates/webapps/tool_shed/repository/tool_form.mako M templates/webapps/tool_shed/repository/view_repository.mako M templates/webapps/tool_shed/role/role.mako M templates/webapps/tool_shed/user/username.mako A test-data/safetar_with_symlink.tar A test-data/testdir.tar A test-data/unsafe.tar A test-data/unsafe.zip A test-data/unsafe_relative_symlink.tar M test/api/test_api_batch.py M test/api/test_dataset_collections.py M test/api/test_histories.py M test/api/test_jobs.py M test/api/test_pages.py M test/api/test_tools.py M test/api/test_tools_upload.py M test/api/test_workflows.py M test/api/test_workflows_from_yaml.py M test/base/api.py M test/base/populators.py A test/base/ssh_util.py M test/base/workflow_fixtures.py R test/base/workflows_format_2/README.txt R test/base/workflows_format_2/__init__.py R test/base/workflows_format_2/converter.py R test/base/workflows_format_2/interface.py R test/base/workflows_format_2/main.py A test/functional/known_broken_tools.txt M test/functional/test_toolbox_pytest.py M test/functional/tools/disambiguate_cond.xml A test/functional/tools/for_workflows/mapper_two.xml A test/functional/tools/identifier_in_conditional.xml M test/functional/tools/job_environment_default.xml M test/functional/tools/job_environment_default_legacy.xml M test/functional/tools/job_environment_explicit_shared_home.xml M test/functional/tools/samples_tool_conf.xml M test/galaxy_selenium/has_driver.py M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/navigation.yml M test/galaxy_selenium/smart_components.py A test/integration/test_cli_runners.py M test/integration/test_job_environments.py M test/integration/test_scripts.py M test/manual/workflows_scaling.py M test/selenium_tests/framework.py M test/selenium_tests/test_collection_builders.py M test/selenium_tests/test_stock_tours.py M test/selenium_tests/test_workflow_run.py M test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py M test/unit/jobs/test_job_wrapper.py A test/unit/test_compression_util.py M test/unit/test_galaxy_mapping.py M test/unit/test_remote_shell.py A test/unit/test_utils.py M test/unit/tools/test_actions.py M test/unit/tools/test_collect_primary_datasets.py M test/unit/tools/test_data_parameters.py M test/unit/tools/test_evaluation.py M test/unit/tools/test_toolbox.py M test/unit/tools/test_toolbox_filters.py M test/unit/workflows/test_extract_summary.py M test/unit/workflows/test_modules.py M test/unit/workflows/test_workflow_progress.py M tools/filters/bed_to_bigbed.xml M tools/filters/join.py M tools/filters/joinWrapper.py M tools/filters/secure_hash_message_digest.py M tools/filters/sff_extract.py M tools/filters/sff_extractor.xml M tools/filters/tailWrapper.xml M tools/filters/uniq.xml M tools/filters/wc_gnu.xml M tools/filters/wig_to_bigwig.xml M tools/genomespace/genomespace_importer.py M tools/maf/maf_limit_to_species.py M tools/maf/maf_split_by_species.xml M tools/maf/maf_to_bed.py M tools/maf/maf_to_bed.xml M tools/maf/maf_to_fasta_multiple_sets.py M tools/maf/maf_to_interval.py M tools/maf/maf_to_interval.xml M tools/next_gen_conversion/solid2fastq.xml M tools/phenotype_association/ldtools.xml M tools/phenotype_association/ldtools_wrapper.sh M tools/phenotype_association/linkToGProfile.pl M tools/phenotype_association/linkToGProfile.xml M tools/phenotype_association/senatag.py M tools/plotting/boxplot.xml M tools/solid_tools/solid_qual_stats.py M tools/solid_tools/solid_qual_stats.xml M tools/stats/aggregate_binned_scores_in_intervals.xml M tools/stats/aggregate_scores_in_intervals.py M tools/stats/grouping.py M tools/stats/gsummary.xml M tox.ini

Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into webpack_4_minimal_flat

Commit: 429ef96a106d0bf094145a7fd8a65143b113e6e5 https://github.com/galaxyproject/galaxy/commit/429ef96a106d0bf094145a7fd8a65... Author: Nate Coraor nate@bx.psu.edu Date: 2018-10-15 (Mon, 15 Oct 2018)

Changed paths: M scripts/cleanup_datasets/pgcleanup.py

Log Message: ----------- WIP pgcleanup improvements

Commit: 941d68ad358155f6577fb89f1778625b805035fe https://github.com/galaxyproject/galaxy/commit/941d68ad358155f6577fb89f17786... Author: Nate Coraor nate@bx.psu.edu Date: 2018-10-15 (Mon, 15 Oct 2018)

Changed paths: M scripts/cleanup_datasets/pgcleanup.py

Log Message: ----------- WIP pgcleanup improvements

Commit: ba83310d53488ccc62dd52907746a3ca63baaf28 https://github.com/galaxyproject/galaxy/commit/ba83310d53488ccc62dd52907746a... Author: Nate Coraor nate@bx.psu.edu Date: 2018-10-15 (Mon, 15 Oct 2018)

Changed paths: M scripts/cleanup_datasets/pgcleanup.py

Log Message: ----------- Mostly refactored pgcleanup.py

Commit: e1a197676ec3f6f35dafaa6cb58d60c7d9d44fb2 https://github.com/galaxyproject/galaxy/commit/e1a197676ec3f6f35dafaa6cb58d6... Author: Nate Coraor nate@bx.psu.edu Date: 2018-10-15 (Mon, 15 Oct 2018)

Changed paths: M scripts/cleanup_datasets/pgcleanup.py

Log Message: ----------- Refactor repetitive HDA purging stuff and add a function to purge HDAs with null history_ids

Commit: 4d0538cc4f74c183495c9df33c1055a9441766d8 https://github.com/galaxyproject/galaxy/commit/4d0538cc4f74c183495c9df33c105... Author: Nate Coraor nate@bx.psu.edu Date: 2018-10-15 (Mon, 15 Oct 2018)

Changed paths: A lib/galaxy/model/migrate/versions/0144_add_cleanup_event_user_table.py

Log Message: ----------- Add a table for logging user cleanup events

Commit: c42cd4b71818783c0d9a6aa77a96fb508e9e34a4 https://github.com/galaxyproject/galaxy/commit/c42cd4b71818783c0d9a6aa77a96f... Author: Martin Cech marten@bx.psu.edu Date: 2018-10-15 (Mon, 15 Oct 2018)

Changed paths: M client/galaxy/scripts/mvc/ui/ui-slider.js

Log Message: ----------- Merge pull request #6870 from guerler/fix_slider_container

Use fluid container for slider to get full width

Commit: 0108a2e6932d631e030b33363ea7564207edc90d https://github.com/galaxyproject/galaxy/commit/0108a2e6932d631e030b33363ea75... Author: Dannon Baker dannon.baker@gmail.com Date: 2018-10-15 (Mon, 15 Oct 2018)

Changed paths: A client/galaxy/images/circle.py A client/galaxy/images/error_icon.svg A client/galaxy/images/galaxy_icons.svg A client/galaxy/images/galaxy_spinner.fla A client/galaxy/images/info_icon.svg A client/galaxy/images/ok_icon.svg A client/galaxy/images/wait_icon.svg A client/galaxy/images/warn_icon.svg M client/galaxy/style/scss/base.scss R client/galaxy/style/source_material/circle.py R client/galaxy/style/source_material/error_icon.svg R client/galaxy/style/source_material/galaxy_icons.svg R client/galaxy/style/source_material/galaxy_spinner.fla R client/galaxy/style/source_material/info_icon.svg R client/galaxy/style/source_material/ok_icon.svg R client/galaxy/style/source_material/wait_icon.svg R client/galaxy/style/source_material/warn_icon.svg

Log Message: ----------- Relocate various source materials.

Commit: 429c29a67166e0718776aee63ee709c60b6130bf https://github.com/galaxyproject/galaxy/commit/429c29a67166e0718776aee63ee70... Author: almahmoud amahmou4@jhu.edu Date: 2018-10-15 (Mon, 15 Oct 2018)

Changed paths: M lib/galaxy/webapps/galaxy/controllers/history.py

Log Message: ----------- History name not escaped

Commit: 4bd6d71ed71643a9f28db9e41a6cf43e1af9a942 https://github.com/galaxyproject/galaxy/commit/4bd6d71ed71643a9f28db9e41a6cf... Author: guerler aysam.guerler@gmail.com Date: 2018-10-15 (Mon, 15 Oct 2018)

Changed paths: M client/galaxy/scripts/mvc/ui/ui-rules-edit.js

Log Message: ----------- Add fix for rule editor element

Commit: 116ce0ddf51654cfbb0923e7afc1ae5b035bd602 https://github.com/galaxyproject/galaxy/commit/116ce0ddf51654cfbb0923e7afc1a... Author: vahid jalili.vahid@gmail.com Date: 2018-10-15 (Mon, 15 Oct 2018)

Changed paths: M lib/galaxy/webapps/galaxy/buildapp.py

Log Message: ----------- Specify `GET` action for cloudauthz index.

Commit: da6c452a9d57ca81594c3c9966bfee19aa4bd01e https://github.com/galaxyproject/galaxy/commit/da6c452a9d57ca81594c3c9966bfe... Author: guerler aysam.guerler@gmail.com Date: 2018-10-15 (Mon, 15 Oct 2018)

Changed paths: M client/galaxy/scripts/mvc/ui/ui-rules-edit.js

Log Message: ----------- Left align rule editor button

Commit: 612e6fc1cfb85e879f846cba90753a50182da5b4 https://github.com/galaxyproject/galaxy/commit/612e6fc1cfb85e879f846cba90753... Author: vahid jalili.vahid@gmail.com Date: 2018-10-15 (Mon, 15 Oct 2018)

Changed paths: M lib/galaxy/webapps/galaxy/buildapp.py

Log Message: ----------- Specify `POST` action for cloudauthz create action.

Commit: 67ee35874e65e5d2bc40caa7fd3cf143bce084c5 https://github.com/galaxyproject/galaxy/commit/67ee35874e65e5d2bc40caa7fd3cf... Author: guerler aysam.guerler@gmail.com Date: 2018-10-15 (Mon, 15 Oct 2018)

Changed paths: M client/galaxy/scripts/ui/editable-text.js

Log Message: ----------- Use small button for editable text fields in history annotation

Commit: e72d52c6dfe9332c5cd1c3f42d4e0276e9a75008 https://github.com/galaxyproject/galaxy/commit/e72d52c6dfe9332c5cd1c3f42d4e0... Author: Nate Coraor nate@bx.psu.edu Date: 2018-10-15 (Mon, 15 Oct 2018)

Changed paths: M lib/galaxy/model/migrate/versions/0144_add_cleanup_event_user_table.py M scripts/cleanup_datasets/pgcleanup.py

Log Message: ----------- Lint

Commit: 23541fcf2ccc87c22c5529020031f7a5cacfe100 https://github.com/galaxyproject/galaxy/commit/23541fcf2ccc87c22c5529020031f... Author: guerler aysam.guerler@gmail.com Date: 2018-10-15 (Mon, 15 Oct 2018)

Changed paths: M client/galaxy/scripts/ui/editable-text.js

Log Message: ----------- Float annotation button to the right

Commit: 1c466e037762618ea33f9a5758469df9015c4047 https://github.com/galaxyproject/galaxy/commit/1c466e037762618ea33f9a5758469... Author: Martin Cech marten@bx.psu.edu Date: 2018-10-15 (Mon, 15 Oct 2018)

Changed paths: M client/galaxy/style/scss/ui.scss M static/style/blue/base.css M templates/admin/jobs.mako M templates/admin/review_tool_migration_stages.mako M templates/admin/tool_shed_repository/browse_repository.mako M templates/admin/tool_shed_repository/browse_tool_dependency.mako M templates/admin/tool_shed_repository/deactivate_or_uninstall_repository.mako M templates/admin/tool_shed_repository/install_tool_dependencies_with_update.mako M templates/admin/tool_shed_repository/manage_repository.mako M templates/admin/tool_shed_repository/manage_repository_tool_dependencies.mako M templates/admin/tool_shed_repository/monitor_repository_installation.mako M templates/admin/tool_shed_repository/purge_repository_confirmation.mako M templates/admin/tool_shed_repository/reselect_tool_panel_section.mako M templates/admin/tool_shed_repository/reset_metadata_on_selected_repositories.mako M templates/admin/tool_shed_repository/select_tool_panel_section.mako M templates/admin/tool_shed_repository/uninstall_tool_dependencies.mako M templates/admin/tool_shed_repository/view_tool_metadata.mako M templates/admin/tool_shed_repository/view_workflow.mako M templates/message.mako M templates/webapps/galaxy/admin/manage_dependencies.mako M templates/webapps/galaxy/admin/sanitize_whitelist.mako M templates/webapps/galaxy/admin/view_display_applications.mako

Log Message: ----------- Merge pull request #6868 from guerler/fix_display_applications

Use card-styles for display applications, job manager and other admin views

Commit: 89dafdcfc00134f4453b987acf21b6790b0751d8 https://github.com/galaxyproject/galaxy/commit/89dafdcfc00134f4453b987acf21b... Author: Sergey Golitsynskiy sgolitsynskiy@gmail.com Date: 2018-10-15 (Mon, 15 Oct 2018)

Changed paths: M client/galaxy/style/scss/jstree.scss A static/style/blue/info_icon.svg

Log Message: ----------- Fix styleguide; change permissions on jstree.scss.

Styleguide: copy info_icon.svg from client/style/source_material/ to static/style/blue/.

Permissions: change client/style/scss/jstree.scss to 644 (same as other scss files in directory.)

Commit: 83bfdf3c95a8ec7afe25b84867ade4f9dca4bd85 https://github.com/galaxyproject/galaxy/commit/83bfdf3c95a8ec7afe25b84867ade... Author: vahid jalili.vahid@gmail.com Date: 2018-10-15 (Mon, 15 Oct 2018)

Changed paths: M lib/galaxy/webapps/galaxy/buildapp.py

Log Message: ----------- Unify `create` and `index` cloudauthz apis.

Commit: 519b994d40ef758ba23d29bc6b84fbc5042aaba8 https://github.com/galaxyproject/galaxy/commit/519b994d40ef758ba23d29bc6b84f... Author: Dannon dannon.baker@gmail.com Date: 2018-10-15 (Mon, 15 Oct 2018)

Changed paths: M client/galaxy/style/scss/jstree.scss A static/style/blue/info_icon.svg

Log Message: ----------- Merge pull request #6879 from ic4f/styleguide_fix

Fix styleguide; change permissions on jstree.scss.

Commit: d144523f7c29ae03e48045fd1cff47b0efc50305 https://github.com/galaxyproject/galaxy/commit/d144523f7c29ae03e48045fd1cff4... Author: Nicola Soranzo nicola.soranzo@earlham.ac.uk Date: 2018-10-16 (Tue, 16 Oct 2018)

Changed paths: M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/upload_util.py M lib/tool_shed/util/hg_util.py

Log Message: ----------- Merge branch 'release_18.09' into dev

Commit: 168032ffc82d0b19f07cbc101ad8d9273daa3d59 https://github.com/galaxyproject/galaxy/commit/168032ffc82d0b19f07cbc101ad8d... Author: John Chilton jmchilton@gmail.com Date: 2018-10-16 (Tue, 16 Oct 2018)

Changed paths: M client/galaxy/scripts/mvc/ui/ui-rules-edit.js

Log Message: ----------- Merge pull request #6874 from guerler/fix_rules_editor

Fix rule editor element alignment

Commit: 877feae8bacd7104add9b31632843c7d3cbd2a39 https://github.com/galaxyproject/galaxy/commit/877feae8bacd7104add9b31632843... Author: Sebastian Kapust sebastian@kapust.org Date: 2018-10-16 (Tue, 16 Oct 2018)

Changed paths: M client/galaxy/scripts/components/admin/DataManager/DataManagerJob.vue M lib/galaxy/webapps/galaxy/controllers/data_manager.py M test/galaxy_selenium/navigation.yml M test/selenium_tests/test_admin_app.py

Log Message: ----------- DataManagerJob: check for empty server data & refactoring

* DataManagerJob - Check for empty server data & refactoring - Fix and numerate data-card ids * job_info - Fix error log in job_info. - Fix redirect in case job is non-existent with empty server response containing an error message and status. * Extend DataManagerJob test

Commit: 1e09f234e77cbca06c91dde4c1fc3af483ee6f1e https://github.com/galaxyproject/galaxy/commit/1e09f234e77cbca06c91dde4c1fc3... Author: Dannon dannon.baker@gmail.com Date: 2018-10-16 (Tue, 16 Oct 2018)

Changed paths: M client/galaxy/scripts/ui/editable-text.js

Log Message: ----------- Merge pull request #6878 from guerler/fix_annotation_button

Use small button for editable text fields in history annotation

Commit: fb0f792f8d50e81b3a2c8b6b9ff49252377c5114 https://github.com/galaxyproject/galaxy/commit/fb0f792f8d50e81b3a2c8b6b9ff49... Author: Dannon dannon.baker@gmail.com Date: 2018-10-16 (Tue, 16 Oct 2018)

Changed paths: M client/README.md A client/galaxy/docs/README.md M client/galaxy/docs/bootstrap.md M client/galaxy/docs/galaxy-buttons.md M client/galaxy/docs/galaxy-forms.md M client/galaxy/docs/galaxy-masthead.md M client/galaxy/docs/galaxy-menus.md M client/galaxy/docs/galaxy-messages.md M client/galaxy/docs/galaxy-panels.md M client/galaxy/docs/galaxy-tables.md M client/galaxy/docs/galaxy-tabs.md

Log Message: ----------- Merge pull request #6848 from ic4f/dev

Indicate language in client docs to enable syntax highlighting.

Commit: 222225d3b017b4af457eb5c59248145899bc01ef https://github.com/galaxyproject/galaxy/commit/222225d3b017b4af457eb5c592481... Author: guerler aysam.guerler@gmail.com Date: 2018-10-16 (Tue, 16 Oct 2018)

Changed paths: M test/galaxy_selenium/navigation.yml

Log Message: ----------- Fix selenium test selectors for alert messages

Commit: 47ad50e1d7738e443c96226f6abe5475c83ef32e https://github.com/galaxyproject/galaxy/commit/47ad50e1d7738e443c96226f6abe5... Author: guerler aysam.guerler@gmail.com Date: 2018-10-16 (Tue, 16 Oct 2018)

Changed paths: M templates/user/register.mako

Log Message: ----------- Align legacy registration mako

Commit: d29e3fc3bed92f856d140241fc0807f7283eea5f https://github.com/galaxyproject/galaxy/commit/d29e3fc3bed92f856d140241fc080... Author: guerler aysam.guerler@gmail.com Date: 2018-10-16 (Tue, 16 Oct 2018)

Changed paths: M templates/user/info.mako

Log Message: ----------- Align legacy user info template

Commit: b13caf14d5529fd44c0debd1da349f7fc8f554c8 https://github.com/galaxyproject/galaxy/commit/b13caf14d5529fd44c0debd1da349... Author: Dannon Baker dannon.baker@gmail.com Date: 2018-10-16 (Tue, 16 Oct 2018)

Changed paths: M client/package.json M client/yarn.lock

Log Message: ----------- Swap to karma-webpack@next (for 4.0 compat -- it actually works!)

Commit: f8c48b83d2fadc8e4df008ce0f0e37f173a07b9d https://github.com/galaxyproject/galaxy/commit/f8c48b83d2fadc8e4df008ce0f0e3... Author: almahmoud amahmou4@jhu.edu Date: 2018-10-16 (Tue, 16 Oct 2018)

Changed paths: M client/galaxy/scripts/apps/analysis.js

Log Message: ----------- Username filtering for published workflows

Commit: f4088c89a0b110a648fe8f504ff4f26669c63613 https://github.com/galaxyproject/galaxy/commit/f4088c89a0b110a648fe8f504ff4f... Author: Martin Cech marten@bx.psu.edu Date: 2018-10-16 (Tue, 16 Oct 2018)

Changed paths: M lib/galaxy/webapps/galaxy/controllers/history.py

Log Message: ----------- Merge pull request #6871 from almahmoud/rename-bug

History name not escaped

Commit: e5186a811032a2c4e8f52865588a0d9033365768 https://github.com/galaxyproject/galaxy/commit/e5186a811032a2c4e8f52865588a0... Author: guerler aysam.guerler@gmail.com Date: 2018-10-16 (Tue, 16 Oct 2018)

Changed paths: M templates/webapps/galaxy/history/share.mako

Log Message: ----------- Align legacy history sharing mako

Commit: 2310a509b2afdd1903a6a00c3df749b4884e66ab https://github.com/galaxyproject/galaxy/commit/2310a509b2afdd1903a6a00c3df74... Author: Martin Cech marten@bx.psu.edu Date: 2018-10-16 (Tue, 16 Oct 2018)

Changed paths: M client/galaxy/scripts/apps/analysis.js

Log Message: ----------- Merge pull request #6882 from almahmoud/published_workflow_bug

Username filtering for published workflows

Commit: 01a124314db553c2b9f646addc18aea3669905de https://github.com/galaxyproject/galaxy/commit/01a124314db553c2b9f646addc18a... Author: vahid jalili.vahid@gmail.com Date: 2018-10-16 (Tue, 16 Oct 2018)

Changed paths: M lib/galaxy/managers/cloud.py R tools/cloud/download.py R tools/cloud/download.xml A tools/cloud/send.py A tools/cloud/send.xml

Log Message: ----------- Rename cloud/download.* to cloud/send.*

Commit: b62e0476be4e27064efffd56a9516860a25e486e https://github.com/galaxyproject/galaxy/commit/b62e0476be4e27064efffd56a9516... Author: vahid jalili.vahid@gmail.com Date: 2018-10-16 (Tue, 16 Oct 2018)

Changed paths: M lib/galaxy/managers/cloud.py M lib/galaxy/tools/__init__.py M tools/cloud/send.xml

Log Message: ----------- cloud Download > Send refactoring in tool wrapper, & related places.

Commit: 8f11f78aa2b9e1e342b03a7b3a8e3f47779eab12 https://github.com/galaxyproject/galaxy/commit/8f11f78aa2b9e1e342b03a7b3a8e3... Author: vahid jalili.vahid@gmail.com Date: 2018-10-16 (Tue, 16 Oct 2018)

Changed paths: M tools/cloud/send.py

Log Message: ----------- download > send refactoring in the tool.

Commit: d304068161dce41eba53a5ec2c4710a203fdf27a https://github.com/galaxyproject/galaxy/commit/d304068161dce41eba53a5ec2c471... Author: vahid jalili.vahid@gmail.com Date: 2018-10-16 (Tue, 16 Oct 2018)

Changed paths: M lib/galaxy/webapps/galaxy/api/cloud.py M lib/galaxy/webapps/galaxy/buildapp.py

Log Message: ----------- Cloud download > send refactoring in the related api.

Commit: 24ed804ab40c931716c5f2f15b76f35160034c56 https://github.com/galaxyproject/galaxy/commit/24ed804ab40c931716c5f2f15b76f... Author: vahid jalili.vahid@gmail.com Date: 2018-10-16 (Tue, 16 Oct 2018)

Changed paths: M lib/galaxy/managers/cloud.py M lib/galaxy/webapps/galaxy/api/cloud.py

Log Message: ----------- Cloud download > send refactoring in cloud manager.

Commit: a35b686dfda36439dd7bdfe632cefb242c383fac https://github.com/galaxyproject/galaxy/commit/a35b686dfda36439dd7bdfe632cef... Author: vahid jalili.vahid@gmail.com Date: 2018-10-16 (Tue, 16 Oct 2018)

Changed paths: M lib/galaxy/managers/cloud.py

Log Message: ----------- Assert if toolbox returns `send` tool before using it.

Commit: 4e0b09499ec58cb90449ef15fb3fea424e58dd3f https://github.com/galaxyproject/galaxy/commit/4e0b09499ec58cb90449ef15fb3fe... Author: vahid jalili.vahid@gmail.com Date: 2018-10-16 (Tue, 16 Oct 2018)

Changed paths: M config/tool_conf.xml.main M config/tool_conf.xml.sample

Log Message: ----------- Refactor cloud download > send in tool config.

Commit: aa20778e0f51b538af684c6b7fc2f39d998c0fb9 https://github.com/galaxyproject/galaxy/commit/aa20778e0f51b538af684c6b7fc2f... Author: vahid jalili.vahid@gmail.com Date: 2018-10-16 (Tue, 16 Oct 2018)

Changed paths: M lib/galaxy/webapps/galaxy/api/cloudauthz.py

Log Message: ----------- remove `/create` from cloudauthz create api docstring.

Commit: 73f691e5b51249b71b5f21b1f0faeea102b1c725 https://github.com/galaxyproject/galaxy/commit/73f691e5b51249b71b5f21b1f0fae... Author: Martin Cech marten@bx.psu.edu Date: 2018-10-16 (Tue, 16 Oct 2018)

Changed paths: M lib/galaxy/managers/cloud.py

Log Message: ----------- reword to reflect refactor

Commit: fbe9e97f19d6f200cdac2548ae5c60e4b9687334 https://github.com/galaxyproject/galaxy/commit/fbe9e97f19d6f200cdac2548ae5c6... Author: Martin Cech marten@bx.psu.edu Date: 2018-10-16 (Tue, 16 Oct 2018)

Changed paths: M lib/galaxy/managers/cloud.py M lib/galaxy/webapps/galaxy/api/cloudauthz.py M lib/galaxy/webapps/galaxy/buildapp.py

Log Message: ----------- Merge pull request #6876 from VJalili/refactor_cloud_authz_api

Specify POST and GET actions for cloudauthz API actions

Commit: e66da36f60c0d1d2b43fe1a5bd9cdf7da7ddc697 https://github.com/galaxyproject/galaxy/commit/e66da36f60c0d1d2b43fe1a5bd9cd... Author: guerler aysam.guerler@gmail.com Date: 2018-10-16 (Tue, 16 Oct 2018)

Changed paths: M lib/galaxy/web/base/controller.py

Log Message: ----------- Use hasattr instead of relying on value

Commit: 53a505eaef3e8d91689ecfeb3b785928c54a8e42 https://github.com/galaxyproject/galaxy/commit/53a505eaef3e8d91689ecfeb3b785... Author: Sebastian Kapust sebastian@kapust.org Date: 2018-10-17 (Wed, 17 Oct 2018)

Changed paths: M client/galaxy/scripts/components/admin/DataManager/DataManager.vue M client/galaxy/scripts/components/admin/DataManager/DataManagerRouter.vue A client/galaxy/scripts/components/admin/DataManager/DataManagerTable.vue M lib/galaxy/webapps/galaxy/controllers/data_manager.py R templates/webapps/galaxy/data_manager/manage_data_table.mako M test/galaxy_selenium/navigation.yml M test/selenium_tests/test_admin_app.py

Log Message: ----------- Vue rewrite of admin data manager (local data): manage data table

* Rewrite (old mako, new json interface, new vue component) - Manage data table page (manage_data_table.mako, tool_data_table_info, DataManagerTable) * Added Selenium test for DataManagerTable component (Manage data table page)

Commit: 6d2a755614239149193d87e8cb695c963c17dc71 https://github.com/galaxyproject/galaxy/commit/6d2a755614239149193d87e8cb695... Author: Sebastian Kapust sebastian@kapust.org Date: 2018-10-17 (Wed, 17 Oct 2018)

Changed paths: M client/README.md A client/galaxy/docs/README.md M client/galaxy/docs/bootstrap.md M client/galaxy/docs/galaxy-buttons.md M client/galaxy/docs/galaxy-forms.md M client/galaxy/docs/galaxy-masthead.md M client/galaxy/docs/galaxy-menus.md M client/galaxy/docs/galaxy-messages.md M client/galaxy/docs/galaxy-panels.md M client/galaxy/docs/galaxy-tables.md M client/galaxy/docs/galaxy-tabs.md M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/mvc/ui/ui-rules-edit.js M client/galaxy/scripts/mvc/ui/ui-slider.js M client/galaxy/scripts/ui/editable-text.js M client/galaxy/style/scss/base.scss M client/galaxy/style/scss/history.scss M client/galaxy/style/scss/jstree.scss M client/galaxy/style/scss/list-item.scss M client/galaxy/style/scss/ui.scss A config/container_resolvers_conf.xml.sample M config/galaxy.yml.sample M doc/source/admin/galaxy_options.rst M doc/source/dev/index.rst A doc/source/releases/18.09.rst A doc/source/releases/18.09_announce.rst A doc/source/releases/19.01_announce.rst M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/upload_util.py M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt M lib/galaxy/jobs/runners/util/cli/shell/local.py M lib/galaxy/jobs/runners/util/cli/shell/rsh.py M lib/galaxy/managers/cloud.py M lib/galaxy/model/metadata.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/util/monitors.py M lib/galaxy/webapps/galaxy/api/cloudauthz.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/tool_shed/util/hg_util.py M scripts/bootstrap_history.py M static/style/blue/base.css A static/style/blue/info_icon.svg M templates/admin/jobs.mako M templates/admin/review_tool_migration_stages.mako M templates/admin/tool_shed_repository/browse_repository.mako M templates/admin/tool_shed_repository/browse_tool_dependency.mako M templates/admin/tool_shed_repository/deactivate_or_uninstall_repository.mako M templates/admin/tool_shed_repository/install_tool_dependencies_with_update.mako M templates/admin/tool_shed_repository/manage_repository.mako M templates/admin/tool_shed_repository/manage_repository_tool_dependencies.mako M templates/admin/tool_shed_repository/monitor_repository_installation.mako M templates/admin/tool_shed_repository/purge_repository_confirmation.mako M templates/admin/tool_shed_repository/reselect_tool_panel_section.mako M templates/admin/tool_shed_repository/reset_metadata_on_selected_repositories.mako M templates/admin/tool_shed_repository/select_tool_panel_section.mako M templates/admin/tool_shed_repository/uninstall_tool_dependencies.mako M templates/admin/tool_shed_repository/view_tool_metadata.mako M templates/admin/tool_shed_repository/view_workflow.mako M templates/message.mako M templates/webapps/galaxy/admin/manage_dependencies.mako M templates/webapps/galaxy/admin/sanitize_whitelist.mako M templates/webapps/galaxy/admin/view_display_applications.mako M test/api/test_tools.py A test/base/ssh_util.py A test/functional/tools/for_workflows/mapper_two.xml M test/functional/tools/job_environment_default.xml M test/functional/tools/job_environment_default_legacy.xml M test/functional/tools/job_environment_explicit_shared_home.xml M test/functional/tools/samples_tool_conf.xml A test/integration/test_cli_runners.py M test/integration/test_job_environments.py M test/unit/test_remote_shell.py

Log Message: ----------- Merge branch 'dev' into admin.data.manager.vue.steps

Commit: 31b484492260f554020ed8eed1d1a20cd98089ef https://github.com/galaxyproject/galaxy/commit/31b484492260f554020ed8eed1d1a... Author: Sebastian Kapust sebastian@kapust.org Date: 2018-10-17 (Wed, 17 Oct 2018)

Changed paths: M lib/galaxy/webapps/galaxy/controllers/data_manager.py

Log Message: ----------- Fix linting error by removing unused import markupsafe escape

Commit: af05cb480b1c49b4cac560cfc086e9638ab7fb1b https://github.com/galaxyproject/galaxy/commit/af05cb480b1c49b4cac560cfc086e... Author: Martin Cech marten@bx.psu.edu Date: 2018-10-17 (Wed, 17 Oct 2018)

Changed paths: M templates/user/info.mako M templates/user/register.mako M templates/webapps/galaxy/history/share.mako M test/galaxy_selenium/navigation.yml

Log Message: ----------- Merge pull request #6881 from guerler/fix_selenium

Fix selenium test selectors for alert messages

Commit: e09b43af0191df4574989c19ec135c51c2934ee3 https://github.com/galaxyproject/galaxy/commit/e09b43af0191df4574989c19ec135... Author: Mason nerdinacan@gmail.com Date: 2018-10-17 (Wed, 17 Oct 2018)

Changed paths: M client/package.json M client/webpack.config.js M client/yarn.lock M templates/js-app.mako

Log Message: ----------- Added OptimizeCssAssetsPlugin fix for sourcemaps + minicss plugin

Commit: ede7d588402d34c363bbff16516171232c70b2f0 https://github.com/galaxyproject/galaxy/commit/ede7d588402d34c363bbff1651617... Author: guerler aysam.guerler@gmail.com Date: 2018-10-17 (Wed, 17 Oct 2018)

Changed paths: M client/galaxy/scripts/mvc/ui/ui-slider.js

Log Message: ----------- Use default input style for slider text field

Commit: 69d31a7f03d0147cd96355c7cec4f9bdafd1937f https://github.com/galaxyproject/galaxy/commit/69d31a7f03d0147cd96355c7cec4f... Author: guerler aysam.guerler@gmail.com Date: 2018-10-17 (Wed, 17 Oct 2018)

Changed paths: M templates/webapps/tool_shed/repository/common.mako

Log Message: ----------- More mako adjustments for the toolshed/galaxy layer

Commit: 8c5ccd328aeccf324c921f6f490c138aee708fba https://github.com/galaxyproject/galaxy/commit/8c5ccd328aeccf324c921f6f490c1... Author: guerler aysam.guerler@gmail.com Date: 2018-10-17 (Wed, 17 Oct 2018)

Changed paths: M templates/webapps/galaxy/history/display.mako

Log Message: ----------- Realign history publishing options

Commit: 8e64ac209a47dd4d07010a3ca8c8da9d7a36f2a7 https://github.com/galaxyproject/galaxy/commit/8e64ac209a47dd4d07010a3ca8c8d... Author: guerler aysam.guerler@gmail.com Date: 2018-10-17 (Wed, 17 Oct 2018)

Changed paths: M templates/webapps/galaxy/visualization/display.mako M templates/webapps/galaxy/visualization/display_in_frame.mako M templates/webapps/galaxy/workflow/display.mako

Log Message: ----------- Restore sharing option alignments

Commit: 443683b80187bf202912e328621573747795316c https://github.com/galaxyproject/galaxy/commit/443683b80187bf202912e32862157... Author: Dannon Baker dannon.baker@gmail.com Date: 2018-10-17 (Wed, 17 Oct 2018)

Changed paths: M client/gulpfile.js M client/package.json M client/yarn.lock

Log Message: ----------- Drop a ton of unused gulp cruft.

Commit: 8ab6dee071756fb13fd841afa23f4aa4e8a643b2 https://github.com/galaxyproject/galaxy/commit/8ab6dee071756fb13fd841afa23f4... Author: Dannon Baker dannon.baker@gmail.com Date: 2018-10-17 (Wed, 17 Oct 2018)

Changed paths: M client/package.json M client/yarn.lock

Log Message: ----------- Still uglify for shipped libs.

Commit: 2bf71d8cc750c60b5516cfe1344a70248dd79a40 https://github.com/galaxyproject/galaxy/commit/2bf71d8cc750c60b5516cfe1344a7... Author: guerler aysam.guerler@gmail.com Date: 2018-10-17 (Wed, 17 Oct 2018)

Changed paths: M client/galaxy/style/scss/base.scss M static/style/blue/base.css

Log Message: ----------- Fix panel padding

Commit: c18e99505f5038b633670eca66a16565ac981232 https://github.com/galaxyproject/galaxy/commit/c18e99505f5038b633670eca66a16... Author: Mason nerdinacan@gmail.com Date: 2018-10-17 (Wed, 17 Oct 2018)

Changed paths: M client/webpack.config.js R static/style/base.css M templates/js-app.mako

Log Message: ----------- exported styles to single file instead of one per entrypoint

Commit: b9d88a2f5afb0cfa49f6cfaa56375e0d229fb8f5 https://github.com/galaxyproject/galaxy/commit/b9d88a2f5afb0cfa49f6cfaa56375... Author: guerler aysam.guerler@gmail.com Date: 2018-10-17 (Wed, 17 Oct 2018)

Changed paths: M templates/display_base.mako M templates/webapps/galaxy/workflow/sharing.mako

Log Message: ----------- Fix container paddings

Commit: ea12d73df12a4a26a423e0c987d27c6ed96e9765 https://github.com/galaxyproject/galaxy/commit/ea12d73df12a4a26a423e0c987d27... Author: Dannon Baker dannon.baker@gmail.com Date: 2018-10-17 (Wed, 17 Oct 2018)

Changed paths: M client/package.json M client/webpack.config.js M client/yarn.lock R static/style/base.css M templates/js-app.mako

Log Message: ----------- Merge remote-tracking branch 'Nerdinacan/webpack_4_mapfix' into unified_webpack4

Commit: ee4908bf57efe03cb85f2ffb846cb05357adc4c5 https://github.com/galaxyproject/galaxy/commit/ee4908bf57efe03cb85f2ffb846cb... Author: Dannon Baker dannon.baker@gmail.com Date: 2018-10-17 (Wed, 17 Oct 2018)

Changed paths: A static/style/base.css R static/style/blue/base.css

Log Message: ----------- Drop style artifact, recreate link to output bundle for backwards compat.

Commit: e273a549db844c3e27645c6dc568cd5f49f389af https://github.com/galaxyproject/galaxy/commit/e273a549db844c3e27645c6dc568c... Author: Dannon Baker dannon.baker@gmail.com Date: 2018-10-17 (Wed, 17 Oct 2018)

Changed paths: M client/package.json M client/yarn.lock

Log Message: ----------- Webpack -> .21

Commit: 658dce066b91ad03379f27f7311bf4e74631be87 https://github.com/galaxyproject/galaxy/commit/658dce066b91ad03379f27f7311bf... Author: Dannon Baker dannon.baker@gmail.com Date: 2018-10-17 (Wed, 17 Oct 2018)

Changed paths: M client/galaxy/scripts/qunit/assets/base.css

Log Message: ----------- Fix link to base.css

Commit: 81f31d1a29e1b1021f7629008d433797b9367267 https://github.com/galaxyproject/galaxy/commit/81f31d1a29e1b1021f7629008d433... Author: Martin Cech marten@bx.psu.edu Date: 2018-10-17 (Wed, 17 Oct 2018)

Changed paths: M lib/galaxy/web/base/controller.py

Log Message: ----------- Merge pull request #6884 from guerler/fix_accessible_links

Improve resilience on handling sharing attributes

Commit: 6c77d715a82bf6b1d461ec0f67744fe76d593cbc https://github.com/galaxyproject/galaxy/commit/6c77d715a82bf6b1d461ec0f67744... Author: Dannon Baker dannon.baker@gmail.com Date: 2018-10-17 (Wed, 17 Oct 2018)

Changed paths: M templates/base.mako

Log Message: ----------- Fix goofed bundle inclusion refactoring

Commit: f98c79ea9568ae7ff4fc1c18b2b598180e5c0285 https://github.com/galaxyproject/galaxy/commit/f98c79ea9568ae7ff4fc1c18b2b59... Author: Dannon Baker dannon.baker@gmail.com Date: 2018-10-17 (Wed, 17 Oct 2018)

Changed paths: M templates/base.mako

Log Message: ----------- include base.css in base mako

Commit: 1b4aa3e47e676ea5d10df74d09f954aad9a22c51 https://github.com/galaxyproject/galaxy/commit/1b4aa3e47e676ea5d10df74d09f95... Author: Dannon Baker dannon.baker@gmail.com Date: 2018-10-17 (Wed, 17 Oct 2018)

Changed paths: M client/galaxy/style/scss/base.scss M templates/js-app.mako

Log Message: ----------- Fix style inclusion for js-app, after poking at merging jquery styles (todo for the future, not worth dealing with now).

Commit: 05da2263d657a7a3cc9454dfd20035743249c11a https://github.com/galaxyproject/galaxy/commit/05da2263d657a7a3cc9454dfd2003... Author: guerler aysam.guerler@gmail.com Date: 2018-10-17 (Wed, 17 Oct 2018)

Changed paths: M client/galaxy/style/scss/base.scss M client/galaxy/style/scss/collection.scss M client/galaxy/style/scss/list-item.scss M static/style/blue/base.css

Log Message: ----------- Adjust collections in history panel

Commit: 21898296a676f39502fb13f2b425a49d978a4c86 https://github.com/galaxyproject/galaxy/commit/21898296a676f39502fb13f2b425a... Author: Dannon Baker dannon.baker@gmail.com Date: 2018-10-17 (Wed, 17 Oct 2018)

Changed paths: A client/galaxy/style/jquery.rating.css R client/galaxy/style/scss/jquery.rating.css A static/style/blue/jquery.rating.css

Log Message: ----------- Fix jquery.rating.css (until it's bundled)

Commit: e7662f7065f0a77dfdd121c133dbfc4ff46cc74b https://github.com/galaxyproject/galaxy/commit/e7662f7065f0a77dfdd121c133dbf... Author: guerler aysam.guerler@gmail.com Date: 2018-10-17 (Wed, 17 Oct 2018)

Changed paths: M templates/display_base.mako M templates/webapps/galaxy/workflow/display.mako

Log Message: ----------- Fix workflow preview

Commit: 55bd9ede5b7b08597725f8f630867f09acca7f7d https://github.com/galaxyproject/galaxy/commit/55bd9ede5b7b08597725f8f630867... Author: Dannon Baker dannon.baker@gmail.com Date: 2018-10-17 (Wed, 17 Oct 2018)

Changed paths: M client/karma.config.js M client/webpack.config.js

Log Message: ----------- Fix js unit tests to work with bundled css (TODO: Make this more robust, this is very brittle right now and will potentially break the tests (obviously) when anyone reorders plugins, for example)

Commit: f1ed67cf3f8325f3f22eb0624d7b9403524a9eaf https://github.com/galaxyproject/galaxy/commit/f1ed67cf3f8325f3f22eb0624d7b9... Author: Dannon Baker dannon.baker@gmail.com Date: 2018-10-17 (Wed, 17 Oct 2018)

Changed paths: M client/karma.config.js

Log Message: ----------- Cleanup, document TODO for loader replacement

Commit: 84ae932e8b7fbb0086dc12a7c44945f37f9e05ed https://github.com/galaxyproject/galaxy/commit/84ae932e8b7fbb0086dc12a7c4494... Author: Dannon Baker dannon.baker@gmail.com Date: 2018-10-17 (Wed, 17 Oct 2018)

Changed paths: A static/style/blue/base.css M test/base/driver_util.py

Log Message: ----------- Add back extra link to base.css for selenium testing (and assumedly other deployments which have custom mappings?). We need to drop all these extra handles eventually, to consolidate the interface to single endpoints with chunked bundles.

Commit: 6775befc6a67a85ff02be4eebdb12a11db2a30ed https://github.com/galaxyproject/galaxy/commit/6775befc6a67a85ff02be4eebdb12... Author: Dannon Baker dannon.baker@gmail.com Date: 2018-10-17 (Wed, 17 Oct 2018)

Changed paths: M client/galaxy/scripts/apps/extended.js

Log Message: ----------- Fix import/export in extended bundle

Commit: 99bb15c1215011dc2d44170e4db2f4f75d74bcbf https://github.com/galaxyproject/galaxy/commit/99bb15c1215011dc2d44170e4db2f... Author: Dannon Baker dannon.baker@gmail.com Date: 2018-10-17 (Wed, 17 Oct 2018)

Changed paths: M templates/base/base_panels.mako

Log Message: ----------- Continue importing base.css in base_panels.mako

Commit: 03b44a84a66e07d720a34764c21241067faec199 https://github.com/galaxyproject/galaxy/commit/03b44a84a66e07d720a34764c2124... Author: Dannon Baker dannon.baker@gmail.com Date: 2018-10-17 (Wed, 17 Oct 2018)

Changed paths: M client/README.md A client/galaxy/docs/README.md M client/galaxy/docs/bootstrap.md M client/galaxy/docs/galaxy-buttons.md M client/galaxy/docs/galaxy-forms.md M client/galaxy/docs/galaxy-masthead.md M client/galaxy/docs/galaxy-menus.md M client/galaxy/docs/galaxy-messages.md M client/galaxy/docs/galaxy-panels.md M client/galaxy/docs/galaxy-tables.md M client/galaxy/docs/galaxy-tabs.md M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/mvc/ui/ui-rules-edit.js M client/galaxy/scripts/mvc/ui/ui-slider.js M client/galaxy/scripts/ui/editable-text.js M client/galaxy/style/scss/jstree.scss M client/galaxy/style/scss/ui.scss M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/upload_util.py M lib/galaxy/managers/cloud.py M lib/galaxy/web/base/controller.py M lib/galaxy/webapps/galaxy/api/cloudauthz.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/tool_shed/util/hg_util.py A static/style/blue/info_icon.svg M templates/admin/jobs.mako M templates/admin/review_tool_migration_stages.mako M templates/admin/tool_shed_repository/browse_repository.mako M templates/admin/tool_shed_repository/browse_tool_dependency.mako M templates/admin/tool_shed_repository/deactivate_or_uninstall_repository.mako M templates/admin/tool_shed_repository/install_tool_dependencies_with_update.mako M templates/admin/tool_shed_repository/manage_repository.mako M templates/admin/tool_shed_repository/manage_repository_tool_dependencies.mako M templates/admin/tool_shed_repository/monitor_repository_installation.mako M templates/admin/tool_shed_repository/purge_repository_confirmation.mako M templates/admin/tool_shed_repository/reselect_tool_panel_section.mako M templates/admin/tool_shed_repository/reset_metadata_on_selected_repositories.mako M templates/admin/tool_shed_repository/select_tool_panel_section.mako M templates/admin/tool_shed_repository/uninstall_tool_dependencies.mako M templates/admin/tool_shed_repository/view_tool_metadata.mako M templates/admin/tool_shed_repository/view_workflow.mako M templates/message.mako M templates/user/info.mako M templates/user/register.mako M templates/webapps/galaxy/admin/manage_dependencies.mako M templates/webapps/galaxy/admin/sanitize_whitelist.mako M templates/webapps/galaxy/admin/view_display_applications.mako M templates/webapps/galaxy/history/share.mako M test/galaxy_selenium/navigation.yml

Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into unified_webpack4

Commit: efc7864cabb0f7adc65929f3bff2f56c3ef14041 https://github.com/galaxyproject/galaxy/commit/efc7864cabb0f7adc65929f3bff2f... Author: Pierrick ROGER pk.roger@icloud.com Date: 2018-10-18 (Thu, 18 Oct 2018)

Changed paths: M .ci/flake8_blacklist.txt A .ci/jenkins/api-py3/run_tests.sh M .ci/jenkins/api/run_tests.sh A .ci/jenkins/framework-py3/run_tests.sh M .ci/jenkins/framework/run_tests.sh A .ci/jenkins/integration-py3/run_tests.sh A .ci/jenkins/main-tools-py3/run_tests.sh A .ci/jenkins/main-tools/run_tests.sh A .ci/jenkins/selenium-py3/run_tests.sh M .ci/jenkins/selenium/run_tests.sh M .ci/jenkins/toolshed/run_tests.sh M .coveragerc M .gitignore M .travis.yml M client/README.md A client/galaxy/docs/README.md M client/galaxy/docs/bootstrap.md A client/galaxy/docs/galaxy-buttons.md A client/galaxy/docs/galaxy-forms.md A client/galaxy/docs/galaxy-masthead.md A client/galaxy/docs/galaxy-menus.md A client/galaxy/docs/galaxy-messages.md A client/galaxy/docs/galaxy-panels.md R client/galaxy/docs/galaxy-styles.md A client/galaxy/docs/galaxy-tables.md A client/galaxy/docs/galaxy-tabs.md M client/galaxy/scripts/admin.toolshed.js M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/apps/panels/admin-panel.js M client/galaxy/scripts/apps/panels/tool-panel.js M client/galaxy/scripts/components/Citations.vue A client/galaxy/scripts/components/DataDialog.vue M client/galaxy/scripts/components/DisplayStructured.vue M client/galaxy/scripts/components/HistoryImport.vue M client/galaxy/scripts/components/HistoryView.vue M client/galaxy/scripts/components/PluginList.vue M client/galaxy/scripts/components/RuleCollectionBuilder.vue M client/galaxy/scripts/components/Sharing.vue M client/galaxy/scripts/components/WorkflowImport.vue M client/galaxy/scripts/components/admin/BaseGrid.vue A client/galaxy/scripts/components/admin/DataTypes.vue R client/galaxy/scripts/components/admin/UserAPIKeys.vue M client/galaxy/scripts/galaxy.pages.js A client/galaxy/scripts/layout/data.js M client/galaxy/scripts/layout/masthead.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/modal.js M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/layout/panel.js M client/galaxy/scripts/layout/scratchbook.js M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M client/galaxy/scripts/mvc/collection/pair-collection-creator.js M client/galaxy/scripts/mvc/dataset/dataset-edit-attributes.js M client/galaxy/scripts/mvc/dataset/dataset-error.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-repeat.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/form/form-wrapper.js M client/galaxy/scripts/mvc/history/history-contents.js M client/galaxy/scripts/mvc/history/history-view-edit-current.js M client/galaxy/scripts/mvc/history/history-view-edit.js M client/galaxy/scripts/mvc/history/history-view.js M client/galaxy/scripts/mvc/history/job-dag.js M client/galaxy/scripts/mvc/history/job-states-model.js M client/galaxy/scripts/mvc/lazy/lazy-limited.js M client/galaxy/scripts/mvc/library/library-folderlist-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/rules/rule-definitions.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/tool/tool-form.js M client/galaxy/scripts/mvc/tool/tools.js M client/galaxy/scripts/mvc/toolshed/categories-view.js R client/galaxy/scripts/mvc/toolshed/repo-queue-view.js M client/galaxy/scripts/mvc/toolshed/repo-status-view.js M client/galaxy/scripts/mvc/toolshed/repositories-view.js M client/galaxy/scripts/mvc/toolshed/repository-queue-view.js M client/galaxy/scripts/mvc/toolshed/repository-view.js M client/galaxy/scripts/mvc/toolshed/shed-list-view.js M client/galaxy/scripts/mvc/toolshed/toolshed-model.js M client/galaxy/scripts/mvc/toolshed/util.js M client/galaxy/scripts/mvc/toolshed/workflows-view.js M client/galaxy/scripts/mvc/tours.js M client/galaxy/scripts/mvc/ui/ui-buttons.js M client/galaxy/scripts/mvc/ui/ui-list.js M client/galaxy/scripts/mvc/ui/ui-misc.js M client/galaxy/scripts/mvc/ui/ui-options.js M client/galaxy/scripts/mvc/ui/ui-popover.js M client/galaxy/scripts/mvc/ui/ui-portlet.js M client/galaxy/scripts/mvc/ui/ui-rules-edit.js M client/galaxy/scripts/mvc/ui/ui-select-content.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/galaxy/scripts/mvc/ui/ui-select-genomespace.js M client/galaxy/scripts/mvc/ui/ui-select-library.js M client/galaxy/scripts/mvc/ui/ui-slider.js M client/galaxy/scripts/mvc/ui/ui-table.js M client/galaxy/scripts/mvc/ui/ui-tabs.js R client/galaxy/scripts/mvc/ui/ui-thumbnails.js M client/galaxy/scripts/mvc/upload/collection/collection-row.js M client/galaxy/scripts/mvc/upload/collection/collection-view.js M client/galaxy/scripts/mvc/upload/composite/composite-row.js M client/galaxy/scripts/mvc/upload/composite/composite-view.js M client/galaxy/scripts/mvc/upload/default/default-row.js M client/galaxy/scripts/mvc/upload/default/default-view.js M client/galaxy/scripts/mvc/upload/upload-extension.js M client/galaxy/scripts/mvc/upload/upload-ftp.js M client/galaxy/scripts/mvc/upload/upload-settings.js M client/galaxy/scripts/mvc/upload/upload-view.js M client/galaxy/scripts/mvc/user/user-custom-builds.js M client/galaxy/scripts/mvc/user/user-preferences.js M client/galaxy/scripts/mvc/visualization/chart/components/model.js M client/galaxy/scripts/mvc/visualization/chart/views/description.js M client/galaxy/scripts/mvc/visualization/chart/views/editor.js M client/galaxy/scripts/mvc/visualization/chart/views/groups.js M client/galaxy/scripts/mvc/visualization/chart/views/menu.js M client/galaxy/scripts/mvc/visualization/chart/views/settings.js M client/galaxy/scripts/mvc/workflow/workflow-canvas.js M client/galaxy/scripts/mvc/workflow/workflow-connector.js M client/galaxy/scripts/mvc/workflow/workflow-forms.js M client/galaxy/scripts/mvc/workflow/workflow-manager.js M client/galaxy/scripts/mvc/workflow/workflow-node.js M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M client/galaxy/scripts/mvc/workflow/workflow-view-data.js M client/galaxy/scripts/mvc/workflow/workflow-view-terminals.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M client/galaxy/scripts/qunit/test.js M client/galaxy/scripts/qunit/tests/form_tests.js M client/galaxy/scripts/qunit/tests/masthead_tests.js R client/galaxy/scripts/qunit/tests/popover_tests.js M client/galaxy/scripts/qunit/tests/ui_tests.js M client/galaxy/scripts/qunit/tests/upload_dialog_tests.js M client/galaxy/scripts/reports/run_stats.js M client/galaxy/scripts/ui/editable-text.js M client/galaxy/scripts/ui/fa-icon-button.js M client/galaxy/scripts/utils/config.js M client/galaxy/scripts/utils/uploadbox.js M client/galaxy/scripts/viz/circster.js M client/galaxy/scripts/viz/sweepster.js M client/galaxy/scripts/viz/trackster/painters.js M client/galaxy/scripts/viz/trackster/tracks.js M client/galaxy/scripts/viz/visualization.js M client/galaxy/style/scss/base.scss M client/galaxy/style/scss/charts.scss M client/galaxy/style/scss/frame.scss R client/galaxy/style/scss/galaxy_bootstrap/overrides.scss R client/galaxy/style/scss/galaxy_bootstrap/variables.scss R client/galaxy/style/scss/galaxy_variables.scss M client/galaxy/style/scss/history.scss M client/galaxy/style/scss/jstree.scss M client/galaxy/style/scss/library.scss M client/galaxy/style/scss/list-item.scss A client/galaxy/style/scss/overrides.scss M client/galaxy/style/scss/theme/blue.scss R client/galaxy/style/scss/theme/plain.scss M client/galaxy/style/scss/ui.scss M client/galaxy/style/scss/upload.scss A 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test/functional/tools/collection_cat_group_tag.xml A test/functional/tools/collection_cat_group_tag_multiple.xml A test/functional/tools/collection_type_source_map_over.xml A test/functional/tools/column_param_configfile.xml M test/functional/tools/disambiguate_cond.xml M test/functional/tools/for_workflows/cat_collection.xml A test/functional/tools/for_workflows/mapper_two.xml A test/functional/tools/identifier_in_conditional.xml A test/functional/tools/inputs_as_json_with_paths.xml M test/functional/tools/job_environment_default.xml M test/functional/tools/job_environment_default_legacy.xml M test/functional/tools/job_environment_explicit_shared_home.xml M test/functional/tools/metadata_biom1.xml M test/functional/tools/multi_data_optional.xml M test/functional/tools/parallelism.xml M test/functional/tools/parallelism_optional.xml M test/functional/tools/samples_tool_conf.xml M test/functional/tools/unicode_stream.xml R test/functional/twilltestcase.py M test/galaxy_selenium/has_driver.py M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/navigation.yml M test/galaxy_selenium/smart_components.py A test/integration/delay_job_conf.xml A test/integration/delay_rules/__init__.py A test/integration/delay_rules/rules.py A test/integration/objectstore_selection_job_conf.xml A test/integration/objectstore_selection_job_resource_parameters_conf.xml A test/integration/objectstore_selection_rules/__init__.py A test/integration/objectstore_selection_rules/rules.py A test/integration/test_cli_runners.py M test/integration/test_data_manager_table_reload.py M test/integration/test_job_environments.py A test/integration/test_job_recovery.py M test/integration/test_job_resubmission.py M test/integration/test_mules_as_job_handlers.py A test/integration/test_objectstore_jobs.py A test/integration/test_objectstore_selection.py M test/integration/test_scripts.py M test/integration/test_upload_configuration_options.py M test/integration/tool_sheds_conf.xml M test/integration/uses_shed.py M test/manual/workflows_scaling.py M test/selenium_tests/framework.py M test/selenium_tests/test_admin_app.py M test/selenium_tests/test_collection_builders.py M test/selenium_tests/test_history_panel_collections.py M test/selenium_tests/test_history_sharing.py M test/selenium_tests/test_published_histories_grid.py M test/selenium_tests/test_saved_histories.py M test/selenium_tests/test_stock_tours.py M test/selenium_tests/test_tool_form.py M test/selenium_tests/test_workflow_run.py M test/shed_functional/base/twilltestcase.py M test/unit/datatypes/dataproviders/test_base_dataproviders.py M test/unit/datatypes/test_bam.py M test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py M test/unit/jobs/test_job_output_checker.py M test/unit/jobs/test_job_wrapper.py M test/unit/jobs/test_runner_params.py M test/unit/managers/test_DatasetManager.py M test/unit/managers/test_HistoryContentsManager.py M test/unit/managers/test_HistoryManager.py A test/unit/managers/test_TagManager.py A test/unit/test_compression_util.py M test/unit/test_galaxy_mapping.py A test/unit/test_model_copy.py M test/unit/test_objectstore.py M test/unit/test_remote_shell.py M test/unit/test_rule_utils.py M test/unit/test_security_helper.py A test/unit/test_utils.py M test/unit/tools/test_actions.py M test/unit/tools/test_collect_primary_datasets.py M test/unit/tools/test_data_parameters.py M test/unit/tools/test_dataset_matcher.py M test/unit/tools/test_evaluation.py M test/unit/tools/test_execution.py M test/unit/tools/test_history_imp_exp.py M test/unit/tools/test_parsing.py M test/unit/tools/test_tool_dependency_description.py M test/unit/tools/test_tool_deps.py M test/unit/tools/test_toolbox.py M test/unit/tools/test_toolbox_filters.py M test/unit/tools/test_wrappers.py M test/unit/unittest_utils/galaxy_mock.py M test/unit/unittest_utils/tempfilecache.py M test/unit/visualizations/plugins/test_VisualizationsRegistry.py M test/unit/web/framework/test_webapp.py M test/unit/workflows/test_extract_summary.py M test/unit/workflows/test_modules.py M test/unit/workflows/test_workflow_progress.py A tool-data/intermine_simple_display.loc.sample M tool-data/shared/ucsc/builds.txt.sample M tool-data/shared/ucsc/ucsc_build_sites.txt.sample A tools/data_source/intermine.xml M tools/data_source/ucsc_tablebrowser_test.xml M tools/data_source/upload.py M tools/filters/bed_to_bigbed.xml M tools/filters/join.py M tools/filters/joinWrapper.py M tools/filters/random_lines_two_pass.py M tools/filters/randomlines.xml M tools/filters/secure_hash_message_digest.py M tools/filters/sff_extract.py M tools/filters/sff_extractor.xml M tools/filters/tailWrapper.xml M tools/filters/uniq.xml M tools/filters/wc_gnu.xml M tools/filters/wig_to_bigwig.xml M tools/genomespace/genomespace_importer.py M tools/maf/maf_limit_to_species.py M tools/maf/maf_split_by_species.xml M tools/maf/maf_to_bed.py M tools/maf/maf_to_bed.xml M tools/maf/maf_to_fasta_multiple_sets.py M tools/maf/maf_to_interval.py M tools/maf/maf_to_interval.xml M tools/next_gen_conversion/solid2fastq.xml M tools/phenotype_association/gpass.xml M tools/phenotype_association/ldtools.xml M tools/phenotype_association/ldtools_wrapper.sh M tools/phenotype_association/linkToGProfile.pl M tools/phenotype_association/linkToGProfile.xml M tools/phenotype_association/lps.xml M tools/phenotype_association/master2gd_snp.xml M tools/phenotype_association/master2pg.xml M tools/phenotype_association/senatag.py M tools/plotting/boxplot.xml M tools/solid_tools/solid_qual_stats.py M tools/solid_tools/solid_qual_stats.xml M tools/stats/aggregate_binned_scores_in_intervals.xml M tools/stats/aggregate_scores_in_intervals.py M tools/stats/filtering.xml M tools/stats/grouping.py M tools/stats/gsummary.xml M tox.ini

Log Message: ----------- Merge branch 'dev' into feature/isa_data_type

Commit: 35093e38fcfe4f9efc3a2914d694cf4a11f24ace https://github.com/galaxyproject/galaxy/commit/35093e38fcfe4f9efc3a2914d694c... Author: Pierrick ROGER pk.roger@icloud.com Date: 2018-10-18 (Thu, 18 Oct 2018)

Changed paths: M test/api/test_tools_upload.py

Log Message: ----------- Remove spaces in blank line.

Commit: a9eb587a3e38849c5044700f9f01c47d53f55a87 https://github.com/galaxyproject/galaxy/commit/a9eb587a3e38849c5044700f9f01c... Author: Pierrick ROGER pk.roger@icloud.com Date: 2018-10-18 (Thu, 18 Oct 2018)

Changed paths: M lib/galaxy/datatypes/isa.py

Log Message: ----------- Various corrections for py34-lint

Add second blank line. Remove useless imports.

Commit: 0c145b3326f2476b05ed8ca7ee66d754099a452f https://github.com/galaxyproject/galaxy/commit/0c145b3326f2476b05ed8ca7ee66d... Author: thobalose lose.thoba@gmail.com Date: 2018-10-18 (Thu, 18 Oct 2018)

Changed paths: M config/plugins/interactive_environments/neo/config/allowed_images.yml.sample M config/plugins/interactive_environments/neo/config/neo.ini.sample M config/plugins/interactive_environments/neo/templates/neo.mako

Log Message: ----------- Updated Neo4j IE to 3.1.9

Commit: 2da38803a3bc12a19e1fa53a1e8cc9e9448eb1b6 https://github.com/galaxyproject/galaxy/commit/2da38803a3bc12a19e1fa53a1e8cc... Author: thobalose lose.thoba@gmail.com Date: 2018-10-18 (Thu, 18 Oct 2018)

Changed paths: M lib/galaxy/visualization/plugins/interactive_environments.py

Log Message: ----------- Catering for shlex.split(cmd_inject) behaviour

Commit: 581e734dfcb9662a6c4c2f0d9288fad2a0707e54 https://github.com/galaxyproject/galaxy/commit/581e734dfcb9662a6c4c2f0d9288f... Author: Dannon Baker dannon.baker@gmail.com Date: 2018-10-18 (Thu, 18 Oct 2018)

Changed paths: M config/plugins/webhooks/demo/tour_generator/config.yml A config/plugins/webhooks/demo/tour_generator/package.json R config/plugins/webhooks/demo/tour_generator/script.js A config/plugins/webhooks/demo/tour_generator/tour_generator.js

Log Message: ----------- Incremental packaging of tour_builder

Commit: 93ac1fc3fff24d280be4a8409515da273c5f6e77 https://github.com/galaxyproject/galaxy/commit/93ac1fc3fff24d280be4a8409515d... Author: Martin Cech marten@bx.psu.edu Date: 2018-10-18 (Thu, 18 Oct 2018)

Changed paths: M lib/galaxy/webapps/galaxy/controllers/history.py

Log Message: ----------- remove sanitization of data being saved in database

Commit: efa375e238d2808639c95f511e7242de0c15453f https://github.com/galaxyproject/galaxy/commit/efa375e238d2808639c95f511e724... Author: Martin Cech marten@bx.psu.edu Date: 2018-10-18 (Thu, 18 Oct 2018)

Changed paths: M lib/galaxy/webapps/galaxy/controllers/history.py

Log Message: ----------- remove unneeded import

Commit: 8c826145d921b72731e611ce1b539372c477a368 https://github.com/galaxyproject/galaxy/commit/8c826145d921b72731e611ce1b539... Author: vahid jalili.vahid@gmail.com Date: 2018-10-18 (Thu, 18 Oct 2018)

Changed paths: M lib/galaxy/webapps/galaxy/api/cloud.py M lib/galaxy/webapps/galaxy/buildapp.py

Log Message: ----------- Refactor cloud "upload">"get" api.

Commit: 6fc3aa35e8e7df9a4c2423b4e76bf90704f66559 https://github.com/galaxyproject/galaxy/commit/6fc3aa35e8e7df9a4c2423b4e76bf... Author: vahid jalili.vahid@gmail.com Date: 2018-10-18 (Thu, 18 Oct 2018)

Changed paths: M lib/galaxy/managers/cloud.py M lib/galaxy/webapps/galaxy/api/cloud.py

Log Message: ----------- Refactor cloud "upload">"get" in cloud manager.

Commit: 571d783517654302a5823487021848166e3a3e10 https://github.com/galaxyproject/galaxy/commit/571d783517654302a582348702184... Author: Dannon Baker dannon.baker@gmail.com Date: 2018-10-18 (Thu, 18 Oct 2018)

Changed paths: M client/galaxy/scripts/onload.js M config/plugins/webhooks/demo/tour_generator/package.json A config/plugins/webhooks/demo/tour_generator/script.js M config/plugins/webhooks/demo/tour_generator/tour_generator.js

Log Message: ----------- Package up tool tour generator as a single artifact that doesn't reach into Galaxy code other than the Galaxy global that's required.

Commit: 65bfe605d0995a5ac177a65ad64e80a597e53e3a https://github.com/galaxyproject/galaxy/commit/65bfe605d0995a5ac177a65ad64e8... Author: Mason nerdinacan@gmail.com Date: 2018-10-18 (Thu, 18 Oct 2018)

Changed paths: M .gitignore A client/package-lock.json M client/package.json M client/webpack.config.js M client/yarn.lock M templates/base.mako M templates/base/base_panels.mako M templates/js-app.mako M templates/webapps/galaxy/galaxy.panels.mako

Log Message: ----------- Single css output from webpack

Commit: de4030fcceebd55a77de3d33a7bc21fb09697895 https://github.com/galaxyproject/galaxy/commit/de4030fcceebd55a77de3d33a7bc2... Author: Dannon Baker dannon.baker@gmail.com Date: 2018-10-18 (Thu, 18 Oct 2018)

Changed paths: M templates/base/base_panels.mako

Log Message: ----------- Fix requirebundled being chunked together.

Commit: 91d13a5a0cc87df1a01c72dca7e835f609e2dabe https://github.com/galaxyproject/galaxy/commit/91d13a5a0cc87df1a01c72dca7e83... Author: Dannon Baker dannon.baker@gmail.com Date: 2018-10-18 (Thu, 18 Oct 2018)

Changed paths: M templates/base/base_panels.mako

Log Message: ----------- We also need base.chunk here.

Commit: 74d1c1fcf809e940bbe9952e29d68f27f3f5af56 https://github.com/galaxyproject/galaxy/commit/74d1c1fcf809e940bbe9952e29d68... Author: vahid jalili.vahid@gmail.com Date: 2018-10-18 (Thu, 18 Oct 2018)

Changed paths: M lib/galaxy/managers/cloud.py M lib/galaxy/webapps/galaxy/api/cloud.py

Log Message: ----------- Update docstring following "upload">"get" refactoring.

Commit: 273bf080b53e2b8cf8acfaa17ab0bcd1bbb82de0 https://github.com/galaxyproject/galaxy/commit/273bf080b53e2b8cf8acfaa17ab0b... Author: Mason nerdinacan@gmail.com Date: 2018-10-18 (Thu, 18 Oct 2018)

Changed paths: M client/webpack.config.js

Log Message: ----------- added in missing priority stats on webpack.config

Commit: ad97c0ce71cf0490dad24ce07c5863d555b9488b https://github.com/galaxyproject/galaxy/commit/ad97c0ce71cf0490dad24ce07c586... Author: guerler aysam.guerler@gmail.com Date: 2018-10-19 (Fri, 19 Oct 2018)

Changed paths: M templates/ind_share_base.mako

Log Message: ----------- Fix style in user sharing

Commit: 754b8f40ff4f95f691acc4024564431f6dde429a https://github.com/galaxyproject/galaxy/commit/754b8f40ff4f95f691acc40245644... Author: guerler aysam.guerler@gmail.com Date: 2018-10-19 (Fri, 19 Oct 2018)

Changed paths: M templates/message.mako

Log Message: ----------- Consolidate message styles

Commit: 09e1bfb98d4b6f88d00e665daf8a63d40224d290 https://github.com/galaxyproject/galaxy/commit/09e1bfb98d4b6f88d00e665daf8a6... Author: Dannon Baker dannon.baker@gmail.com Date: 2018-10-19 (Fri, 19 Oct 2018)

Changed paths: R client/package-lock.json M client/yarn.lock

Log Message: ----------- Drop package-lock.json; regenerate yarn.lock

Commit: 99bc4b33d2fa14a42f9ee7f4a9afe4dcf867c851 https://github.com/galaxyproject/galaxy/commit/99bc4b33d2fa14a42f9ee7f4a9afe... Author: Martin Cech marten@bx.psu.edu Date: 2018-10-19 (Fri, 19 Oct 2018)

Changed paths: M config/datatypes_conf.xml.sample A lib/galaxy/datatypes/isa.py M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt A test-data/MTBLS6.zip M test/api/test_tools_upload.py M tools/data_source/upload.py

Log Message: ----------- Merge pull request #5787 from phnmnl/feature/isa_data_type

Feature/isa data type

Commit: 016a7935a3189e717f58b93bd64aaed8b240795e https://github.com/galaxyproject/galaxy/commit/016a7935a3189e717f58b93bd64aa... Author: Pierrick Roger pk.roger@icloud.com Date: 2018-10-22 (Mon, 22 Oct 2018)

Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/proteomics.py

Log Message: ----------- nmrML data type.

Commit: 77f742d7ffd95167b3c4905ef4bdcb4e678e8158 https://github.com/galaxyproject/galaxy/commit/77f742d7ffd95167b3c4905ef4bdc... Author: guerler aysam.guerler@gmail.com Date: 2018-10-22 (Mon, 22 Oct 2018)

Changed paths: M config/plugins/visualizations/scatterplot/package.json M config/plugins/visualizations/scatterplot/src/scatterplot.js M config/plugins/visualizations/scatterplot/static/scatterplot.css M config/plugins/visualizations/scatterplot/static/scatterplot.js

Log Message: ----------- Adjust scatterplot interface style

Commit: 4e426ce25621736c6e6c7a7d91fcf1845f46db03 https://github.com/galaxyproject/galaxy/commit/4e426ce25621736c6e6c7a7d91fcf... Author: guerler aysam.guerler@gmail.com Date: 2018-10-22 (Mon, 22 Oct 2018)

Changed paths: M config/plugins/visualizations/scatterplot/src/scatterplot.js M config/plugins/visualizations/scatterplot/static/scatterplot.js M config/plugins/visualizations/scatterplot/templates/scatterplot.mako

Log Message: ----------- Fix scatterplot saving feature

Commit: dac9d14311ec27b40432a64b35e68cab892078d6 https://github.com/galaxyproject/galaxy/commit/dac9d14311ec27b40432a64b35e68... Author: Dannon Baker dannon.baker@gmail.com Date: 2018-10-22 (Mon, 22 Oct 2018)

Changed paths: M client/package.json M client/yarn.lock

Log Message: ----------- Minor webpack upgrade.

Commit: cd92dd2819ef3e789e0f25e9b1c99dcc8404d486 https://github.com/galaxyproject/galaxy/commit/cd92dd2819ef3e789e0f25e9b1c99... Author: Martin Cech marten@bx.psu.edu Date: 2018-10-22 (Mon, 22 Oct 2018)

Changed paths: M lib/galaxy/dependencies/pipfiles/default/Pipfile

Log Message: ----------- add isa-rwal to default pipfile

it is in pinned already

Commit: a38fc541d14712b4a81e9aaf42a8041efc17c803 https://github.com/galaxyproject/galaxy/commit/a38fc541d14712b4a81e9aaf42a80... Author: Nicola Soranzo nicola.soranzo@earlham.ac.uk Date: 2018-10-23 (Tue, 23 Oct 2018)

Changed paths: M lib/galaxy/tools/error_reports/plugins/biostars.py M lib/galaxy/tools/error_reports/plugins/email.py M lib/galaxy/tools/error_reports/plugins/github.py M lib/galaxy/tools/error_reports/plugins/influxdb.py M lib/galaxy/tools/error_reports/plugins/json.py M lib/galaxy/tools/error_reports/plugins/sentry.py

Log Message: ----------- Simplify imports

Commit: cbf8a6658d8bf386c6133213883d0f833049d445 https://github.com/galaxyproject/galaxy/commit/cbf8a6658d8bf386c6133213883d0... Author: Nicola Soranzo nicola.soranzo@earlham.ac.uk Date: 2018-10-23 (Tue, 23 Oct 2018)

Changed paths: M doc/source/admin/special_topics/bug_reports.rst

Log Message: ----------- Update Bug Reports docs to use YAML syntax

Commit: 3759db3297b2d277ae3039f54e203dc7493cb3dc https://github.com/galaxyproject/galaxy/commit/3759db3297b2d277ae3039f54e203... Author: John Chilton jmchilton@gmail.com Date: 2018-10-23 (Tue, 23 Oct 2018)

Changed paths: A lib/galaxy/model/migrate/versions/0144_add_cleanup_event_user_table.py M scripts/cleanup_datasets/pgcleanup.py

Log Message: ----------- Merge pull request #6877 from natefoo/pgcleanup-inactive-users

Refactor pgcleanup.py and add new routines

Commit: 02c71e2429bad6caf07ce9a66e788d26af8b21b3 https://github.com/galaxyproject/galaxy/commit/02c71e2429bad6caf07ce9a66e788... Author: Nicola Soranzo nicola.soranzo@earlham.ac.uk Date: 2018-10-23 (Tue, 23 Oct 2018)

Changed paths: M config/galaxy.yml.sample M doc/source/admin/galaxy_options.rst M doc/source/releases/18.09.rst M doc/source/releases/18.09_announce.rst M lib/galaxy/datatypes/data.py M lib/galaxy/webapps/galaxy/config_schema.yml

Log Message: ----------- Merge branch 'release_18.09' into dev

Commit: 7244fb5153b39ba285ac3bf5a4128e2705c1279a https://github.com/galaxyproject/galaxy/commit/7244fb5153b39ba285ac3bf5a4128... Author: Dannon Baker dannon.baker@gmail.com Date: 2018-10-23 (Tue, 23 Oct 2018)

Changed paths: M client/galaxy/scripts/onload.js

Log Message: ----------- Swap back to bundled jquery-ui, sort this out later (or purge it with fire)

Commit: ade72dd8b638292392f057767ad41f9ed4330eb9 https://github.com/galaxyproject/galaxy/commit/ade72dd8b638292392f057767ad41... Author: John Chilton jmchilton@gmail.com Date: 2018-10-23 (Tue, 23 Oct 2018)

Changed paths: M config/plugins/visualizations/scatterplot/package.json M config/plugins/visualizations/scatterplot/src/scatterplot.js M config/plugins/visualizations/scatterplot/static/scatterplot.css M config/plugins/visualizations/scatterplot/static/scatterplot.js M config/plugins/visualizations/scatterplot/templates/scatterplot.mako

Log Message: ----------- Merge pull request #6905 from guerler/viz_frame

Fixes for built-in Scatterplot plugin

Commit: 096fe9b7b9c37e066abe1d31f4a1eeb360b95097 https://github.com/galaxyproject/galaxy/commit/096fe9b7b9c37e066abe1d31f4a1e... Author: John Chilton jmchilton@gmail.com Date: 2018-10-23 (Tue, 23 Oct 2018)

Changed paths: M doc/source/admin/special_topics/bug_reports.rst M lib/galaxy/tools/error_reports/plugins/biostars.py M lib/galaxy/tools/error_reports/plugins/email.py M lib/galaxy/tools/error_reports/plugins/github.py M lib/galaxy/tools/error_reports/plugins/influxdb.py M lib/galaxy/tools/error_reports/plugins/json.py M lib/galaxy/tools/error_reports/plugins/sentry.py

Log Message: ----------- Merge pull request #6909 from nsoranzo/error_reports

Update Bug Reports docs to use YAML syntax

Commit: 47b41d1bb058244bcb06b88a5c612a4371d45e1f https://github.com/galaxyproject/galaxy/commit/47b41d1bb058244bcb06b88a5c612... Author: vahid jalili.vahid@gmail.com Date: 2018-10-23 (Tue, 23 Oct 2018)

Changed paths: M tools/cloud/send.py

Log Message: ----------- Add timestamp, and transfer ET & rate to the Send to cloud tool's log.

Commit: 00632a5295cd705b8a744adcf37c5c083812a059 https://github.com/galaxyproject/galaxy/commit/00632a5295cd705b8a744adcf37c5... Author: Nicola Soranzo nicola.soranzo@earlham.ac.uk Date: 2018-10-24 (Wed, 24 Oct 2018)

Changed paths: M Makefile M scripts/bootstrap_history.py

Log Message: ----------- Fix ``expr: non-integer argument`` error when running ``make``

when `VERSION_MINOR` in `lib/galaxy/version.py` is e.g. `rc1`.

Also: - Do not require awk - Remove unused functions - Do not require the presence of `~/.github.json` file

Commit: 5dfb743ae160f873db670bff26d3ba19d85d4ce9 https://github.com/galaxyproject/galaxy/commit/5dfb743ae160f873db670bff26d3b... Author: Nicola Soranzo nicola.soranzo@earlham.ac.uk Date: 2018-10-24 (Wed, 24 Oct 2018)

Changed paths: M lib/galaxy/tools/parameters/dynamic_options.py

Log Message: ----------- Allow ``remove_value`` filter on data tables

The `RemoveValueFilter.filter_options()` method was expecting `options` to be a list of lists, where each inner list contains exactly 3-elements (name, value, selected), which is the format returned by the `data_meta` filter. In fact, the only known use of the `remove_falue` filter is in the tool `tools/maf/maf_to_interval.xml`, to filter dataset metadata.

This commit generalises the filter to look for a column of the dynamic options named `value`, and use it during the filtering.

Fix https://github.com/galaxyproject/tools-iuc/issues/2151

Commit: 4a82c43270670d4d4cc7bd30e6301c4a3516f48c https://github.com/galaxyproject/galaxy/commit/4a82c43270670d4d4cc7bd30e6301... Author: Nicola Soranzo nicola.soranzo@earlham.ac.uk Date: 2018-10-24 (Wed, 24 Oct 2018)

Changed paths: M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt

Log Message: ----------- make update-dependencies

Commit: b01ff7c2289bbfe7e6e9e543f0a98fd18f9a05f2 https://github.com/galaxyproject/galaxy/commit/b01ff7c2289bbfe7e6e9e543f0a98... Author: vahid jalili.vahid@gmail.com Date: 2018-10-23 (Tue, 23 Oct 2018)

Changed paths: M lib/galaxy/authnz/managers.py

Log Message: ----------- Log cloudauthz exceptions as `info`, not as an `exception`.

Commit: b9771b7ccc417b9e4326151058f0fd221a21ff80 https://github.com/galaxyproject/galaxy/commit/b9771b7ccc417b9e4326151058f0f... Author: vahid jalili.vahid@gmail.com Date: 2018-10-23 (Tue, 23 Oct 2018)

Changed paths: M lib/galaxy/authnz/managers.py

Log Message: ----------- Log entire cloudauthz exception, not just its message.

Commit: 26680e0ca1ace0ad8c857ab712f60d2fc4bf8c1b https://github.com/galaxyproject/galaxy/commit/26680e0ca1ace0ad8c857ab712f60... Author: mvdbeek m.vandenbeek@gmail.com Date: 2018-10-24 (Wed, 24 Oct 2018)

Changed paths: A test/functional/tools/remove_value.xml M test/functional/tools/samples_tool_conf.xml

Log Message: ----------- Add test for remove_value form dynamic options

Unfortunately you can select an invalid value (in the API, not the UI) and Galaxy will replace the invalid value with the first valid value.

Commit: 7c81daa073dea39785144b9228b53b2cd9f6fdbe https://github.com/galaxyproject/galaxy/commit/7c81daa073dea39785144b9228b53... Author: Nicola Soranzo nicola.soranzo@gmail.com Date: 2018-10-24 (Wed, 24 Oct 2018)

Changed paths: M lib/galaxy/tools/parameters/dynamic_options.py

Log Message: ----------- Fix assertion in ``RemoveValueFilter``

Commit: 19c98b27455862e7f50570bbc147a28667182e31 https://github.com/galaxyproject/galaxy/commit/19c98b27455862e7f50570bbc147a... Author: mvdbeek m.vandenbeek@gmail.com Date: 2018-10-24 (Wed, 24 Oct 2018)

Changed paths: M test/functional/tools/remove_value.xml

Log Message: ----------- Fix tests and name tool more appropriately

Commit: 51ca8dc0f5d4cb9ba4221cba5d2067f467087caa https://github.com/galaxyproject/galaxy/commit/51ca8dc0f5d4cb9ba4221cba5d206... Author: Nicola Soranzo nicola.soranzo@earlham.ac.uk Date: 2018-10-24 (Wed, 24 Oct 2018)

Changed paths: M lib/galaxy/jobs/runners/drmaa.py M lib/galaxy/tools/data/__init__.py M lib/galaxy/util/__init__.py M lib/tool_shed/capsule/capsule_manager.py M lib/tool_shed/galaxy_install/tools/data_manager.py M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py M lib/tool_shed/metadata/metadata_generator.py M lib/tool_shed/util/xml_util.py

Log Message: ----------- Merge branch 'release_18.09' into dev

Commit: 949dcfdbc34331de7f0aa321e67e1255a7627306 https://github.com/galaxyproject/galaxy/commit/949dcfdbc34331de7f0aa321e67e1... Author: Nicola Soranzo nicola.soranzo@earlham.ac.uk Date: 2018-10-24 (Wed, 24 Oct 2018)

Changed paths: M lib/galaxy/authnz/managers.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/drmaa.py M lib/galaxy/managers/cloud.py M lib/galaxy/model/migrate/versions/0141_add_oidc_tables.py M lib/galaxy/model/migrate/versions/0142_change_numeric_metric_precision.py M lib/galaxy/model/migrate/versions/0143_add_cloudauthz_tables.py M lib/galaxy/objectstore/cloud.py M lib/galaxy/tools/__init__.py M lib/galaxy/util/pastescript/serve.py M lib/galaxy/webapps/galaxy/api/cloudauthz.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py M lib/tool_shed/util/readme_util.py M scripts/tool_shed/api/reset_metadata_on_repositories.py M test/base/populators.py M tools/data_source/upload.py

Log Message: ----------- Do not log exceptions twice

`logging.exception()` already adds the the exception information after the supplied message.

Also: the `message` attribute of `Exception` class has been dropped in Python 3, always use `str(e)`.

xref. https://github.com/galaxyproject/galaxy/issues/1715

Commit: 014b9d76f76c2eb959266bc271ad0539a1ab0f6d https://github.com/galaxyproject/galaxy/commit/014b9d76f76c2eb959266bc271ad0... Author: Marius van den Beek m.vandenbeek@gmail.com Date: 2018-10-24 (Wed, 24 Oct 2018)

Changed paths: M lib/galaxy/tools/parameters/dynamic_options.py A test/functional/tools/remove_value.xml M test/functional/tools/samples_tool_conf.xml

Log Message: ----------- Merge pull request #6914 from nsoranzo/remove_value

Allow ``remove_value`` filter on data tables

Commit: 2dcd126e82fc6db51c8ab9cacb39abd496504d51 https://github.com/galaxyproject/galaxy/commit/2dcd126e82fc6db51c8ab9cacb39a... Author: Marius van den Beek m.vandenbeek@gmail.com Date: 2018-10-24 (Wed, 24 Oct 2018)

Changed paths: M lib/galaxy/dependencies/pipfiles/default/Pipfile M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt

Log Message: ----------- Merge pull request #6906 from martenson/isa-req

add isa-rwal to default pipfile

Commit: 9d94c0da95c833c49c21537336b62371420eb671 https://github.com/galaxyproject/galaxy/commit/9d94c0da95c833c49c21537336b62... Author: Dannon Baker dannon.baker@gmail.com Date: 2018-10-24 (Wed, 24 Oct 2018)

Changed paths: A client/galaxy/images/light_gray_grid.gif M client/galaxy/style/scss/base.scss R static/images/light_gray_grid.gif M templates/webapps/galaxy/workflow/editor.mako

Log Message: ----------- Stage workflow editor images via webpacked styles (todo is relevant in here, it should be refactored, but I'm taking minimal steps here to get things working correctly)

Commit: b1fe6fee9373f025341e25b248ffa003a10213b3 https://github.com/galaxyproject/galaxy/commit/b1fe6fee9373f025341e25b248ffa... Author: John Chilton jmchilton@gmail.com Date: 2018-10-24 (Wed, 24 Oct 2018)

Changed paths: M lib/galaxy/tools/parameters/history_query.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run.py M test/unit/workflows/test_workflow_progress.py

Log Message: ----------- Refactor collection mapping workflows toward independence from tools.

Refactor get_data_inputs into get_all_inputs and use the resulting dictionaries to reason about if collection mapping should occur during invocation of tools. Using these dictionaries instead of explicit tool input objects should allow reuse within other module types since they may produce the same interface.

Commit: c2a49de6cee056d6cd942e3b392ffbd15961fb42 https://github.com/galaxyproject/galaxy/commit/c2a49de6cee056d6cd942e3b392ff... Author: John Chilton jmchilton@gmail.com Date: 2018-10-24 (Wed, 24 Oct 2018)

Changed paths: M config/datatypes_conf.xml.sample A lib/galaxy/datatypes/converters/tar_to_directory.xml M lib/galaxy/datatypes/data.py M lib/galaxy/tools/__init__.py M test/functional/tools/sample_datatypes_conf.xml M test/integration/test_upload_configuration_options.py

Log Message: ----------- Directory datatype for Galaxy.

Commit: 210cdc998a8f8929362d881bfaded32ac1e45aef https://github.com/galaxyproject/galaxy/commit/210cdc998a8f8929362d881bfaded... Author: Marius van den Beek m.vandenbeek@gmail.com Date: 2018-10-24 (Wed, 24 Oct 2018)

Changed paths: M lib/galaxy/authnz/managers.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/drmaa.py M lib/galaxy/managers/cloud.py M lib/galaxy/model/migrate/versions/0141_add_oidc_tables.py M lib/galaxy/model/migrate/versions/0142_change_numeric_metric_precision.py M lib/galaxy/model/migrate/versions/0143_add_cloudauthz_tables.py M lib/galaxy/objectstore/cloud.py M lib/galaxy/tools/__init__.py M lib/galaxy/util/pastescript/serve.py M lib/galaxy/webapps/galaxy/api/cloudauthz.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py M lib/tool_shed/util/readme_util.py M scripts/tool_shed/api/reset_metadata_on_repositories.py M test/base/populators.py M tools/data_source/upload.py

Log Message: ----------- Merge pull request #6916 from nsoranzo/fix_exception_logging

Do not log exception info twice

Commit: dd6b185ab82b7e251ba7ad3b69abbda7ab4018b9 https://github.com/galaxyproject/galaxy/commit/dd6b185ab82b7e251ba7ad3b69abb... Author: John Chilton jmchilton@gmail.com Date: 2018-10-24 (Wed, 24 Oct 2018)

Changed paths: M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/util/compression_utils.py M test/api/test_tools.py M test/api/test_tools_upload.py M tools/data_source/upload.py M tools/data_source/upload.xml

Log Message: ----------- Implement composite uploads on arbitrary datatypes.

Prior to this, composite uploads were only allowed for select data types. As far as I can tell, the framework itself allows arbitrary datatypes to have extra files. This allows the upload API to take in extra files for datatypes that aren't explicitly annotated has having extra files.

These may be specified one at a time or in directory structures via tar files.

Commit: e3bc005a8602a47e542129b5be53aa6316525e90 https://github.com/galaxyproject/galaxy/commit/e3bc005a8602a47e542129b5be53a... Author: John Chilton jmchilton@gmail.com Date: 2018-10-24 (Wed, 24 Oct 2018)

Changed paths: M lib/galaxy/webapps/galaxy/api/datasets.py M lib/galaxy/webapps/galaxy/buildapp.py M test/api/test_tools.py M test/base/populators.py

Log Message: ----------- Implement API endpoint for indexing extra files in a dataset.

Commit: 1970d2d29c07aa50ef3713307eccd02861d44810 https://github.com/galaxyproject/galaxy/commit/1970d2d29c07aa50ef3713307eccd... Author: Dannon Baker dannon.baker@gmail.com Date: 2018-10-24 (Wed, 24 Oct 2018)

Changed paths: M client/galaxy/scripts/onload.js

Log Message: ----------- Add jquery drop plugin to onload, seems to have been lost along the way.

Commit: 129153a542ea6e4438ddbc1e7137e4c4e60759d8 https://github.com/galaxyproject/galaxy/commit/129153a542ea6e4438ddbc1e7137e... Author: Dannon Baker dannon.baker@gmail.com Date: 2018-10-24 (Wed, 24 Oct 2018)

Changed paths: M client/package.json M client/yarn.lock

Log Message: ----------- Fix problem with rxjs dep listing in yarn.lock, bump webpack (minor)

Commit: 743d3b32f2426b39640d19c6dcd550727a549287 https://github.com/galaxyproject/galaxy/commit/743d3b32f2426b39640d19c6dcd55... Author: Dannon Baker dannon.baker@gmail.com Date: 2018-10-24 (Wed, 24 Oct 2018)

Changed paths: A client/galaxy/images/delete.gif A client/galaxy/images/star.gif R client/galaxy/style/jquery.rating.css M client/galaxy/style/scss/base.scss A client/galaxy/style/scss/jquery.rating.scss R static/images/delete.gif R static/images/star.gif

Log Message: ----------- fix rating styles -- this isn't great, but the loaders just work better this way, calling it scss and customizing it slightly.

Commit: 6a2999e109d79420d261e165e366d16bcbfdf685 https://github.com/galaxyproject/galaxy/commit/6a2999e109d79420d261e165e366d... Author: Dannon Baker dannon.baker@gmail.com Date: 2018-10-24 (Wed, 24 Oct 2018)

Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/polyfills.js M client/galaxy/style/scss/select2.scss M client/galaxy/style/scss/sprite-fugue.scss M client/galaxy/style/scss/sprite-history-buttons.scss M client/galaxy/style/scss/sprite-history-states.scss

Log Message: ----------- Client format.

Commit: 1939154622db826d3e91f6bf51573b2947308181 https://github.com/galaxyproject/galaxy/commit/1939154622db826d3e91f6bf51573... Author: Nicola Soranzo nicola.soranzo@earlham.ac.uk Date: 2018-10-24 (Wed, 24 Oct 2018)

Changed paths: M lib/galaxy/dependencies/pipfiles/default/pinned-dev-requirements.txt M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt M lib/galaxy/dependencies/pipfiles/flake8/pinned-requirements.txt M lib/galaxy/dependencies/pipfiles/update.sh

Log Message: ----------- Update all dependencies

with `make update-dependencies` using pipenv 2018.10.13 .

Also remove `python_version` pin for `monotonic` and `python-dateutil` packages.

Commit: f4203ca051b385a449fec5273b9777de51fd3c6e https://github.com/galaxyproject/galaxy/commit/f4203ca051b385a449fec5273b977... Author: Nicola Soranzo nicola.soranzo@earlham.ac.uk Date: 2018-10-24 (Wed, 24 Oct 2018)

Changed paths: M lib/galaxy/containers/docker.py M lib/galaxy/containers/docker_model.py M lib/galaxy/containers/docker_swarm.py M lib/galaxy/datatypes/assembly.py M lib/galaxy/datatypes/genetics.py M lib/galaxy/datatypes/molecules.py M lib/galaxy/datatypes/proteomics.py M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/text.py M lib/galaxy/datatypes/util/gff_util.py M lib/galaxy/datatypes/xml.py M lib/galaxy/jobs/dynamic_tool_destination.py M lib/galaxy/jobs/handler.py M lib/galaxy/jobs/metrics/instrumenters/env.py M lib/galaxy/jobs/runners/kubernetes.py M lib/galaxy/jobs/runners/util/cli/job/slurm_torque.py M lib/galaxy/managers/collections.py M lib/galaxy/managers/rbac_secured.py M lib/galaxy/managers/sharable.py M lib/galaxy/managers/tags.py M lib/galaxy/model/search.py M lib/galaxy/security/validate_user_input.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/brew_exts.py M lib/galaxy/tools/deps/containers.py M lib/galaxy/tools/deps/views.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/verify/asserts/__init__.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/inflection.py M lib/galaxy/util/json.py M lib/galaxy/visualization/data_providers/genome.py M lib/galaxy/visualization/data_providers/phyloviz/newickparser.py M lib/galaxy/web/base/controller.py M lib/galaxy/web/framework/middleware/batch.py M lib/galaxy/webapps/galaxy/api/uploads.py M lib/galaxy/webapps/galaxy/api/users.py M lib/galaxy/webapps/galaxy/controllers/forms.py M lib/galaxy/webapps/galaxy/controllers/page.py M lib/galaxy/webapps/tool_shed/api/tools.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/galaxy/webapps/tool_shed/controllers/upload.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M lib/tool_shed/util/commit_util.py M lib/tool_shed/util/repository_util.py M scripts/bootstrap_history.py M scripts/check_python.py M scripts/runtime_stats.py M scripts/summarize_timings.py M scripts/tool_shed/bootstrap_tool_shed/create_user_with_api_key.py M scripts/transfer.py M setup.cfg M test/functional/webhooks/phdcomics/__init__.py M test/selenium_tests/test_uploads.py M test/shed_functional/base/twilltestcase.py M test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py M test/unit/web/framework/test_webapp.py M tools/data_source/upload.py M tools/extract/extract_genomic_dna.py M tools/filters/convert_characters.py M tools/filters/grep.py M tools/filters/uniq.py M tools/stats/filtering.py M tools/stats/gsummary.py

Log Message: ----------- Fix errors reported by flake8 3.6.0

Ignore W504.

Commit: 8543231b401bf3eec4d44d63f41c68e7b4ad8e02 https://github.com/galaxyproject/galaxy/commit/8543231b401bf3eec4d44d63f41c6... Author: vahid jalili.vahid@gmail.com Date: 2018-10-24 (Wed, 24 Oct 2018)

Changed paths: M tools/cloud/send.xml

Log Message: ----------- Surround getting cloudauthz cred. in Send tool in a try-catch block.

Commit: 8c95f174ba0d61c9632a03e9bec243509ca63a19 https://github.com/galaxyproject/galaxy/commit/8c95f174ba0d61c9632a03e9bec24... Author: vahid jalili.vahid@gmail.com Date: 2018-10-24 (Wed, 24 Oct 2018)

Changed paths: M tools/cloud/send.py

Log Message: ----------- Fix lint issues.

Commit: 0c8344ee4fda3a54606bb84a23b2e1d24bfcd54e https://github.com/galaxyproject/galaxy/commit/0c8344ee4fda3a54606bb84a23b2e... Author: Dannon Baker dannon.baker@gmail.com Date: 2018-10-25 (Thu, 25 Oct 2018)

Changed paths: A client/galaxy/images/fugue/application-dock-270-bw.png A client/galaxy/images/fugue/application-dock-270.png A client/galaxy/images/fugue/arrow-000-small-bw.png A client/galaxy/images/fugue/arrow-090.png A client/galaxy/images/fugue/arrow-circle.png A client/galaxy/images/fugue/arrow-resize-090-bw.png A client/galaxy/images/fugue/arrow-resize-090.png A client/galaxy/images/fugue/arrow-split-bw.png A client/galaxy/images/fugue/arrow-split.png A client/galaxy/images/fugue/arrow-transition-270-bw.png A client/galaxy/images/fugue/arrow-transition-bw.png A client/galaxy/images/fugue/asterisk-small-outline.png A client/galaxy/images/fugue/asterisk-small-yellow.png A client/galaxy/images/fugue/asterisk-small.png A client/galaxy/images/fugue/block--plus-bw.png A client/galaxy/images/fugue/block--plus.png A client/galaxy/images/fugue/bookmarks-bw.png A client/galaxy/images/fugue/bookmarks.png A client/galaxy/images/fugue/bug.png A client/galaxy/images/fugue/chart.png A client/galaxy/images/fugue/chevron-expand-bw.png A client/galaxy/images/fugue/chevron-expand.png A client/galaxy/images/fugue/chevron.png A client/galaxy/images/fugue/control-270.png A client/galaxy/images/fugue/cross-button.png A client/galaxy/images/fugue/cross-circle-bw.png A client/galaxy/images/fugue/cross-circle.png A client/galaxy/images/fugue/cross-small-bw.png A client/galaxy/images/fugue/cross.png A client/galaxy/images/fugue/disk--arrow-bw.png A client/galaxy/images/fugue/disk--arrow.png A client/galaxy/images/fugue/disk.png A client/galaxy/images/fugue/exclamation.png A client/galaxy/images/fugue/external.png A client/galaxy/images/fugue/eye.png A client/galaxy/images/fugue/gear-bw.png A client/galaxy/images/fugue/gear.png A client/galaxy/images/fugue/globe-bw.png A client/galaxy/images/fugue/globe.png A client/galaxy/images/fugue/hammer-bw.png A client/galaxy/images/fugue/hammer.png A client/galaxy/images/fugue/information-white.png A 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static/images/fugue/application-dock-270.png R static/images/fugue/arrow-000-small-bw.png R static/images/fugue/arrow-090.png R static/images/fugue/arrow-circle.png R static/images/fugue/arrow-resize-090-bw.png R static/images/fugue/arrow-resize-090.png R static/images/fugue/arrow-split-bw.png R static/images/fugue/arrow-split.png R static/images/fugue/arrow-transition-270-bw.png R static/images/fugue/arrow-transition-bw.png R static/images/fugue/asterisk-small-outline.png R static/images/fugue/asterisk-small-yellow.png R static/images/fugue/asterisk-small.png R static/images/fugue/block--plus-bw.png R static/images/fugue/block--plus.png R static/images/fugue/bookmarks-bw.png R static/images/fugue/bookmarks.png R static/images/fugue/bug.png R static/images/fugue/chart.png R static/images/fugue/chevron-expand-bw.png R static/images/fugue/chevron-expand.png R static/images/fugue/chevron.png R static/images/fugue/control-270.png R static/images/fugue/cross-button.png R static/images/fugue/cross-circle-bw.png R static/images/fugue/cross-circle.png R static/images/fugue/cross-small-bw.png R static/images/fugue/cross.png R static/images/fugue/disk--arrow-bw.png R static/images/fugue/disk--arrow.png R static/images/fugue/disk.png R static/images/fugue/exclamation.png R static/images/fugue/external.png R static/images/fugue/eye.png R static/images/fugue/gear-bw.png R static/images/fugue/gear.png R static/images/fugue/globe-bw.png R static/images/fugue/globe.png R static/images/fugue/hammer-bw.png R static/images/fugue/hammer.png R static/images/fugue/information-white.png R static/images/fugue/layer-transparent-bw.png R static/images/fugue/layer-transparent.png R static/images/fugue/layers-stack-bw.png R static/images/fugue/layers-stack.png R static/images/fugue/magnifier-left.png R static/images/fugue/magnifier-zoom-out.png R static/images/fugue/magnifier-zoom.png R static/images/fugue/navigation.png R static/images/fugue/pencil-small.png R static/images/fugue/pencil.png R static/images/fugue/plus-button-bw.png R static/images/fugue/plus-button.png R static/images/fugue/plus-circle.png R static/images/fugue/sticky-note-text.png R static/images/fugue/tag--plus.png R static/images/fugue/tag-label.png R static/images/fugue/tags.png R static/images/fugue/toggle-bw.png R static/images/fugue/toggle-expand-bw.png R static/images/fugue/toggle-expand.png R static/images/fugue/toggle.png R static/images/fugue/toolbox-bw.png R static/images/fugue/toolbox.png R static/images/fugue/ui-slider-050-bw.png R static/images/fugue/ui-slider-050.png R static/images/tipsy.gif A static/images/tracks R static/images/tracks/block.png R static/images/tracks/close_btn.gif R static/images/tracks/diag_bg.gif R static/images/tracks/go_btn.gif R static/images/tracks/handle-left.gif R static/images/tracks/handle-right.gif R static/images/tracks/pan_left.gif R static/images/tracks/pan_right.gif R static/images/tracks/show_history.gif R static/images/tracks/zoom_in.gif R static/images/tracks/zoom_in_full.gif R static/images/tracks/zoom_out.gif R static/images/tracks/zoom_out_full.gif

Log Message: ----------- Stage trackster (and potentially other fugue-consumers, which we should be getting rid of) via webpack.

Commit: a38a0add24a4602fa4ac58e59d9276c85955013d https://github.com/galaxyproject/galaxy/commit/a38a0add24a4602fa4ac58e59d927... Author: Nicola Soranzo nicola.soranzo@earlham.ac.uk Date: 2018-10-25 (Thu, 25 Oct 2018)

Changed paths: M lib/galaxy/datatypes/isa.py

Log Message: ----------- Fix Python3 compatibility for ISA datatype

Follow-up on https://github.com/galaxyproject/galaxy/pull/5787 .

xref. https://github.com/galaxyproject/galaxy/issues/1715

Commit: f7fa5a94ba945d56e916deba84353bcf5b44c746 https://github.com/galaxyproject/galaxy/commit/f7fa5a94ba945d56e916deba84353... Author: Nate Coraor nate@bx.psu.edu Date: 2018-10-25 (Thu, 25 Oct 2018)

Changed paths: M lib/galaxy/jobs/handler.py

Log Message: ----------- Don't mask exceptions during job runner work thread shutdown

Commit: 93b93a789ae51a5478553f062a50d74050c49ef5 https://github.com/galaxyproject/galaxy/commit/93b93a789ae51a5478553f062a50d... Author: Nate Coraor nate@bx.psu.edu Date: 2018-10-25 (Thu, 25 Oct 2018)

Changed paths: M lib/galaxy/jobs/runners/__init__.py

Log Message: ----------- Modify job runner work thread shutdown behavior from "wait at least this long per thread" to "wait at least (but pretty close to) this long for all threads"

Commit: 33c3b74bf56f9c197e4d15cc4cd6f94882fc1240 https://github.com/galaxyproject/galaxy/commit/33c3b74bf56f9c197e4d15cc4cd6f... Author: Nate Coraor nate@bx.psu.edu Date: 2018-10-25 (Thu, 25 Oct 2018)

Changed paths: M config/galaxy.yml.sample M doc/source/admin/galaxy_options.rst M doc/source/admin/scaling.md M lib/galaxy/config.py M lib/galaxy/webapps/galaxy/config_schema.yml

Log Message: ----------- Increase the value of monitor_thread_join_timeout to 30 now that it is the total wait time. Add more documentation about it and the uWSGI and supervisord options that changing it will have an effect upon.

Commit: e7156bdd23a0621b3a98d50687041af2403241f3 https://github.com/galaxyproject/galaxy/commit/e7156bdd23a0621b3a98d50687041... Author: Nate Coraor nate@bx.psu.edu Date: 2018-10-25 (Thu, 25 Oct 2018)

Changed paths: M test/base/driver_util.py

Log Message: ----------- Restore monitor_thread_join_timeout to 5 for tests

Commit: 5076f1d2d198cef9300751183289156a0360299b https://github.com/galaxyproject/galaxy/commit/5076f1d2d198cef93007511832891... Author: Dannon Baker dannon.baker@gmail.com Date: 2018-10-25 (Thu, 25 Oct 2018)

Changed paths: M doc/source/releases/18.09.rst M doc/source/releases/18.09_announce.rst

Log Message: ----------- Merge branch 'release_18.09' into dev

Commit: 56d8c634b02088ecb9d5744254004a7d951c4e5d https://github.com/galaxyproject/galaxy/commit/56d8c634b02088ecb9d5744254004... Author: Dannon Baker dannon.baker@gmail.com Date: 2018-10-25 (Thu, 25 Oct 2018)

Changed paths:

Log Message: ----------- Merge branch 'release_18.09' into dev

Commit: 7c6b184557dcfd052abf1424fc024f77838c4a70 https://github.com/galaxyproject/galaxy/commit/7c6b184557dcfd052abf1424fc024... Author: Nate Coraor nate@bx.psu.edu Date: 2018-10-25 (Thu, 25 Oct 2018)

Changed paths: M config/galaxy.yml.sample M doc/source/admin/galaxy_options.rst M doc/source/admin/scaling.md M lib/galaxy/webapps/galaxy/config_schema.yml

Log Message: ----------- Clarify that maximum job runner worker shutdown time is a multiple of `monitor_thread_join_timeout` based on the configured number of runner plugins.

Commit: ae12cc92eb12cada527cb44dc5c66ae7b355545e https://github.com/galaxyproject/galaxy/commit/ae12cc92eb12cada527cb44dc5c66... Author: Nate Coraor nate@bx.psu.edu Date: 2018-10-25 (Thu, 25 Oct 2018)

Changed paths: M lib/galaxy/jobs/handler.py

Log Message: ----------- Catch all exceptions around runner shutdown so it doesn't prevent other runners from attempting shutdown.

Commit: a6215ea68e4b8accfef5a5cec2133f440fec9fe0 https://github.com/galaxyproject/galaxy/commit/a6215ea68e4b8accfef5a5cec2133... Author: Nate Coraor nate@bx.psu.edu Date: 2018-10-25 (Thu, 25 Oct 2018)

Changed paths: M lib/galaxy/jobs/handler.py

Log Message: ----------- In fixing the incorrect behavior of what was previously in the handler shutdown method, I made the same mistake in a slightly different way.

Commit: d4d659a85191bbf8e7683c8840c716a96c09d85b https://github.com/galaxyproject/galaxy/commit/d4d659a85191bbf8e7683c8840c71... Author: vahid jalili.vahid@gmail.com Date: 2018-10-25 (Thu, 25 Oct 2018)

Changed paths: M tools/cloud/send.xml

Log Message: ----------- Replace the hardcoded msg with the exception msg in the cloud send tool.

Commit: b72e08e8b8f1d5c47aee6bc42a9bb292ff304ab5 https://github.com/galaxyproject/galaxy/commit/b72e08e8b8f1d5c47aee6bc42a9bb... Author: vahid jalili.vahid@gmail.com Date: 2018-10-25 (Thu, 25 Oct 2018)

Changed paths: M client/README.md A client/galaxy/docs/README.md M client/galaxy/docs/bootstrap.md M client/galaxy/docs/galaxy-buttons.md M client/galaxy/docs/galaxy-forms.md M client/galaxy/docs/galaxy-masthead.md M client/galaxy/docs/galaxy-menus.md M client/galaxy/docs/galaxy-messages.md M client/galaxy/docs/galaxy-panels.md M client/galaxy/docs/galaxy-tables.md M client/galaxy/docs/galaxy-tabs.md M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/mvc/ui/ui-rules-edit.js M client/galaxy/scripts/mvc/ui/ui-slider.js M client/galaxy/scripts/ui/editable-text.js M client/galaxy/style/scss/base.scss M client/galaxy/style/scss/history.scss M client/galaxy/style/scss/jstree.scss M client/galaxy/style/scss/list-item.scss M client/galaxy/style/scss/ui.scss A config/container_resolvers_conf.xml.sample M config/datatypes_conf.xml.sample M config/galaxy.yml.sample M config/plugins/interactive_environments/bam_iobio/templates/bam_iobio.mako M config/plugins/interactive_environments/hicbrowser/templates/hicbrowser.mako M config/plugins/interactive_environments/neo/templates/neo.mako M config/plugins/visualizations/scatterplot/package.json M config/plugins/visualizations/scatterplot/src/scatterplot.js M config/plugins/visualizations/scatterplot/static/scatterplot.css M config/plugins/visualizations/scatterplot/static/scatterplot.js M config/plugins/visualizations/scatterplot/templates/scatterplot.mako M doc/source/admin/galaxy_options.rst M doc/source/admin/special_topics/bug_reports.rst M doc/source/admin/special_topics/interactive_environments.rst M doc/source/dev/index.rst M doc/source/dev/interactive_environments.rst A doc/source/releases/18.09.rst A doc/source/releases/18.09_announce.rst A doc/source/releases/19.01_announce.rst M lib/galaxy/authnz/managers.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/data.py A lib/galaxy/datatypes/isa.py M lib/galaxy/datatypes/upload_util.py M lib/galaxy/dependencies/pipfiles/default/Pipfile M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt M lib/galaxy/exceptions/__init__.py M lib/galaxy/exceptions/error_codes.json M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/drmaa.py M lib/galaxy/jobs/runners/util/cli/shell/local.py M lib/galaxy/jobs/runners/util/cli/shell/rsh.py M lib/galaxy/managers/cloud.py M lib/galaxy/managers/context.py M lib/galaxy/model/metadata.py M lib/galaxy/model/migrate/versions/0141_add_oidc_tables.py M lib/galaxy/model/migrate/versions/0142_change_numeric_metric_precision.py M lib/galaxy/model/migrate/versions/0143_add_cloudauthz_tables.py A lib/galaxy/model/migrate/versions/0144_add_cleanup_event_user_table.py M lib/galaxy/objectstore/cloud.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/actions/history_imp_exp.py M lib/galaxy/tools/actions/metadata.py M lib/galaxy/tools/actions/model_operations.py M lib/galaxy/tools/actions/upload.py M lib/galaxy/tools/data/__init__.py M lib/galaxy/tools/error_reports/plugins/biostars.py M lib/galaxy/tools/error_reports/plugins/email.py M lib/galaxy/tools/error_reports/plugins/github.py M lib/galaxy/tools/error_reports/plugins/influxdb.py M lib/galaxy/tools/error_reports/plugins/json.py M lib/galaxy/tools/error_reports/plugins/sentry.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/dynamic_options.py M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/util/__init__.py M lib/galaxy/util/monitors.py M lib/galaxy/util/pastescript/serve.py M lib/galaxy/web/base/controller.py M lib/galaxy/webapps/galaxy/api/cloudauthz.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/config_schema.yml M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/tool_shed/capsule/capsule_manager.py M lib/tool_shed/galaxy_install/tools/data_manager.py M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py M lib/tool_shed/metadata/metadata_generator.py M lib/tool_shed/util/hg_util.py M lib/tool_shed/util/readme_util.py M lib/tool_shed/util/xml_util.py M scripts/bootstrap_history.py M scripts/cleanup_datasets/pgcleanup.py M scripts/tool_shed/api/reset_metadata_on_repositories.py M static/style/blue/base.css A static/style/blue/info_icon.svg M templates/admin/jobs.mako M templates/admin/review_tool_migration_stages.mako M templates/admin/tool_shed_repository/browse_repository.mako M templates/admin/tool_shed_repository/browse_tool_dependency.mako M templates/admin/tool_shed_repository/deactivate_or_uninstall_repository.mako M templates/admin/tool_shed_repository/install_tool_dependencies_with_update.mako M templates/admin/tool_shed_repository/manage_repository.mako M templates/admin/tool_shed_repository/manage_repository_tool_dependencies.mako M templates/admin/tool_shed_repository/monitor_repository_installation.mako M templates/admin/tool_shed_repository/purge_repository_confirmation.mako M templates/admin/tool_shed_repository/reselect_tool_panel_section.mako M templates/admin/tool_shed_repository/reset_metadata_on_selected_repositories.mako M templates/admin/tool_shed_repository/select_tool_panel_section.mako M templates/admin/tool_shed_repository/uninstall_tool_dependencies.mako M templates/admin/tool_shed_repository/view_tool_metadata.mako M templates/admin/tool_shed_repository/view_workflow.mako M templates/message.mako M templates/user/info.mako M templates/user/register.mako M templates/webapps/galaxy/admin/manage_dependencies.mako M templates/webapps/galaxy/admin/sanitize_whitelist.mako M templates/webapps/galaxy/admin/view_display_applications.mako M templates/webapps/galaxy/history/share.mako A test-data/MTBLS6.zip M test/api/test_tools.py M test/api/test_tools_upload.py M test/base/populators.py A test/base/ssh_util.py A test/functional/tools/for_workflows/mapper_two.xml M test/functional/tools/job_environment_default.xml M test/functional/tools/job_environment_default_legacy.xml M test/functional/tools/job_environment_explicit_shared_home.xml A test/functional/tools/remove_value.xml M test/functional/tools/samples_tool_conf.xml M test/galaxy_selenium/navigation.yml A test/integration/test_cli_runners.py M test/integration/test_job_environments.py M test/unit/test_remote_shell.py M test/unit/tools/test_actions.py M tools/data_source/upload.py

Log Message: ----------- Merge and resolve conflicts.

Commit: a236c64ea79ac45ed8bcde67c586f16d92e7e70a https://github.com/galaxyproject/galaxy/commit/a236c64ea79ac45ed8bcde67c586f... Author: vahid jalili.vahid@gmail.com Date: 2018-10-25 (Thu, 25 Oct 2018)

Changed paths: M tools/cloud/send.xml

Log Message: ----------- Repalce "sys.exc_info" with "Exception as e" in cloud Send tool wrapper.

Commit: 79da3e554c946abaaf63804da283570844aa7122 https://github.com/galaxyproject/galaxy/commit/79da3e554c946abaaf63804da2835... Author: Marius van den Beek m.vandenbeek@gmail.com Date: 2018-10-26 (Fri, 26 Oct 2018)

Changed paths: M Makefile M scripts/bootstrap_history.py

Log Message: ----------- Merge pull request #6913 from nsoranzo/bootstrap_fixes

Fix ``expr: non-integer argument`` error when running ``make``

Commit: fc6ae3c35eb83fb0e0ca0fd798481b926a1ea2f7 https://github.com/galaxyproject/galaxy/commit/fc6ae3c35eb83fb0e0ca0fd798481... Author: David Johnson djcomlab@gmail.com Date: 2018-10-26 (Fri, 26 Oct 2018)

Changed paths: M config/datatypes_conf.xml.sample

Log Message: ----------- Add NmrML to sniffers section

Commit: 2be4f3b2a145136aeea49b93482c0ba5c06b2c84 https://github.com/galaxyproject/galaxy/commit/2be4f3b2a145136aeea49b93482c0... Author: Marius van den Beek m.vandenbeek@gmail.com Date: 2018-10-26 (Fri, 26 Oct 2018)

Changed paths: M lib/galaxy/containers/docker.py M lib/galaxy/containers/docker_model.py M lib/galaxy/containers/docker_swarm.py M lib/galaxy/datatypes/assembly.py M lib/galaxy/datatypes/genetics.py M lib/galaxy/datatypes/isa.py M lib/galaxy/datatypes/molecules.py M lib/galaxy/datatypes/proteomics.py M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/text.py M lib/galaxy/datatypes/util/gff_util.py M lib/galaxy/datatypes/xml.py M lib/galaxy/dependencies/pipfiles/default/pinned-dev-requirements.txt M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt M lib/galaxy/dependencies/pipfiles/flake8/pinned-requirements.txt M lib/galaxy/dependencies/pipfiles/update.sh M lib/galaxy/jobs/dynamic_tool_destination.py M lib/galaxy/jobs/handler.py M lib/galaxy/jobs/metrics/instrumenters/env.py M lib/galaxy/jobs/runners/kubernetes.py M lib/galaxy/jobs/runners/util/cli/job/slurm_torque.py M lib/galaxy/managers/collections.py M lib/galaxy/managers/rbac_secured.py M lib/galaxy/managers/sharable.py M lib/galaxy/managers/tags.py M lib/galaxy/model/search.py M lib/galaxy/security/validate_user_input.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/brew_exts.py M lib/galaxy/tools/deps/containers.py M lib/galaxy/tools/deps/views.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/verify/asserts/__init__.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/inflection.py M lib/galaxy/util/json.py M lib/galaxy/visualization/data_providers/genome.py M lib/galaxy/visualization/data_providers/phyloviz/newickparser.py M lib/galaxy/web/base/controller.py M lib/galaxy/web/framework/middleware/batch.py M lib/galaxy/webapps/galaxy/api/uploads.py M lib/galaxy/webapps/galaxy/api/users.py M lib/galaxy/webapps/galaxy/controllers/forms.py M lib/galaxy/webapps/galaxy/controllers/page.py M lib/galaxy/webapps/tool_shed/api/tools.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/galaxy/webapps/tool_shed/controllers/upload.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M lib/tool_shed/util/commit_util.py M lib/tool_shed/util/repository_util.py M scripts/bootstrap_history.py M scripts/check_python.py M scripts/runtime_stats.py M scripts/summarize_timings.py M scripts/tool_shed/bootstrap_tool_shed/create_user_with_api_key.py M scripts/transfer.py M setup.cfg M test/functional/webhooks/phdcomics/__init__.py M test/selenium_tests/test_uploads.py M test/shed_functional/base/twilltestcase.py M test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py M test/unit/web/framework/test_webapp.py M tools/data_source/upload.py M tools/extract/extract_genomic_dna.py M tools/filters/convert_characters.py M tools/filters/grep.py M tools/filters/uniq.py M tools/stats/filtering.py M tools/stats/gsummary.py

Log Message: ----------- Merge pull request #6921 from nsoranzo/dependencies_update

Update all dependencies

Commit: 7b591bc2098f24d52d2c2cb9d5e32f56cc96afda https://github.com/galaxyproject/galaxy/commit/7b591bc2098f24d52d2c2cb9d5e32... Author: David Johnson djcomlab@gmail.com Date: 2018-10-26 (Fri, 26 Oct 2018)

Changed paths: M lib/galaxy/datatypes/proteomics.py

Log Message: ----------- Insert lines to address pep8 problems

Commit: 74bf467f71a45ab2b46b9e45faa0f744c696de4a https://github.com/galaxyproject/galaxy/commit/74bf467f71a45ab2b46b9e45faa0f... Author: Marius van den Beek m.vandenbeek@gmail.com Date: 2018-10-26 (Fri, 26 Oct 2018)

Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/proteomics.py

Log Message: ----------- Merge pull request #6903 from phnmnl/feature/nmrml_data_type

nmrML data type.

Commit: 6e3f731d5cafd3992de34eb52aaa26cb22c7a31e https://github.com/galaxyproject/galaxy/commit/6e3f731d5cafd3992de34eb52aaa2... Author: Marius van den Beek m.vandenbeek@gmail.com Date: 2018-10-26 (Fri, 26 Oct 2018)

Changed paths: M client/galaxy/scripts/mvc/ui/ui-slider.js M client/galaxy/style/scss/base.scss M client/galaxy/style/scss/collection.scss M client/galaxy/style/scss/list-item.scss M static/style/blue/base.css M templates/display_base.mako M templates/ind_share_base.mako M templates/message.mako M templates/webapps/galaxy/history/display.mako M templates/webapps/galaxy/visualization/display.mako M templates/webapps/galaxy/visualization/display_in_frame.mako M templates/webapps/galaxy/workflow/display.mako M templates/webapps/galaxy/workflow/sharing.mako M templates/webapps/tool_shed/repository/common.mako

Log Message: ----------- Merge pull request #6883 from guerler/style_fixes

Align toolshed makos used in the admin panel, fix slider height

Commit: dda297c4089fba323cd0043abafc09da773b7388 https://github.com/galaxyproject/galaxy/commit/dda297c4089fba323cd0043abafc0... Author: Marius van den Beek m.vandenbeek@gmail.com Date: 2018-10-26 (Fri, 26 Oct 2018)

Changed paths: M lib/galaxy/config.py M lib/galaxy/managers/workflows.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/config_schema.yml M run.sh M test/api/test_workflows.py M test/api/test_workflows_from_yaml.py M test/base/driver_util.py M test/base/populators.py M test/base/workflow_fixtures.py

Log Message: ----------- Merge pull request #6776 from jmchilton/gxformat2_integration

Allow API import/export of format 2 workflows.

Commit: 4919805f815ef0e7f780b094ffd6c91f6d54c4b4 https://github.com/galaxyproject/galaxy/commit/4919805f815ef0e7f780b094ffd6c... Author: John Chilton jmchilton@gmail.com Date: 2018-10-26 (Fri, 26 Oct 2018)

Changed paths: M config/galaxy.yml.sample M doc/source/admin/galaxy_options.rst M doc/source/admin/scaling.md M lib/galaxy/config.py M lib/galaxy/jobs/handler.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/webapps/galaxy/config_schema.yml M test/base/driver_util.py

Log Message: ----------- Merge pull request #6924 from natefoo/quiesce-handler

Be more precise with the job runner worker thread join timeout and improve documentation

Commit: 7bbe0e98cd0fdb1c0a952cdb0c6c99e121c1f1e2 https://github.com/galaxyproject/galaxy/commit/7bbe0e98cd0fdb1c0a952cdb0c6c9... Author: John Chilton jmchilton@gmail.com Date: 2018-10-26 (Fri, 26 Oct 2018)

Changed paths: M .ci/jenkins/selenium-py3/run_tests.sh

Log Message: ----------- Allocate more memory for selenium Python 3 client.

Matching Python 2 fix in 4054ffc31165b533cb292c58edafac49b59de9de.

Commit: 7bd7abb5eeb1e3e73effde03498aedc979744939 https://github.com/galaxyproject/galaxy/commit/7bd7abb5eeb1e3e73effde03498ae... Author: John Chilton jmchilton@gmail.com Date: 2018-10-26 (Fri, 26 Oct 2018)

Changed paths: M test/api/test_workflows_from_yaml.py

Log Message: ----------- Fix linting of dev.

Commit: 395778390c692cab247853a82a8d3ebfd6d7edd0 https://github.com/galaxyproject/galaxy/commit/395778390c692cab247853a82a8d3... Author: Martin Cech marten@bx.psu.edu Date: 2018-10-26 (Fri, 26 Oct 2018)

Changed paths: M test/api/test_workflows_from_yaml.py

Log Message: ----------- Merge pull request #6928 from jmchilton/fix_linting_dev

Fix linting of dev.

Commit: 91e2e841f71734f1ad90c1679f5427fb4826336c https://github.com/galaxyproject/galaxy/commit/91e2e841f71734f1ad90c1679f542... Author: Marius van den Beek m.vandenbeek@gmail.com Date: 2018-10-26 (Fri, 26 Oct 2018)

Changed paths: M .ci/jenkins/selenium-py3/run_tests.sh

Log Message: ----------- Merge pull request #6927 from jmchilton/py3_sel_fix

Allocate more memory for selenium Python 3 client.

Commit: 9319ddf989aa33158b5a02e7a80e879e9e1bc10d https://github.com/galaxyproject/galaxy/commit/9319ddf989aa33158b5a02e7a80e8... Author: jra001k jra001k@gmail.com Date: 2018-10-26 (Fri, 26 Oct 2018)

Changed paths: M test/base/populators.py

Log Message: ----------- Rename "Test Dataset".

Rename test dataset from "Test Dataset" to "Test_Dataset" to prevent CWL error below: <-- if not ACCEPTLIST_RE.match(f["basename"]): raise WorkflowException("Invalid filename: '%s' contains illegal characters" % (f["basename"])) ---> This error occur when running the test below: test/api/test_workflows_cwl.py:CwlWorkflowsTestCase.test_simplest_wf

Commit: f0bf1694c54b8cbb06d90e11737c3a7859ffc571 https://github.com/galaxyproject/galaxy/commit/f0bf1694c54b8cbb06d90e11737c3... Author: John Chilton jmchilton@gmail.com Date: 2018-10-26 (Fri, 26 Oct 2018)

Changed paths: M test/base/populators.py

Log Message: ----------- Tweak testing toward being a bit more robust.

Commit: e30460049ff2ab7ec64b703fca590dab88db3ec7 https://github.com/galaxyproject/galaxy/commit/e30460049ff2ab7ec64b703fca590... Author: vahid jalili.vahid@gmail.com Date: 2018-10-28 (Sun, 28 Oct 2018)

Changed paths: M tools/cloud/send.xml

Log Message: ----------- Remove _ and capitalize each work in "overwrite_existing".

Commit: ef70f20a58828b892e6af9b6b7515dbfd8f24e15 https://github.com/galaxyproject/galaxy/commit/ef70f20a58828b892e6af9b6b7515... Author: vahid jalili.vahid@gmail.com Date: 2018-10-28 (Sun, 28 Oct 2018)

Changed paths: M tools/cloud/send.xml

Log Message: ----------- Swap authz_id and bucket; bucket is the first parameter now.

Commit: 6f56ff10b9bc341fdaae879dec281e99fce6b1fc https://github.com/galaxyproject/galaxy/commit/6f56ff10b9bc341fdaae879dec281... Author: vahid jalili.vahid@gmail.com Date: 2018-10-28 (Sun, 28 Oct 2018)

Changed paths: M tools/cloud/send.py

Log Message: ----------- Remove `@` & msec from send tool timestamp.

Commit: 39bdb67273700b0766250241801112a27dbc4b87 https://github.com/galaxyproject/galaxy/commit/39bdb67273700b076625024180111... Author: vahid jalili.vahid@gmail.com Date: 2018-10-28 (Sun, 28 Oct 2018)

Changed paths: M tools/cloud/send.py

Log Message: ----------- Make duplicate object timestamp shorter and use `_` instead of `-`.

Commit: 7433e2640bc87fc76381eb7fcdcf07a1fde4671a https://github.com/galaxyproject/galaxy/commit/7433e2640bc87fc76381eb7fcdcf0... Author: vahid jalili.vahid@gmail.com Date: 2018-10-28 (Sun, 28 Oct 2018)

Changed paths: M tools/cloud/send.xml

Log Message: ----------- Extend the help section and refactor `Authz` to `Cloud Authorization`.

Commit: 2d7e54831944246b327f06f93cfc22343ae5f9c9 https://github.com/galaxyproject/galaxy/commit/2d7e54831944246b327f06f93cfc2... Author: John Chilton jmchilton@gmail.com Date: 2018-10-29 (Mon, 29 Oct 2018)

Changed paths: M test/base/populators.py

Log Message: ----------- Merge pull request #6929 from jmchilton/testing_tweaks

Small testing tweaks from the CWL branch.

Commit: 09e6b1dcde5eb30a76e7487eba9ee75475b29753 https://github.com/galaxyproject/galaxy/commit/09e6b1dcde5eb30a76e7487eba9ee... Author: John Chilton jmchilton@gmail.com Date: 2018-10-29 (Mon, 29 Oct 2018)

Changed paths: M test/base/populators.py

Log Message: ----------- Eliminate some mutable defaults in populators.py.

Commit: f1a3a44b444d9914a97d26a0b0f5667efc211ac5 https://github.com/galaxyproject/galaxy/commit/f1a3a44b444d9914a97d26a0b0f56... Author: M Bernt m.bernt@ufz.de Date: 2018-10-29 (Mon, 29 Oct 2018)

Changed paths: M lib/galaxy/tools/verify/interactor.py

Log Message: ----------- galaxy test needs to count data sets and collection outputs

Commit: 1ec18484df22ec0d226415a6aa9379bb176fe329 https://github.com/galaxyproject/galaxy/commit/1ec18484df22ec0d226415a6aa937... Author: M Bernt m.bernt@ufz.de Date: 2018-10-29 (Mon, 29 Oct 2018)

Changed paths: M test/functional/tools/output_filter.xml

Log Message: ----------- added test

Commit: 6f6fffe9134e7becfd698340899a96c1cbd8a4fe https://github.com/galaxyproject/galaxy/commit/6f6fffe9134e7becfd698340899a9... Author: Dannon Baker dannon.baker@gmail.com Date: 2018-10-29 (Mon, 29 Oct 2018)

Changed paths: M doc/source/releases/18.09.rst M doc/source/releases/index.rst M lib/galaxy/webapps/tool_shed/api/tools.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/tool_shed/tools/tool_validator.py M lib/tool_shed/util/workflow_util.py

Log Message: ----------- Merge remote-tracking branch 'upstream/release_18.09' into dev

Commit: 30ac5d90d937a28dc61aef5d4a6b6cb05c1a05bf https://github.com/galaxyproject/galaxy/commit/30ac5d90d937a28dc61aef5d4a6b6... Author: Dannon Baker dannon.baker@gmail.com Date: 2018-10-29 (Mon, 29 Oct 2018)

Changed paths: M scripts/bootstrap_history.py

Log Message: ----------- Release scaffold tweaks.

Commit: 66b05cbfc591a5de2d5d248c1f060a67ff369c44 https://github.com/galaxyproject/galaxy/commit/66b05cbfc591a5de2d5d248c1f060... Author: Dannon Baker dannon.baker@gmail.com Date: 2018-10-29 (Mon, 29 Oct 2018)

Changed paths: M scripts/bootstrap_history.py

Log Message: ----------- Minor clarification

Commit: 5d51492a538dddb5eb5c45dc117f090104f70652 https://github.com/galaxyproject/galaxy/commit/5d51492a538dddb5eb5c45dc117f0... Author: Dannon Baker dannon.baker@gmail.com Date: 2018-10-29 (Mon, 29 Oct 2018)

Changed paths: M scripts/bootstrap_history.py

Log Message: ----------- Getgalaxy links

Commit: 2fb4ea1e689e03a44712fd18942d86717e773e36 https://github.com/galaxyproject/galaxy/commit/2fb4ea1e689e03a44712fd18942d8... Author: Martin Cech marten@bx.psu.edu Date: 2018-10-29 (Mon, 29 Oct 2018)

Changed paths: M scripts/bootstrap_history.py

Log Message: ----------- Merge pull request #6935 from dannon/release-scaffold-tweaks

Release issue scaffold tweaks.

Commit: c3dfdb0dc73bbc5339e285500dcaf345e5c67d60 https://github.com/galaxyproject/galaxy/commit/c3dfdb0dc73bbc5339e285500dcaf... Author: Nate Coraor nate@bx.psu.edu Date: 2018-10-29 (Mon, 29 Oct 2018)

Changed paths: M config/migrated_tools_conf.xml.sample M config/shed_tool_conf.xml.sample M doc/source/admin/tool_panel.rst M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/tool_shed/galaxy_install/migrate/check.py M lib/tool_shed/util/common_util.py

Log Message: ----------- Default shed tool installation to database/shed_tools instead of ../shed_tools

Commit: adc62f6ba7d8f6ef462cc42c914743044ed9d2ee https://github.com/galaxyproject/galaxy/commit/adc62f6ba7d8f6ef462cc42c91474... Author: Martin Cech marten@bx.psu.edu Date: 2018-10-29 (Mon, 29 Oct 2018)

Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/molecules.py A lib/galaxy/datatypes/test/5e5z.pqr

Log Message: ----------- Merge pull request #6816 from jj-umn/datatype_pqr

Datatype pqr

Commit: a71db8384cc512efd95c4ac89695d1584899874f https://github.com/galaxyproject/galaxy/commit/a71db8384cc512efd95c4ac89695d... Author: vahid jalili.vahid@gmail.com Date: 2018-10-29 (Mon, 29 Oct 2018)

Changed paths: M lib/galaxy/managers/cloud.py

Log Message: ----------- Raise an exception in cloud get/send managers if OIDC is not enabled.

Commit: e89773a20d5c3f18fd9b4766c1c7deb6485e88da https://github.com/galaxyproject/galaxy/commit/e89773a20d5c3f18fd9b4766c1c7d... Author: Martin Cech marten@bx.psu.edu Date: 2018-10-29 (Mon, 29 Oct 2018)

Changed paths: M lib/galaxy/tools/verify/interactor.py M test/functional/tools/output_filter.xml

Log Message: ----------- Merge pull request #6931 from bernt-matthias/topic/test-colouts

tests need to count data sets and collections

Commit: 43e5a1828d2ba1ed11b7a5c7321fe075f06b9c0b https://github.com/galaxyproject/galaxy/commit/43e5a1828d2ba1ed11b7a5c7321fe... Author: vahid jalili.vahid@gmail.com Date: 2018-10-29 (Mon, 29 Oct 2018)

Changed paths: M tools/cloud/send.py

Log Message: ----------- In Cloud send tool: surround error raising blocks of code in try-catch.

Commit: c5916912093ffaca57281db486c263108f263e88 https://github.com/galaxyproject/galaxy/commit/c5916912093ffaca57281db486c26... Author: Nicola Soranzo nicola.soranzo@earlham.ac.uk Date: 2018-10-29 (Mon, 29 Oct 2018)

Changed paths: M scripts/bootstrap_history.py

Log Message: ----------- Fix typos in ``scripts/bootstrap_history.py``

Commit: a4abbb1d8a244e260412df8551f9f3d0f25f78c7 https://github.com/galaxyproject/galaxy/commit/a4abbb1d8a244e260412df8551f9f... Author: Nicola Soranzo nicola.soranzo@earlham.ac.uk Date: 2018-10-29 (Mon, 29 Oct 2018)

Changed paths: M lib/galaxy/datatypes/molecules.py

Log Message: ----------- Fix flake8 errors introduced in #6816

Commit: d41837cd9ccde259941c8b643ebf1c38ebed871b https://github.com/galaxyproject/galaxy/commit/d41837cd9ccde259941c8b643ebf1... Author: Dannon dannon.baker@gmail.com Date: 2018-10-29 (Mon, 29 Oct 2018)

Changed paths: M test/base/populators.py

Log Message: ----------- Merge pull request #6933 from jmchilton/mutable_default

Eliminate some mutable defaults in populators.py.

Commit: 8e8ff78b459c68c4b54c0c722ed5619f9d117c62 https://github.com/galaxyproject/galaxy/commit/8e8ff78b459c68c4b54c0c722ed56... Author: Dannon dannon.baker@gmail.com Date: 2018-10-29 (Mon, 29 Oct 2018)

Changed paths: M lib/galaxy/datatypes/molecules.py M scripts/bootstrap_history.py

Log Message: ----------- Merge pull request #6941 from nsoranzo/bootstrap_history_typos

Fix typos in ``scripts/bootstrap_history.py``

Commit: 734c39d4f58cfc96c637d9121b88b14398a9c4b2 https://github.com/galaxyproject/galaxy/commit/734c39d4f58cfc96c637d9121b88b... Author: Mason nerdinacan@gmail.com Date: 2018-10-29 (Mon, 29 Oct 2018)

Changed paths: M .gitignore A client/galaxy/jsconfig.json M client/galaxy/scripts/galaxy.js A client/galaxy/scripts/galaxy.monitor.js R client/galaxy/scripts/onload.js A client/galaxy/scripts/onload/index.js A client/galaxy/scripts/onload/loadConfig.js A client/galaxy/scripts/utils/installMonitor.js A client/galaxy/scripts/utils/mock.js A client/galaxy/scripts/utils/serverPath.js M client/webpack.config.js M test/galaxy_selenium/navigates_galaxy.py

Log Message: ----------- added global monitor for window.Galaxy

Commit: 0cdf78956f29abf53e9e2233a6545dc1fba71f5c https://github.com/galaxyproject/galaxy/commit/0cdf78956f29abf53e9e2233a6545... Author: Mason nerdinacan@gmail.com Date: 2018-10-29 (Mon, 29 Oct 2018)

Changed paths: M client/galaxy/scripts/onload/loadConfig.js M client/galaxy/scripts/utils/installMonitor.js

Log Message: ----------- Corrected instructions, removed config function that is not used yet.

Commit: 712aa6cb8742674777c4bc0ee36df9f361bfbeab https://github.com/galaxyproject/galaxy/commit/712aa6cb8742674777c4bc0ee36df... Author: Mason nerdinacan@gmail.com Date: 2018-10-29 (Mon, 29 Oct 2018)

Changed paths: M client/galaxy/scripts/utils/installMonitor.js

Log Message: ----------- Removed debugger statements

Commit: 4c13d204c454203b17194c6174177de642c0a2ae https://github.com/galaxyproject/galaxy/commit/4c13d204c454203b17194c6174177... Author: Mason nerdinacan@gmail.com Date: 2018-10-29 (Mon, 29 Oct 2018)

Changed paths: M client/galaxy/scripts/utils/installMonitor.js

Log Message: ----------- Corrected monitor value storage initialization

Commit: ef5e01da82e532a819a343457ea31bf0cb16baa7 https://github.com/galaxyproject/galaxy/commit/ef5e01da82e532a819a343457ea31... Author: Mason nerdinacan@gmail.com Date: 2018-10-29 (Mon, 29 Oct 2018)

Changed paths: M test/galaxy_selenium/navigates_galaxy.py

Log Message: ----------- White space awesomeness

Commit: 3cf9dd85f4c20801807d0aef74b4628c26ca3f97 https://github.com/galaxyproject/galaxy/commit/3cf9dd85f4c20801807d0aef74b46... Author: Mason nerdinacan@gmail.com Date: 2018-10-29 (Mon, 29 Oct 2018)

Changed paths: M client/.babelrc M client/galaxy/scripts/polyfills.js M client/package.json M client/yarn.lock

Log Message: ----------- Updating babel for proxy support with karma

Commit: 9a24338d12001cdcea336703ce41ac4032c275b8 https://github.com/galaxyproject/galaxy/commit/9a24338d12001cdcea336703ce41a... Author: mvdbeek m.vandenbeek@gmail.com Date: 2018-10-30 (Tue, 30 Oct 2018)

Changed paths: M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/sniff.py R lib/galaxy/datatypes/test/1.vcf.gz A lib/galaxy/datatypes/test/1.vcf_bgzip R lib/galaxy/datatypes/test/Acanium.hmm A lib/galaxy/datatypes/test/Acanium.snaphmm R lib/galaxy/datatypes/test/biom2_sparse_otu_table_hdf5.biom A lib/galaxy/datatypes/test/biom2_sparse_otu_table_hdf5.biom2 R lib/galaxy/datatypes/test/test.CEL A lib/galaxy/datatypes/test/test.cel R lib/galaxy/datatypes/test/test.idpDB A lib/galaxy/datatypes/test/test.idpdb R lib/galaxy/datatypes/test/test_ensembl.tab A lib/galaxy/datatypes/test/test_ensembl.tabular A test/integration/test_datatype_upload.py M test/unit/datatypes/test_vcf.py

Log Message: ----------- Name datatype test files according to datatype extension

Commit: b2276319d409c7d88bf3af7ff0cfa8cd4df2ab98 https://github.com/galaxyproject/galaxy/commit/b2276319d409c7d88bf3af7ff0cfa... Author: mvdbeek m.vandenbeek@gmail.com Date: 2018-10-30 (Tue, 30 Oct 2018)

Changed paths: M lib/galaxy/datatypes/binary.py

Log Message: ----------- Change more biom2 instances

Commit: 7ce69df57c7a2bb6e7c34108a8e2e0b67487cd5d https://github.com/galaxyproject/galaxy/commit/7ce69df57c7a2bb6e7c34108a8e2e... Author: mvdbeek m.vandenbeek@gmail.com Date: 2018-10-30 (Tue, 30 Oct 2018)

Changed paths: M test/integration/test_datatype_upload.py

Log Message: ----------- Add integration test for uploading datasets of known datatype

We upload everything in lib/galaxy/datatypes/test and make sure that we get the correct datatype. For datatypes that have a sniffer we use `auto`, otherwise we set the correct datatype.

This is fairly basic for now, but it would be trivial to extend this to also verify file integrity and metadata elements as well as testing options that affect uploads, like `auto_decompress` settings.

Commit: f2d8218a5366f25601dac8342601c02a74ca6f22 https://github.com/galaxyproject/galaxy/commit/f2d8218a5366f25601dac8342601c... Author: mvdbeek m.vandenbeek@gmail.com Date: 2018-10-30 (Tue, 30 Oct 2018)

Changed paths: M lib/galaxy/datatypes/binary.py

Log Message: ----------- Fix uncompressed bcf

This actually also fails, but at least doesn't crash the interpreter.

Commit: 63eb6a145c9683651532fc7afaded7a5d930743a https://github.com/galaxyproject/galaxy/commit/63eb6a145c9683651532fc7afaded... Author: mvdbeek m.vandenbeek@gmail.com Date: 2018-10-30 (Tue, 30 Oct 2018)

Changed paths: M lib/galaxy/datatypes/sequence.py

Log Message: ----------- Tighten up memepsp sniffer

Values need to be floats, but float("1") also doesn't raise an exception. This prevents 454qual files to be sniffed as memepsp.

Commit: f7773c39b1fb7d9ac31115b69c60f5f487e40a13 https://github.com/galaxyproject/galaxy/commit/f7773c39b1fb7d9ac31115b69c60f... Author: mvdbeek m.vandenbeek@gmail.com Date: 2018-10-30 (Tue, 30 Oct 2018)

Changed paths: M lib/galaxy/datatypes/blast.py A lib/galaxy/datatypes/test/tblastn_four_human_vs_rhodopsin.blastxml R lib/galaxy/datatypes/test/tblastn_four_human_vs_rhodopsin.xml

Log Message: ----------- Move tblastn_four_human_vs_rhodopsin.xml to tblastn_four_human_vs_rhodopsin.blastxml

Commit: 38e18c9daff58a02f1da0be23329ec9ec5d4cbe7 https://github.com/galaxyproject/galaxy/commit/38e18c9daff58a02f1da0be23329e... Author: mvdbeek m.vandenbeek@gmail.com Date: 2018-10-30 (Tue, 30 Oct 2018)

Changed paths: M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/sniff.py A lib/galaxy/datatypes/test/gff.gff3 R lib/galaxy/datatypes/test/gff_version_3.gff

Log Message: ----------- Rename gff3 test file

Commit: 3529295d5512bee68e7981d036147b18a518fc6c https://github.com/galaxyproject/galaxy/commit/3529295d5512bee68e7981d036147... Author: mvdbeek m.vandenbeek@gmail.com Date: 2018-10-30 (Tue, 30 Oct 2018)

Changed paths: R lib/galaxy/datatypes/test/sequence.qual

Log Message: ----------- Delete unused test file

Commit: bc0a3c5244181a5b6af2a4d394a0d4375ceff453 https://github.com/galaxyproject/galaxy/commit/bc0a3c5244181a5b6af2a4d394a0d... Author: mvdbeek m.vandenbeek@gmail.com Date: 2018-10-30 (Tue, 30 Oct 2018)

Changed paths: M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/sniff.py A lib/galaxy/datatypes/test/interv1.bed R lib/galaxy/datatypes/test/interval1.bed

Log Message: ----------- Rename interval1.bed to interv1.bed

Otherwise guess_datatype would expect interval as the datatype.

Commit: 81155c635a38eb0ad1201f92bb70fbdf9faf170b https://github.com/galaxyproject/galaxy/commit/81155c635a38eb0ad1201f92bb70f... Author: mvdbeek m.vandenbeek@gmail.com Date: 2018-10-30 (Tue, 30 Oct 2018)

Changed paths: R lib/galaxy/datatypes/test/2.shuffled.bam A lib/galaxy/datatypes/test/2.shuffled.unsorted.bam M test/unit/datatypes/test_bam.py

Log Message: ----------- Rename 2.shuffled.bam to 2.shuffled.unsorted.bam

Commit: a151b63a622424c1f5f21f97169121b4c7bcc5d5 https://github.com/galaxyproject/galaxy/commit/a151b63a622424c1f5f21f9716912... Author: mvdbeek m.vandenbeek@gmail.com Date: 2018-10-30 (Tue, 30 Oct 2018)

Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/sequence.py R lib/galaxy/datatypes/test/2.fastqsanger A lib/galaxy/datatypes/test/3.fastq

Log Message: ----------- Tighten up fastq sniffers significantly

This requires the sequence regex to match over the entire sequence, which precludes fastqcssanger files to be sniffed as fastqsanger (fixes https://github.com/galaxyproject/galaxy/issues/6734). Further adds a sniffer for FastqCSSanger, which contains numbers in the sequence and so shouldn't interfere with the other fastq datatypes.

Commit: b74f225f189688ea885ea6b52bf0f36367cd8d03 https://github.com/galaxyproject/galaxy/commit/b74f225f189688ea885ea6b52bf0f... Author: mvdbeek m.vandenbeek@gmail.com Date: 2018-10-30 (Tue, 30 Oct 2018)

Changed paths: M test/integration/test_datatype_upload.py

Log Message: ----------- Map fastqsolex to fastq datatype in integration test

Commit: 720386999828150ed3b639c3600f491e75c7217b https://github.com/galaxyproject/galaxy/commit/720386999828150ed3b639c3600f4... Author: mvdbeek m.vandenbeek@gmail.com Date: 2018-10-30 (Tue, 30 Oct 2018)

Changed paths: M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/test/1.bcf_uncompressed

Log Message: ----------- Drop index file for bcf_uncompressed

Even `bcftools index` complains that the file is not compressed. I think this is just not supported.

Commit: 85a47ccc47b6f3504360e9f4a0486cefe3f6faa8 https://github.com/galaxyproject/galaxy/commit/85a47ccc47b6f3504360e9f4a0486... Author: mvdbeek m.vandenbeek@gmail.com Date: 2018-10-30 (Tue, 30 Oct 2018)

Changed paths: M lib/galaxy/datatypes/sequence.py

Log Message: ----------- Fix totally broken memepsp sniffer

The sniffer could never reach 100 sniffed lines, and the test file contains an empty line, so the comment and code that says that empty lines are not valid is wrong, but was never called.

Commit: 48bdc97fce177c5f867cd31e3600ad5670a6c958 https://github.com/galaxyproject/galaxy/commit/48bdc97fce177c5f867cd31e3600a... Author: mvdbeek m.vandenbeek@gmail.com Date: 2018-10-30 (Tue, 30 Oct 2018)

Changed paths: M test/base/populators.py M test/integration/test_datatype_upload.py

Log Message: ----------- Verify state of uploaded datasets and download datasets to verify that the file is intact after upload

Commit: be939310fbd4736eaaf8e3ecb00081e7fc080463 https://github.com/galaxyproject/galaxy/commit/be939310fbd4736eaaf8e3ecb0008... Author: mvdbeek m.vandenbeek@gmail.com Date: 2018-10-30 (Tue, 30 Oct 2018)

Changed paths: A lib/galaxy/datatypes/test/1.fastqcssanger

Log Message: ----------- Add a fastqcssanger test file

Commit: 7b955277566a8cb647b1a689cf1c0d18fba274f2 https://github.com/galaxyproject/galaxy/commit/7b955277566a8cb647b1a689cf1c0... Author: mvdbeek m.vandenbeek@gmail.com Date: 2018-10-30 (Tue, 30 Oct 2018)

Changed paths: M lib/galaxy/datatypes/sniff.py

Log Message: ----------- Missed one idpDB instance

Commit: dd6a4bb2f33e39889577e9a0b60a6314355eab6b https://github.com/galaxyproject/galaxy/commit/dd6a4bb2f33e39889577e9a0b60a6... Author: mvdbeek m.vandenbeek@gmail.com Date: 2018-10-30 (Tue, 30 Oct 2018)

Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/tabular.py A lib/galaxy/datatypes/test/1.excel.xls R lib/galaxy/datatypes/test/1.xls

Log Message: ----------- Move xls file to excel.xls and change xls to be excel.xls

Commit: d80e4bd0a13dc5996c35cd5ecbca9c4439e5e2a1 https://github.com/galaxyproject/galaxy/commit/d80e4bd0a13dc5996c35cd5ecbca9... Author: mvdbeek m.vandenbeek@gmail.com Date: 2018-10-30 (Tue, 30 Oct 2018)

Changed paths: M test/base/populators.py M test/integration/test_datatype_upload.py

Log Message: ----------- Fix test logic

Commit: e01e6ba2bdcf557668995f402812ff8b93474134 https://github.com/galaxyproject/galaxy/commit/e01e6ba2bdcf557668995f402812f... Author: mvdbeek m.vandenbeek@gmail.com Date: 2018-10-30 (Tue, 30 Oct 2018)

Changed paths: M lib/galaxy/datatypes/test/1.afg M lib/galaxy/datatypes/test/1.fastq M lib/galaxy/datatypes/test/1.fastqsanger M lib/galaxy/datatypes/test/1.fastqsolexa M lib/galaxy/datatypes/test/1.owl M lib/galaxy/datatypes/test/1.stockholm M lib/galaxy/datatypes/test/2.fastq M lib/galaxy/datatypes/test/2.fastqsolexa M lib/galaxy/datatypes/test/2.txt M lib/galaxy/datatypes/test/3.fastq M lib/galaxy/datatypes/test/3.txt M lib/galaxy/datatypes/test/454Score.pdf M lib/galaxy/datatypes/test/alignment.lav M lib/galaxy/datatypes/test/interv1.bed M lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.filter M lib/galaxy/datatypes/test/sequence.qual454 M lib/galaxy/datatypes/test/sequence.qualsolid M lib/galaxy/datatypes/test/test_tab.bed M lib/galaxy/datatypes/test/ucsc.customtrack M lib/galaxy/datatypes/test/wiggle.wig

Log Message: ----------- Fix up various test datasets

Commit: ec193d929fd81b8f0438c097ebbb3aa3fb55e224 https://github.com/galaxyproject/galaxy/commit/ec193d929fd81b8f0438c097ebbb3... Author: mvdbeek m.vandenbeek@gmail.com Date: 2018-10-30 (Tue, 30 Oct 2018)

Changed paths: M lib/galaxy/datatypes/sequence.py

Log Message: ----------- Fix minor typo

Commit: d3cd57e29975b66ca3883b6e8dfb63839a49aaee https://github.com/galaxyproject/galaxy/commit/d3cd57e29975b66ca3883b6e8dfb6... Author: mvdbeek m.vandenbeek@gmail.com Date: 2018-10-30 (Tue, 30 Oct 2018)

Changed paths: M lib/galaxy/model/custom_types.py

Log Message: ----------- Safe JSON encoding of MetadataParameters, JSONType

This fixes a couple of upload tests on python 3 (loom, Biom2).

Commit: 09601ad4efdd877375dfda3e62e2657899101ae2 https://github.com/galaxyproject/galaxy/commit/09601ad4efdd877375dfda3e62e26... Author: mvdbeek m.vandenbeek@gmail.com Date: 2018-10-30 (Tue, 30 Oct 2018)

Changed paths: M lib/galaxy/datatypes/sniff.py

Log Message: ----------- Skip newlines/space2tab conversion for binary datatypes that fail is_binary check

Commit: d168042b366dcdbacabfabe692f120e9118a2de9 https://github.com/galaxyproject/galaxy/commit/d168042b366dcdbacabfabe692f12... Author: mvdbeek m.vandenbeek@gmail.com Date: 2018-10-30 (Tue, 30 Oct 2018)

Changed paths: M lib/galaxy/datatypes/sniff.py

Log Message: ----------- Fix newline conversion on python 3 if no encoding is set

Commit: 738bde01278c50a62f4d97c7afc6e4f8b919254f https://github.com/galaxyproject/galaxy/commit/738bde01278c50a62f4d97c7afc6e... Author: mvdbeek m.vandenbeek@gmail.com Date: 2018-10-30 (Tue, 30 Oct 2018)

Changed paths: M lib/galaxy/util/checkers.py

Log Message: ----------- Fix check_html on python 3

We can open the file in binary mode and then use unicodify on the lines, as we have to do that anyway if `chunks` is provided. Also adds the unicode flag to re.compile.

Commit: 1a407429ba7ffe1476317c5ac0f5b1ad19f1e0d7 https://github.com/galaxyproject/galaxy/commit/1a407429ba7ffe1476317c5ac0f5b... Author: mvdbeek m.vandenbeek@gmail.com Date: 2018-10-30 (Tue, 30 Oct 2018)

Changed paths: M lib/galaxy/datatypes/mothur.py M lib/galaxy/datatypes/phylip.py

Log Message: ----------- Tighten up mothur and phylip sniffers

Commit: c50a0fccace2d94565ba85f0703e516139132b4b https://github.com/galaxyproject/galaxy/commit/c50a0fccace2d94565ba85f0703e5... Author: mvdbeek m.vandenbeek@gmail.com Date: 2018-10-30 (Tue, 30 Oct 2018)

Changed paths: M lib/galaxy/datatypes/text.py

Log Message: ----------- Don't sniff simple json types

These should instead be text.

Commit: 0fae117e672e626cc7093d0169dae241c4f54128 https://github.com/galaxyproject/galaxy/commit/0fae117e672e626cc7093d0169dae... Author: mvdbeek m.vandenbeek@gmail.com Date: 2018-10-30 (Tue, 30 Oct 2018)

Changed paths: M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py

Log Message: ----------- Use raw strings in regex and allow lowercase fastq sequences

Commit: ecc02bb659ce89e78b1a5aeb49dd020280864617 https://github.com/galaxyproject/galaxy/commit/ecc02bb659ce89e78b1a5aeb49dd0... Author: mvdbeek m.vandenbeek@gmail.com Date: 2018-10-30 (Tue, 30 Oct 2018)

Changed paths: M lib/galaxy/datatypes/upload_util.py

Log Message: ----------- Fix UploadProblemException

Commit: ba5d76eb934598227102ae1cb0ff4e89e0ab0b9c https://github.com/galaxyproject/galaxy/commit/ba5d76eb934598227102ae1cb0ff4... Author: mvdbeek m.vandenbeek@gmail.com Date: 2018-10-30 (Tue, 30 Oct 2018)

Changed paths: M lib/galaxy/datatypes/sequence.py

Log Message: ----------- Avoid exception if no match

This fixes the sniffing unit test, the datatype framework would just continue anyway.

Commit: 16962ad6a16c5b5dcc5b3d06921d2c4c89c6d9d0 https://github.com/galaxyproject/galaxy/commit/16962ad6a16c5b5dcc5b3d06921d2... Author: mvdbeek m.vandenbeek@gmail.com Date: 2018-10-30 (Tue, 30 Oct 2018)

Changed paths: M lib/galaxy/datatypes/test/5e5z.pqr

Log Message: ----------- Add newline to lib/galaxy/datatypes/test/5e5z.pqr

Commit: 0de9c738cf8cb11b814d1d758268f0bcf9b71652 https://github.com/galaxyproject/galaxy/commit/0de9c738cf8cb11b814d1d758268f... Author: Marius van den Beek m.vandenbeek@gmail.com Date: 2018-10-30 (Tue, 30 Oct 2018)

Changed paths: M client/galaxy/style/scss/base.scss M static/style/blue/base.css M static/welcome.html.sample

Log Message: ----------- Merge pull request #6833 from martenson/tinies

adjust the panel resize cursor, update docs link

Commit: a1b7105b389e8a7b8f9ed9aab630c8b543825da4 https://github.com/galaxyproject/galaxy/commit/a1b7105b389e8a7b8f9ed9aab630c... Author: Saskia Hiltemann zazkia@gmail.com Date: 2018-10-30 (Tue, 30 Oct 2018)

Changed paths: M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js

Log Message: ----------- add option to strip url prefix from pair names

Commit: 9713556b16acb3e4218fc9e28463cdaba654a0c5 https://github.com/galaxyproject/galaxy/commit/9713556b16acb3e4218fc9e28463c... Author: John Chilton jmchilton@gmail.com Date: 2018-10-30 (Tue, 30 Oct 2018)

Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/blast.py M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/mothur.py M lib/galaxy/datatypes/phylip.py M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/test/1.afg M lib/galaxy/datatypes/test/1.bcf_uncompressed A lib/galaxy/datatypes/test/1.excel.xls M lib/galaxy/datatypes/test/1.fastq A lib/galaxy/datatypes/test/1.fastqcssanger M lib/galaxy/datatypes/test/1.fastqsanger M lib/galaxy/datatypes/test/1.fastqsolexa M lib/galaxy/datatypes/test/1.owl M lib/galaxy/datatypes/test/1.stockholm R lib/galaxy/datatypes/test/1.vcf.gz A lib/galaxy/datatypes/test/1.vcf_bgzip R lib/galaxy/datatypes/test/1.xls M lib/galaxy/datatypes/test/2.fastq R lib/galaxy/datatypes/test/2.fastqsanger M lib/galaxy/datatypes/test/2.fastqsolexa R lib/galaxy/datatypes/test/2.shuffled.bam A lib/galaxy/datatypes/test/2.shuffled.unsorted.bam M lib/galaxy/datatypes/test/2.txt A lib/galaxy/datatypes/test/3.fastq M lib/galaxy/datatypes/test/3.txt M lib/galaxy/datatypes/test/454Score.pdf M lib/galaxy/datatypes/test/5e5z.pqr R lib/galaxy/datatypes/test/Acanium.hmm A lib/galaxy/datatypes/test/Acanium.snaphmm M lib/galaxy/datatypes/test/alignment.lav R lib/galaxy/datatypes/test/biom2_sparse_otu_table_hdf5.biom A lib/galaxy/datatypes/test/biom2_sparse_otu_table_hdf5.biom2 A lib/galaxy/datatypes/test/gff.gff3 R lib/galaxy/datatypes/test/gff_version_3.gff A lib/galaxy/datatypes/test/interv1.bed R lib/galaxy/datatypes/test/interval1.bed M lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.filter R lib/galaxy/datatypes/test/sequence.qual M lib/galaxy/datatypes/test/sequence.qual454 M lib/galaxy/datatypes/test/sequence.qualsolid A lib/galaxy/datatypes/test/tblastn_four_human_vs_rhodopsin.blastxml R lib/galaxy/datatypes/test/tblastn_four_human_vs_rhodopsin.xml R lib/galaxy/datatypes/test/test.CEL A lib/galaxy/datatypes/test/test.cel R lib/galaxy/datatypes/test/test.idpDB A lib/galaxy/datatypes/test/test.idpdb R lib/galaxy/datatypes/test/test_ensembl.tab A lib/galaxy/datatypes/test/test_ensembl.tabular M lib/galaxy/datatypes/test/test_tab.bed M lib/galaxy/datatypes/test/ucsc.customtrack M lib/galaxy/datatypes/test/wiggle.wig M lib/galaxy/datatypes/text.py M lib/galaxy/datatypes/upload_util.py M lib/galaxy/model/custom_types.py M lib/galaxy/util/checkers.py M test/base/populators.py A test/integration/test_datatype_upload.py M test/unit/datatypes/test_bam.py M test/unit/datatypes/test_vcf.py

Log Message: ----------- Merge pull request #6869 from mvdbeek/datatype_upload_integration_test

Datatype upload integration test and fixes

Commit: 41d60f576122a74a87ca060a6813d0e6ca903c05 https://github.com/galaxyproject/galaxy/commit/41d60f576122a74a87ca060a6813d... Author: Saskia Hiltemann zazkia@gmail.com Date: 2018-10-30 (Tue, 30 Oct 2018)

Changed paths: M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js

Log Message: ----------- always strip url prefix

Commit: 04242c75034637f064173eca0c1e2f415343fe93 https://github.com/galaxyproject/galaxy/commit/04242c75034637f064173eca0c1e2... Author: Mason nerdinacan@gmail.com Date: 2018-10-30 (Tue, 30 Oct 2018)

Changed paths: M test/galaxy_selenium/navigates_galaxy.py

Log Message: ----------- Renamed selenium utility function

Commit: b27b3fe2af116301e96247576814728d525b275e https://github.com/galaxyproject/galaxy/commit/b27b3fe2af116301e962475768147... Author: Dannon Baker dannon.baker@gmail.com Date: 2018-10-30 (Tue, 30 Oct 2018)

Changed paths: A lib/galaxy/datatypes/test/test.cel A lib/galaxy/datatypes/test/test.idpdb

Log Message: ----------- Move test files for upstream merge (case sensitivity in git)

Commit: 46f24df8e1b67dcc92d71c6849c922e57f8ffcdd https://github.com/galaxyproject/galaxy/commit/46f24df8e1b67dcc92d71c6849c92... Author: Dannon Baker dannon.baker@gmail.com Date: 2018-10-30 (Tue, 30 Oct 2018)

Changed paths: A static/images/visualization

Log Message: ----------- For simplicity, just symlink viz images for now

Commit: 51273658fb5420c9e6748ed2b08e6769e33158eb https://github.com/galaxyproject/galaxy/commit/51273658fb5420c9e6748ed2b08e6... Author: Dannon Baker dannon.baker@gmail.com Date: 2018-10-30 (Tue, 30 Oct 2018)

Changed paths: M .ci/jenkins/selenium-py3/run_tests.sh M Makefile M client/galaxy/scripts/mvc/ui/ui-slider.js M client/galaxy/style/scss/base.scss M client/galaxy/style/scss/collection.scss M client/galaxy/style/scss/list-item.scss M config/datatypes_conf.xml.sample M config/galaxy.yml.sample M config/plugins/visualizations/scatterplot/package.json M config/plugins/visualizations/scatterplot/src/scatterplot.js M config/plugins/visualizations/scatterplot/static/scatterplot.css M config/plugins/visualizations/scatterplot/static/scatterplot.js M config/plugins/visualizations/scatterplot/templates/scatterplot.mako M doc/source/admin/galaxy_options.rst M doc/source/admin/scaling.md M doc/source/admin/special_topics/bug_reports.rst M doc/source/releases/18.09.rst M doc/source/releases/18.09_announce.rst M doc/source/releases/index.rst M lib/galaxy/authnz/managers.py M lib/galaxy/config.py M lib/galaxy/containers/docker.py M lib/galaxy/containers/docker_model.py M lib/galaxy/containers/docker_swarm.py M lib/galaxy/datatypes/assembly.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/blast.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/genetics.py M lib/galaxy/datatypes/interval.py A lib/galaxy/datatypes/isa.py M lib/galaxy/datatypes/molecules.py M lib/galaxy/datatypes/mothur.py M lib/galaxy/datatypes/phylip.py M lib/galaxy/datatypes/proteomics.py M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/test/1.afg M lib/galaxy/datatypes/test/1.bcf_uncompressed A lib/galaxy/datatypes/test/1.excel.xls M lib/galaxy/datatypes/test/1.fastq A lib/galaxy/datatypes/test/1.fastqcssanger M lib/galaxy/datatypes/test/1.fastqsanger M lib/galaxy/datatypes/test/1.fastqsolexa M lib/galaxy/datatypes/test/1.owl M lib/galaxy/datatypes/test/1.stockholm R lib/galaxy/datatypes/test/1.vcf.gz A lib/galaxy/datatypes/test/1.vcf_bgzip R lib/galaxy/datatypes/test/1.xls M lib/galaxy/datatypes/test/2.fastq R lib/galaxy/datatypes/test/2.fastqsanger M lib/galaxy/datatypes/test/2.fastqsolexa R lib/galaxy/datatypes/test/2.shuffled.bam A lib/galaxy/datatypes/test/2.shuffled.unsorted.bam M lib/galaxy/datatypes/test/2.txt A lib/galaxy/datatypes/test/3.fastq M lib/galaxy/datatypes/test/3.txt M lib/galaxy/datatypes/test/454Score.pdf A lib/galaxy/datatypes/test/5e5z.pqr R lib/galaxy/datatypes/test/Acanium.hmm A lib/galaxy/datatypes/test/Acanium.snaphmm M lib/galaxy/datatypes/test/alignment.lav R lib/galaxy/datatypes/test/biom2_sparse_otu_table_hdf5.biom A lib/galaxy/datatypes/test/biom2_sparse_otu_table_hdf5.biom2 A lib/galaxy/datatypes/test/gff.gff3 R lib/galaxy/datatypes/test/gff_version_3.gff A lib/galaxy/datatypes/test/interv1.bed R lib/galaxy/datatypes/test/interval1.bed M lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.filter R lib/galaxy/datatypes/test/sequence.qual M lib/galaxy/datatypes/test/sequence.qual454 M lib/galaxy/datatypes/test/sequence.qualsolid A lib/galaxy/datatypes/test/tblastn_four_human_vs_rhodopsin.blastxml R lib/galaxy/datatypes/test/tblastn_four_human_vs_rhodopsin.xml R lib/galaxy/datatypes/test/test.CEL R lib/galaxy/datatypes/test/test.idpDB R lib/galaxy/datatypes/test/test_ensembl.tab A lib/galaxy/datatypes/test/test_ensembl.tabular M lib/galaxy/datatypes/test/test_tab.bed M lib/galaxy/datatypes/test/ucsc.customtrack M lib/galaxy/datatypes/test/wiggle.wig M lib/galaxy/datatypes/text.py M lib/galaxy/datatypes/upload_util.py M lib/galaxy/datatypes/util/gff_util.py M lib/galaxy/datatypes/xml.py M lib/galaxy/dependencies/pipfiles/default/Pipfile M lib/galaxy/dependencies/pipfiles/default/pinned-dev-requirements.txt M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt M lib/galaxy/dependencies/pipfiles/flake8/pinned-requirements.txt M lib/galaxy/dependencies/pipfiles/update.sh M lib/galaxy/jobs/dynamic_tool_destination.py M lib/galaxy/jobs/handler.py M lib/galaxy/jobs/metrics/instrumenters/env.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/drmaa.py M lib/galaxy/jobs/runners/kubernetes.py M lib/galaxy/jobs/runners/util/cli/job/slurm_torque.py M lib/galaxy/managers/cloud.py M lib/galaxy/managers/collections.py M lib/galaxy/managers/rbac_secured.py M lib/galaxy/managers/sharable.py M lib/galaxy/managers/tags.py M lib/galaxy/managers/workflows.py M lib/galaxy/model/custom_types.py M lib/galaxy/model/migrate/versions/0141_add_oidc_tables.py M lib/galaxy/model/migrate/versions/0142_change_numeric_metric_precision.py M lib/galaxy/model/migrate/versions/0143_add_cloudauthz_tables.py A lib/galaxy/model/migrate/versions/0144_add_cleanup_event_user_table.py M lib/galaxy/model/search.py M lib/galaxy/objectstore/cloud.py M lib/galaxy/security/validate_user_input.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/data/__init__.py M lib/galaxy/tools/deps/brew_exts.py M lib/galaxy/tools/deps/containers.py M lib/galaxy/tools/deps/views.py M lib/galaxy/tools/error_reports/plugins/biostars.py M lib/galaxy/tools/error_reports/plugins/email.py M lib/galaxy/tools/error_reports/plugins/github.py M lib/galaxy/tools/error_reports/plugins/influxdb.py M lib/galaxy/tools/error_reports/plugins/json.py M lib/galaxy/tools/error_reports/plugins/sentry.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/dynamic_options.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/verify/asserts/__init__.py M lib/galaxy/tools/verify/interactor.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/inflection.py M lib/galaxy/util/json.py M lib/galaxy/util/pastescript/serve.py M lib/galaxy/visualization/data_providers/genome.py M lib/galaxy/visualization/data_providers/phyloviz/newickparser.py M lib/galaxy/web/base/controller.py M lib/galaxy/web/framework/middleware/batch.py M lib/galaxy/webapps/galaxy/api/cloudauthz.py M lib/galaxy/webapps/galaxy/api/uploads.py M lib/galaxy/webapps/galaxy/api/users.py M lib/galaxy/webapps/galaxy/api/workflows.py M 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/forms.py M lib/galaxy/webapps/galaxy/controllers/page.py M lib/galaxy/webapps/tool_shed/api/tools.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/galaxy/webapps/tool_shed/controllers/upload.py M lib/tool_shed/capsule/capsule_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M lib/tool_shed/galaxy_install/tools/data_manager.py M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py M lib/tool_shed/metadata/metadata_generator.py M lib/tool_shed/tools/tool_validator.py M lib/tool_shed/util/commit_util.py M lib/tool_shed/util/readme_util.py M lib/tool_shed/util/repository_util.py M lib/tool_shed/util/workflow_util.py M lib/tool_shed/util/xml_util.py M run.sh M scripts/bootstrap_history.py M scripts/check_python.py M scripts/cleanup_datasets/pgcleanup.py M scripts/runtime_stats.py M scripts/summarize_timings.py M scripts/tool_shed/api/reset_metadata_on_repositories.py M scripts/tool_shed/bootstrap_tool_shed/create_user_with_api_key.py M scripts/transfer.py M setup.cfg M static/style/blue/base.css M static/welcome.html.sample M templates/display_base.mako M templates/ind_share_base.mako M templates/message.mako M templates/webapps/galaxy/history/display.mako M templates/webapps/galaxy/visualization/display.mako M templates/webapps/galaxy/visualization/display_in_frame.mako M templates/webapps/galaxy/workflow/display.mako M templates/webapps/galaxy/workflow/sharing.mako M templates/webapps/tool_shed/repository/common.mako A test-data/MTBLS6.zip M test/api/test_tools_upload.py M test/api/test_workflows.py M test/api/test_workflows_from_yaml.py M test/base/driver_util.py M test/base/populators.py M test/base/workflow_fixtures.py M test/functional/tools/output_filter.xml A test/functional/tools/remove_value.xml M test/functional/tools/samples_tool_conf.xml M test/functional/webhooks/phdcomics/__init__.py A test/integration/test_datatype_upload.py M test/selenium_tests/test_uploads.py M test/shed_functional/base/twilltestcase.py M test/unit/datatypes/test_bam.py M test/unit/datatypes/test_vcf.py M test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py M test/unit/web/framework/test_webapp.py M tools/data_source/upload.py M tools/extract/extract_genomic_dna.py M tools/filters/convert_characters.py M tools/filters/grep.py M tools/filters/uniq.py M tools/stats/filtering.py M tools/stats/gsummary.py

Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into unified_webpack4

Commit: 17efac853ad1b5a7f319e010b00a79d4694a09ac https://github.com/galaxyproject/galaxy/commit/17efac853ad1b5a7f319e010b00a7... Author: John Chilton jmchilton@gmail.com Date: 2018-10-30 (Tue, 30 Oct 2018)

Changed paths: M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js

Log Message: ----------- Merge pull request #6943 from shiltemann/collection-strip-urlprefix

Collection builder: add option to strip url prefix from pair names

Commit: 2bf5b9b84e5f1391c8a0640255293e23f82042e1 https://github.com/galaxyproject/galaxy/commit/2bf5b9b84e5f1391c8a0640255293... Author: guerler aysam.guerler@gmail.com Date: 2018-10-30 (Tue, 30 Oct 2018)

Changed paths: M templates/webapps/galaxy/admin/tool_sheds.mako

Log Message: ----------- Fix style for legacy toolshed selection page

Commit: 7dbc81ca825adbae503d076c88a838336790067f https://github.com/galaxyproject/galaxy/commit/7dbc81ca825adbae503d076c88a83... Author: Dannon Baker dannon.baker@gmail.com Date: 2018-10-30 (Tue, 30 Oct 2018)

Changed paths: M scripts/get_uwsgi_args.py

Log Message: ----------- Add images to default static-safe location

Commit: dbdce6d37b075720d9d936921ae72edd66211bc1 https://github.com/galaxyproject/galaxy/commit/dbdce6d37b075720d9d936921ae72... Author: Dannon Baker dannon.baker@gmail.com Date: 2018-10-30 (Tue, 30 Oct 2018)

Changed paths: M .gitignore A static/images/delete_tag_icon_gray.png A static/style/blue/ok_small.png

Log Message: ----------- Stage two more images after inclusion in scripts. We'll inevitably find more of these, and they should all be removed, but this gives us a way to transition as things are rewritten.

Commit: 4d5285b65921e8a25689d7813872619dbd6e9b23 https://github.com/galaxyproject/galaxy/commit/4d5285b65921e8a25689d78138726... Author: Dannon Baker dannon.baker@gmail.com Date: 2018-10-30 (Tue, 30 Oct 2018)

Changed paths: A static/style/blue/question-octagon-frame.png

Log Message: ----------- Another image link for admin_toolshed stuff.

Commit: b47efd4adedb781056423bda4112a5b46a72489b https://github.com/galaxyproject/galaxy/commit/b47efd4adedb781056423bda4112a... Author: Nicola Soranzo nicola.soranzo@earlham.ac.uk Date: 2018-10-31 (Wed, 31 Oct 2018)

Changed paths: M doc/source/releases/18.09_announce.rst M lib/galaxy/datatypes/binary.py M lib/galaxy/jobs/runners/kubernetes.py

Log Message: ----------- Merge branch 'release_18.09' into dev

Commit: ddeef3fbc2f884d8ad1af95adc164ca8e5bc15c3 https://github.com/galaxyproject/galaxy/commit/ddeef3fbc2f884d8ad1af95adc164... Author: mvdbeek m.vandenbeek@gmail.com Date: 2018-10-31 (Wed, 31 Oct 2018)

Changed paths: M lib/galaxy/datatypes/binary.py A lib/galaxy/datatypes/test/1.qname_sorted.bam

Log Message: ----------- Fix sniffing of readname sorted BAM files

This fixes https://github.com/galaxyproject/galaxy/issues/6949. The problem is that `super` would fall back to the BamInputSorted sniffer, which prevents sniffing. Includes a test file for the new datatype upload testing framework.

Commit: c78f704c230a694d42c769bacdb23d20eb2ea810 https://github.com/galaxyproject/galaxy/commit/c78f704c230a694d42c769bacdb23... Author: mvdbeek m.vandenbeek@gmail.com Date: 2018-10-31 (Wed, 31 Oct 2018)

Changed paths: A lib/galaxy/datatypes/test/0.txt A lib/galaxy/datatypes/test/1.json

Log Message: ----------- Add two test files that exercise json and txt sniffing

Commit: f40bb68141ebff020401740b8bf9b3b1fc73db60 https://github.com/galaxyproject/galaxy/commit/f40bb68141ebff020401740b8bf9b... Author: John Chilton jmchilton@gmail.com Date: 2018-10-31 (Wed, 31 Oct 2018)

Changed paths: M lib/galaxy/datatypes/binary.py A lib/galaxy/datatypes/test/0.txt A lib/galaxy/datatypes/test/1.json A lib/galaxy/datatypes/test/1.qname_sorted.bam

Log Message: ----------- Merge pull request #6950 from mvdbeek/qname_sorted_sniffer

Fix sniffing of readname sorted BAM files

Commit: 341f7d6372aa62bc6e84527925e0fb96622d1b84 https://github.com/galaxyproject/galaxy/commit/341f7d6372aa62bc6e84527925e0f... Author: vahid jalili.vahid@gmail.com Date: 2018-10-31 (Wed, 31 Oct 2018)

Changed paths: M tools/cloud/send.xml

Log Message: ----------- Update output label & tool name to compose a more intuitive log label.

Commit: 6c07a0370dadfdf0b9352c63b2d6f3357c33853d https://github.com/galaxyproject/galaxy/commit/6c07a0370dadfdf0b9352c63b2d6f... Author: vahid jalili.vahid@gmail.com Date: 2018-10-31 (Wed, 31 Oct 2018)

Changed paths: M tools/cloud/send.xml

Log Message: ----------- Update description on send tool wrapper.

Commit: 3e57fb172fbf580da04131355326681e118cc82b https://github.com/galaxyproject/galaxy/commit/3e57fb172fbf580da041313553266... Author: Dannon Baker dannon.baker@gmail.com Date: 2018-10-31 (Wed, 31 Oct 2018)

Changed paths: M client/galaxy/scripts/mvc/history/options-menu.js M client/galaxy/scripts/mvc/user/user-preferences.js M lib/galaxy/webapps/galaxy/controllers/history.py

Log Message: ----------- Quick 'make everything private' implementation. Takes a single history or operates on all of a user's histories. Intentionally doesn't use an API, rather a simple webcontroller endpoint, because I think we'll want to handle this with group operations and the like down the road, and will enhance existing APIs

Commit: a07a1c3a566571b9b83dc7a99fae1ed0d275f020 https://github.com/galaxyproject/galaxy/commit/a07a1c3a566571b9b83dc7a99fae1... Author: Dannon Baker dannon.baker@gmail.com Date: 2018-10-31 (Wed, 31 Oct 2018)

Changed paths: M lib/galaxy/webapps/galaxy/controllers/history.py

Log Message: ----------- Make logic more concise, fix typo, add commentary.

Commit: 43689c1f3fc8e2fc49c3d6dfc033f70fe06e4c32 https://github.com/galaxyproject/galaxy/commit/43689c1f3fc8e2fc49c3d6dfc033f... Author: Dannon Baker dannon.baker@gmail.com Date: 2018-10-31 (Wed, 31 Oct 2018)

Changed paths: M lib/galaxy/webapps/galaxy/controllers/history.py

Log Message: ----------- Update message to reflect all histories functionality.

Commit: 31905f1402d9ba8af82d0ae723eaccc20d1d621c https://github.com/galaxyproject/galaxy/commit/31905f1402d9ba8af82d0ae723eac... Author: Martin Cech marten@bx.psu.edu Date: 2018-10-31 (Wed, 31 Oct 2018)

Changed paths: M .gitignore M client/.babelrc R client/GruntFile.js A client/galaxy/images/Armitagep_manhattan.png A client/galaxy/images/Armitagep_qqplot.png A client/galaxy/images/add_icon.png A client/galaxy/images/add_icon_dark.png A client/galaxy/images/aggregate_history1.png A client/galaxy/images/aggregate_history2.png A client/galaxy/images/bar_chart.png A client/galaxy/images/base_bg.png A client/galaxy/images/bed_warn.png A client/galaxy/images/button_bar_bg_light.png A client/galaxy/images/circle.py A client/galaxy/images/closebox.png A client/galaxy/images/dat_points_table_brows_1.png A client/galaxy/images/data_empty.png A client/galaxy/images/data_error.png A client/galaxy/images/data_ok.png A client/galaxy/images/data_queued.png A client/galaxy/images/data_running.gif A client/galaxy/images/ddarrowsplit.png A client/galaxy/images/delete.gif A client/galaxy/images/delete_tag_icon_gray.png A client/galaxy/images/delete_tag_icon_white.png A 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Log Message: ----------- Merge pull request #6917 from dannon/unified_webpack4

Unified webpack4

Commit: 66a7db94053763bfb1cc23ba5df1e537f0177219 https://github.com/galaxyproject/galaxy/commit/66a7db94053763bfb1cc23ba5df1e... Author: Mason nerdinacan@gmail.com Date: 2018-10-31 (Wed, 31 Oct 2018)

Changed paths: M .gitignore M client/.babelrc R client/GruntFile.js A client/galaxy/images/Armitagep_manhattan.png A client/galaxy/images/Armitagep_qqplot.png A client/galaxy/images/add_icon.png A client/galaxy/images/add_icon_dark.png A client/galaxy/images/aggregate_history1.png A client/galaxy/images/aggregate_history2.png A client/galaxy/images/bar_chart.png A client/galaxy/images/base_bg.png A client/galaxy/images/bed_warn.png A client/galaxy/images/button_bar_bg_light.png A client/galaxy/images/circle.py A client/galaxy/images/closebox.png A client/galaxy/images/dat_points_table_brows_1.png A client/galaxy/images/data_empty.png A client/galaxy/images/data_error.png A client/galaxy/images/data_ok.png A client/galaxy/images/data_queued.png A client/galaxy/images/data_running.gif A client/galaxy/images/ddarrowsplit.png A client/galaxy/images/delete.gif A client/galaxy/images/delete_tag_icon_gray.png A client/galaxy/images/delete_tag_icon_white.png A client/galaxy/images/documents-stack-faded.png A client/galaxy/images/documents-stack.png A client/galaxy/images/done_message_icon.png A client/galaxy/images/dropdownarrow.png A client/galaxy/images/error_bg.png A client/galaxy/images/error_icon.svg A client/galaxy/images/error_large.png A client/galaxy/images/error_message_icon.png A client/galaxy/images/error_small.png A client/galaxy/images/fetchTax.png A client/galaxy/images/footer_title_bg.png A client/galaxy/images/form_body_bg.png A client/galaxy/images/form_title_bg.png A client/galaxy/images/fugue.png A client/galaxy/images/fugue/application-dock-270-bw.png A client/galaxy/images/fugue/application-dock-270.png A client/galaxy/images/fugue/arrow-000-small-bw.png A client/galaxy/images/fugue/arrow-090.png A client/galaxy/images/fugue/arrow-circle.png A client/galaxy/images/fugue/arrow-resize-090-bw.png A client/galaxy/images/fugue/arrow-resize-090.png A client/galaxy/images/fugue/arrow-split-bw.png A 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static/style/blue/warn_message_icon.png R static/style/blue/warn_small.png R static/style/blue/workflow_circle_drag.png R static/style/blue/workflow_circle_green.png R static/style/blue/workflow_circle_open.png R static/style/shared_images/data_running.gif R static/style/shared_images/error_large.png R static/style/shared_images/error_small.png R static/style/shared_images/info_large.png R static/style/shared_images/info_small.png R static/style/shared_images/ok_large.png R static/style/shared_images/ok_small.png R static/style/shared_images/wait_large.png R static/style/shared_images/wait_small.png R static/style/shared_images/warn_large.png R static/style/shared_images/warn_small.png M static/welcome.html.sample M templates/admin/tool_shed_repository/browse_repository.mako M templates/admin/tool_shed_repository/browse_tool_dependency.mako M templates/admin/tool_shed_repository/manage_repository.mako M templates/admin/tool_shed_repository/reselect_tool_panel_section.mako M templates/admin/tool_shed_repository/select_tool_panel_section.mako M templates/base.mako M templates/base/base_panels.mako M templates/galaxy_client_app.mako M templates/js-app.mako M templates/legacy/grid_base.mako M templates/webapps/galaxy/galaxy.panels.mako M templates/webapps/galaxy/visualization/display.mako M templates/webapps/galaxy/visualization/gie.mako M templates/webapps/galaxy/visualization/sweepster.mako M templates/webapps/galaxy/workflow/editor.mako M templates/webapps/reports/run_stats.mako M templates/webapps/tool_shed/repository/browse_repository.mako M templates/webapps/tool_shed/repository/manage_repository.mako M templates/webapps/tool_shed/repository/preview_tools_in_changeset.mako M templates/webapps/tool_shed/repository/rate_repository.mako M templates/webapps/tool_shed/repository/upload.mako M templates/webapps/tool_shed/repository/view_changelog.mako M templates/webapps/tool_shed/repository/view_changeset.mako M templates/webapps/tool_shed/repository/view_repository.mako M templates/webapps/tool_shed/repository_review/browse_review.mako M templates/webapps/tool_shed/repository_review/edit_review.mako M templates/webapps/tool_shed/repository_review/reviews_of_changeset_revision.mako M templates/webapps/tool_shed/repository_review/reviews_of_repository.mako M templates/webapps/tool_shed/repository_review/select_previous_review.mako M test/base/driver_util.py M test/base/populators.py A test/integration/test_datatype_upload.py M test/unit/datatypes/test_bam.py M test/unit/datatypes/test_vcf.py

Log Message: ----------- Merged dev

Commit: 294cfbf6716dbac554da36f0c410276669c1dce9 https://github.com/galaxyproject/galaxy/commit/294cfbf6716dbac554da36f0c4102... Author: Mason nerdinacan@gmail.com Date: 2018-10-31 (Wed, 31 Oct 2018)

Changed paths: M client/webpack.config.js

Log Message: ----------- Updated provide monitored proxy for Galaxy references

Commit: 20f3c04a421d007ad04a78e39a74c967b61b10fd https://github.com/galaxyproject/galaxy/commit/20f3c04a421d007ad04a78e39a74c... Author: guerler aysam.guerler@gmail.com Date: 2018-10-31 (Wed, 31 Oct 2018)

Changed paths: M client/galaxy/style/scss/ui.scss M templates/admin/tool_shed_repository/monitor_repository_installation.mako M templates/webapps/galaxy/admin/manage_dependencies.mako M templates/webapps/galaxy/admin/sanitize_whitelist.mako M templates/webapps/galaxy/admin/view_display_applications.mako

Log Message: ----------- Use existing overflow utility instead of overwriting card defaults

Commit: 3f7425ad9308a6e1946225d155351ccc05aa4fab https://github.com/galaxyproject/galaxy/commit/3f7425ad9308a6e1946225d155351... Author: Martin Cech marten@bx.psu.edu Date: 2018-10-31 (Wed, 31 Oct 2018)

Changed paths: M client/galaxy/style/scss/ui.scss M templates/admin/tool_shed_repository/monitor_repository_installation.mako M templates/webapps/galaxy/admin/manage_dependencies.mako M templates/webapps/galaxy/admin/sanitize_whitelist.mako M templates/webapps/galaxy/admin/view_display_applications.mako

Log Message: ----------- Merge pull request #6948 from guerler/add_overflow_auto

Use recently introduced overflow utility instead of overwriting card defaults

Commit: e8a64a862212af970690fcd1969ac8f5ebaaf407 https://github.com/galaxyproject/galaxy/commit/e8a64a862212af970690fcd1969ac... Author: Mason nerdinacan@gmail.com Date: 2018-10-31 (Wed, 31 Oct 2018)

Changed paths: A client/galaxy/scripts/apps/sample.test.js A client/galaxy/scripts/unitTestBundle.js A client/karma.config.base.js R client/karma.config.js A client/karma.config.mocha.js A client/karma.config.qunit.js M client/package.json A client/webpack.config.test.js M client/yarn.lock

Log Message: ----------- Split qunit and mocha tests, clean up karma configs

Commit: 1490b6ae839bd704af45b7a415ba70d7fc013df3 https://github.com/galaxyproject/galaxy/commit/1490b6ae839bd704af45b7a415ba7... Author: Mason nerdinacan@gmail.com Date: 2018-10-31 (Wed, 31 Oct 2018)

Changed paths: M client/galaxy/style/scss/ui.scss M templates/admin/tool_shed_repository/monitor_repository_installation.mako M templates/webapps/galaxy/admin/manage_dependencies.mako M templates/webapps/galaxy/admin/sanitize_whitelist.mako M templates/webapps/galaxy/admin/view_display_applications.mako

Log Message: ----------- Merge branch 'dev' into karma_chromeheadless

Commit: 3108bd3b37298417df5e9851d7e126c6c1b4878f https://github.com/galaxyproject/galaxy/commit/3108bd3b37298417df5e9851d7e12... Author: Dannon dannon.baker@gmail.com Date: 2018-11-01 (Thu, 01 Nov 2018)

Changed paths: M templates/webapps/galaxy/admin/tool_sheds.mako

Log Message: ----------- Merge pull request #6910 from guerler/toolshed_selection

Fix style for legacy toolshed selection page

Commit: c312c1014d0e85920f630bf3d3e02e508c636b84 https://github.com/galaxyproject/galaxy/commit/c312c1014d0e85920f630bf3d3e02... Author: John Chilton jmchilton@gmail.com Date: 2018-11-01 (Thu, 01 Nov 2018)

Changed paths: M config/migrated_tools_conf.xml.sample M config/shed_tool_conf.xml.sample M doc/source/admin/tool_panel.rst M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/tool_shed/galaxy_install/migrate/check.py M lib/tool_shed/util/common_util.py

Log Message: ----------- Merge pull request #6937 from natefoo/shed-tools-relocate

Default shed tool installation to database/shed_tools

Commit: d4b6bf28b5c834dc82591761a98a1aeefc0ed412 https://github.com/galaxyproject/galaxy/commit/d4b6bf28b5c834dc82591761a98a1... Author: John Chilton jmchilton@gmail.com Date: 2018-11-01 (Thu, 01 Nov 2018)

Changed paths: M test/api/test_workflows.py

Log Message: ----------- Test for parameter replacement of GUI-style normalized parameters.

Commit: 06aea92eb8614faa06afdeaeffe91565e1390774 https://github.com/galaxyproject/galaxy/commit/06aea92eb8614faa06afdeaeffe91... Author: John Chilton jmchilton@gmail.com Date: 2018-11-01 (Thu, 01 Nov 2018)

Changed paths: M test/api/test_workflows.py

Log Message: ----------- cleaner test test_run_subworkflow_runtime_parameters

Commit: f035d642ceb2a4835d774996f3b3d78588318834 https://github.com/galaxyproject/galaxy/commit/f035d642ceb2a4835d774996f3b3d... Author: John Chilton jmchilton@gmail.com Date: 2018-11-01 (Thu, 01 Nov 2018)

Changed paths: M config/datatypes_conf.xml.sample A lib/galaxy/datatypes/converters/tar_to_directory.xml M lib/galaxy/datatypes/data.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/util/compression_utils.py M lib/galaxy/webapps/galaxy/api/datasets.py M lib/galaxy/webapps/galaxy/buildapp.py M test/api/test_tools.py M test/api/test_tools_upload.py M test/base/populators.py M test/functional/tools/sample_datatypes_conf.xml M test/integration/test_upload_configuration_options.py M tools/data_source/upload.py M tools/data_source/upload.xml

Log Message: ----------- Merge pull request #6844 from jmchilton/compressed_types_and_extra_files

Infrastructure/API Support for Composite Uploads/Downloads

Commit: cc8e1c211ee5c7f6af3d358619b44b3a14ce4deb https://github.com/galaxyproject/galaxy/commit/cc8e1c211ee5c7f6af3d358619b44... Author: M Bernt m.bernt@ufz.de Date: 2018-11-01 (Thu, 01 Nov 2018)

Changed paths: M lib/galaxy/tools/data/__init__.py

Log Message: ----------- fix empty loc file bug

Commit: 13a4238510de2330bcf460519eac2198f66e0c33 https://github.com/galaxyproject/galaxy/commit/13a4238510de2330bcf460519eac2... Author: M Bernt m.bernt@ufz.de Date: 2018-11-01 (Thu, 01 Nov 2018)

Changed paths: M lib/galaxy/tools/data/__init__.py

Log Message: ----------- removed debug output

Commit: b52b2d8c4817295f9dad56a057fe9d5a095d3a37 https://github.com/galaxyproject/galaxy/commit/b52b2d8c4817295f9dad56a057fe9... Author: Mason nerdinacan@gmail.com Date: 2018-11-01 (Thu, 01 Nov 2018)

Changed paths: M config/datatypes_conf.xml.sample M config/migrated_tools_conf.xml.sample M config/shed_tool_conf.xml.sample M doc/source/admin/tool_panel.rst A lib/galaxy/datatypes/converters/tar_to_directory.xml M lib/galaxy/datatypes/data.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/util/compression_utils.py M lib/galaxy/webapps/galaxy/api/datasets.py M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/tool_shed/galaxy_install/migrate/check.py M lib/tool_shed/util/common_util.py M templates/webapps/galaxy/admin/tool_sheds.mako M test/api/test_tools.py M test/api/test_tools_upload.py M test/base/populators.py M test/functional/tools/sample_datatypes_conf.xml M test/integration/test_upload_configuration_options.py M tools/data_source/upload.py M tools/data_source/upload.xml

Log Message: ----------- Merge branch 'dev' into karma_chromeheadless

Commit: 0beac8fdf4835271ccafefd6a50f928afa055c2c https://github.com/galaxyproject/galaxy/commit/0beac8fdf4835271ccafefd6a50f9... Author: M Bernt m.bernt@ufz.de Date: 2018-11-01 (Thu, 01 Nov 2018)

Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py A lib/galaxy/datatypes/test/diamond.rma

Log Message: ----------- rma: add RMA6 data type (MEGAN6 read-match archive)

Commit: dcae06624a7561d082a7630917d095925795d30e https://github.com/galaxyproject/galaxy/commit/dcae06624a7561d082a7630917d09... Author: M Bernt m.bernt@ufz.de Date: 2018-11-01 (Thu, 01 Nov 2018)

Changed paths: M config/datatypes_conf.xml.sample

Log Message: ----------- rma: RMA->RMA6

Commit: 2cc0417530cb33dfa43cb0c0d64f2f807d5396d5 https://github.com/galaxyproject/galaxy/commit/2cc0417530cb33dfa43cb0c0d64f2... Author: Mason nerdinacan@gmail.com Date: 2018-11-01 (Thu, 01 Nov 2018)

Changed paths: M .travis.yml M client/karma.config.base.js

Log Message: ----------- Added chrome to qunit build, tried no sandbox flag on chrome

Commit: b637c7575a6cdd17960b57e803cabcaa9fe5972c https://github.com/galaxyproject/galaxy/commit/b637c7575a6cdd17960b57e803cab... Author: Mason nerdinacan@gmail.com Date: 2018-11-01 (Thu, 01 Nov 2018)

Changed paths: M Makefile M client/karma.config.base.js M client/package.json

Log Message: ----------- Modified test script calls

Commit: 31d3c97e757fd9e9206c815d7b0c9b9d22d0d7a8 https://github.com/galaxyproject/galaxy/commit/31d3c97e757fd9e9206c815d7b0c9... Author: Mason nerdinacan@gmail.com Date: 2018-11-01 (Thu, 01 Nov 2018)

Changed paths: M client/karma.config.qunit.js

Log Message: ----------- Remove one failing test just to check build

Commit: e92ce870928700917d69e9c3d939087d6d48eb56 https://github.com/galaxyproject/galaxy/commit/e92ce870928700917d69e9c3d9390... Author: Mason nerdinacan@gmail.com Date: 2018-11-01 (Thu, 01 Nov 2018)

Changed paths: M client/galaxy/scripts/qunit/test.js M client/karma.config.qunit.js

Log Message: ----------- Removed bad test just to test build

Commit: b06957e90619b3b7c4cf1f7b989ae32242b55f83 https://github.com/galaxyproject/galaxy/commit/b06957e90619b3b7c4cf1f7b989ae... Author: Mason nerdinacan@gmail.com Date: 2018-11-01 (Thu, 01 Nov 2018)

Changed paths: M client/karma.config.mocha.js

Log Message: ----------- Added existing mocha tests back

Commit: a7a73bcfcd32de2b89a6cd4119ba64db8be045ef https://github.com/galaxyproject/galaxy/commit/a7a73bcfcd32de2b89a6cd4119ba6... Author: Mason nerdinacan@gmail.com Date: 2018-11-01 (Thu, 01 Nov 2018)

Changed paths: M client/karma.config.base.js M client/karma.config.mocha.js M client/karma.config.qunit.js M client/package.json A client/webpack.config.qunit.js R client/webpack.config.test.js A client/webpack.config.unittest.js M client/yarn.lock

Log Message: ----------- Documented differences bretween different webpack configs, used cleaner tool and ignore-loader for true unit-tests

Commit: c2f71c3a3ec31fd6af7479db9ae13f8b0975d584 https://github.com/galaxyproject/galaxy/commit/c2f71c3a3ec31fd6af7479db9ae13... Author: Mason nerdinacan@gmail.com Date: 2018-11-01 (Thu, 01 Nov 2018)

Changed paths: M client/webpack.config.qunit.js

Log Message: ----------- Added missing settings on special qunit webpack config

Commit: 09de6fe4961adcfe09f8701989ac37b8f8df1930 https://github.com/galaxyproject/galaxy/commit/09de6fe4961adcfe09f8701989ac3... Author: M Bernt m.bernt@ufz.de Date: 2018-11-02 (Fri, 02 Nov 2018)

Changed paths: M lib/galaxy/datatypes/binary.py

Log Message: ----------- rma: fix test

Commit: d6af6b7bd1ef9c9429d1362ac9473168be7ba471 https://github.com/galaxyproject/galaxy/commit/d6af6b7bd1ef9c9429d1362ac9473... Author: Nicola Soranzo nicola.soranzo@earlham.ac.uk Date: 2018-11-02 (Fri, 02 Nov 2018)

Changed paths: M config/datatypes_conf.xml.sample

Log Message: ----------- Merge branch 'release_18.09' into dev

Commit: ee0038a01f8ddd9f8b99d0612497fc6681a14acc https://github.com/galaxyproject/galaxy/commit/ee0038a01f8ddd9f8b99d0612497f... Author: M Bernt m.bernt@ufz.de Date: 2018-11-02 (Fri, 02 Nov 2018)

Changed paths: M config/datatypes_conf.xml.sample

Log Message: ----------- rma: extension rma6 for consistency

Commit: 8789713b9584c8ee58692b4dc02a282f32484502 https://github.com/galaxyproject/galaxy/commit/8789713b9584c8ee58692b4dc02a2... Author: Sebastian Kapust sebastian@kapust.org Date: 2018-11-03 (Sat, 03 Nov 2018)

Changed paths: M .ci/jenkins/selenium-py3/run_tests.sh M .gitignore M Makefile M client/.babelrc R client/GruntFile.js A client/galaxy/images/Armitagep_manhattan.png A client/galaxy/images/Armitagep_qqplot.png A client/galaxy/images/add_icon.png A client/galaxy/images/add_icon_dark.png A client/galaxy/images/aggregate_history1.png A client/galaxy/images/aggregate_history2.png A client/galaxy/images/bar_chart.png A client/galaxy/images/base_bg.png A client/galaxy/images/bed_warn.png A client/galaxy/images/button_bar_bg_light.png A client/galaxy/images/circle.py A client/galaxy/images/closebox.png A client/galaxy/images/dat_points_table_brows_1.png A client/galaxy/images/data_empty.png A client/galaxy/images/data_error.png A client/galaxy/images/data_ok.png A client/galaxy/images/data_queued.png A client/galaxy/images/data_running.gif A client/galaxy/images/ddarrowsplit.png A client/galaxy/images/delete.gif A client/galaxy/images/delete_tag_icon_gray.png A client/galaxy/images/delete_tag_icon_white.png A client/galaxy/images/documents-stack-faded.png A client/galaxy/images/documents-stack.png A client/galaxy/images/done_message_icon.png A client/galaxy/images/dropdownarrow.png A client/galaxy/images/error_bg.png A client/galaxy/images/error_icon.svg A client/galaxy/images/error_large.png A client/galaxy/images/error_message_icon.png A client/galaxy/images/error_small.png A client/galaxy/images/fetchTax.png A client/galaxy/images/footer_title_bg.png A client/galaxy/images/form_body_bg.png A client/galaxy/images/form_title_bg.png A client/galaxy/images/fugue.png A client/galaxy/images/fugue/application-dock-270-bw.png A client/galaxy/images/fugue/application-dock-270.png A client/galaxy/images/fugue/arrow-000-small-bw.png A client/galaxy/images/fugue/arrow-090.png A client/galaxy/images/fugue/arrow-circle.png A client/galaxy/images/fugue/arrow-resize-090-bw.png A client/galaxy/images/fugue/arrow-resize-090.png A client/galaxy/images/fugue/arrow-split-bw.png A client/galaxy/images/fugue/arrow-split.png A client/galaxy/images/fugue/arrow-transition-270-bw.png A client/galaxy/images/fugue/arrow-transition-bw.png A client/galaxy/images/fugue/asterisk-small-outline.png A client/galaxy/images/fugue/asterisk-small-yellow.png A client/galaxy/images/fugue/asterisk-small.png A client/galaxy/images/fugue/block--plus-bw.png A client/galaxy/images/fugue/block--plus.png A client/galaxy/images/fugue/bookmarks-bw.png A client/galaxy/images/fugue/bookmarks.png A client/galaxy/images/fugue/bug.png A client/galaxy/images/fugue/chart.png A client/galaxy/images/fugue/chevron-expand-bw.png A client/galaxy/images/fugue/chevron-expand.png A client/galaxy/images/fugue/chevron.png A client/galaxy/images/fugue/control-270.png A client/galaxy/images/fugue/cross-button.png A client/galaxy/images/fugue/cross-circle-bw.png A client/galaxy/images/fugue/cross-circle.png A client/galaxy/images/fugue/cross-small-bw.png A 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static/welcome.html.sample M templates/admin/tool_shed_repository/browse_repository.mako M templates/admin/tool_shed_repository/browse_tool_dependency.mako M templates/admin/tool_shed_repository/manage_repository.mako M templates/admin/tool_shed_repository/monitor_repository_installation.mako M templates/admin/tool_shed_repository/reselect_tool_panel_section.mako M templates/admin/tool_shed_repository/select_tool_panel_section.mako M templates/base.mako M templates/base/base_panels.mako M templates/display_base.mako M templates/galaxy_client_app.mako M templates/ind_share_base.mako M templates/js-app.mako M templates/legacy/grid_base.mako M templates/message.mako M templates/user/info.mako M templates/user/register.mako M templates/webapps/galaxy/admin/manage_dependencies.mako M templates/webapps/galaxy/admin/sanitize_whitelist.mako M templates/webapps/galaxy/admin/tool_sheds.mako M templates/webapps/galaxy/admin/view_display_applications.mako M templates/webapps/galaxy/galaxy.panels.mako M templates/webapps/galaxy/history/display.mako M templates/webapps/galaxy/history/share.mako M templates/webapps/galaxy/visualization/display.mako M templates/webapps/galaxy/visualization/display_in_frame.mako M templates/webapps/galaxy/visualization/gie.mako M templates/webapps/galaxy/visualization/sweepster.mako M templates/webapps/galaxy/workflow/display.mako M templates/webapps/galaxy/workflow/editor.mako M templates/webapps/galaxy/workflow/sharing.mako M templates/webapps/reports/run_stats.mako M templates/webapps/tool_shed/repository/browse_repository.mako M templates/webapps/tool_shed/repository/common.mako M templates/webapps/tool_shed/repository/manage_repository.mako M templates/webapps/tool_shed/repository/preview_tools_in_changeset.mako M templates/webapps/tool_shed/repository/rate_repository.mako M templates/webapps/tool_shed/repository/upload.mako M templates/webapps/tool_shed/repository/view_changelog.mako M templates/webapps/tool_shed/repository/view_changeset.mako M templates/webapps/tool_shed/repository/view_repository.mako M templates/webapps/tool_shed/repository_review/browse_review.mako M templates/webapps/tool_shed/repository_review/edit_review.mako M templates/webapps/tool_shed/repository_review/reviews_of_changeset_revision.mako M templates/webapps/tool_shed/repository_review/reviews_of_repository.mako M templates/webapps/tool_shed/repository_review/select_previous_review.mako A test-data/MTBLS6.zip M test/api/test_tools.py M test/api/test_tools_upload.py M test/api/test_workflows.py M test/api/test_workflows_from_yaml.py M test/base/driver_util.py M test/base/populators.py M test/base/workflow_fixtures.py M test/functional/tools/output_filter.xml A test/functional/tools/remove_value.xml M test/functional/tools/sample_datatypes_conf.xml M test/functional/tools/samples_tool_conf.xml M test/functional/webhooks/phdcomics/__init__.py M test/galaxy_selenium/navigation.yml A test/integration/test_datatype_upload.py M test/integration/test_upload_configuration_options.py M test/selenium_tests/test_uploads.py M test/shed_functional/base/twilltestcase.py M test/unit/datatypes/test_bam.py M test/unit/datatypes/test_vcf.py M test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py M test/unit/web/framework/test_webapp.py M tools/data_source/upload.py M tools/data_source/upload.xml M tools/extract/extract_genomic_dna.py M tools/filters/convert_characters.py M tools/filters/grep.py M tools/filters/uniq.py M tools/stats/filtering.py M tools/stats/gsummary.py

Log Message: ----------- Merge branch 'dev' into admin.data.manager.vue.steps

Commit: 91df3971be62419620c3cd08b0c9162ec6989856 https://github.com/galaxyproject/galaxy/commit/91df3971be62419620c3cd08b0c91... Author: Sebastian Kapust sebastian@kapust.org Date: 2018-11-03 (Sat, 03 Nov 2018)

Changed paths: M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/components/admin/DataManager/DataManager.vue M client/galaxy/scripts/components/admin/DataManager/DataManagerJobs.vue M client/galaxy/scripts/components/admin/DataManager/DataManagerRouter.vue M lib/galaxy/webapps/galaxy/buildapp.py

Log Message: ----------- DataManagerRouter, DataManager, DataManagerJobs: Fix routing problem

* Forward path following the data manager url to DataManagerRouter * encode id in DataManager and DataManagerJobs

Commit: 45d0f161c92c6fdac103ca3eecec421ac3fa3db3 https://github.com/galaxyproject/galaxy/commit/45d0f161c92c6fdac103ca3eecec4... Author: Sebastian Kapust sebastian@kapust.org Date: 2018-11-03 (Sat, 03 Nov 2018)

Changed paths: M test/shed_functional/base/twilltestcase.py M test/shed_functional/functional/test_1460_data_managers.py

Log Message: ----------- Fix functional test case test_1460_data_managers

Commit: 19b2fdd73ba82d0eb3ae38141134915d8a745827 https://github.com/galaxyproject/galaxy/commit/19b2fdd73ba82d0eb3ae381411349... Author: Mason nerdinacan@gmail.com Date: 2018-11-03 (Sat, 03 Nov 2018)

Changed paths: R client/galaxy/scripts/apps/sample.test.js A client/galaxy/scripts/sample.test.js R client/karma.config.base.js R client/karma.config.mocha.js R client/karma.config.qunit.js A client/karma/karma.config.base.js A client/karma/karma.config.mocha.js A client/karma/karma.config.qunit.js A client/karma/webpack.config.qunit.js A client/karma/webpack.config.unittest.js M client/package.json R client/webpack.config.qunit.js R client/webpack.config.unittest.js

Log Message: ----------- Reorganized config scripts, fleshed out comments and instructions

Commit: 0ede377925c415cf5b7805de03d57d8d0bd2bca4 https://github.com/galaxyproject/galaxy/commit/0ede377925c415cf5b7805de03d57... Author: Marius van den Beek m.vandenbeek@gmail.com Date: 2018-11-04 (Sun, 04 Nov 2018)

Changed paths: M lib/galaxy/tools/data/__init__.py

Log Message: ----------- Merge pull request #6957 from bernt-matthias/topic/empty-data-table

Topic/empty data table

Commit: 562b10b7efc93c5ab15bd3a3d5918f32491d934d https://github.com/galaxyproject/galaxy/commit/562b10b7efc93c5ab15bd3a3d5918... Author: M Bernt m.bernt@ufz.de Date: 2018-11-05 (Mon, 05 Nov 2018)

Changed paths: M lib/galaxy/datatypes/binary.py R lib/galaxy/datatypes/test/diamond.rma A lib/galaxy/datatypes/test/diamond.rma6

Log Message: ----------- rma: renamed test data to rma6

Commit: a3f213e3c5319bd8125e4856e0094fd3cd7ef737 https://github.com/galaxyproject/galaxy/commit/a3f213e3c5319bd8125e4856e0094... Author: Marius van den Beek m.vandenbeek@gmail.com Date: 2018-11-05 (Mon, 05 Nov 2018)

Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py A lib/galaxy/datatypes/test/diamond.rma6

Log Message: ----------- Merge pull request #6962 from bernt-matthias/topic/rma

add RMA6 data type (MEGAN6 read-match archive)

Commit: c1e4b0111a70e3bae63791f60a44e6b14b259a5c https://github.com/galaxyproject/galaxy/commit/c1e4b0111a70e3bae63791f60a44e... Author: Marius van den Beek m.vandenbeek@gmail.com Date: 2018-11-05 (Mon, 05 Nov 2018)

Changed paths: M lib/galaxy/tools/parameters/history_query.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run.py M test/unit/workflows/test_workflow_progress.py

Log Message: ----------- Merge pull request #6911 from jmchilton/workflow_mapping_refactor

Refactor collection mapping workflows toward independence from tools.

Commit: c3dc2392ce1a3c9ca91369caf63fa0b6008820d2 https://github.com/galaxyproject/galaxy/commit/c3dc2392ce1a3c9ca91369caf63fa... Author: Marius van den Beek m.vandenbeek@gmail.com Date: 2018-11-05 (Mon, 05 Nov 2018)

Changed paths: M test/api/test_workflows.py

Log Message: ----------- Merge pull request #6954 from jmchilton/workflow_tests_2

Small API Workflow Test Improvements.

Commit: a53de291fefd34ca9fcdf1a03bacd9739f768edf https://github.com/galaxyproject/galaxy/commit/a53de291fefd34ca9fcdf1a03bacd... Author: Martin Cech marten@bx.psu.edu Date: 2018-11-05 (Mon, 05 Nov 2018)

Changed paths: M .travis.yml M Makefile M client/galaxy/scripts/qunit/test.js A client/galaxy/scripts/sample.test.js A client/galaxy/scripts/unitTestBundle.js R client/karma.config.js A client/karma/karma.config.base.js A client/karma/karma.config.mocha.js A client/karma/karma.config.qunit.js A client/karma/webpack.config.qunit.js A client/karma/webpack.config.unittest.js M client/package.json M client/yarn.lock

Log Message: ----------- Merge pull request #6959 from Nerdinacan/karma_chromeheadless

Switch from PhantomJS to Chrome Headless for unit tests

Commit: d7d5e04f9276ba3c1cd9ef2c1a09ede1fc9f5ed0 https://github.com/galaxyproject/galaxy/commit/d7d5e04f9276ba3c1cd9ef2c1a09e... Author: Mason nerdinacan@gmail.com Date: 2018-11-05 (Mon, 05 Nov 2018)

Changed paths: M client/galaxy/scripts/utils/installMonitor.js

Log Message: ----------- Changed toggle to installation toggle instead of logging toggle

Commit: 5ffd438ebfef26c55b9b11da2f24abd6c2772b43 https://github.com/galaxyproject/galaxy/commit/5ffd438ebfef26c55b9b11da2f24a... Author: Mason nerdinacan@gmail.com Date: 2018-11-05 (Mon, 05 Nov 2018)

Changed paths: M client/galaxy/scripts/utils/installMonitor.js

Log Message: ----------- Updated install console functions and instructions

Commit: 11375a5692fe541e3df257f3ce2e36cd6f39a1f8 https://github.com/galaxyproject/galaxy/commit/11375a5692fe541e3df257f3ce2e3... Author: Mason nerdinacan@gmail.com Date: 2018-11-05 (Mon, 05 Nov 2018)

Changed paths: M .travis.yml M Makefile M client/galaxy/scripts/qunit/test.js A client/galaxy/scripts/sample.test.js A client/galaxy/scripts/unitTestBundle.js M client/galaxy/style/scss/ui.scss R client/karma.config.js A client/karma/karma.config.base.js A client/karma/karma.config.mocha.js A client/karma/karma.config.qunit.js A client/karma/webpack.config.qunit.js A client/karma/webpack.config.unittest.js M client/package.json M client/yarn.lock M config/datatypes_conf.xml.sample M config/migrated_tools_conf.xml.sample M config/shed_tool_conf.xml.sample M doc/source/admin/tool_panel.rst M lib/galaxy/datatypes/binary.py A lib/galaxy/datatypes/converters/tar_to_directory.xml M lib/galaxy/datatypes/data.py A lib/galaxy/datatypes/test/diamond.rma6 M lib/galaxy/tools/__init__.py M lib/galaxy/tools/data/__init__.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/tools/parameters/history_query.py M lib/galaxy/util/compression_utils.py M lib/galaxy/webapps/galaxy/api/datasets.py M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run.py M lib/tool_shed/galaxy_install/migrate/check.py M lib/tool_shed/util/common_util.py M templates/admin/tool_shed_repository/monitor_repository_installation.mako M templates/webapps/galaxy/admin/manage_dependencies.mako M templates/webapps/galaxy/admin/sanitize_whitelist.mako M templates/webapps/galaxy/admin/tool_sheds.mako M templates/webapps/galaxy/admin/view_display_applications.mako M test/api/test_tools.py M test/api/test_tools_upload.py M test/api/test_workflows.py M test/base/populators.py M test/functional/tools/sample_datatypes_conf.xml M test/integration/test_upload_configuration_options.py M test/unit/workflows/test_workflow_progress.py M tools/data_source/upload.py M tools/data_source/upload.xml

Log Message: ----------- Merge branch 'dev' into window_monitor

Commit: cd1a6b2ef8f1169f39505bf67644100657b4a64c https://github.com/galaxyproject/galaxy/commit/cd1a6b2ef8f1169f39505bf676441... Author: guerler aysam.guerler@gmail.com Date: 2018-11-05 (Mon, 05 Nov 2018)

Changed paths: M client/galaxy/style/scss/base.scss M templates/webapps/galaxy/workflow/editor.mako

Log Message: ----------- Move disabled tool style from mako to scss

Commit: 551ac053dd8a5d75f53681a314e4aeed161c629f https://github.com/galaxyproject/galaxy/commit/551ac053dd8a5d75f53681a314e4a... Author: guerler aysam.guerler@gmail.com Date: 2018-11-05 (Mon, 05 Nov 2018)

Changed paths: M templates/webapps/galaxy/workflow/editor.mako

Log Message: ----------- Remove unused post job action form styles

Commit: 3e3021d6f3cbfa4871e6c8836a6ac051f9c3041d https://github.com/galaxyproject/galaxy/commit/3e3021d6f3cbfa4871e6c8836a6ac... Author: guerler aysam.guerler@gmail.com Date: 2018-11-05 (Mon, 05 Nov 2018)

Changed paths: M client/galaxy/style/scss/base.scss M templates/webapps/galaxy/workflow/editor.mako

Log Message: ----------- Remove title and row styles from mako to scss

Commit: 6247955ebb0b3755057a5b41c58175a6effaeec8 https://github.com/galaxyproject/galaxy/commit/6247955ebb0b3755057a5b41c5817... Author: guerler aysam.guerler@gmail.com Date: 2018-11-05 (Mon, 05 Nov 2018)

Changed paths: M client/galaxy/style/scss/base.scss M templates/webapps/galaxy/workflow/editor.mako

Log Message: ----------- Move panel margins from mako to scss

Commit: c7f65aee677fe5cc8c9322e99f5388e842191b39 https://github.com/galaxyproject/galaxy/commit/c7f65aee677fe5cc8c9322e99f538... Author: guerler aysam.guerler@gmail.com Date: 2018-11-05 (Mon, 05 Nov 2018)

Changed paths: M templates/webapps/galaxy/workflow/editor.mako

Log Message: ----------- Remove custom body panel margins

Commit: 1f82b33e704be5121c5c9b2eba4dfa59d8a586aa https://github.com/galaxyproject/galaxy/commit/1f82b33e704be5121c5c9b2eba4df... Author: guerler aysam.guerler@gmail.com Date: 2018-11-05 (Mon, 05 Nov 2018)

Changed paths: M client/galaxy/style/scss/base.scss M templates/webapps/galaxy/workflow/editor.mako

Log Message: ----------- Move ruler style to scss

Commit: 496e353e86aef3868c68756ec0184fe38942ef0c https://github.com/galaxyproject/galaxy/commit/496e353e86aef3868c68756ec0184... Author: guerler aysam.guerler@gmail.com Date: 2018-11-05 (Mon, 05 Nov 2018)

Changed paths: M client/galaxy/style/scss/base.scss M templates/webapps/galaxy/workflow/editor.mako

Log Message: ----------- Move callout for hidden outputs to scss

Commit: 5e0921cc9edd5ea0067b8da02bc119528eed2340 https://github.com/galaxyproject/galaxy/commit/5e0921cc9edd5ea0067b8da02bc11... Author: guerler aysam.guerler@gmail.com Date: 2018-11-05 (Mon, 05 Nov 2018)

Changed paths: M client/galaxy/style/scss/base.scss M templates/webapps/galaxy/workflow/editor.mako

Log Message: ----------- Consolidate module step titles

Commit: 4c2bc2222f5aadd102293cbd081b41511d15cd80 https://github.com/galaxyproject/galaxy/commit/4c2bc2222f5aadd102293cbd081b4... Author: guerler aysam.guerler@gmail.com Date: 2018-11-05 (Mon, 05 Nov 2018)

Changed paths: M templates/webapps/galaxy/workflow/editor.mako

Log Message: ----------- Remove unused form-row-clear specification

Commit: e9255599bd7de37ba57a6b72cad681e7c25a956a https://github.com/galaxyproject/galaxy/commit/e9255599bd7de37ba57a6b72cad68... Author: guerler aysam.guerler@gmail.com Date: 2018-11-05 (Mon, 05 Nov 2018)

Changed paths: M client/galaxy/style/scss/base.scss M templates/webapps/galaxy/workflow/editor.mako

Log Message: ----------- Remove unused title row specification

Commit: e0d891b2741f9e65c526d95bcb3c4474d8a8b9d0 https://github.com/galaxyproject/galaxy/commit/e0d891b2741f9e65c526d95bcb3c4... Author: guerler aysam.guerler@gmail.com Date: 2018-11-05 (Mon, 05 Nov 2018)

Changed paths: M client/galaxy/style/scss/base.scss M templates/webapps/galaxy/workflow/editor.mako

Log Message: ----------- Move error highlighting to scss

Commit: c01f7d2b63cc120cea419eaf06f2ef99879d0b99 https://github.com/galaxyproject/galaxy/commit/c01f7d2b63cc120cea419eaf06f2e... Author: guerler aysam.guerler@gmail.com Date: 2018-11-05 (Mon, 05 Nov 2018)

Changed paths: M client/galaxy/style/scss/base.scss M templates/webapps/galaxy/workflow/editor.mako

Log Message: ----------- Move custom step margins to scss

Commit: 6e41c8a404280e8bd13082b5ea6b7495da7002dd https://github.com/galaxyproject/galaxy/commit/6e41c8a404280e8bd13082b5ea6b7... Author: guerler aysam.guerler@gmail.com Date: 2018-11-05 (Mon, 05 Nov 2018)

Changed paths: M client/galaxy/style/scss/base.scss

Log Message: ----------- Fix callout style, currently global, attached to body

Commit: ec97b380df757fb2c8282850a6b5178430d45ec5 https://github.com/galaxyproject/galaxy/commit/ec97b380df757fb2c8282850a6b51... Author: guerler aysam.guerler@gmail.com Date: 2018-11-05 (Mon, 05 Nov 2018)

Changed paths: M client/galaxy/style/scss/base.scss M templates/webapps/galaxy/workflow/editor.mako

Log Message: ----------- Remove duplicate border highlighting for module forms

Commit: 4417632cea7f90e21962a9f8f4d014644cf219f5 https://github.com/galaxyproject/galaxy/commit/4417632cea7f90e21962a9f8f4d01... Author: guerler aysam.guerler@gmail.com Date: 2018-11-05 (Mon, 05 Nov 2018)

Changed paths: M client/galaxy/style/scss/base.scss M templates/webapps/galaxy/workflow/editor.mako

Log Message: ----------- Consolidate module representation specifications

Commit: f19ac2d05270d06d7f1e5506471d53743506b733 https://github.com/galaxyproject/galaxy/commit/f19ac2d05270d06d7f1e5506471d5... Author: guerler aysam.guerler@gmail.com Date: 2018-11-05 (Mon, 05 Nov 2018)

Changed paths: M templates/webapps/galaxy/workflow/editor.mako

Log Message: ----------- Remove unused panel button styles

Commit: cfc4ed879997670c7963da095b85a06aea6f17ce https://github.com/galaxyproject/galaxy/commit/cfc4ed879997670c7963da095b85a... Author: guerler aysam.guerler@gmail.com Date: 2018-11-05 (Mon, 05 Nov 2018)

Changed paths: M client/galaxy/style/scss/base.scss M templates/webapps/galaxy/workflow/editor.mako

Log Message: ----------- Move callout button specification to scss

Commit: 3fc6191f9562da97bd993816a7d0104046dbc8d7 https://github.com/galaxyproject/galaxy/commit/3fc6191f9562da97bd993816a7d01... Author: guerler aysam.guerler@gmail.com Date: 2018-11-05 (Mon, 05 Nov 2018)

Changed paths: M templates/webapps/galaxy/workflow/editor.mako

Log Message: ----------- Remove unused canvas area styles

Commit: 4b3606f1acd57064c3b4a2da6842a58d5d634a9b https://github.com/galaxyproject/galaxy/commit/4b3606f1acd57064c3b4a2da6842a... Author: Dannon Baker dannon.baker@gmail.com Date: 2018-11-05 (Mon, 05 Nov 2018)

Changed paths: M client/galaxy/scripts/components/admin/DataManager/DataManagerJobs.vue

Log Message: ----------- Target top with rerun to avoid nested Galaxy.

Commit: e9f269393346175c2d88dd6e190d3d00547ef3c6 https://github.com/galaxyproject/galaxy/commit/e9f269393346175c2d88dd6e190d3... Author: Dannon dannon.baker@gmail.com Date: 2018-11-05 (Mon, 05 Nov 2018)

Changed paths: M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/panels/admin-panel.js A client/galaxy/scripts/components/Alert.vue A client/galaxy/scripts/components/admin/DataManager/DataManager.vue A client/galaxy/scripts/components/admin/DataManager/DataManagerJob.vue A client/galaxy/scripts/components/admin/DataManager/DataManagerJobs.vue A client/galaxy/scripts/components/admin/DataManager/DataManagerRouter.vue A client/galaxy/scripts/components/admin/DataManager/DataManagerTable.vue A client/galaxy/scripts/components/admin/DataManager/DataManagerView.vue M client/package.json M client/yarn.lock M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/data_manager.py R templates/webapps/galaxy/data_manager/index.mako R templates/webapps/galaxy/data_manager/manage_data_manager.mako R templates/webapps/galaxy/data_manager/manage_data_table.mako R templates/webapps/galaxy/data_manager/view_job.mako M test/galaxy_selenium/navigation.yml M test/selenium_tests/test_admin_app.py M test/shed_functional/base/twilltestcase.py M test/shed_functional/functional/test_1460_data_managers.py

Log Message: ----------- Merge pull request #6729 from scrathat/admin.data.manager.vue.steps

Vue rewrite of admin data manager (local data) in steps

Commit: 566ffaf9d549e3d1096db4996fc9133f133dee19 https://github.com/galaxyproject/galaxy/commit/566ffaf9d549e3d1096db4996fc91... Author: Enis Afgan afgane@gmail.com Date: 2018-11-05 (Mon, 05 Nov 2018)

Changed paths: M tools/cloud/send.xml

Log Message: ----------- Update send tool help text

Commit: 38e9225aff0997efe3b023cf28ec869faa09d161 https://github.com/galaxyproject/galaxy/commit/38e9225aff0997efe3b023cf28ec8... Author: Dannon Baker dannon.baker@gmail.com Date: 2018-11-05 (Mon, 05 Nov 2018)

Changed paths: M client/galaxy/jsconfig.json M client/galaxy/scripts/onload/index.js M client/galaxy/scripts/sample.test.js M client/galaxy/scripts/unitTestBundle.js M client/galaxy/scripts/utils/installMonitor.js M client/galaxy/scripts/utils/mock.js

Log Message: ----------- Client format

Commit: 4405d15fea61b2610045ecfe4a6a1a0922142df8 https://github.com/galaxyproject/galaxy/commit/4405d15fea61b2610045ecfe4a6a1... Author: Dannon Baker dannon.baker@gmail.com Date: 2018-11-05 (Mon, 05 Nov 2018)

Changed paths: M .gitignore A client/galaxy/jsconfig.json M client/galaxy/scripts/galaxy.js A client/galaxy/scripts/galaxy.monitor.js R client/galaxy/scripts/onload.js A client/galaxy/scripts/onload/index.js A client/galaxy/scripts/onload/loadConfig.js M client/galaxy/scripts/sample.test.js M client/galaxy/scripts/unitTestBundle.js A client/galaxy/scripts/utils/installMonitor.js A client/galaxy/scripts/utils/mock.js A client/galaxy/scripts/utils/serverPath.js M client/webpack.config.js M test/galaxy_selenium/navigates_galaxy.py

Log Message: ----------- Merge branch 'window_monitor' into dev

Commit: 199fe7e0fccbeeb55501bad54f8ae4e44e7c100c https://github.com/galaxyproject/galaxy/commit/199fe7e0fccbeeb55501bad54f8ae... Author: mvdbeek m.vandenbeek@gmail.com Date: 2018-11-05 (Mon, 05 Nov 2018)

Changed paths: M lib/galaxy/managers/workflows.py

Log Message: ----------- Allow saving workflows with input parameters

Commit: 638b1b7581d38b9044e17937f308c82fd36663ee https://github.com/galaxyproject/galaxy/commit/638b1b7581d38b9044e17937f308c... Author: mvdbeek m.vandenbeek@gmail.com Date: 2018-11-05 (Mon, 05 Nov 2018)

Changed paths: M lib/galaxy/workflow/modules.py

Log Message: ----------- Allow inserting input parameter into workflow

Commit: c09d1bc150775909f0e2a8f1c48ad0b2b70afea0 https://github.com/galaxyproject/galaxy/commit/c09d1bc150775909f0e2a8f1c48ad... Author: mvdbeek m.vandenbeek@gmail.com Date: 2018-11-05 (Mon, 05 Nov 2018)

Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-node.js M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M client/galaxy/scripts/mvc/workflow/workflow-view-data.js M client/galaxy/scripts/mvc/workflow/workflow-view-node.js M client/galaxy/scripts/mvc/workflow/workflow-view-terminals.js M lib/galaxy/managers/workflows.py M lib/galaxy/workflow/modules.py

Log Message: ----------- WIP: add StepParameter inputs to workflow editor

In the current state when a text, integer, float, boolean or boolean parameter is set as "Set at Runtime" a new connectable input appears for the tool node, to which a Parameter can be properly dragged and connected.

This still needs a little more separation from data inputs/outputs, and the new connection isn't persisted in a meaningful way.

Commit: 99c270fd77367a813af6202465d5453be78ac4eb https://github.com/galaxyproject/galaxy/commit/99c270fd77367a813af6202465d54... Author: mvdbeek m.vandenbeek@gmail.com Date: 2018-11-05 (Mon, 05 Nov 2018)

Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-node.js M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/workflow/modules.py

Log Message: ----------- Fix rebuilding parameter node

Commit: b0d64a8f09e6dc3d29c069edcb2abe77ee9c3662 https://github.com/galaxyproject/galaxy/commit/b0d64a8f09e6dc3d29c069edcb2ab... Author: mvdbeek m.vandenbeek@gmail.com Date: 2018-11-05 (Mon, 05 Nov 2018)

Changed paths: M lib/galaxy/workflow/modules.py

Log Message: ----------- Fix selecting the correct item from select list

select lists don't take a `value` argument.

Commit: c624cc4bce8b7b2bea9eaf61ecbf8bea485c4640 https://github.com/galaxyproject/galaxy/commit/c624cc4bce8b7b2bea9eaf61ecbf8... Author: mvdbeek m.vandenbeek@gmail.com Date: 2018-11-05 (Mon, 05 Nov 2018)

Changed paths: M lib/galaxy/workflow/modules.py

Log Message: ----------- Fix getting correct type

Commit: 83a25c90e66b52890fcd8ad9288059d87b4f4932 https://github.com/galaxyproject/galaxy/commit/83a25c90e66b52890fcd8ad928805... Author: mvdbeek m.vandenbeek@gmail.com Date: 2018-11-05 (Mon, 05 Nov 2018)

Changed paths: M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py

Log Message: ----------- Fix restoring saved non-data connections in workflow editor

Commit: 4e3004bb250f86b8c16a1c94c8599f497488e732 https://github.com/galaxyproject/galaxy/commit/4e3004bb250f86b8c16a1c94c8599... Author: mvdbeek m.vandenbeek@gmail.com Date: 2018-11-05 (Mon, 05 Nov 2018)

Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-node.js

Log Message: ----------- Fix node.addOuputParameter

Commit: e135fac159e80549ce611a40f4c66598f51632d2 https://github.com/galaxyproject/galaxy/commit/e135fac159e80549ce611a40f4c66... Author: mvdbeek m.vandenbeek@gmail.com Date: 2018-11-05 (Mon, 05 Nov 2018)

Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-node.js

Log Message: ----------- Don't render data inputs on parameter_input node

Commit: 0340dcb18a99d9d7984eb7566b3826290fe90025 https://github.com/galaxyproject/galaxy/commit/0340dcb18a99d9d7984eb7566b382... Author: mvdbeek m.vandenbeek@gmail.com Date: 2018-11-05 (Mon, 05 Nov 2018)

Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-node.js

Log Message: ----------- More defensive runtime check

Commit: 5a5b4abb5bd4b1b142601a94b4498556c4f14946 https://github.com/galaxyproject/galaxy/commit/5a5b4abb5bd4b1b142601a94b4498... Author: mvdbeek m.vandenbeek@gmail.com Date: 2018-11-05 (Mon, 05 Nov 2018)

Changed paths: M lib/galaxy/workflow/modules.py

Log Message: ----------- Allow loading in test-data workfows

Commit: 4812586156b4cf01fe8ee1cb743306cc91ba2c84 https://github.com/galaxyproject/galaxy/commit/4812586156b4cf01fe8ee1cb74330... Author: John Chilton jmchilton@gmail.com Date: 2018-11-05 (Mon, 05 Nov 2018)

Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-view-data.js

Log Message: ----------- Add label to input parameters without labels.

Commit: dbe4033abe74035082b510c862c7729212367341 https://github.com/galaxyproject/galaxy/commit/dbe4033abe74035082b510c862c77... Author: John Chilton jmchilton@gmail.com Date: 2018-11-05 (Mon, 05 Nov 2018)

Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-icons.js

Log Message: ----------- Give parameter inputs a workflow icon.

Commit: 00b8776db521cab884a107f8b66441690f644f88 https://github.com/galaxyproject/galaxy/commit/00b8776db521cab884a107f8b6644... Author: John Chilton jmchilton@gmail.com Date: 2018-11-05 (Mon, 05 Nov 2018)

Changed paths: M lib/galaxy/workflow/run_request.py

Log Message: ----------- Convert raw parameters from map into formal parameters when invoking wfs.

Commit: d74b959419a667b2ff3192c9fde07a2cddc5e90d https://github.com/galaxyproject/galaxy/commit/d74b959419a667b2ff3192c9fde07... Author: John Chilton jmchilton@gmail.com Date: 2018-11-05 (Mon, 05 Nov 2018)

Changed paths: M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py

Log Message: ----------- Revert non-data connection handling, send connections unfiltered to editor.

Commit: 85d777dbe704ccdbf71898853e542c1c2df05303 https://github.com/galaxyproject/galaxy/commit/85d777dbe704ccdbf71898853e542... Author: John Chilton jmchilton@gmail.com Date: 2018-11-05 (Mon, 05 Nov 2018)

Changed paths: M client/galaxy/scripts/mvc/form/form-data.js M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/workflow/workflow-forms.js M client/galaxy/scripts/mvc/workflow/workflow-node.js M lib/galaxy/managers/workflows.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/workflow/modules.py

Log Message: ----------- Separate RuntimeValue into RuntimeValue and ConnectedValue.

Use ConnectedValue values to determine what non-data parameters to display connections for.

Commit: dd8d74f364770a1272555a3753f5d1e1288315e1 https://github.com/galaxyproject/galaxy/commit/dd8d74f364770a1272555a3753f5d... Author: John Chilton jmchilton@gmail.com Date: 2018-11-05 (Mon, 05 Nov 2018)

Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-node.js M client/galaxy/scripts/mvc/workflow/workflow-view-node.js M client/galaxy/scripts/qunit/tests/workflow_editor_tests.js M lib/galaxy/managers/workflows.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run.py M test/api/test_workflows.py

Log Message: ----------- Unify data/non-data input/output handling for workflow editor.

Don't treat data and non-data inputs/outputs different at the API boundary or at the workflow-manager.js level. Keep differences at the level of walking inputs/outputs in the workflow module on the backend and at the terminal definition (models and views) level on the frontend. Make the code and interfaces more consistent in my opinion and is more compatible with future directions I'd like to take things with mix-mode inputs/outputs for CWL.

Commit: 5a99ebd5af9d68f028b86d295846a1c4cefccfb4 https://github.com/galaxyproject/galaxy/commit/5a99ebd5af9d68f028b86d295846a... Author: John Chilton jmchilton@gmail.com Date: 2018-11-05 (Mon, 05 Nov 2018)

Changed paths: M lib/galaxy/managers/workflows.py

Log Message: ----------- Remove filtering of connections for workflow editor.

Things not matching should be handled there.

Commit: 29950be83f8240acba05685b4a057b38d803b445 https://github.com/galaxyproject/galaxy/commit/29950be83f8240acba05685b4a057... Author: John Chilton jmchilton@gmail.com Date: 2018-11-05 (Mon, 05 Nov 2018)

Changed paths: M test/galaxy_selenium/navigation.yml M test/selenium_tests/test_workflow_editor.py

Log Message: ----------- Workflow editor testing for step parameters/connections.

- Fixes and refactoring for existing input tests (toward reuse). - Add simple test for non-data input.

Commit: c42ea4d9c5e38bc365b54d97f51c96def0f3def7 https://github.com/galaxyproject/galaxy/commit/c42ea4d9c5e38bc365b54d97f51c9... Author: Mason nerdinacan@gmail.com Date: 2018-11-05 (Mon, 05 Nov 2018)

Changed paths: M client/galaxy/scripts/onload/index.js M client/galaxy/scripts/qunit/test.js M client/galaxy/scripts/qunit/tests/page_tests.js M client/galaxy/scripts/utils/installMonitor.js M client/webpack.config.js M client/yarn.lock

Log Message: ----------- Fixed monitor Proxy set function

Commit: 9b7b6ab04d4f0eaa6500cabacf632ef45acf5bcf https://github.com/galaxyproject/galaxy/commit/9b7b6ab04d4f0eaa6500cabacf632... Author: Mason nerdinacan@gmail.com Date: 2018-11-05 (Mon, 05 Nov 2018)

Changed paths: A client/galaxy/scripts/libs/jquery.custom.js

Log Message: ----------- Added jquery.custom.js to lib folder

Commit: 258ada862ece5a06b8a86530cd9f22c355a80ac1 https://github.com/galaxyproject/galaxy/commit/258ada862ece5a06b8a86530cd9f2... Author: Slugger70 slugger70@gmail.com Date: 2018-11-06 (Tue, 06 Nov 2018)

Changed paths: M lib/galaxy/datatypes/text.py

Log Message: ----------- Added a metadata element to the biom1 datatype

Commit: 789f7b2d8dd72833e2c295535ca58fb9f46806b5 https://github.com/galaxyproject/galaxy/commit/789f7b2d8dd72833e2c295535ca58... Author: Nicola Soranzo nicola.soranzo@gmail.com Date: 2018-11-06 (Tue, 06 Nov 2018)

Changed paths: M lib/galaxy/datatypes/text.py

Log Message: ----------- As per review

Co-Authored-By: Slugger70 slugger70@gmail.com

Commit: fc53123a94c2ba625c1e6075e0e3a284bddf2d29 https://github.com/galaxyproject/galaxy/commit/fc53123a94c2ba625c1e6075e0e3a... Author: Slugger70 slugger70@gmail.com Date: 2018-11-06 (Tue, 06 Nov 2018)

Changed paths: M lib/galaxy/datatypes/text.py

Log Message: ----------- Changes as per review

Commit: 9d9bc9e27269d347e87846374492ce4a5290dad1 https://github.com/galaxyproject/galaxy/commit/9d9bc9e27269d347e87846374492c... Author: Slugger70 slugger70@gmail.com Date: 2018-11-06 (Tue, 06 Nov 2018)

Changed paths:

Log Message: ----------- Made changes as per review

Commit: 58e705a547fc53a91e46abad12c2ab77838228c2 https://github.com/galaxyproject/galaxy/commit/58e705a547fc53a91e46abad12c2a... Author: M Bernt m.bernt@ufz.de Date: 2018-11-06 (Tue, 06 Nov 2018)

Changed paths: M lib/galaxy/tools/parser/xml.py

Log Message: ----------- changed exit code and regex parsing

- stdio are always prepended to command tag derived exit codes and regexes

Commit: 443170e9128cd785dcfc24f73bddc5bcc1035fa3 https://github.com/galaxyproject/galaxy/commit/443170e9128cd785dcfc24f73bddc... Author: Bjoern Gruening bjoern.gruening@gmail.com Date: 2018-11-06 (Tue, 06 Nov 2018)

Changed paths: M client/galaxy/images/Armitagep_manhattan.png M client/galaxy/images/Armitagep_qqplot.png M client/galaxy/images/add_icon.png M client/galaxy/images/add_icon_dark.png M client/galaxy/images/aggregate_history1.png M client/galaxy/images/aggregate_history2.png M client/galaxy/images/bar_chart.png M client/galaxy/images/bed_warn.png M client/galaxy/images/closebox.png M client/galaxy/images/dat_points_table_brows_1.png M client/galaxy/images/data_empty.png M client/galaxy/images/data_error.png M client/galaxy/images/data_ok.png M client/galaxy/images/data_queued.png M client/galaxy/images/ddarrowsplit.png M client/galaxy/images/delete_tag_icon_gray.png M client/galaxy/images/delete_tag_icon_white.png M client/galaxy/images/documents-stack-faded.png M client/galaxy/images/dropdownarrow.png M client/galaxy/images/error_large.png M client/galaxy/images/error_small.png M client/galaxy/images/fetchTax.png M client/galaxy/images/form_body_bg.png M client/galaxy/images/fugue.png M client/galaxy/images/hatch-023858.png M client/galaxy/images/histogram.png M client/galaxy/images/histogram2.png M client/galaxy/images/history-buttons.png M client/galaxy/images/history-states.png M client/galaxy/images/info_large.png M client/galaxy/images/info_small.png M client/galaxy/images/kendall.png M client/galaxy/images/mag_glass.png M client/galaxy/images/masthead_bg.png M client/galaxy/images/mutation_visualization_example.png M client/galaxy/images/ok_large.png M client/galaxy/images/ok_small.png M client/galaxy/images/overview_arrows.png M client/galaxy/images/question-octagon-frame.png M client/galaxy/images/scatter.png M client/galaxy/images/scatterplot.png M client/galaxy/images/solid_qual.png M client/galaxy/images/sprite-fugue.png M client/galaxy/images/sprite-history-buttons.png M client/galaxy/images/sprite-history-states.png M client/galaxy/images/thumbtack_icon.png M client/galaxy/images/thumbtack_icon_dark.png M client/galaxy/images/wait_large.png M client/galaxy/images/wait_small.png

Log Message: ----------- optimize images with optipng

Commit: f12e548872b0087b4ba8b5828bc80b6aa10207e4 https://github.com/galaxyproject/galaxy/commit/f12e548872b0087b4ba8b5828bc80... Author: John Chilton jmchilton@gmail.com Date: 2018-11-06 (Tue, 06 Nov 2018)

Changed paths: M lib/galaxy/workflow/run.py M test/galaxy_selenium/navigation.yml M test/selenium_tests/test_workflow_run.py

Log Message: ----------- Step parameter workflow run test case and fix.

Commit: 82a8eb05d6f955b027b8c3b9b436171b6da158ea https://github.com/galaxyproject/galaxy/commit/82a8eb05d6f955b027b8c3b9b4361... Author: John Chilton jmchilton@gmail.com Date: 2018-11-06 (Tue, 06 Nov 2018)

Changed paths: M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M client/galaxy/scripts/nls/zh/locale.js M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/blast.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/molecules.py M lib/galaxy/datatypes/neo4j.py M lib/galaxy/jobs/__init__.py M test/api/test_workflows.py

Log Message: ----------- Merge remote-tracking branch 'jmchilton/release_18.09' into dev_merge_1

Commit: b7c8bd47c9079ddb7094eee0ad69005705850488 https://github.com/galaxyproject/galaxy/commit/b7c8bd47c9079ddb7094eee0ad690... Author: Dannon dannon.baker@gmail.com Date: 2018-11-06 (Tue, 06 Nov 2018)

Changed paths: M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M client/galaxy/scripts/nls/zh/locale.js M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/blast.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/molecules.py M lib/galaxy/datatypes/neo4j.py M lib/galaxy/jobs/__init__.py M test/api/test_workflows.py

Log Message: ----------- Merge pull request #6979 from jmchilton/dev_merge_1

Merge 18.09 into dev

Commit: a4f21fca773c91032e11804e4a4c71646c213da0 https://github.com/galaxyproject/galaxy/commit/a4f21fca773c91032e11804e4a4c7... Author: Dannon dannon.baker@gmail.com Date: 2018-11-06 (Tue, 06 Nov 2018)

Changed paths: M client/galaxy/images/Armitagep_manhattan.png M client/galaxy/images/Armitagep_qqplot.png M client/galaxy/images/add_icon.png M client/galaxy/images/add_icon_dark.png M client/galaxy/images/aggregate_history1.png M client/galaxy/images/aggregate_history2.png M client/galaxy/images/bar_chart.png M client/galaxy/images/bed_warn.png M client/galaxy/images/closebox.png M client/galaxy/images/dat_points_table_brows_1.png M client/galaxy/images/data_empty.png M client/galaxy/images/data_error.png M client/galaxy/images/data_ok.png M client/galaxy/images/data_queued.png M client/galaxy/images/ddarrowsplit.png M client/galaxy/images/delete_tag_icon_gray.png M client/galaxy/images/delete_tag_icon_white.png M client/galaxy/images/documents-stack-faded.png M client/galaxy/images/dropdownarrow.png M client/galaxy/images/error_large.png M client/galaxy/images/error_small.png M client/galaxy/images/fetchTax.png M client/galaxy/images/form_body_bg.png M client/galaxy/images/fugue.png M client/galaxy/images/hatch-023858.png M client/galaxy/images/histogram.png M client/galaxy/images/histogram2.png M client/galaxy/images/history-buttons.png M client/galaxy/images/history-states.png M client/galaxy/images/info_large.png M client/galaxy/images/info_small.png M client/galaxy/images/kendall.png M client/galaxy/images/mag_glass.png M client/galaxy/images/masthead_bg.png M client/galaxy/images/mutation_visualization_example.png M client/galaxy/images/ok_large.png M client/galaxy/images/ok_small.png M client/galaxy/images/overview_arrows.png M client/galaxy/images/question-octagon-frame.png M client/galaxy/images/scatter.png M client/galaxy/images/scatterplot.png M client/galaxy/images/solid_qual.png M client/galaxy/images/sprite-fugue.png M client/galaxy/images/sprite-history-buttons.png M client/galaxy/images/sprite-history-states.png M client/galaxy/images/thumbtack_icon.png M client/galaxy/images/thumbtack_icon_dark.png M client/galaxy/images/wait_large.png M client/galaxy/images/wait_small.png

Log Message: ----------- Merge pull request #6980 from bgruening/optipng

optimize images with optipng

Commit: eb57469eef96f7225192128bd846237443e9b437 https://github.com/galaxyproject/galaxy/commit/eb57469eef96f7225192128bd8462... Author: Dannon dannon.baker@gmail.com Date: 2018-11-06 (Tue, 06 Nov 2018)

Changed paths: A client/galaxy/scripts/libs/jquery.custom.js M client/galaxy/scripts/onload/index.js M client/galaxy/scripts/qunit/test.js M client/galaxy/scripts/qunit/tests/page_tests.js M client/galaxy/scripts/utils/installMonitor.js M client/webpack.config.js M client/yarn.lock

Log Message: ----------- Merge pull request #6970 from Nerdinacan/jquery_bundle

Normalized jquery bundle

Commit: 2f2153292b39d3a2718c0950303f2b48b18838c9 https://github.com/galaxyproject/galaxy/commit/2f2153292b39d3a2718c0950303f2... Author: Enis Afgan afgane@gmail.com Date: 2018-11-06 (Tue, 06 Nov 2018)

Changed paths: M config/tool_conf.xml.main M config/tool_conf.xml.sample M lib/galaxy/authnz/managers.py M lib/galaxy/managers/cloud.py M lib/galaxy/tools/__init__.py M lib/galaxy/webapps/galaxy/api/cloud.py M lib/galaxy/webapps/galaxy/buildapp.py A tools/cloud/send.py A tools/cloud/send.xml

Log Message: ----------- Merge pull request #6583 from VJalili/cloud_download_tool

Send data to cloud

Commit: a8eb9463a6778772b7c00cf3e80364cdb5956edd https://github.com/galaxyproject/galaxy/commit/a8eb9463a6778772b7c00cf3e8036... Author: Mason nerdinacan@gmail.com Date: 2018-11-06 (Tue, 06 Nov 2018)

Changed paths: M test/selenium_tests/test_library_contents.py

Log Message: ----------- test/selenium_tests/test_library_contents.py

Commit: 0bc6e35ad60a1f3b4e5db5691cc26fb67728d2bc https://github.com/galaxyproject/galaxy/commit/0bc6e35ad60a1f3b4e5db5691cc26... Author: Slugger70 slugger70@gmail.com Date: 2018-11-07 (Wed, 07 Nov 2018)

Changed paths: M lib/galaxy/datatypes/text.py

Log Message: ----------- Minor alteration for flake8

Commit: 10723c789f83f2a3ec9e4ba73ec3d08321d02ed3 https://github.com/galaxyproject/galaxy/commit/10723c789f83f2a3ec9e4ba73ec3d... Author: Mason nerdinacan@gmail.com Date: 2018-11-06 (Tue, 06 Nov 2018)

Changed paths: M test/selenium_tests/test_library_contents.py

Log Message: ----------- Added white space to pass linter

Commit: 1b18e9ea2dcc403d44a972433c0f75c823107a8c https://github.com/galaxyproject/galaxy/commit/1b18e9ea2dcc403d44a972433c0f7... Author: Mason nerdinacan@gmail.com Date: 2018-11-06 (Tue, 06 Nov 2018)

Changed paths: M test/selenium_tests/test_library_contents.py

Log Message: ----------- More linting fun

Commit: 649d8bad5280174c2f9a74bd847a44ba7158ec3f https://github.com/galaxyproject/galaxy/commit/649d8bad5280174c2f9a74bd847a4... Author: Nuwan Goonasekera nuwan.ag@gmail.com Date: 2018-11-07 (Wed, 07 Nov 2018)

Changed paths: M lib/galaxy/jobs/mapper.py

Log Message: ----------- Added support for overriding the rules module per destination

Commit: 9f8c29520df53ca42e241d69718ddd2e1d37a987 https://github.com/galaxyproject/galaxy/commit/9f8c29520df53ca42e241d69718dd... Author: mvdbeek m.vandenbeek@gmail.com Date: 2018-11-07 (Wed, 07 Nov 2018)

Changed paths: M doc/source/admin/framework_dependencies.rst M scripts/common_startup.sh

Log Message: ----------- Use virtualenv when conda is on PATH

This uses our proper pinned requirements and is sginificantly easier to set up and maintain.

Commit: 09186c991ae88f9f4edf67f4ba98cc73286831b3 https://github.com/galaxyproject/galaxy/commit/09186c991ae88f9f4edf67f4ba98c... Author: Martin Cech marten@bx.psu.edu Date: 2018-11-07 (Wed, 07 Nov 2018)

Changed paths: M test/selenium_tests/test_library_contents.py

Log Message: ----------- Merge pull request #6982 from Nerdinacan/selenium_test_library_contents

Update test/selenium_tests/test_library_contents.py

Commit: be87d2402d09cee0f2e43677f7073f7333876c94 https://github.com/galaxyproject/galaxy/commit/be87d2402d09cee0f2e43677f7073... Author: Nicola Soranzo nicola.soranzo@earlham.ac.uk Date: 2018-11-07 (Wed, 07 Nov 2018)

Changed paths: M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt

Log Message: ----------- Merge branch 'release_18.09' into dev

Commit: fcf451fb887cfb9e86c8b93c11f775793cfce65a https://github.com/galaxyproject/galaxy/commit/fcf451fb887cfb9e86c8b93c11f77... Author: Dannon Baker dannon.baker@gmail.com Date: 2018-11-07 (Wed, 07 Nov 2018)

Changed paths: M config/plugins/visualizations/common/templates/chart_entry_point.mako

Log Message: ----------- Fix charts entrypoint for compatibility with newer chunk changes.

Commit: f0df34eacadf5d6f23bc4791d612352de6fe102c https://github.com/galaxyproject/galaxy/commit/f0df34eacadf5d6f23bc4791d6123... Author: Dannon dannon.baker@gmail.com Date: 2018-11-07 (Wed, 07 Nov 2018)

Changed paths: M client/galaxy/style/scss/base.scss M templates/webapps/galaxy/workflow/editor.mako

Log Message: ----------- Merge pull request #6967 from guerler/workflow_style_1

Refactor workflow editor styles and move from mako to css

Commit: 840e760877c1f232603695d9c9099a8a309957c0 https://github.com/galaxyproject/galaxy/commit/840e760877c1f232603695d9c9099... Author: guerler aysam.guerler@gmail.com Date: 2018-11-07 (Wed, 07 Nov 2018)

Changed paths: M client/galaxy/style/scss/base.scss

Log Message: ----------- Use card styles

Commit: 58a1b4589250866d2de6ffdd2213232cb0d7c9cb https://github.com/galaxyproject/galaxy/commit/58a1b4589250866d2de6ffdd22132... Author: guerler aysam.guerler@gmail.com Date: 2018-11-07 (Wed, 07 Nov 2018)

Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-connector.js M client/galaxy/style/scss/base.scss

Log Message: ----------- Style revision workflow editor

Commit: 2ef314ccd0e10d88ce1f4d1d52220c5cc5c51bc2 https://github.com/galaxyproject/galaxy/commit/2ef314ccd0e10d88ce1f4d1d52220... Author: guerler aysam.guerler@gmail.com Date: 2018-11-07 (Wed, 07 Nov 2018)

Changed paths: R client/galaxy/images/workflow_circle_drag.png R client/galaxy/images/workflow_circle_green.png R client/galaxy/images/workflow_circle_open.png M client/galaxy/scripts/mvc/workflow/workflow-connector.js M client/galaxy/scripts/mvc/workflow/workflow-view-terminals.js M client/galaxy/style/scss/base.scss

Log Message: ----------- Remove legacy png files for workflow editor

Commit: 656433f42802a92ce0fae086d7863b66ac8c4c12 https://github.com/galaxyproject/galaxy/commit/656433f42802a92ce0fae086d7863... Author: guerler aysam.guerler@gmail.com Date: 2018-11-07 (Wed, 07 Nov 2018)

Changed paths: R client/galaxy/images/fugue/asterisk-small-outline.png R client/galaxy/images/fugue/asterisk-small-yellow.png R client/galaxy/images/fugue/asterisk-small.png M client/galaxy/scripts/mvc/workflow/workflow-manager.js M client/galaxy/scripts/mvc/workflow/workflow-view-data.js M client/galaxy/style/scss/base.scss

Log Message: ----------- Replace asterisk png for marked terminal marking with fontawesome icon

Commit: ba2dc44d9db3e9a0881c65e2358cb233c6683a8d https://github.com/galaxyproject/galaxy/commit/ba2dc44d9db3e9a0881c65e2358cb... Author: guerler aysam.guerler@gmail.com Date: 2018-11-07 (Wed, 07 Nov 2018)

Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-view-terminals.js M client/galaxy/style/scss/base.scss

Log Message: ----------- Use icon instead of i as tag for terminal icons

Commit: 64da2ca1f4794befc7ab8634fac63b6b393936b3 https://github.com/galaxyproject/galaxy/commit/64da2ca1f4794befc7ab8634fac63... Author: guerler aysam.guerler@gmail.com Date: 2018-11-07 (Wed, 07 Nov 2018)

Changed paths: M client/galaxy/style/scss/base.scss

Log Message: ----------- Remove fixed icon height

Commit: 9d559753af9c756e90154c11b6c286bbeb593077 https://github.com/galaxyproject/galaxy/commit/9d559753af9c756e90154c11b6c28... Author: guerler aysam.guerler@gmail.com Date: 2018-11-07 (Wed, 07 Nov 2018)

Changed paths: M client/galaxy/style/scss/base.scss M client/galaxy/style/scss/library.scss M client/galaxy/style/scss/list-item.scss M client/galaxy/style/scss/ui/icon-btn.scss

Log Message: ----------- Replace custom maroon highlighting by brand color

Commit: a61017dbc70479d73f6ca944f7f2b1ab793e3df3 https://github.com/galaxyproject/galaxy/commit/a61017dbc70479d73f6ca944f7f2b... Author: guerler aysam.guerler@gmail.com Date: 2018-11-07 (Wed, 07 Nov 2018)

Changed paths: M client/galaxy/style/scss/base.scss

Log Message: ----------- Use panel color for module header backgrounds

Commit: fbf514d2a022a02e3f1cc763451981ff6f73ddb9 https://github.com/galaxyproject/galaxy/commit/fbf514d2a022a02e3f1cc76345198... Author: guerler aysam.guerler@gmail.com Date: 2018-11-07 (Wed, 07 Nov 2018)

Changed paths: M client/galaxy/style/scss/base.scss M client/galaxy/style/scss/theme/blue.scss

Log Message: ----------- Add editor background color to theme file

Commit: 5506acc2f709954aa64a51b85912b8a90e33bfd2 https://github.com/galaxyproject/galaxy/commit/5506acc2f709954aa64a51b85912b... Author: guerler aysam.guerler@gmail.com Date: 2018-11-07 (Wed, 07 Nov 2018)

Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-canvas.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M client/galaxy/style/scss/base.scss M client/galaxy/style/scss/theme/blue.scss M templates/webapps/galaxy/workflow/editor.mako

Log Message: ----------- Revise workflow editor overview panel

Commit: 6dd098f747c89ba3494b64bb5a64dc078bb3d5db https://github.com/galaxyproject/galaxy/commit/6dd098f747c89ba3494b64bb5a64d... Author: Nicola Soranzo nicola.soranzo@gmail.com Date: 2018-11-07 (Wed, 07 Nov 2018)

Changed paths: M lib/galaxy/datatypes/text.py

Log Message: ----------- Simplify code

Commit: 0a6117bcda7baa691d7ec17e89d6e36fdf3e437a https://github.com/galaxyproject/galaxy/commit/0a6117bcda7baa691d7ec17e89d6e... Author: Aysam Guerler aysam.guerler@gmail.com Date: 2018-11-07 (Wed, 07 Nov 2018)

Changed paths: M config/plugins/visualizations/common/templates/chart_entry_point.mako

Log Message: ----------- Merge pull request #6984 from dannon/fix-charts

Fix charts entrypoint for compatibility with newer chunk changes.

Commit: d28ce7686d12b0f0b2b9f6125cd0b78fc745a967 https://github.com/galaxyproject/galaxy/commit/d28ce7686d12b0f0b2b9f6125cd0b... Author: Martin Cech marten@bx.psu.edu Date: 2018-11-07 (Wed, 07 Nov 2018)

Changed paths: M lib/galaxy/webapps/galaxy/controllers/history.py

Log Message: ----------- Merge pull request #6898 from martenson/no-sanitization-db

prevent sanitized history names being saved in database

Commit: dc9c34bef3487e899d5cbeeb7afa1109618a0c64 https://github.com/galaxyproject/galaxy/commit/dc9c34bef3487e899d5cbeeb7afa1... Author: guerler aysam.guerler@gmail.com Date: 2018-11-07 (Wed, 07 Nov 2018)

Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-manager.js M client/galaxy/scripts/mvc/workflow/workflow-view-data.js M client/galaxy/scripts/mvc/workflow/workflow-view-terminals.js M client/galaxy/style/scss/base.scss

Log Message: ----------- Revise connector deletion option, remove from body and move to node, improve css specificity

Commit: 6a9437b5c39d3ab554885c4cfe5f2cb926dfe6e3 https://github.com/galaxyproject/galaxy/commit/6a9437b5c39d3ab554885c4cfe5f2... Author: guerler aysam.guerler@gmail.com Date: 2018-11-07 (Wed, 07 Nov 2018)

Changed paths: M client/galaxy/style/scss/base.scss

Log Message: ----------- Remove unused z-index, previously used for global dom node features

Commit: 3379d3e98116f9904f72076db4c46beb1ae614e1 https://github.com/galaxyproject/galaxy/commit/3379d3e98116f9904f72076db4c46... Author: guerler aysam.guerler@gmail.com Date: 2018-11-07 (Wed, 07 Nov 2018)

Changed paths: M client/galaxy/scripts/layout/panel.js M client/galaxy/style/scss/base.scss M templates/webapps/galaxy/workflow/editor.mako

Log Message: ----------- Move style spec for panel buttons from mako to scss file, revise editor workflow title

Commit: 21599376501e7a740f8d2700b2463024f02ca58e https://github.com/galaxyproject/galaxy/commit/21599376501e7a740f8d2700b2463... Author: Jim Johnson jj@umn.edu Date: 2018-11-07 (Wed, 07 Nov 2018)

Changed paths: M .ci/jenkins/selenium-py3/run_tests.sh M .gitignore M .travis.yml M Makefile M client/.babelrc R client/GruntFile.js M client/README.md A client/galaxy/docs/README.md M client/galaxy/docs/bootstrap.md M client/galaxy/docs/galaxy-buttons.md M client/galaxy/docs/galaxy-forms.md M client/galaxy/docs/galaxy-masthead.md M client/galaxy/docs/galaxy-menus.md M client/galaxy/docs/galaxy-messages.md M client/galaxy/docs/galaxy-panels.md M client/galaxy/docs/galaxy-tables.md M client/galaxy/docs/galaxy-tabs.md A client/galaxy/images/Armitagep_manhattan.png A client/galaxy/images/Armitagep_qqplot.png A client/galaxy/images/add_icon.png A client/galaxy/images/add_icon_dark.png A client/galaxy/images/aggregate_history1.png A client/galaxy/images/aggregate_history2.png A client/galaxy/images/bar_chart.png A client/galaxy/images/base_bg.png A client/galaxy/images/bed_warn.png A client/galaxy/images/button_bar_bg_light.png A client/galaxy/images/circle.py A client/galaxy/images/closebox.png A client/galaxy/images/dat_points_table_brows_1.png A client/galaxy/images/data_empty.png A client/galaxy/images/data_error.png A client/galaxy/images/data_ok.png A client/galaxy/images/data_queued.png A client/galaxy/images/data_running.gif A client/galaxy/images/ddarrowsplit.png A client/galaxy/images/delete.gif A client/galaxy/images/delete_tag_icon_gray.png A client/galaxy/images/delete_tag_icon_white.png A client/galaxy/images/documents-stack-faded.png A client/galaxy/images/documents-stack.png A client/galaxy/images/done_message_icon.png A client/galaxy/images/dropdownarrow.png A client/galaxy/images/error_bg.png A client/galaxy/images/error_icon.svg A client/galaxy/images/error_large.png A client/galaxy/images/error_message_icon.png A client/galaxy/images/error_small.png A client/galaxy/images/fetchTax.png A client/galaxy/images/footer_title_bg.png A client/galaxy/images/form_body_bg.png A client/galaxy/images/form_title_bg.png A client/galaxy/images/fugue.png A client/galaxy/images/fugue/application-dock-270-bw.png A client/galaxy/images/fugue/application-dock-270.png A client/galaxy/images/fugue/arrow-000-small-bw.png A client/galaxy/images/fugue/arrow-090.png A client/galaxy/images/fugue/arrow-circle.png A client/galaxy/images/fugue/arrow-resize-090-bw.png A client/galaxy/images/fugue/arrow-resize-090.png A client/galaxy/images/fugue/arrow-split-bw.png A client/galaxy/images/fugue/arrow-split.png A client/galaxy/images/fugue/arrow-transition-270-bw.png A client/galaxy/images/fugue/arrow-transition-bw.png A client/galaxy/images/fugue/asterisk-small-outline.png A client/galaxy/images/fugue/asterisk-small-yellow.png A client/galaxy/images/fugue/asterisk-small.png A client/galaxy/images/fugue/block--plus-bw.png A client/galaxy/images/fugue/block--plus.png A client/galaxy/images/fugue/bookmarks-bw.png A client/galaxy/images/fugue/bookmarks.png A client/galaxy/images/fugue/bug.png A client/galaxy/images/fugue/chart.png A client/galaxy/images/fugue/chevron-expand-bw.png A client/galaxy/images/fugue/chevron-expand.png A client/galaxy/images/fugue/chevron.png A client/galaxy/images/fugue/control-270.png A client/galaxy/images/fugue/cross-button.png A client/galaxy/images/fugue/cross-circle-bw.png A client/galaxy/images/fugue/cross-circle.png A client/galaxy/images/fugue/cross-small-bw.png A client/galaxy/images/fugue/cross.png A client/galaxy/images/fugue/disk--arrow-bw.png A client/galaxy/images/fugue/disk--arrow.png A client/galaxy/images/fugue/disk.png A client/galaxy/images/fugue/exclamation.png A client/galaxy/images/fugue/external.png A client/galaxy/images/fugue/eye.png A client/galaxy/images/fugue/gear-bw.png A client/galaxy/images/fugue/gear.png A client/galaxy/images/fugue/globe-bw.png A client/galaxy/images/fugue/globe.png A client/galaxy/images/fugue/hammer-bw.png A client/galaxy/images/fugue/hammer.png A client/galaxy/images/fugue/information-white.png A client/galaxy/images/fugue/layer-transparent-bw.png A client/galaxy/images/fugue/layer-transparent.png A client/galaxy/images/fugue/layers-stack-bw.png A client/galaxy/images/fugue/layers-stack.png A client/galaxy/images/fugue/magnifier-left.png A client/galaxy/images/fugue/magnifier-zoom-out.png A client/galaxy/images/fugue/magnifier-zoom.png A client/galaxy/images/fugue/navigation.png A client/galaxy/images/fugue/pencil-small.png A client/galaxy/images/fugue/pencil.png A client/galaxy/images/fugue/plus-button-bw.png A client/galaxy/images/fugue/plus-button.png A client/galaxy/images/fugue/plus-circle.png A client/galaxy/images/fugue/sticky-note-text.png A client/galaxy/images/fugue/tag--plus.png A client/galaxy/images/fugue/tag-label.png A client/galaxy/images/fugue/tags.png A client/galaxy/images/fugue/toggle-bw.png A client/galaxy/images/fugue/toggle-expand-bw.png A client/galaxy/images/fugue/toggle-expand.png A client/galaxy/images/fugue/toggle.png A client/galaxy/images/fugue/toolbox-bw.png A client/galaxy/images/fugue/toolbox.png A client/galaxy/images/fugue/ui-slider-050-bw.png A client/galaxy/images/fugue/ui-slider-050.png A client/galaxy/images/galaxy_icons.svg A client/galaxy/images/galaxy_spinner.fla A client/galaxy/images/gray_bg.png A client/galaxy/images/hatch-023858.png A client/galaxy/images/hgrad.png A client/galaxy/images/hgrad_over.png A client/galaxy/images/histogram.png A client/galaxy/images/histogram2.png A client/galaxy/images/history-buttons.png A client/galaxy/images/history-states.png A client/galaxy/images/info_icon.svg A client/galaxy/images/info_large.png A client/galaxy/images/info_message_icon.png A client/galaxy/images/info_small.png A client/galaxy/images/jstree/32px.png A client/galaxy/images/jstree/40px.png A client/galaxy/images/jstree/throbber.gif A client/galaxy/images/kendall.png A client/galaxy/images/largespinner.gif A client/galaxy/images/layout_callout_top.png A 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Log Message: ----------- Merge remote-tracking branch 'galaxyproject/dev' into dev

Commit: d5b46e99d234a615d06b1376bf57e1ada49154c9 https://github.com/galaxyproject/galaxy/commit/d5b46e99d234a615d06b1376bf57e... Author: Jim Johnson jj@umn.edu Date: 2018-11-07 (Wed, 07 Nov 2018)

Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/sequence.py A lib/galaxy/datatypes/test/sequence.fastg

Log Message: ----------- datatype_fastg

FASTG is a format for faithfully representing genome assemblies in the face of allelic polymorphism and assembly uncertainty. http://fastg.sourceforge.net/FASTG_Spec_v1.00.pdf This format can be an output for metagenomics applications metapades and megahit. It is a required input for Graph2Pro-var application that generates putative protein sequences for the variant assemblies described by the FASTG format file.

Commit: e4c00af38d387ee860050916e6b2c28f57b2fd4e https://github.com/galaxyproject/galaxy/commit/e4c00af38d387ee860050916e6b2c... Author: Nicola Soranzo nicola.soranzo@earlham.ac.uk Date: 2018-11-08 (Thu, 08 Nov 2018)

Changed paths: M doc/schema_template.md M lib/galaxy/tools/xsd/galaxy.xsd

Log Message: ----------- Merge branch 'release_18.09' into dev

Commit: f9a84b0ffe36a79df7c83d7fcca23efa30f07d89 https://github.com/galaxyproject/galaxy/commit/f9a84b0ffe36a79df7c83d7fcca23... Author: Nicola Soranzo nicola.soranzo@gmail.com Date: 2018-11-08 (Thu, 08 Nov 2018)

Changed paths: M lib/galaxy/datatypes/text.py

Log Message: ----------- Merge pull request #6972 from Slugger70/biom_datatype_changes

Added a metadata element to the biom1 datatype

Commit: ff4232b8b65b91969ae09f315b2955d44fcc4348 https://github.com/galaxyproject/galaxy/commit/ff4232b8b65b91969ae09f315b295... Author: Nicola Soranzo nicola.soranzo@earlham.ac.uk Date: 2018-11-08 (Thu, 08 Nov 2018)

Changed paths: M lib/galaxy/datatypes/set_metadata_tool.xml

Log Message: ----------- Use ``detect_errors="exit_code"`` in ``__SET_METADATA__`` tool

Commit: ebb6e78f0d86555be0b53d635f076cae3d945eb2 https://github.com/galaxyproject/galaxy/commit/ebb6e78f0d86555be0b53d635f076... Author: John Chilton jmchilton@gmail.com Date: 2018-11-08 (Thu, 08 Nov 2018)

Changed paths: M .ci/jenkins/api/run_tests.sh M .ci/jenkins/framework/run_tests.sh M .ci/jenkins/integration/run_tests.sh M .ci/jenkins/main-tools/run_tests.sh M .ci/jenkins/selenium/run_tests.sh M .ci/jenkins/toolshed/run_tests.sh

Log Message: ----------- Don't mount external /tmp for tests.

Nate wants the file busy errors back ;).

Commit: e8dbb8c58ab78a75044b5a5ebdd9f8dfb442aeac https://github.com/galaxyproject/galaxy/commit/e8dbb8c58ab78a75044b5a5ebdd9f... Author: Dannon Baker dannon.baker@gmail.com Date: 2018-11-08 (Thu, 08 Nov 2018)

Changed paths: M scripts/common_startup.sh

Log Message: ----------- Upgrade nodeenv's nodejs to 10.13.0 LTS, now that the client build works fine with v10

Commit: a3badf62478f975bb0f9b1ca339d14f74116c4be https://github.com/galaxyproject/galaxy/commit/a3badf62478f975bb0f9b1ca339d1... Author: Marius van den Beek m.vandenbeek@gmail.com Date: 2018-11-08 (Thu, 08 Nov 2018)

Changed paths: M config/datatypes_conf.xml.sample

Log Message: ----------- Update config/datatypes_conf.xml.sample

Co-Authored-By: jj-umn jj@umn.edu

Commit: 8dc824e4831aca566d65e3f488cd8f0e8224c014 https://github.com/galaxyproject/galaxy/commit/8dc824e4831aca566d65e3f488cd8... Author: Jim Johnson jj@umn.edu Date: 2018-11-08 (Thu, 08 Nov 2018)

Changed paths: M lib/galaxy/datatypes/sequence.py

Log Message: ----------- Update sequence.py

Fix typo for properties.

Commit: 7966ca5a95d57ee986621bd180e3ff8858e1624c https://github.com/galaxyproject/galaxy/commit/7966ca5a95d57ee986621bd180e3f... Author: Marius van den Beek m.vandenbeek@gmail.com Date: 2018-11-08 (Thu, 08 Nov 2018)

Changed paths: M .ci/jenkins/api/run_tests.sh M .ci/jenkins/framework/run_tests.sh M .ci/jenkins/integration/run_tests.sh M .ci/jenkins/main-tools/run_tests.sh M .ci/jenkins/selenium/run_tests.sh M .ci/jenkins/toolshed/run_tests.sh

Log Message: ----------- Merge pull request #6990 from jmchilton/skip_mounting_external_tmp_in_ci_tests

Don't mount external /tmp for tests.

Commit: 03794ce21aabe40bc942eed7ef3442ec9b0960b6 https://github.com/galaxyproject/galaxy/commit/03794ce21aabe40bc942eed7ef344... Author: Sergey Golitsynskiy sgolitsynskiy@gmail.com Date: 2018-11-08 (Thu, 08 Nov 2018)

Changed paths: M doc/source/admin/jobs.md

Log Message: ----------- Fix broken links on Job Configuration page

Commit: 46126cda099095c70079f3f297201f01e1350df1 https://github.com/galaxyproject/galaxy/commit/46126cda099095c70079f3f297201... Author: Martin Cech marten@bx.psu.edu Date: 2018-11-08 (Thu, 08 Nov 2018)

Changed paths: M doc/source/admin/jobs.md

Log Message: ----------- Merge pull request #6992 from ic4f/dev

Fix broken links on Job Configuration page (documentation)

Commit: 4c71bb43a36ad173718c2f89b4fabaa632e11515 https://github.com/galaxyproject/galaxy/commit/4c71bb43a36ad173718c2f89b4fab... Author: Jim Johnson jj@umn.edu Date: 2018-11-08 (Thu, 08 Nov 2018)

Changed paths: M lib/galaxy/datatypes/sequence.py

Log Message: ----------- Update sequence.py

remove extraneous line that was pasted in.

Commit: 65979e473c5623a5116819bd93c182744117e6f0 https://github.com/galaxyproject/galaxy/commit/65979e473c5623a5116819bd93c18... Author: Nuwan Goonasekera nuwan.ag@gmail.com Date: 2018-11-09 (Fri, 09 Nov 2018)

Changed paths: M test/unit/jobs/test_mapper.py A test/unit/jobs/test_rules_override/10_rule.py A test/unit/jobs/test_rules_override/__init__.py

Log Message: ----------- Added test for rules module overriding

Commit: 33b7f0f9d1e105dfbcbdab0a92081a9302cfe7eb https://github.com/galaxyproject/galaxy/commit/33b7f0f9d1e105dfbcbdab0a92081... Author: Nuwan Goonasekera nuwan.ag@gmail.com Date: 2018-11-09 (Fri, 09 Nov 2018)

Changed paths: M lib/galaxy/jobs/mapper.py

Log Message: ----------- Refactor to use importlib

Commit: 4b5312fe80fe4d8bc0a429229d84366b630d8eac https://github.com/galaxyproject/galaxy/commit/4b5312fe80fe4d8bc0a429229d843... Author: Nuwan Goonasekera nuwan.ag@gmail.com Date: 2018-11-09 (Fri, 09 Nov 2018)

Changed paths: M lib/galaxy/queue_worker.py M lib/galaxy/webapps/galaxy/config_watchers.py M test/unit/unittest_utils/galaxy_mock.py

Log Message: ----------- Updated watchers to reload rule module overrides

Commit: bf1f2fe0ab5248acd86d646f1c80314561c0cdc2 https://github.com/galaxyproject/galaxy/commit/bf1f2fe0ab5248acd86d646f1c803... Author: Nuwan Goonasekera nuwan.ag@gmail.com Date: 2018-11-09 (Fri, 09 Nov 2018)

Changed paths: M lib/galaxy/containers/__init__.py M lib/galaxy/jobs/mapper.py M lib/galaxy/jobs/runners/state_handler_factory.py M lib/galaxy/tools/lint.py M lib/galaxy/util/plugin_config.py M lib/galaxy/util/submodules.py M lib/galaxy/webapps/galaxy/config_watchers.py M test/unit/jobs/test_mapper.py

Log Message: ----------- Refactor submodule imports

Commit: 302a16da00d2c3c31a07160bbfe8d94552bce0a4 https://github.com/galaxyproject/galaxy/commit/302a16da00d2c3c31a07160bbfe8d... Author: guerler aysam.guerler@gmail.com Date: 2018-11-08 (Thu, 08 Nov 2018)

Changed paths: M client/galaxy/scripts/qunit/tests/workflow_editor_tests.js

Log Message: ----------- Fix qunit test color

Commit: e6faaa427e2a9f01540429d949d8b978961a09bc https://github.com/galaxyproject/galaxy/commit/e6faaa427e2a9f01540429d949d8b... Author: guerler aysam.guerler@gmail.com Date: 2018-11-08 (Thu, 08 Nov 2018)

Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-view-terminals.js

Log Message: ----------- Remove hard-coded style attribute from drag terminal

Commit: f21a3dd81572d341ae28e2bd62512fb849e6fecc https://github.com/galaxyproject/galaxy/commit/f21a3dd81572d341ae28e2bd62512... Author: Jim Johnson jj@umn.edu Date: 2018-11-08 (Thu, 08 Nov 2018)

Changed paths: M lib/galaxy/datatypes/sequence.py

Log Message: ----------- Update sequence.py

Line after header must not be empty or start with '>'

Commit: 8ea6fff8d82ad230689cf2fd47e39c8e9b158b47 https://github.com/galaxyproject/galaxy/commit/8ea6fff8d82ad230689cf2fd47e39... Author: guerler aysam.guerler@gmail.com Date: 2018-11-08 (Thu, 08 Nov 2018)

Changed paths: M test/galaxy_selenium/navigation.yml

Log Message: ----------- Fix selenium tests

Commit: 4add47b2642a9719351e417e016945eadd3cfd27 https://github.com/galaxyproject/galaxy/commit/4add47b2642a9719351e417e01694... Author: Mason nerdinacan@gmail.com Date: 2018-11-08 (Thu, 08 Nov 2018)

Changed paths: M client/galaxy/scripts/apps/extended.js M client/galaxy/scripts/galaxy.pages.js M client/galaxy/scripts/libs/jquery.custom.js R client/galaxy/scripts/libs/jquery/jstorage.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M client/galaxy/scripts/qunit/test-app.js M client/galaxy/scripts/utils/metrics-logger.js M client/package.json M client/webpack.config.js M client/yarn.lock M templates/admin/tool_shed_repository/manage_repository.mako M templates/admin/tool_shed_repository/reselect_tool_panel_section.mako M templates/admin/tool_shed_repository/select_tool_panel_section.mako M templates/webapps/tool_shed/repository/common.mako M templates/webapps/tool_shed/repository/manage_repository.mako M templates/webapps/tool_shed/repository/preview_tools_in_changeset.mako M templates/webapps/tool_shed/repository/view_repository.mako

Log Message: ----------- Replaced jStorage with store

Commit: 99ca7939acec122a252c15733ff0da18814f880b https://github.com/galaxyproject/galaxy/commit/99ca7939acec122a252c15733ff0d... Author: guerler aysam.guerler@gmail.com Date: 2018-11-08 (Thu, 08 Nov 2018)

Changed paths: M client/galaxy/style/scss/base.scss

Log Message: ----------- Improve delete option alignment

Commit: fc66e88642d0d1c00c24b4507a317ca3c65dd348 https://github.com/galaxyproject/galaxy/commit/fc66e88642d0d1c00c24b4507a317... Author: Mason nerdinacan@gmail.com Date: 2018-11-09 (Fri, 09 Nov 2018)

Changed paths: M client/galaxy/scripts/libs/jquery.custom.js

Log Message: ----------- Update jquery.custom.js

Committing just to make the tests run again.

Commit: f8d50824acf2a8f6cf6bd324f5607ebb99379629 https://github.com/galaxyproject/galaxy/commit/f8d50824acf2a8f6cf6bd324f5607... Author: Mason nerdinacan@gmail.com Date: 2018-11-09 (Fri, 09 Nov 2018)

Changed paths: M templates/webapps/tool_shed/repository/common.mako

Log Message: ----------- Removed debugger statement

Commit: a64fa50c760484d5710588c89600a4597caba10c https://github.com/galaxyproject/galaxy/commit/a64fa50c760484d5710588c89600a... Author: Mason nerdinacan@gmail.com Date: 2018-11-09 (Fri, 09 Nov 2018)

Changed paths: M client/galaxy/scripts/libs/jquery.custom.js

Log Message: ----------- Merge branch 'replace_jstorage' of https://github.com/Nerdinacan/galaxy into replace_jstorage

Commit: fc87b19a1cdd14965ed85fe750b17698bea30ebd https://github.com/galaxyproject/galaxy/commit/fc87b19a1cdd14965ed85fe750b17... Author: Martin Cech marten@bx.psu.edu Date: 2018-11-09 (Fri, 09 Nov 2018)

Changed paths: M client/galaxy/scripts/apps/extended.js M client/galaxy/scripts/galaxy.pages.js M client/galaxy/scripts/libs/jquery.custom.js R client/galaxy/scripts/libs/jquery/jstorage.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M client/galaxy/scripts/qunit/test-app.js M client/galaxy/scripts/utils/metrics-logger.js M client/package.json M client/webpack.config.js M client/yarn.lock M templates/admin/tool_shed_repository/manage_repository.mako M templates/admin/tool_shed_repository/reselect_tool_panel_section.mako M templates/admin/tool_shed_repository/select_tool_panel_section.mako M templates/webapps/tool_shed/repository/common.mako M templates/webapps/tool_shed/repository/manage_repository.mako M templates/webapps/tool_shed/repository/preview_tools_in_changeset.mako M templates/webapps/tool_shed/repository/view_repository.mako

Log Message: ----------- Merge pull request #6994 from Nerdinacan/replace_jstorage

Replaced jStorage with store

Commit: e5c5cd284d6ed927667f330bfd579092f281e5d6 https://github.com/galaxyproject/galaxy/commit/e5c5cd284d6ed927667f330bfd579... Author: Jim Johnson jj@umn.edu Date: 2018-11-09 (Fri, 09 Nov 2018)

Changed paths: M lib/galaxy/datatypes/sequence.py

Log Message: ----------- Update sequence.py

Fix a couple of typos.

Commit: 588dbfaa68d5a39cd7a153b785f0dcb097bb39af https://github.com/galaxyproject/galaxy/commit/588dbfaa68d5a39cd7a153b785f0d... Author: Martin Cech marten@bx.psu.edu Date: 2018-11-09 (Fri, 09 Nov 2018)

Changed paths: M lib/galaxy/tools/data_manager/manager.py

Log Message: ----------- Merge pull request #6682 from pvanheus/patch-5

Trim whitespace from data manager conf paths

Commit: 97ba92f3cffd0c17353595c61bd5d22c7a4e8c4e https://github.com/galaxyproject/galaxy/commit/97ba92f3cffd0c17353595c61bd5d... Author: M Bernt m.bernt@ufz.de Date: 2018-11-09 (Fri, 09 Nov 2018)

Changed paths: M scripts/drmaa_external_runner.py

Log Message: ----------- external_runner: load json template first

if the JSON is loaded first the cluster_files_directory does not need to be accessible by the real user (ie all users)

Commit: c95cc50282873761f83ae930bcb3f652922a690a https://github.com/galaxyproject/galaxy/commit/c95cc50282873761f83ae930bcb3f... Author: guerler aysam.guerler@gmail.com Date: 2018-11-09 (Fri, 09 Nov 2018)

Changed paths: M .ci/jenkins/api/run_tests.sh M .ci/jenkins/framework/run_tests.sh M .ci/jenkins/integration/run_tests.sh M .ci/jenkins/main-tools/run_tests.sh M .ci/jenkins/selenium/run_tests.sh M .ci/jenkins/toolshed/run_tests.sh M client/galaxy/scripts/apps/extended.js M client/galaxy/scripts/galaxy.pages.js M client/galaxy/scripts/libs/jquery.custom.js R client/galaxy/scripts/libs/jquery/jstorage.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M client/galaxy/scripts/qunit/test-app.js M client/galaxy/scripts/utils/metrics-logger.js M client/package.json M client/webpack.config.js M client/yarn.lock M config/plugins/visualizations/common/templates/chart_entry_point.mako M doc/schema_template.md M doc/source/admin/jobs.md M lib/galaxy/datatypes/text.py M lib/galaxy/tools/data_manager/manager.py M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/webapps/galaxy/controllers/history.py M templates/admin/tool_shed_repository/manage_repository.mako M templates/admin/tool_shed_repository/reselect_tool_panel_section.mako M templates/admin/tool_shed_repository/select_tool_panel_section.mako M templates/webapps/tool_shed/repository/common.mako M templates/webapps/tool_shed/repository/manage_repository.mako M templates/webapps/tool_shed/repository/preview_tools_in_changeset.mako M templates/webapps/tool_shed/repository/view_repository.mako

Log Message: ----------- Merge branch 'dev' into workflow_style_2

Commit: a882ccc88b1b79cd78550161b40507a9da1b2075 https://github.com/galaxyproject/galaxy/commit/a882ccc88b1b79cd78550161b4050... Author: Dannon Baker dannon.baker@gmail.com Date: 2018-11-09 (Fri, 09 Nov 2018)

Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-view-data.js M client/galaxy/scripts/mvc/workflow/workflow-view-terminals.js M client/galaxy/style/scss/base.scss

Log Message: ----------- Client format

Commit: 4e8922298010deee8879862200989de1902aff48 https://github.com/galaxyproject/galaxy/commit/4e8922298010deee8879862200989... Author: Dannon dannon.baker@gmail.com Date: 2018-11-09 (Fri, 09 Nov 2018)

Changed paths: M lib/galaxy/managers/cloud.py M lib/galaxy/webapps/galaxy/api/cloud.py M lib/galaxy/webapps/galaxy/buildapp.py

Log Message: ----------- Merge pull request #6899 from VJalili/refactor_cloud_upload

Refactor cloud "Upload" > "Get"

Commit: fdb571f57dadb3ab23a61cc369f766ef1e16fe12 https://github.com/galaxyproject/galaxy/commit/fdb571f57dadb3ab23a61cc369f76... Author: Martin Cech marten@bx.psu.edu Date: 2018-11-09 (Fri, 09 Nov 2018)

Changed paths: M scripts/common_startup.sh

Log Message: ----------- Merge pull request #6991 from dannon/node_lts_upgrade

Upgrade nodeenv's nodejs to 10.13.0 LTS

Commit: 346b1bbfae5674a0212f626a5b9e4bd929fac889 https://github.com/galaxyproject/galaxy/commit/346b1bbfae5674a0212f626a5b9e4... Author: Martin Cech marten@bx.psu.edu Date: 2018-11-09 (Fri, 09 Nov 2018)

Changed paths: M lib/galaxy/model/__init__.py

Log Message: ----------- Merge pull request #6757 from natefoo/repr-model-objects

Give all model objects with an id a __repr__ that includes the id

Commit: eeca6f37a3b1c406f2389a32939b62269b682561 https://github.com/galaxyproject/galaxy/commit/eeca6f37a3b1c406f2389a32939b6... Author: Martin Cech marten@bx.psu.edu Date: 2018-11-09 (Fri, 09 Nov 2018)

Changed paths: M lib/galaxy/model/__init__.py

Log Message: ----------- Merge pull request #6784 from dpryan79/purged_library_datasets

Prevent errors when a library dataset has been purged from disk

Commit: 880605f17d9bd337789b783840c0fb4d35ddbe9d https://github.com/galaxyproject/galaxy/commit/880605f17d9bd337789b783840c0f... Author: Qiang Gu guqiang01@gmail.com Date: 2018-11-09 (Fri, 09 Nov 2018)

Changed paths: M tools/filters/joiner.xml

Log Message: ----------- change join two dataset output format to auto

Commit: a3fd7084e2f02a9e9bc5383cd7f76532450774e9 https://github.com/galaxyproject/galaxy/commit/a3fd7084e2f02a9e9bc5383cd7f76... Author: Dannon Baker dannon.baker@gmail.com Date: 2018-11-09 (Fri, 09 Nov 2018)

Changed paths: M lib/galaxy/webapps/galaxy/controllers/history.py

Log Message: ----------- Exclude library associated datasets from history make-all-private functionality.

Commit: cc53b07253538e192b8196dee300aefaf8e2fde5 https://github.com/galaxyproject/galaxy/commit/cc53b07253538e192b8196dee300a... Author: Dannon Baker dannon.baker@gmail.com Date: 2018-11-09 (Fri, 09 Nov 2018)

Changed paths: M client/galaxy/scripts/mvc/history/options-menu.js M client/galaxy/scripts/mvc/user/user-preferences.js

Log Message: ----------- Update messaging to indicate library datasets are not included in the privacy pass.

Commit: d2f01b3d000d68378e456aa46e5ec32a9fea506c https://github.com/galaxyproject/galaxy/commit/d2f01b3d000d68378e456aa46e5ec... Author: Qiang Gu 36086881+qiagu@users.noreply.github.com Date: 2018-11-09 (Fri, 09 Nov 2018)

Changed paths: M tools/filters/joiner.xml

Log Message: ----------- Update joiner.xml

Commit: 5d38e558f27b2ec14088376ec1a07c3bf4b25d08 https://github.com/galaxyproject/galaxy/commit/5d38e558f27b2ec14088376ec1a07... Author: Dannon Baker dannon.baker@gmail.com Date: 2018-11-09 (Fri, 09 Nov 2018)

Changed paths: M client/galaxy/scripts/mvc/history/options-menu.js M lib/galaxy/webapps/galaxy/controllers/history.py

Log Message: ----------- Resolve two issues from refactoring.

Commit: 9b481ba9d7d34e101d54ae1ed0821f6a05b27be0 https://github.com/galaxyproject/galaxy/commit/9b481ba9d7d34e101d54ae1ed0821... Author: Dannon Baker dannon.baker@gmail.com Date: 2018-11-09 (Fri, 09 Nov 2018)

Changed paths: M client/galaxy/scripts/apps/analysis.js

Log Message: ----------- Client format

Commit: 4960e08d2ab285e8d02f8498d773a393198a7e01 https://github.com/galaxyproject/galaxy/commit/4960e08d2ab285e8d02f8498d773a... Author: Martin Cech marten@bx.psu.edu Date: 2018-11-09 (Fri, 09 Nov 2018)

Changed paths: M client/galaxy/scripts/layout/data.js

Log Message: ----------- Merge pull request #6693 from guerler/create_history_entry

Add utility function to create history entries

Commit: 5f2c785d66f76467dff23c6cc2edfcf9785e0bdd https://github.com/galaxyproject/galaxy/commit/5f2c785d66f76467dff23c6cc2edf... Author: Martin Cech marten@bx.psu.edu Date: 2018-11-09 (Fri, 09 Nov 2018)

Changed paths: M lib/galaxy/datatypes/set_metadata_tool.xml

Log Message: ----------- Merge pull request #6989 from nsoranzo/set_metadata_detect_errors

Use ``detect_errors="exit_code"`` in ``__SET_METADATA__`` tool

Commit: aaf49d6d067e84dbf31b52a45dbe7d7156dd59f3 https://github.com/galaxyproject/galaxy/commit/aaf49d6d067e84dbf31b52a45dbe7... Author: Marius van den Beek m.vandenbeek@gmail.com Date: 2018-11-09 (Fri, 09 Nov 2018)

Changed paths: M tools/filters/joiner.xml

Log Message: ----------- Update tools/filters/joiner.xml

Co-Authored-By: qiagu 36086881+qiagu@users.noreply.github.com

Commit: 3ed0ce862bf9397aefa3b3d58552e2013fcd098c https://github.com/galaxyproject/galaxy/commit/3ed0ce862bf9397aefa3b3d58552e... Author: Dannon dannon.baker@gmail.com Date: 2018-11-09 (Fri, 09 Nov 2018)

Changed paths: M doc/source/admin/framework_dependencies.rst M scripts/common_startup.sh

Log Message: ----------- Merge pull request #6975 from mvdbeek/conda_run_sh

Use virtualenv when conda is on PATH

Commit: 35bc1b387a3371e46b42c16c7b5664c33474d4fd https://github.com/galaxyproject/galaxy/commit/35bc1b387a3371e46b42c16c7b566... Author: Dannon Baker dannon.baker@gmail.com Date: 2018-11-09 (Fri, 09 Nov 2018)

Changed paths: M doc/source/admin/framework_dependencies.rst

Log Message: ----------- Typos in admin docs.

Commit: cfacaae8b50c9650e4d365063a177fbda9c0895c https://github.com/galaxyproject/galaxy/commit/cfacaae8b50c9650e4d365063a177... Author: Martin Cech marten@bx.psu.edu Date: 2018-11-09 (Fri, 09 Nov 2018)

Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/sequence.py A lib/galaxy/datatypes/test/sequence.fastg

Log Message: ----------- Merge pull request #6987 from jj-umn/dev

datatype_fastg

Commit: e9ab7add6e8e3ab31cf858e344bd0c568fc5fd83 https://github.com/galaxyproject/galaxy/commit/e9ab7add6e8e3ab31cf858e344bd0... Author: Dannon Baker dannon.baker@gmail.com Date: 2018-11-09 (Fri, 09 Nov 2018)

Changed paths: M doc/source/admin/nginx.md

Log Message: ----------- Another typo in admin/nginx

Commit: b57c25622b74b51b70cfe71d477a86a1f85b05a9 https://github.com/galaxyproject/galaxy/commit/b57c25622b74b51b70cfe71d477a8... Author: Martin Cech marten@bx.psu.edu Date: 2018-11-09 (Fri, 09 Nov 2018)

Changed paths: M doc/source/admin/framework_dependencies.rst M doc/source/admin/nginx.md

Log Message: ----------- Merge pull request #6999 from dannon/typo_fix

Fix several typos in admin docs.

Commit: a4ce326d8e8bbf812f5573bfe6c14fb566b2be1a https://github.com/galaxyproject/galaxy/commit/a4ce326d8e8bbf812f5573bfe6c14... Author: Mason nerdinacan@gmail.com Date: 2018-11-10 (Sat, 10 Nov 2018)

Changed paths: A client/galaxy/scripts/app/galaxy.js A client/galaxy/scripts/app/index.js A client/galaxy/scripts/app/monitor.js A client/galaxy/scripts/app/singleton.js R client/galaxy/scripts/galaxy.js R client/galaxy/scripts/galaxy.monitor.js M client/galaxy/scripts/onload/index.js M client/galaxy/scripts/utils/add-logging.js M client/galaxy/scripts/utils/config.js M client/galaxy/scripts/utils/deferred.js M client/galaxy/scripts/utils/installMonitor.js M client/galaxy/scripts/utils/serverPath.js M client/galaxy/scripts/utils/uploadbox.js M client/galaxy/scripts/utils/utils.js M client/webpack.config.js

Log Message: ----------- added singleton functions

Commit: 4ed27cf13145a77b4f8f1bcd57acbf1bb867886a https://github.com/galaxyproject/galaxy/commit/4ed27cf13145a77b4f8f1bcd57acb... Author: Mason nerdinacan@gmail.com Date: 2018-11-10 (Sat, 10 Nov 2018)

Changed paths: M client/galaxy/scripts/qunit/test-app.js M client/galaxy/scripts/qunit/test-data/bootstrapped.js M client/galaxy/scripts/qunit/test-data/fakeserver.js M client/galaxy/scripts/qunit/test-data/job-dag-1.js A client/galaxy/scripts/qunit/test-data/json/datatypes.json A client/galaxy/scripts/qunit/test-data/json/datatypes.mapping.json A client/galaxy/scripts/qunit/test-data/json/tools.test.build.json M client/galaxy/scripts/qunit/test-data/paired-collection-creator.data.js M client/galaxy/scripts/qunit/test.js M client/galaxy/scripts/qunit/tests/form_tests.js M client/galaxy/scripts/qunit/tests/galaxy_app_base_tests.js M client/galaxy/scripts/qunit/tests/graph_tests.js M client/galaxy/scripts/qunit/tests/hda_base_tests.js M client/galaxy/scripts/qunit/tests/history_contents_model_tests.js M client/galaxy/scripts/qunit/tests/job_dag_tests.js A client/galaxy/scripts/qunit/tests/jquery_plugin_tests.js M client/galaxy/scripts/qunit/tests/list_of_pairs_collection_creator_tests.js M client/galaxy/scripts/qunit/tests/masthead_tests.js M client/galaxy/scripts/qunit/tests/metrics_logger_tests.js M client/galaxy/scripts/qunit/tests/modal_tests.js M client/galaxy/scripts/qunit/tests/page_tests.js M client/galaxy/scripts/qunit/tests/ui_tests.js M client/galaxy/scripts/qunit/tests/upload_dialog_tests.js M client/galaxy/scripts/qunit/tests/utils_tests.js M client/galaxy/scripts/qunit/tests/workflow_editor_tests.js

Log Message: ----------- Added qunit tests

Commit: d4ab893441a5dd8f7a82df902323a5940e1698d7 https://github.com/galaxyproject/galaxy/commit/d4ab893441a5dd8f7a82df902323a... Author: Mason nerdinacan@gmail.com Date: 2018-11-10 (Sat, 10 Nov 2018)

Changed paths: M templates/base.mako M templates/galaxy_client_app.mako M templates/js-app.mako M templates/webapps/galaxy/galaxy.masthead.mako M templates/webapps/galaxy/galaxy.panels.mako

Log Message: ----------- Modified python templates

Commit: 969263e94805ff1c2b4568c3bf127d4183515cb4 https://github.com/galaxyproject/galaxy/commit/969263e94805ff1c2b4568c3bf127... Author: Mason nerdinacan@gmail.com Date: 2018-11-10 (Sat, 10 Nov 2018)

Changed paths: M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/apps/extended.js M client/galaxy/scripts/apps/login.js M client/galaxy/scripts/apps/panels/admin-panel.js M client/galaxy/scripts/apps/panels/history-panel.js M client/galaxy/scripts/apps/panels/tool-panel.js

Log Message: ----------- Updated entry points to use singleton

Commit: 964875f58a39c36032b7d958d5f3739643ea0dc2 https://github.com/galaxyproject/galaxy/commit/964875f58a39c36032b7d958d5f37... Author: Mason nerdinacan@gmail.com Date: 2018-11-10 (Sat, 10 Nov 2018)

Changed paths: M client/galaxy/scripts/admin.toolshed.js M client/galaxy/scripts/components/Citations.vue M client/galaxy/scripts/components/DataDialog.vue M client/galaxy/scripts/components/DisplayStructured.vue M client/galaxy/scripts/components/HistoryImport.vue M client/galaxy/scripts/components/HistoryView.vue M client/galaxy/scripts/components/PluginList.vue M client/galaxy/scripts/components/RuleCollectionBuilder.vue M client/galaxy/scripts/components/Sharing.vue M client/galaxy/scripts/components/WorkflowImport.vue M client/galaxy/scripts/components/admin/DataManager/DataManager.vue M client/galaxy/scripts/components/admin/DataManager/DataManagerJob.vue M client/galaxy/scripts/components/admin/DataManager/DataManagerJobs.vue M client/galaxy/scripts/components/admin/DataManager/DataManagerRouter.vue M client/galaxy/scripts/components/admin/DataManager/DataManagerTable.vue M client/galaxy/scripts/components/admin/DataTables.vue M client/galaxy/scripts/components/admin/DataTypes.vue M client/galaxy/scripts/galaxy.library.js M client/galaxy/scripts/layout/communication-server-view.js M client/galaxy/scripts/layout/masthead.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/layout/panel.js M client/galaxy/scripts/layout/router.js M client/galaxy/scripts/layout/scratchbook.js M client/galaxy/scripts/mvc/base/controlled-fetch-collection.js M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/collection/collection-view-edit.js M client/galaxy/scripts/mvc/collection/collection-view.js M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M client/galaxy/scripts/mvc/dataset/data.js M client/galaxy/scripts/mvc/dataset/dataset-edit-attributes.js M client/galaxy/scripts/mvc/dataset/dataset-error.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/dataset/dataset-model.js M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/form/form-wrapper.js M client/galaxy/scripts/mvc/grid/grid-shared.js M client/galaxy/scripts/mvc/grid/grid-view.js M client/galaxy/scripts/mvc/history/copy-dialog.js M client/galaxy/scripts/mvc/history/history-content-model.js M client/galaxy/scripts/mvc/history/history-contents.js M client/galaxy/scripts/mvc/history/history-list.js M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/history-view-edit-current.js M client/galaxy/scripts/mvc/history/history-view-edit.js M client/galaxy/scripts/mvc/history/history-view.js M client/galaxy/scripts/mvc/history/job-states-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/job/job-model.js M client/galaxy/scripts/mvc/job/job-params.js M client/galaxy/scripts/mvc/library/library-dataset-view.js M client/galaxy/scripts/mvc/library/library-folder-view.js M client/galaxy/scripts/mvc/library/library-folderrow-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/library/library-library-view.js M client/galaxy/scripts/mvc/library/library-librarylist-view.js M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js M client/galaxy/scripts/mvc/library/library-model.js M client/galaxy/scripts/mvc/tag.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/tool/tool-form.js M client/galaxy/scripts/mvc/tool/tool-genomespace.js M client/galaxy/scripts/mvc/tool/tools.js M client/galaxy/scripts/mvc/toolshed/categories-view.js M client/galaxy/scripts/mvc/toolshed/repositories-view.js M client/galaxy/scripts/mvc/toolshed/repository-queue-view.js M client/galaxy/scripts/mvc/toolshed/repository-view.js M client/galaxy/scripts/mvc/toolshed/toolshed-model.js M client/galaxy/scripts/mvc/toolshed/util.js M client/galaxy/scripts/mvc/toolshed/workflows-view.js M client/galaxy/scripts/mvc/tours.js M client/galaxy/scripts/mvc/ui/error-modal.js M client/galaxy/scripts/mvc/ui/ui-frames.js M client/galaxy/scripts/mvc/ui/ui-rules-edit.js M client/galaxy/scripts/mvc/ui/ui-select-ftp.js M client/galaxy/scripts/mvc/ui/ui-select-library.js M client/galaxy/scripts/mvc/upload/collection/rules-input-view.js M client/galaxy/scripts/mvc/upload/default/default-view.js M client/galaxy/scripts/mvc/upload/upload-ftp.js M client/galaxy/scripts/mvc/upload/upload-utils.js M client/galaxy/scripts/mvc/upload/upload-view.js M client/galaxy/scripts/mvc/user/user-custom-builds.js M client/galaxy/scripts/mvc/user/user-model.js M client/galaxy/scripts/mvc/user/user-preferences.js M client/galaxy/scripts/mvc/visualization/chart/chart-client.js M client/galaxy/scripts/mvc/visualization/chart/utilities/datasets.js M client/galaxy/scripts/mvc/visualization/chart/utilities/jobs.js M client/galaxy/scripts/mvc/visualization/chart/views/description.js M client/galaxy/scripts/mvc/visualization/chart/views/groups.js M client/galaxy/scripts/mvc/visualization/visualization-model.js M client/galaxy/scripts/mvc/webhooks.js M client/galaxy/scripts/mvc/workflow/workflow-forms.js M client/galaxy/scripts/mvc/workflow/workflow-manager.js M client/galaxy/scripts/mvc/workflow/workflow-model.js M client/galaxy/scripts/mvc/workflow/workflow-node.js M client/galaxy/scripts/mvc/workflow/workflow-view-data.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M client/galaxy/scripts/mvc/workflow/workflow.js M client/galaxy/scripts/toolshed/groups/group-model.js M client/galaxy/scripts/viz/bbi-data-manager.js M client/galaxy/scripts/viz/circster.js M client/galaxy/scripts/viz/sweepster.js M client/galaxy/scripts/viz/trackster.js M client/galaxy/scripts/viz/trackster/tracks.js M client/galaxy/scripts/viz/visualization.js M client/karma/karma.config.qunit.js M client/karma/webpack.config.unittest.js

Log Message: ----------- Removed global references to Galaxy

Commit: e98f63caf2d2adfd7857ff9fcba6df0b5923b668 https://github.com/galaxyproject/galaxy/commit/e98f63caf2d2adfd7857ff9fcba6d... Author: Marius van den Beek m.vandenbeek@gmail.com Date: 2018-11-10 (Sat, 10 Nov 2018)

Changed paths: M client/galaxy/scripts/mvc/form/form-data.js M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/workflow/workflow-forms.js M client/galaxy/scripts/mvc/workflow/workflow-icons.js M client/galaxy/scripts/mvc/workflow/workflow-node.js M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M client/galaxy/scripts/mvc/workflow/workflow-view-data.js M client/galaxy/scripts/mvc/workflow/workflow-view-node.js M client/galaxy/scripts/mvc/workflow/workflow-view-terminals.js M client/galaxy/scripts/qunit/tests/workflow_editor_tests.js M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run.py M lib/galaxy/workflow/run_request.py M test/api/test_workflows.py M test/galaxy_selenium/navigation.yml M test/selenium_tests/test_workflow_editor.py M test/selenium_tests/test_workflow_run.py

Log Message: ----------- Merge pull request #6925 from jmchilton/workflow_step_parameters_3

Add workflow step parameters to workflow editor (try 3)

Commit: 773a9bef892ede8f464a14de5f89469045568ec3 https://github.com/galaxyproject/galaxy/commit/773a9bef892ede8f464a14de5f894... Author: mvdbeek m.vandenbeek@gmail.com Date: 2018-11-10 (Sat, 10 Nov 2018)

Changed paths: M lib/galaxy/datatypes/sequence.py

Log Message: ----------- Fix fastq set_metadata on python 3

Commit: acfbca32dd7dc381750f6a9362b48ddaa4abd5a5 https://github.com/galaxyproject/galaxy/commit/acfbca32dd7dc381750f6a9362b48... Author: John Chilton jmchilton@gmail.com Date: 2018-11-10 (Sat, 10 Nov 2018)

Changed paths: M lib/galaxy/datatypes/sequence.py

Log Message: ----------- Merge pull request #7001 from mvdbeek/fastq_fix

Fix set_peek for fastg datatype

Commit: be76d9f8017efa14f133ee8fb49c0f3b490bdd2a https://github.com/galaxyproject/galaxy/commit/be76d9f8017efa14f133ee8fb49c0... Author: Marius van den Beek m.vandenbeek@gmail.com Date: 2018-11-11 (Sun, 11 Nov 2018)

Changed paths: M scripts/drmaa_external_runner.py

Log Message: ----------- Merge pull request #6995 from bernt-matthias/topic/external-runner-json-load-order

external_runner: load json template first

Commit: 020bbe92763e98c39c9d345a661dcf5475218d86 https://github.com/galaxyproject/galaxy/commit/020bbe92763e98c39c9d345a661dc... Author: Mason nerdinacan@gmail.com Date: 2018-11-12 (Mon, 12 Nov 2018)

Changed paths: M client/galaxy/scripts/mvc/form/form-data.js M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/workflow/workflow-forms.js M client/galaxy/scripts/mvc/workflow/workflow-icons.js M client/galaxy/scripts/mvc/workflow/workflow-node.js M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M client/galaxy/scripts/mvc/workflow/workflow-view-data.js M client/galaxy/scripts/mvc/workflow/workflow-view-node.js M client/galaxy/scripts/mvc/workflow/workflow-view-terminals.js M client/galaxy/scripts/qunit/tests/workflow_editor_tests.js M lib/galaxy/datatypes/sequence.py M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run.py M lib/galaxy/workflow/run_request.py M scripts/drmaa_external_runner.py M test/api/test_workflows.py M test/galaxy_selenium/navigation.yml M test/selenium_tests/test_workflow_editor.py M test/selenium_tests/test_workflow_run.py

Log Message: ----------- Merged dev, noted unused variables in workflow-node.js but harmless

Commit: 57abad3fa603fdb8325d1eeea61709959eb1dcdb https://github.com/galaxyproject/galaxy/commit/57abad3fa603fdb8325d1eeea6170... Author: Mason nerdinacan@gmail.com Date: 2018-11-12 (Mon, 12 Nov 2018)

Changed paths: M client/galaxy/scripts/app/singleton.js

Log Message: ----------- Replaced string-based type comparison with instanceof, fixed production-only build issue where constructor names become uglified

Commit: ab75fe8a37c4aaef2724bb1746f0fb7bb32c6fab https://github.com/galaxyproject/galaxy/commit/ab75fe8a37c4aaef2724bb1746f0f... Author: Nicola Soranzo nicola.soranzo@earlham.ac.uk Date: 2018-11-12 (Mon, 12 Nov 2018)

Changed paths: M lib/galaxy/dependencies/pipfiles/default/Pipfile M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt

Log Message: ----------- Update pysam to v0.15.1

For Python 3.7 compatibility.

Reported by @wm75.

Commit: a53629ebae992e685020676f72cbcb55c954b677 https://github.com/galaxyproject/galaxy/commit/a53629ebae992e685020676f72cbc... Author: Nicola Soranzo nicola.soranzo@earlham.ac.uk Date: 2018-11-13 (Tue, 13 Nov 2018)

Changed paths: M scripts/common_startup.sh

Log Message: ----------- Update virtualenv installation to v16.1.0

which bundles `wheel` 0.32.2.

The old virtualenv 13.1.2 included wheel 0.24.0, where tagging is broken for Python >=3.5, producing tracebacks like:

``` Traceback (most recent call last): File "<string>", line 1, in <module> File "/tmp/pip-install-c53eutpg/uwsgi/setup.py", line 138, in <module> 'Programming Language :: Python :: 3.6', File "/tmp/wheel_venv/lib/python3.7/site-packages/setuptools/__init__.py", line 143, in setup return distutils.core.setup(**attrs) File "/usr/lib/python3.7/distutils/core.py", line 148, in setup dist.run_commands() File "/usr/lib/python3.7/distutils/dist.py", line 966, in run_commands self.run_command(cmd) File "/usr/lib/python3.7/distutils/dist.py", line 985, in run_command cmd_obj.run() File "/tmp/wheel_venv/lib/python3.7/site-packages/wheel/bdist_wheel.py", line 213, in run archive_basename = self.get_archive_basename() File "/tmp/wheel_venv/lib/python3.7/site-packages/wheel/bdist_wheel.py", line 161, in get_archive_basename impl_tag, abi_tag, plat_tag = self.get_tag() File "/tmp/wheel_venv/lib/python3.7/site-packages/wheel/bdist_wheel.py", line 155, in get_tag assert tag == supported_tags[0] AssertionError ```

This was fixed in wheel 0.25.0. Reported by @wm75.

Also update `urlretrieve` import for Python 3.

Commit: 5385ca0473be64f4cde24fef07b5a38f47e9444f https://github.com/galaxyproject/galaxy/commit/5385ca0473be64f4cde24fef07b5a... Author: Pablo Moreno pcm32@users.noreply.github.com Date: 2018-11-13 (Tue, 13 Nov 2018)

Changed paths: M lib/galaxy/jobs/runners/util/cli/job/lsf.py

Log Message: ----------- Fix handling of forgotten LSF jobs in cli

Previous case assumed that "is not found" was part of the STDOUT when in fact is in the STDERR (and STDOUT is empty).

Commit: bdf5c06f04ab4743a5e18872446d4af96f9877db https://github.com/galaxyproject/galaxy/commit/bdf5c06f04ab4743a5e18872446d4... Author: Dannon Baker dannon.baker@gmail.com Date: 2018-11-13 (Tue, 13 Nov 2018)

Changed paths: M client/galaxy/scripts/admin.toolshed.js M client/galaxy/scripts/app/index.js M client/galaxy/scripts/app/monitor.js M client/galaxy/scripts/app/singleton.js M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/apps/login.js M client/galaxy/scripts/apps/panels/history-panel.js M client/galaxy/scripts/layout/data.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/scratchbook.js M client/galaxy/scripts/mvc/dataset/data.js M client/galaxy/scripts/mvc/dataset/dataset-error.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/history/history-content-model.js M client/galaxy/scripts/mvc/history/history-contents.js M client/galaxy/scripts/mvc/history/history-list.js M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/history-view-edit.js M client/galaxy/scripts/mvc/history/history-view.js M client/galaxy/scripts/mvc/history/multi-panel.js M client/galaxy/scripts/mvc/history/options-menu.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/tool/tool-form.js M client/galaxy/scripts/mvc/tool/tools.js M client/galaxy/scripts/mvc/toolshed/toolshed-model.js M client/galaxy/scripts/mvc/tours.js M client/galaxy/scripts/mvc/ui/error-modal.js M client/galaxy/scripts/mvc/ui/ui-frames.js M client/galaxy/scripts/mvc/upload/default/default-view.js M client/galaxy/scripts/mvc/upload/upload-ftp.js M client/galaxy/scripts/mvc/visualization/chart/chart-client.js M client/galaxy/scripts/mvc/visualization/chart/utilities/jobs.js M client/galaxy/scripts/mvc/workflow/workflow-node.js M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M client/galaxy/scripts/mvc/workflow/workflow-view-data.js M client/galaxy/scripts/mvc/workflow/workflow-view-terminals.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M client/galaxy/scripts/mvc/workflow/workflow.js M client/galaxy/scripts/onload/index.js M client/galaxy/scripts/qunit/test-app.js M client/galaxy/scripts/qunit/test-data/bootstrapped.js M client/galaxy/scripts/qunit/test-data/fakeserver.js M client/galaxy/scripts/qunit/test-data/job-dag-1.js M client/galaxy/scripts/qunit/test-data/paired-collection-creator.data.js M client/galaxy/scripts/qunit/test.js M client/galaxy/scripts/qunit/tests/form_tests.js M client/galaxy/scripts/qunit/tests/galaxy_app_base_tests.js M client/galaxy/scripts/qunit/tests/list_of_pairs_collection_creator_tests.js M client/galaxy/scripts/qunit/tests/metrics_logger_tests.js M client/galaxy/scripts/qunit/tests/ui_tests.js M client/galaxy/scripts/qunit/tests/workflow_editor_tests.js M client/galaxy/scripts/utils/installMonitor.js M client/galaxy/scripts/utils/uploadbox.js M client/galaxy/scripts/utils/utils.js M client/galaxy/scripts/viz/circster.js M client/galaxy/scripts/viz/trackster.js M client/galaxy/scripts/viz/visualization.js

Log Message: ----------- Client format.

Commit: c2ac98b9bb48d938fbebc5c70ce563fcb4717ad4 https://github.com/galaxyproject/galaxy/commit/c2ac98b9bb48d938fbebc5c70ce56... Author: Dannon Baker dannon.baker@gmail.com Date: 2018-11-13 (Tue, 13 Nov 2018)

Changed paths: M client/galaxy/scripts/layout/data.js

Log Message: ----------- Update layout/data to use getGalaxyInstance/etc

Commit: 4ea20bc95915c5a1f4046f31d3b50e11516540d0 https://github.com/galaxyproject/galaxy/commit/4ea20bc95915c5a1f4046f31d3b50... Author: Dannon dannon.baker@gmail.com Date: 2018-11-13 (Tue, 13 Nov 2018)

Changed paths: M client/galaxy/scripts/admin.toolshed.js A client/galaxy/scripts/app/galaxy.js A client/galaxy/scripts/app/index.js A client/galaxy/scripts/app/monitor.js A client/galaxy/scripts/app/singleton.js M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/apps/extended.js M client/galaxy/scripts/apps/login.js M client/galaxy/scripts/apps/panels/admin-panel.js M client/galaxy/scripts/apps/panels/history-panel.js M client/galaxy/scripts/apps/panels/tool-panel.js M client/galaxy/scripts/components/Citations.vue M client/galaxy/scripts/components/DataDialog.vue M client/galaxy/scripts/components/DisplayStructured.vue M client/galaxy/scripts/components/HistoryImport.vue M client/galaxy/scripts/components/HistoryView.vue M client/galaxy/scripts/components/PluginList.vue M client/galaxy/scripts/components/RuleCollectionBuilder.vue M client/galaxy/scripts/components/Sharing.vue M client/galaxy/scripts/components/WorkflowImport.vue M client/galaxy/scripts/components/admin/DataManager/DataManager.vue M client/galaxy/scripts/components/admin/DataManager/DataManagerJob.vue M client/galaxy/scripts/components/admin/DataManager/DataManagerJobs.vue M client/galaxy/scripts/components/admin/DataManager/DataManagerRouter.vue M client/galaxy/scripts/components/admin/DataManager/DataManagerTable.vue M client/galaxy/scripts/components/admin/DataTables.vue M client/galaxy/scripts/components/admin/DataTypes.vue R client/galaxy/scripts/galaxy.js M client/galaxy/scripts/galaxy.library.js R client/galaxy/scripts/galaxy.monitor.js M client/galaxy/scripts/layout/communication-server-view.js M client/galaxy/scripts/layout/data.js M client/galaxy/scripts/layout/masthead.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/layout/panel.js M client/galaxy/scripts/layout/router.js M client/galaxy/scripts/layout/scratchbook.js M client/galaxy/scripts/mvc/base/controlled-fetch-collection.js M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/collection/collection-view-edit.js M client/galaxy/scripts/mvc/collection/collection-view.js M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M client/galaxy/scripts/mvc/dataset/data.js M client/galaxy/scripts/mvc/dataset/dataset-edit-attributes.js M client/galaxy/scripts/mvc/dataset/dataset-error.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/dataset/dataset-model.js M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/form/form-wrapper.js M client/galaxy/scripts/mvc/grid/grid-shared.js M client/galaxy/scripts/mvc/grid/grid-view.js M client/galaxy/scripts/mvc/history/copy-dialog.js M client/galaxy/scripts/mvc/history/history-content-model.js M client/galaxy/scripts/mvc/history/history-contents.js M client/galaxy/scripts/mvc/history/history-list.js M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/history-view-edit-current.js M client/galaxy/scripts/mvc/history/history-view-edit.js M client/galaxy/scripts/mvc/history/history-view.js M client/galaxy/scripts/mvc/history/job-states-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/job/job-model.js M client/galaxy/scripts/mvc/job/job-params.js M client/galaxy/scripts/mvc/library/library-dataset-view.js M client/galaxy/scripts/mvc/library/library-folder-view.js M client/galaxy/scripts/mvc/library/library-folderrow-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/library/library-library-view.js M client/galaxy/scripts/mvc/library/library-librarylist-view.js M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js M client/galaxy/scripts/mvc/library/library-model.js M client/galaxy/scripts/mvc/tag.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/tool/tool-form.js M client/galaxy/scripts/mvc/tool/tool-genomespace.js M client/galaxy/scripts/mvc/tool/tools.js M client/galaxy/scripts/mvc/toolshed/categories-view.js M client/galaxy/scripts/mvc/toolshed/repositories-view.js M client/galaxy/scripts/mvc/toolshed/repository-queue-view.js M client/galaxy/scripts/mvc/toolshed/repository-view.js M client/galaxy/scripts/mvc/toolshed/toolshed-model.js M client/galaxy/scripts/mvc/toolshed/util.js M client/galaxy/scripts/mvc/toolshed/workflows-view.js M client/galaxy/scripts/mvc/tours.js M client/galaxy/scripts/mvc/ui/error-modal.js M client/galaxy/scripts/mvc/ui/ui-frames.js M client/galaxy/scripts/mvc/ui/ui-rules-edit.js M client/galaxy/scripts/mvc/ui/ui-select-ftp.js M client/galaxy/scripts/mvc/ui/ui-select-library.js M client/galaxy/scripts/mvc/upload/collection/rules-input-view.js M client/galaxy/scripts/mvc/upload/default/default-view.js M client/galaxy/scripts/mvc/upload/upload-ftp.js M client/galaxy/scripts/mvc/upload/upload-utils.js M client/galaxy/scripts/mvc/upload/upload-view.js M client/galaxy/scripts/mvc/user/user-custom-builds.js M client/galaxy/scripts/mvc/user/user-model.js M client/galaxy/scripts/mvc/user/user-preferences.js M client/galaxy/scripts/mvc/visualization/chart/chart-client.js M client/galaxy/scripts/mvc/visualization/chart/utilities/datasets.js M client/galaxy/scripts/mvc/visualization/chart/utilities/jobs.js M client/galaxy/scripts/mvc/visualization/chart/views/description.js M client/galaxy/scripts/mvc/visualization/chart/views/groups.js M client/galaxy/scripts/mvc/visualization/visualization-model.js M client/galaxy/scripts/mvc/webhooks.js M client/galaxy/scripts/mvc/workflow/workflow-forms.js M client/galaxy/scripts/mvc/workflow/workflow-manager.js M client/galaxy/scripts/mvc/workflow/workflow-model.js M client/galaxy/scripts/mvc/workflow/workflow-node.js M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M client/galaxy/scripts/mvc/workflow/workflow-view-data.js M client/galaxy/scripts/mvc/workflow/workflow-view-terminals.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M client/galaxy/scripts/mvc/workflow/workflow.js M client/galaxy/scripts/onload/index.js M client/galaxy/scripts/qunit/test-app.js M client/galaxy/scripts/qunit/test-data/bootstrapped.js M client/galaxy/scripts/qunit/test-data/fakeserver.js M client/galaxy/scripts/qunit/test-data/job-dag-1.js A client/galaxy/scripts/qunit/test-data/json/datatypes.json A client/galaxy/scripts/qunit/test-data/json/datatypes.mapping.json A client/galaxy/scripts/qunit/test-data/json/tools.test.build.json M client/galaxy/scripts/qunit/test-data/paired-collection-creator.data.js M client/galaxy/scripts/qunit/test.js M client/galaxy/scripts/qunit/tests/form_tests.js M client/galaxy/scripts/qunit/tests/galaxy_app_base_tests.js M client/galaxy/scripts/qunit/tests/graph_tests.js M client/galaxy/scripts/qunit/tests/hda_base_tests.js M client/galaxy/scripts/qunit/tests/history_contents_model_tests.js M client/galaxy/scripts/qunit/tests/job_dag_tests.js A client/galaxy/scripts/qunit/tests/jquery_plugin_tests.js M client/galaxy/scripts/qunit/tests/list_of_pairs_collection_creator_tests.js M client/galaxy/scripts/qunit/tests/masthead_tests.js M client/galaxy/scripts/qunit/tests/metrics_logger_tests.js M client/galaxy/scripts/qunit/tests/modal_tests.js M client/galaxy/scripts/qunit/tests/page_tests.js M client/galaxy/scripts/qunit/tests/ui_tests.js M client/galaxy/scripts/qunit/tests/upload_dialog_tests.js M client/galaxy/scripts/qunit/tests/utils_tests.js M client/galaxy/scripts/qunit/tests/workflow_editor_tests.js M client/galaxy/scripts/toolshed/groups/group-model.js M client/galaxy/scripts/utils/add-logging.js M client/galaxy/scripts/utils/config.js M client/galaxy/scripts/utils/deferred.js M client/galaxy/scripts/utils/installMonitor.js M client/galaxy/scripts/utils/serverPath.js M client/galaxy/scripts/utils/uploadbox.js M client/galaxy/scripts/utils/utils.js M client/galaxy/scripts/viz/bbi-data-manager.js M client/galaxy/scripts/viz/circster.js M client/galaxy/scripts/viz/sweepster.js M client/galaxy/scripts/viz/trackster.js M client/galaxy/scripts/viz/trackster/tracks.js M client/galaxy/scripts/viz/visualization.js M client/karma/karma.config.qunit.js M client/karma/webpack.config.unittest.js M client/webpack.config.js M templates/base.mako M templates/galaxy_client_app.mako M templates/js-app.mako M templates/webapps/galaxy/galaxy.masthead.mako M templates/webapps/galaxy/galaxy.panels.mako

Log Message: ----------- Merge pull request #7005 from Nerdinacan/app_singleton_cleaned

Replace global Galaxy references with galaxy singleton accessor/setter

Commit: 688bf3d524f7495afaf9c202a3601101baffb760 https://github.com/galaxyproject/galaxy/commit/688bf3d524f7495afaf9c202a3601... Author: Dannon Baker dannon.baker@gmail.com Date: 2018-11-13 (Tue, 13 Nov 2018)

Changed paths: M client/galaxy/scripts/layout/data.js

Log Message: ----------- Fix getAppRoot in layout/data.js

Commit: 0395fcabf083525beb1155c631a27046fa02d3a6 https://github.com/galaxyproject/galaxy/commit/0395fcabf083525beb1155c631a27... Author: Aysam Guerler aysam.guerler@gmail.com Date: 2018-11-13 (Tue, 13 Nov 2018)

Changed paths: M client/galaxy/scripts/layout/data.js

Log Message: ----------- Merge pull request #7009 from dannon/app_singleton_cleaned

Fix getAppRoot in layout/data.js

Commit: d88f2b63daa91f1fce1ca161f9a9192ce20a5cd5 https://github.com/galaxyproject/galaxy/commit/d88f2b63daa91f1fce1ca161f9a91... Author: John Chilton jmchilton@gmail.com Date: 2018-11-13 (Tue, 13 Nov 2018)

Changed paths: M lib/galaxy/dependencies/pipfiles/default/Pipfile M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt M scripts/common_startup.sh

Log Message: ----------- Merge pull request #7008 from nsoranzo/python3.7

Fixes for Python 3.7

Commit: cf86049c0c46908fa6fd87c7b1221e86b1faf13f https://github.com/galaxyproject/galaxy/commit/cf86049c0c46908fa6fd87c7b1221... Author: Qiang Gu guqiang01@gmail.com Date: 2018-11-13 (Tue, 13 Nov 2018)

Changed paths: M tools/filters/joiner.xml

Log Message: ----------- update help of joiner two datasets tool

Commit: 55f5235ab8b444a2ef20b03b9a03183cb5266ebb https://github.com/galaxyproject/galaxy/commit/55f5235ab8b444a2ef20b03b9a031... Author: M Bernt m.bernt@ufz.de Date: 2018-11-14 (Wed, 14 Nov 2018)

Changed paths: M lib/galaxy/dependencies/__init__.py M lib/galaxy/jobs/runners/drmaa.py A lib/galaxy/jobs/runners/univa.py M lib/galaxy/jobs/runners/util/job_script/MEMORY_STATEMENT.sh

Log Message: ----------- A new runner for DRMAA (currently UNIVA)

Reimplementation of the DRMAA runner inspired by the SLURM runner. Currently tested only for the UNIVA grid engine (but I'm optimistic that it should work as well for other drmaa systems).

This solves the problem that the current DRMAAJobRunner does not work when jobs are submitted as real user (because jobs that are started in a different drmaa session can not be accessed from the session that is open in galaxy): - this is done by resorting to command line tools qstat and qacct if the drmaa library can not be used to check the job status and to get run time information. - this has the additional advantage that if the drmaa library functions are not working (DRMAAJobRunner had implemented a repeated checking to handle this problem) the runner can still use the command line tools.

Furthermore (in contrast to the original drmaa runner) the new one tests for run time and memory violations: - memory violations are determined by comparing the used and the requested memory - run time violations are determined by checking the signal that killed the job and by comparing the used and the requested run time Where the used memory and time are determined with drmaa.wait() or qacct

Open (or better perspective): - adaptions to other grid engines. the current implementation (the command line calls and result parsing) might be specific for the Univa grid engine. to include other GEs one could determine the GE (+ version) and make the calls and result parsing depending on this.

Implementation note:

The changes in drmaa.py do not change the functionality at all, but only reorganize the code. In particular part of the function `check_watched_items` was put into a new function `check_watched_item` in order to make subclassing more convenient.

Replaces #6931 (which replaced #4275), since I did mess up with git again (there were some duplicated commits).

Commit: 53c3785986f68b5d65ec037381568a1092adbccb https://github.com/galaxyproject/galaxy/commit/53c3785986f68b5d65ec037381568... Author: M Bernt m.bernt@ufz.de Date: 2018-11-14 (Wed, 14 Nov 2018)

Changed paths: M lib/galaxy/jobs/runners/drmaa.py

Log Message: ----------- drmaa: soft catch of external runner fails

Commit: 876b460178bfb52936dc9f1d6c22149fea1f2513 https://github.com/galaxyproject/galaxy/commit/876b460178bfb52936dc9f1d6c221... Author: M Bernt m.bernt@ufz.de Date: 2018-11-14 (Wed, 14 Nov 2018)

Changed paths: M lib/galaxy/jobs/runners/__init__.py M test/unit/jobs/test_runner_local.py

Log Message: ----------- reclaim ownership for failed jobs

Commit: bfa7b200526bccf4dc0ffe888972ffe879f688bc https://github.com/galaxyproject/galaxy/commit/bfa7b200526bccf4dc0ffe888972f... Author: Marius van den Beek m.vandenbeek@gmail.com Date: 2018-11-15 (Thu, 15 Nov 2018)

Changed paths: M lib/galaxy/jobs/runners/util/cli/job/lsf.py

Log Message: ----------- Add log warning for missing LSF jobs.

Co-Authored-By: pcm32 pcm32@users.noreply.github.com

Commit: eaacc5bc9f351b8a01281ffa3462e1c653db3826 https://github.com/galaxyproject/galaxy/commit/eaacc5bc9f351b8a01281ffa3462e... Author: Nicola Soranzo nicola.soranzo@earlham.ac.uk Date: 2018-11-15 (Thu, 15 Nov 2018)

Changed paths: M run.sh M run_reports.sh M run_tool_shed.sh M scripts/common_startup_functions.sh

Log Message: ----------- Merge branch 'release_18.09' into dev

Commit: f04342541d3b43adacf8b9f194069e72dc77ec61 https://github.com/galaxyproject/galaxy/commit/f04342541d3b43adacf8b9f194069... Author: Frederik Coppens frederik.coppens@psb.vib-ugent.be Date: 2018-11-15 (Thu, 15 Nov 2018)

Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py

Log Message: ----------- workflows api call made public

Commit: 17299356f011b80dcf575399be5d6803a1f31cc7 https://github.com/galaxyproject/galaxy/commit/17299356f011b80dcf575399be5d6... Author: John Chilton jmchilton@gmail.com Date: 2018-11-15 (Thu, 15 Nov 2018)

Changed paths: M lib/galaxy/jobs/runners/util/cli/job/lsf.py

Log Message: ----------- Merge pull request #7007 from pcm32/patch-2

Fix handling of forgotten LSF jobs in cli

Commit: 265a43507ebda1bac9bc5dbe2ac601912bef66d8 https://github.com/galaxyproject/galaxy/commit/265a43507ebda1bac9bc5dbe2ac60... Author: John Chilton jmchilton@gmail.com Date: 2018-11-15 (Thu, 15 Nov 2018)

Changed paths: M lib/galaxy/containers/__init__.py M lib/galaxy/jobs/mapper.py M lib/galaxy/jobs/runners/state_handler_factory.py M lib/galaxy/queue_worker.py M lib/galaxy/tools/lint.py M lib/galaxy/util/plugin_config.py M lib/galaxy/util/submodules.py M lib/galaxy/webapps/galaxy/config_watchers.py M test/unit/jobs/test_mapper.py A test/unit/jobs/test_rules_override/10_rule.py A test/unit/jobs/test_rules_override/__init__.py M test/unit/unittest_utils/galaxy_mock.py

Log Message: ----------- Merge pull request #6993 from nuwang/allow_rules_module_override

Allow rules module override and refactor submodule imports

Commit: 7a10f5ce0ed809ba1ab836f6a295c4fca9a637de https://github.com/galaxyproject/galaxy/commit/7a10f5ce0ed809ba1ab836f6a295c... Author: John Chilton jmchilton@gmail.com Date: 2018-11-15 (Thu, 15 Nov 2018)

Changed paths: M tools/filters/joiner.xml

Log Message: ----------- Merge pull request #6998 from qiagu/join1

Change join two dataset output format to tabular

Commit: b8c97f108681e0e0963efc95a16af13be84642f9 https://github.com/galaxyproject/galaxy/commit/b8c97f108681e0e0963efc95a16af... Author: Nuwan Goonasekera nuwan.ag@gmail.com Date: 2018-11-15 (Thu, 15 Nov 2018)

Changed paths: M lib/galaxy/jobs/mapper.py M test/unit/jobs/test_mapper.py M test/unit/jobs/test_rules/10_site.py

Log Message: ----------- Added support for chaining dynamic destinations

Commit: f46ab5a5dc21c1e8dd115ec3d9a37e0e3ee26a56 https://github.com/galaxyproject/galaxy/commit/f46ab5a5dc21c1e8dd115ec3d9a37... Author: Nuwan Goonasekera nuwan.ag@gmail.com Date: 2018-11-15 (Thu, 15 Nov 2018)

Changed paths: M lib/galaxy/jobs/mapper.py

Log Message: ----------- Fix debug logging

Commit: f6c0e6ff9fdbf66a2af6d6538ad816274ecb93b3 https://github.com/galaxyproject/galaxy/commit/f6c0e6ff9fdbf66a2af6d6538ad81... Author: Nuwan Goonasekera nuwan.ag@gmail.com Date: 2018-11-15 (Thu, 15 Nov 2018)

Changed paths: M lib/galaxy/jobs/mapper.py

Log Message: ----------- Fixed issue with job_destination caching and added documentation

Commit: c114ba4f43cb4e73fbff470f1283aed103e91fc2 https://github.com/galaxyproject/galaxy/commit/c114ba4f43cb4e73fbff470f1283a... Author: Nuwan Goonasekera nuwan.ag@gmail.com Date: 2018-11-15 (Thu, 15 Nov 2018)

Changed paths: M lib/galaxy/jobs/mapper.py M test/unit/jobs/test_mapper.py

Log Message: ----------- Added test for cached_job_destination to prevent regression

Commit: 766039adbd17490bf6e758311329b03917fefa18 https://github.com/galaxyproject/galaxy/commit/766039adbd17490bf6e758311329b... Author: Nuwan Goonasekera nuwan.ag@gmail.com Date: 2018-11-15 (Thu, 15 Nov 2018)

Changed paths: M config/job_conf.xml.sample_advanced

Log Message: ----------- Added usage example of dynamic rule chaining

Commit: c06a142e04a9e034b3d991010fb910a775cabb21 https://github.com/galaxyproject/galaxy/commit/c06a142e04a9e034b3d991010fb91... Author: John Chilton jmchilton@gmail.com Date: 2018-11-15 (Thu, 15 Nov 2018)

Changed paths: M test/api/test_workflows.py

Log Message: ----------- Workflow test case, inputs as outputs.

Commit: aa9fe3cb500603b7aaf5cc11b4875953d2c8e6ab https://github.com/galaxyproject/galaxy/commit/aa9fe3cb500603b7aaf5cc11b4875... Author: guerler aysam.guerler@gmail.com Date: 2018-11-15 (Thu, 15 Nov 2018)

Changed paths: M templates/user/login.mako

Log Message: ----------- Use cards for login forms

Commit: b697e0921182bacf249085138148b9e22cc1c8d7 https://github.com/galaxyproject/galaxy/commit/b697e0921182bacf249085138148b... Author: guerler aysam.guerler@gmail.com Date: 2018-11-15 (Thu, 15 Nov 2018)

Changed paths: M client/galaxy/style/scss/trackster.scss

Log Message: ----------- Restore button defaults

Commit: 1b4358653d7a7d5552a634fc34ffeba61b6b6228 https://github.com/galaxyproject/galaxy/commit/1b4358653d7a7d5552a634fc34ffe... Author: guerler aysam.guerler@gmail.com Date: 2018-11-15 (Thu, 15 Nov 2018)

Changed paths: M templates/user/reset_password.mako

Log Message: ----------- Use card for password reset form

Commit: 15e2c7ff8b31ce397a2c9fdfc98dcdcbdfe9d6d0 https://github.com/galaxyproject/galaxy/commit/15e2c7ff8b31ce397a2c9fdfc98dc... Author: guerler aysam.guerler@gmail.com Date: 2018-11-15 (Thu, 15 Nov 2018)

Changed paths: M templates/user/register.mako

Log Message: ----------- Use card for registration forms

Commit: 9a9b815d8fc9810600668ca358f72e0130e37d8f https://github.com/galaxyproject/galaxy/commit/9a9b815d8fc9810600668ca358f72... Author: Qiang Gu guqiang01@gmail.com Date: 2018-11-15 (Thu, 15 Nov 2018)

Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-edit-attributes.js M lib/galaxy/webapps/galaxy/controllers/dataset.py

Log Message: ----------- add datatype sniff button in edit dataset attributes page

Commit: 67efd072ae98d6a34cbbc7f2270743524126bf8a https://github.com/galaxyproject/galaxy/commit/67efd072ae98d6a34cbbc7f227074... Author: John Chilton jmchilton@gmail.com Date: 2018-11-15 (Thu, 15 Nov 2018)

Changed paths: M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py M lib/galaxy/model/migrate/versions/0136_collection_and_workflow_state.py A lib/galaxy/model/migrate/versions/0145_add_workflow_step_input.py M lib/galaxy/webapps/tool_shed/model/__init__.py M lib/galaxy/workflow/extract.py M lib/galaxy/workflow/modules.py M lib/tool_shed/util/workflow_util.py M test/api/test_workflows.py M test/unit/test_galaxy_mapping.py M test/unit/workflows/test_modules.py M test/unit/workflows/test_render.py M test/unit/workflows/test_workflow_progress.py M test/unit/workflows/workflow_support.py

Log Message: ----------- Track workflow step input definitions in our model.

We don't track workflow step inputs in any formal way in our model currently. This has resulted in some current hacks and prevents future enhancements. This commit splits WorkflowStepConnection into two models WorkflowStepInput and WorkflowStepConnection - normalizing the previous table workflow_step_connection on input step and input name.

In terms of current hacks forced on it by restricting all of tool state to be confined to a big JSON blob in the database - we have problems distinguishing keys and values when walking tool state. As we store more and more JSON blobs inside of the giant tool state blob - the worse this problem gets. Take for instance checking for runtime parameters or the rules parameter values - these both use JSON blobs that aren't simple values, so it is hard to tell looking at the tool state blob in the database or the workflow export to tell what is a key or what is a value. Tracking state as normalized inputs with default values and explicit attributes runtime values should allow much more percise state definition and construction.

This variant of the models would also potentially allow defining runtime values with non-tool default values (so default values defined for the workflow but still explicitly settable at runtime). The combinations of overriding defaults and defining runtime values were not representable before.

In terms of future enhancements, there is a lot we cannot track with the current models - such as map/reduce options for collection operations (https://github.com/galaxyproject/galaxy/issues/4623#issuecomment-389544980). This should enable a lot of that. Obviously there are a lot of attributes defined here that are not yet utilized, but I'm using most (all?) of them downstream in the CWL branch. I'd rather populate this table fully realized and fill in the implementation around it as work continues to stream in from the CWL branch - to keep things simple and avoid extra database migrations. But I understand if this feels like speculative complexity we want to avoid despite the implementation being readily available for inspection downstream.

Commit: 017ad2ccfbb2434bd036b8ff1a36c25bfba827dd https://github.com/galaxyproject/galaxy/commit/017ad2ccfbb2434bd036b8ff1a36c... Author: John Chilton jmchilton@gmail.com Date: 2018-11-15 (Thu, 15 Nov 2018)

Changed paths: M client/galaxy/style/scss/trackster.scss M templates/user/login.mako M templates/user/register.mako M templates/user/reset_password.mako

Log Message: ----------- Merge pull request #7017 from guerler/login_style

Fix login and registration form appearance

Commit: 170ed2a8c2a4d324ceac6fabf2a115d6eb801c16 https://github.com/galaxyproject/galaxy/commit/170ed2a8c2a4d324ceac6fabf2a11... Author: Qiang Gu guqiang01@gmail.com Date: 2018-11-15 (Thu, 15 Nov 2018)

Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-edit-attributes.js M lib/galaxy/webapps/galaxy/controllers/dataset.py

Log Message: ----------- fix style and wording

Commit: 952847aad1eb00f6150761127cce4456e2f880a5 https://github.com/galaxyproject/galaxy/commit/952847aad1eb00f6150761127cce4... Author: Nicola Soranzo nicola.soranzo@gmail.com Date: 2018-11-16 (Fri, 16 Nov 2018)

Changed paths: M test/api/test_workflows.py

Log Message: ----------- Merge pull request #7016 from jmchilton/input_output_test_case

Workflow test case - test marking inputs as outputs.

Commit: ca7e2b9e68900e26a3be444f7269e21399176b10 https://github.com/galaxyproject/galaxy/commit/ca7e2b9e68900e26a3be444f7269e... Author: Nuwan Goonasekera nuwan.ag@gmail.com Date: 2018-11-16 (Fri, 16 Nov 2018)

Changed paths: A test/integration/chained_dyndest_job_conf.xml A test/integration/chained_dyndest_rules/__init__.py A test/integration/chained_dyndest_rules/rules.py A test/integration/test_chained_dynamic_destinations.py

Log Message: ----------- Added integration test for chained destinations

Commit: 5ba1c24a1475c13f977fc2d1a6e02b5dc8158bb6 https://github.com/galaxyproject/galaxy/commit/5ba1c24a1475c13f977fc2d1a6e02... Author: Nuwan Goonasekera nuwan.ag@gmail.com Date: 2018-11-16 (Fri, 16 Nov 2018)

Changed paths: M test/integration/chained_dyndest_job_conf.xml A test/integration/chained_dyndest_rules/module1/__init__.py A test/integration/chained_dyndest_rules/module1/rules.py A test/integration/chained_dyndest_rules/module2/__init__.py A test/integration/chained_dyndest_rules/module2/rules.py A test/integration/chained_dyndest_rules/module3/__init__.py A test/integration/chained_dyndest_rules/module3/rules.py R test/integration/chained_dyndest_rules/rules.py

Log Message: ----------- Added integration test for rules_module overrides

Commit: 15c43e777b7c66614fd9d157ab2fcabb54d7f759 https://github.com/galaxyproject/galaxy/commit/15c43e777b7c66614fd9d157ab2fc... Author: Nicola Soranzo nicola.soranzo@gmail.com Date: 2018-11-16 (Fri, 16 Nov 2018)

Changed paths: M lib/galaxy/model/mapping.py

Log Message: ----------- Update lib/galaxy/model/mapping.py

Co-Authored-By: jmchilton jmchilton@gmail.com

Commit: a94d22a7b3767217cbc90fda118f1e27ded1962c https://github.com/galaxyproject/galaxy/commit/a94d22a7b3767217cbc90fda118f1... Author: Frederik Coppens frederik.coppens@psb.vib-ugent.be Date: 2018-11-16 (Fri, 16 Nov 2018)

Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py

Log Message: ----------- published workflows accessible through API endpoint

Commit: 0a18ed62977b8a81932841361f7fa126f8dca2dc https://github.com/galaxyproject/galaxy/commit/0a18ed62977b8a81932841361f7fa... Author: Nicola Soranzo nicola.soranzo@gmail.com Date: 2018-11-16 (Fri, 16 Nov 2018)

Changed paths: M lib/galaxy/model/migrate/versions/0145_add_workflow_step_input.py

Log Message: ----------- Update lib/galaxy/model/migrate/versions/0145_add_workflow_step_input.py

Co-Authored-By: jmchilton jmchilton@gmail.com

Commit: ae7869170762b08425c264b0d9777df0efd977ea https://github.com/galaxyproject/galaxy/commit/ae7869170762b08425c264b0d9777... Author: Marius van den Beek m.vandenbeek@gmail.com Date: 2018-11-16 (Fri, 16 Nov 2018)

Changed paths: M test/integration/test_chained_dynamic_destinations.py

Log Message: ----------- Update test/integration/test_chained_dynamic_destinations.py

Co-Authored-By: nuwang nuwan.goonasekera@gmail.com

Commit: 983f490f9e2928a0abcdd74086952db3043ac1bf https://github.com/galaxyproject/galaxy/commit/983f490f9e2928a0abcdd74086952... Author: Frederik Coppens frederik.coppens@psb.vib-ugent.be Date: 2018-11-16 (Fri, 16 Nov 2018)

Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py

Log Message: ----------- show_published only defaults to True when not logged in

Commit: 00af4e21dee168fd6c54ac925414bcb95b8e7930 https://github.com/galaxyproject/galaxy/commit/00af4e21dee168fd6c54ac925414b... Author: Nicola Soranzo nicola.soranzo@gmail.com Date: 2018-11-16 (Fri, 16 Nov 2018)

Changed paths: M lib/galaxy/model/migrate/versions/0145_add_workflow_step_input.py

Log Message: ----------- Update lib/galaxy/model/migrate/versions/0145_add_workflow_step_input.py

Co-Authored-By: jmchilton jmchilton@gmail.com

Commit: b0bc14a90524a01a162f803b5604cbb361dac386 https://github.com/galaxyproject/galaxy/commit/b0bc14a90524a01a162f803b5604c... Author: M Bernt m.bernt@ufz.de Date: 2018-11-16 (Fri, 16 Nov 2018)

Changed paths: M lib/galaxy/jobs/runners/drmaa.py

Log Message: ----------- drmaa: make external_runjob return stripped stdio

Commit: f2c17e589b734afedcb807d038d0f1b8caf27f52 https://github.com/galaxyproject/galaxy/commit/f2c17e589b734afedcb807d038d0f... Author: Nicola Soranzo nicola.soranzo@earlham.ac.uk Date: 2018-11-16 (Fri, 16 Nov 2018)

Changed paths: M lib/galaxy/model/mapping.py M lib/galaxy/model/migrate/versions/0145_add_workflow_step_input.py

Log Message: ----------- Preserve updated content in migration 145 downgrade

Also add UNIQUE constraint to `("workflow_step_id", "name")` to the new `workflow_step_input` table.

Commit: 7695569b50b7bb1ae249a248743612debd519f10 https://github.com/galaxyproject/galaxy/commit/7695569b50b7bb1ae249a24874361... Author: Marius van den Beek m.vandenbeek@gmail.com Date: 2018-11-16 (Fri, 16 Nov 2018)

Changed paths: M config/job_conf.xml.sample_advanced M lib/galaxy/jobs/mapper.py A test/integration/chained_dyndest_job_conf.xml A test/integration/chained_dyndest_rules/__init__.py A test/integration/chained_dyndest_rules/module1/__init__.py A test/integration/chained_dyndest_rules/module1/rules.py A test/integration/chained_dyndest_rules/module2/__init__.py A test/integration/chained_dyndest_rules/module2/rules.py A test/integration/chained_dyndest_rules/module3/__init__.py A test/integration/chained_dyndest_rules/module3/rules.py A test/integration/test_chained_dynamic_destinations.py M test/unit/jobs/test_mapper.py M test/unit/jobs/test_rules/10_site.py

Log Message: ----------- Merge pull request #7006 from nuwang/chained_dynamic_destinations

Added support for chaining dynamic destinations

Commit: f9685459a45f2e2b3395077cbfa11e9a45245021 https://github.com/galaxyproject/galaxy/commit/f9685459a45f2e2b3395077cbfa11... Author: Nicola Soranzo nicola.soranzo@gmail.com Date: 2018-11-16 (Fri, 16 Nov 2018)

Changed paths: M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py M lib/galaxy/model/migrate/versions/0136_collection_and_workflow_state.py A lib/galaxy/model/migrate/versions/0145_add_workflow_step_input.py M lib/galaxy/webapps/tool_shed/model/__init__.py M lib/galaxy/workflow/extract.py M lib/galaxy/workflow/modules.py M lib/tool_shed/util/workflow_util.py M test/api/test_workflows.py M test/unit/test_galaxy_mapping.py M test/unit/workflows/test_modules.py M test/unit/workflows/test_render.py M test/unit/workflows/test_workflow_progress.py M test/unit/workflows/workflow_support.py

Log Message: ----------- Merge pull request #6850 from jmchilton/workflows_track_step_inputs

Track workflow step input definitions in our model.

Commit: 306b114191a1d326afcbdca68f489b015ba07660 https://github.com/galaxyproject/galaxy/commit/306b114191a1d326afcbdca68f489... Author: Nicola Soranzo nicola.soranzo@earlham.ac.uk Date: 2018-11-17 (Sat, 17 Nov 2018)

Changed paths: M lib/galaxy/jobs/handler.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/chronos.py M lib/galaxy/jobs/runners/cli.py M lib/galaxy/jobs/runners/condor.py M lib/galaxy/jobs/runners/drmaa.py M lib/galaxy/jobs/runners/godocker.py M lib/galaxy/jobs/runners/kubernetes.py M lib/galaxy/jobs/runners/local.py M lib/galaxy/jobs/runners/pbs.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/jobs/runners/tasks.py M test/unit/jobs/test_runner_local.py

Log Message: ----------- Pass a ``JobWrapper`` instead of a ``Job`` to ``stop_job()`` methods

Commit: 0ddc5aeba1827833991cd782a9d806fa9ccd414e https://github.com/galaxyproject/galaxy/commit/0ddc5aeba1827833991cd782a9d80... Author: Nicola Soranzo nicola.soranzo@earlham.ac.uk Date: 2018-11-17 (Sat, 17 Nov 2018)

Changed paths: M lib/galaxy/jobs/handler.py M lib/galaxy/jobs/runners/drmaa.py M lib/galaxy/jobs/runners/local.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/jobs/runners/tasks.py M lib/galaxy/model/__init__.py

Log Message: ----------- Drop ``get_id()`` method

Commit: 183d84e5dc8ce4530835852292f3d20318dc9980 https://github.com/galaxyproject/galaxy/commit/183d84e5dc8ce4530835852292f3d... Author: Nicola Soranzo nicola.soranzo@earlham.ac.uk Date: 2018-11-17 (Sat, 17 Nov 2018)

Changed paths: M lib/galaxy/jobs/__init__.py

Log Message: ----------- 2 small simplifications in ``JobWrapper``

After commit eeb1dae5b71200ffe9f2056b2a7fd8ed560033c1, `JobWrapper.job_destination()` does not call `self._job_dataset_path_rewriter()` any more.

Commit: 72b2781d4b22cf1c6a312912ffc5333fe5db10b7 https://github.com/galaxyproject/galaxy/commit/72b2781d4b22cf1c6a312912ffc53... Author: John Chilton jmchilton@gmail.com Date: 2018-11-19 (Mon, 19 Nov 2018)

Changed paths: M lib/galaxy/dependencies/__init__.py M lib/galaxy/jobs/runners/drmaa.py A lib/galaxy/jobs/runners/univa.py M lib/galaxy/jobs/runners/util/job_script/MEMORY_STATEMENT.sh

Log Message: ----------- Merge pull request #7004 from bernt-matthias/topic/univa3

A new runner for DRMAA (currently UNIVA)

Commit: eb3664316ce9d7ab3f6d5d2c637b6901138c19a3 https://github.com/galaxyproject/galaxy/commit/eb3664316ce9d7ab3f6d5d2c637b6... Author: Nicola Soranzo nicola.soranzo@earlham.ac.uk Date: 2018-11-20 (Tue, 20 Nov 2018)

Changed paths: M lib/galaxy/model/migrate/versions/0145_add_workflow_step_input.py

Log Message: ----------- Only migrate distinct (input_step_id, input_name) pairs

otherwise the UNIQUE constraint on the `workflow_step_input` table is violated.

Follow-up on #6850.

Reported by @mvdbeek.

Commit: 797c2c5b270bb544773025e0d0d85855aba62d6b https://github.com/galaxyproject/galaxy/commit/797c2c5b270bb544773025e0d0d85... Author: Nicola Soranzo nicola.soranzo@earlham.ac.uk Date: 2018-11-20 (Tue, 20 Nov 2018)

Changed paths: M lib/galaxy/model/mapping.py M lib/galaxy/model/migrate/versions/0006_change_qual_datatype.py

Log Message: ----------- Simplification of SQLAlchemy session handling

Commit: 4ff3c95e38d1c62a5d1b85994e2dde909a2f7e38 https://github.com/galaxyproject/galaxy/commit/4ff3c95e38d1c62a5d1b85994e2dd... Author: Qiang Gu guqiang01@gmail.com Date: 2018-11-19 (Mon, 19 Nov 2018)

Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-edit-attributes.js

Log Message: ----------- fix a typo error

Commit: 1b5fd373cb2f260c9f29afd2ed7722bbc0cd6299 https://github.com/galaxyproject/galaxy/commit/1b5fd373cb2f260c9f29afd2ed772... Author: guerler aysam.guerler@gmail.com Date: 2018-11-20 (Tue, 20 Nov 2018)

Changed paths: M templates/js-app.mako

Log Message: ----------- Restore jquery style for text field autocomplete options

Commit: d35a07689891b5cff03976ca36e928cf10827594 https://github.com/galaxyproject/galaxy/commit/d35a07689891b5cff03976ca36e92... Author: mvdbeek m.vandenbeek@gmail.com Date: 2018-11-20 (Tue, 20 Nov 2018)

Changed paths: M lib/galaxy/tools/wrappers.py M test/functional/tools/identifier_collection.xml

Log Message: ----------- Provide element_identifier attribute in DatsetCollectionWrapper

This allows accessing `$input1.element_identifier` for an `input1` of collection_type `list:pair`.

Commit: d13792d64605bc3480eae5e877e933b1c111e28f https://github.com/galaxyproject/galaxy/commit/d13792d64605bc3480eae5e877e93... Author: John Chilton jmchilton@gmail.com Date: 2018-11-20 (Tue, 20 Nov 2018)

Changed paths: M lib/galaxy/model/mapping.py M lib/galaxy/model/migrate/versions/0006_change_qual_datatype.py M lib/galaxy/model/migrate/versions/0145_add_workflow_step_input.py

Log Message: ----------- Merge pull request #7029 from nsoranzo/followup_on_6850

Follow-up on #6850

Commit: 9bac3c44faf51e0e4c396d7f1d3470f7aa4a588e https://github.com/galaxyproject/galaxy/commit/9bac3c44faf51e0e4c396d7f1d347... Author: John Chilton jmchilton@gmail.com Date: 2018-11-20 (Tue, 20 Nov 2018)

Changed paths: M lib/galaxy/managers/workflows.py M lib/galaxy/model/mapping.py A lib/galaxy/model/migrate/versions/0146_workflow_paths.py M lib/galaxy/web/base/controller.py M lib/galaxy/webapps/galaxy/api/workflows.py M test/api/test_workflows.py M test/base/populators.py M test/base/workflow_fixtures.py M test/integration/test_dockerized_jobs.py A test/integration/test_workflow_sync.py

Log Message: ----------- Path-aware workflows.

- Allow workflows to be uploaded via path using the GUI and and API for admins. - Track the path and resync workflows on save (both .ga and format 2 workflows) - this will allow Planemo to leverage the Galaxy workflow editor to interactively save workflows.

Commit: cd0b7a9347c8cbe9df913cf65a6059157e6de3f0 https://github.com/galaxyproject/galaxy/commit/cd0b7a9347c8cbe9df913cf65a605... Author: John Chilton jmchilton@gmail.com Date: 2018-11-20 (Tue, 20 Nov 2018)

Changed paths: M lib/galaxy/tools/wrappers.py M test/functional/tools/identifier_collection.xml

Log Message: ----------- Merge pull request #7031 from mvdbeek/element_identifer_everywhere

Provide element_identifier attribute in DatsetCollectionWrapper

Commit: 6778fa47ed899eefe1418139f43832f225760e0f https://github.com/galaxyproject/galaxy/commit/6778fa47ed899eefe1418139f4383... Author: John Chilton jmchilton@gmail.com Date: 2018-11-20 (Tue, 20 Nov 2018)

Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/handler.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/chronos.py M lib/galaxy/jobs/runners/cli.py M lib/galaxy/jobs/runners/condor.py M lib/galaxy/jobs/runners/drmaa.py M lib/galaxy/jobs/runners/godocker.py M lib/galaxy/jobs/runners/kubernetes.py M lib/galaxy/jobs/runners/local.py M lib/galaxy/jobs/runners/pbs.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/jobs/runners/tasks.py M lib/galaxy/model/__init__.py M test/unit/jobs/test_runner_local.py

Log Message: ----------- Merge pull request #7023 from nsoranzo/stop_job_wrapper

Pass a ``JobWrapper`` instead of a ``Job`` to ``stop_job()`` methods

Commit: fe671f67ec6ba222115bb4c5c5a3705ca868b3a6 https://github.com/galaxyproject/galaxy/commit/fe671f67ec6ba222115bb4c5c5a37... Author: John Chilton jmchilton@gmail.com Date: 2018-11-20 (Tue, 20 Nov 2018)

Changed paths: M templates/js-app.mako

Log Message: ----------- Merge pull request #7027 from guerler/fix_text_options

Use solid background for text field autocomplete options

Commit: 5f04dbd996f4034aa9db45037c6c6e43518bcd1f https://github.com/galaxyproject/galaxy/commit/5f04dbd996f4034aa9db45037c6c6... Author: guerler aysam.guerler@gmail.com Date: 2018-11-20 (Tue, 20 Nov 2018)

Changed paths: M client/galaxy/scripts/components/HistoryImport.vue M client/galaxy/scripts/components/PluginList.vue M client/galaxy/scripts/components/WorkflowImport.vue

Log Message: ----------- Fix typo in import error messages

Commit: c7bd5c794b3c0f6a34fe01c7928ca5dbf43284d5 https://github.com/galaxyproject/galaxy/commit/c7bd5c794b3c0f6a34fe01c7928ca... Author: Martin Cech marten@bx.psu.edu Date: 2018-11-20 (Tue, 20 Nov 2018)

Changed paths: M client/galaxy/scripts/components/HistoryImport.vue M client/galaxy/scripts/components/PluginList.vue M client/galaxy/scripts/components/WorkflowImport.vue

Log Message: ----------- Merge pull request #7033 from guerler/import_typos

Fix typos in import error messages

Commit: 45345533fb6495a109c49b6fe058f1a26609fe15 https://github.com/galaxyproject/galaxy/commit/45345533fb6495a109c49b6fe058f... Author: John Chilton jmchilton@gmail.com Date: 2018-11-21 (Wed, 21 Nov 2018)

Changed paths: M test/api/test_workflows.py

Log Message: ----------- Test cases for public WF access to published workflows.

Commit: 8470e91296931ea9d23f4b655a4a2be7d1d51b4c https://github.com/galaxyproject/galaxy/commit/8470e91296931ea9d23f4b655a4a2... Author: John Chilton jmchilton@gmail.com Date: 2018-11-21 (Wed, 21 Nov 2018)

Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py M test/api/test_workflows.py

Log Message: ----------- Merge pull request #7020 from frederikcoppens/public_api_wf

Expose published workflows through API

Commit: b082daa39f2cd47d75872d9176af0bbde6b94311 https://github.com/galaxyproject/galaxy/commit/b082daa39f2cd47d75872d9176af0... Author: Martin Cech marten@bx.psu.edu Date: 2018-11-21 (Wed, 21 Nov 2018)

Changed paths: M .travis.yml

Log Message: ----------- remove sudo from travis, it will stop being supported soon

https://blog.travis-ci.com/2018-11-19-required-linux-infrastructure-migratio...

Commit: 7474eeadf6375b90fd66bb7545970fd2eb05afe8 https://github.com/galaxyproject/galaxy/commit/7474eeadf6375b90fd66bb7545970... Author: Jelle Scholtalbers j.scholtalbers@gmail.com Date: 2018-11-22 (Thu, 22 Nov 2018)

Changed paths: M lib/galaxy/tools/deps/mulled/mulled_build.py

Log Message: ----------- fix error when building images where conda channels is passed as a string instead of a list

Commit: 855ccb12791a649d72598ba2433491bd5d705899 https://github.com/galaxyproject/galaxy/commit/855ccb12791a649d72598ba243349... Author: Helena Rasche hxr@hx42.org Date: 2018-11-23 (Fri, 23 Nov 2018)

Changed paths: M scripts/grt/export.py M scripts/grt/grt.yml.sample

Log Message: ----------- GRT: Rip out all parameters, round file sizes

Commit: a2b7521140f74b443c7339cf3ef605fde4bae187 https://github.com/galaxyproject/galaxy/commit/a2b7521140f74b443c7339cf3ef60... Author: John Chilton jmchilton@gmail.com Date: 2018-11-23 (Fri, 23 Nov 2018)

Changed paths: M lib/galaxy/jobs/runners/state_handlers/resubmit.py A test/functional/tools/exit_code_from_env.xml M test/functional/tools/samples_tool_conf.xml A test/integration/resubmission_tool_detected_always_error_job_conf.xml A test/integration/resubmission_tool_detected_resubmit_job_conf.xml M test/integration/test_job_resubmission.py

Log Message: ----------- Fix resubmission on tool error detection.

Parts of this were wired up before but pieces were missing and so it was broken.

Commit: 536f7c9c6b24b027731cddbcced600aedc518de6 https://github.com/galaxyproject/galaxy/commit/536f7c9c6b24b027731cddbcced60... Author: guerler aysam.guerler@gmail.com Date: 2018-11-23 (Fri, 23 Nov 2018)

Changed paths: M lib/galaxy/tools/__init__.py

Log Message: ----------- Do not replace mismatching data-reference based input parameters with default values

Commit: 90076617651b8159fc75bfeefff2ab5db85cab59 https://github.com/galaxyproject/galaxy/commit/90076617651b8159fc75bfeefff2a... Author: Nicola Soranzo nicola.soranzo@earlham.ac.uk Date: 2018-11-23 (Fri, 23 Nov 2018)

Changed paths: M scripts/common_startup_functions.sh

Log Message: ----------- Merge branch 'release_18.09' into dev

Commit: dcfbedaa53ddc488b2ac74a63c8bae5a3d206abc https://github.com/galaxyproject/galaxy/commit/dcfbedaa53ddc488b2ac74a63c8ba... Author: Martin Cech marten@bx.psu.edu Date: 2018-11-23 (Fri, 23 Nov 2018)

Changed paths: M lib/galaxy/tools/deps/container_resolvers/__init__.py M lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/tools/deps/mulled/mulled_build.py

Log Message: ----------- Merge pull request #7038 from nsoranzo/release_18.09_fix/mulled_container_default_channels

[18.09] Fix error when building images

Commit: 12dbbb81a7c76b5de0d195f25f0a7b46992db9e0 https://github.com/galaxyproject/galaxy/commit/12dbbb81a7c76b5de0d195f25f0a7... Author: Martin Cech marten@bx.psu.edu Date: 2018-11-23 (Fri, 23 Nov 2018)

Changed paths:

Log Message: ----------- Merge pull request #7036 from scholtalbers/fix/mulled_container_default_channels

Fix error when building images

Commit: 03acc98576085039ab1363b8248369ca646a031d https://github.com/galaxyproject/galaxy/commit/03acc98576085039ab1363b824836... Author: Nicola Soranzo nicola.soranzo@earlham.ac.uk Date: 2018-11-25 (Sun, 25 Nov 2018)

Changed paths:

Log Message: ----------- Merge branch 'release_18.09' into dev

Commit: 81e337622580d22b8170f9a85ad4f825ea30c440 https://github.com/galaxyproject/galaxy/commit/81e337622580d22b8170f9a85ad4f... Author: Nicola Soranzo nicola.soranzo@earlham.ac.uk Date: 2018-11-26 (Mon, 26 Nov 2018)

Changed paths: M .travis.yml

Log Message: ----------- Add workaround for https://github.com/travis-ci/travis-ci/issues/7940

Commit: 284e906df0a0cf4215483088f0120c14ca1f1b24 https://github.com/galaxyproject/galaxy/commit/284e906df0a0cf4215483088f0120... Author: Martin Cech marten@bx.psu.edu Date: 2018-11-26 (Mon, 26 Nov 2018)

Changed paths: M lib/galaxy/tools/__init__.py

Log Message: ----------- Merge pull request #7043 from guerler/column_match

Avoid replacing data-referenced input values with default values

Commit: 015b8547ad3b56e32decf0bc803d1a800b35182c https://github.com/galaxyproject/galaxy/commit/015b8547ad3b56e32decf0bc803d1... Author: Martin Cech marten@bx.psu.edu Date: 2018-11-26 (Mon, 26 Nov 2018)

Changed paths: M .travis.yml

Log Message: ----------- Merge pull request #7035 from martenson/remove-sudo

Remove ``sudo: false`` from .travis.yml, it will stop being supported soon

Commit: 8033f0cd6d3882b3373e31470d7fd0ae6c37c467 https://github.com/galaxyproject/galaxy/commit/8033f0cd6d3882b3373e31470d7fd... Author: Helena Rasche hxr@hx42.org Date: 2018-11-27 (Tue, 27 Nov 2018)

Changed paths: M lib/galaxy/jobs/runners/state_handlers/resubmit.py A test/functional/tools/exit_code_from_env.xml M test/functional/tools/samples_tool_conf.xml A test/integration/resubmission_tool_detected_always_error_job_conf.xml A test/integration/resubmission_tool_detected_resubmit_job_conf.xml M test/integration/test_job_resubmission.py

Log Message: ----------- Merge pull request #7040 from jmchilton/fix_tool_detected_error_resubmission

Fix resubmission on tool error detection.

Commit: 5a62a5c091a9c73ffd6647af7a81e1781c59aa17 https://github.com/galaxyproject/galaxy/commit/5a62a5c091a9c73ffd6647af7a81e... Author: Dannon Baker dannon.baker@gmail.com Date: 2018-11-27 (Tue, 27 Nov 2018)

Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/webapps/galaxy/api/workflows.py

Log Message: ----------- Merge remote-tracking branch 'upstream/release_18.09' into dev

Commit: 2376d7f2fd57fcf9ae00264c4244ba06d63b8906 https://github.com/galaxyproject/galaxy/commit/2376d7f2fd57fcf9ae00264c4244b... Author: John Chilton jmchilton@gmail.com Date: 2018-11-27 (Tue, 27 Nov 2018)

Changed paths: M lib/galaxy/tools/parser/xml.py

Log Message: ----------- Merge pull request #6977 from bernt-matthias/topic/stdio-add

changed exit code and regex parsing

Commit: c4c8af036fda560d5340e77d9f38782754729eb1 https://github.com/galaxyproject/galaxy/commit/c4c8af036fda560d5340e77d9f387... Author: M Bernt m.bernt@ufz.de Date: 2018-11-27 (Tue, 27 Nov 2018)

Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd

Log Message: ----------- doc: updated error parsing docs

see https://github.com/galaxyproject/galaxy/pull/697://github.com/galaxyproject/...

Commit: 83417cab622309f9b53d8881c6946bc11e6cb3ba https://github.com/galaxyproject/galaxy/commit/83417cab622309f9b53d8881c6946... Author: Ivan Kuzmin inkuzm@gmail.com Date: 2018-11-28 (Wed, 28 Nov 2018)

Changed paths: A client/galaxy/scripts/components/GalaxyLoader.vue

Log Message: ----------- Add styled loader vue component

Commit: 356d949199359a974a96d531db0dc39d97007df6 https://github.com/galaxyproject/galaxy/commit/356d949199359a974a96d531db0dc... Author: Nuwan Goonasekera 2070605+nuwang@users.noreply.github.com Date: 2018-11-28 (Wed, 28 Nov 2018)

Changed paths: M lib/galaxy/jobs/runners/pulsar.py

Log Message: ----------- Allow pulsar jobs to be resubmitted on connection failures

Commit: 263d10ca1c7577f3138df83f19468c1c20b85ea0 https://github.com/galaxyproject/galaxy/commit/263d10ca1c7577f3138df83f19468... Author: Nuwan Goonasekera 2070605+nuwang@users.noreply.github.com Date: 2018-11-28 (Wed, 28 Nov 2018)

Changed paths: A test/integration/resubmission_pulsar_job_conf.xml M test/integration/test_job_resubmission.py

Log Message: ----------- Added test for pulsar resubmission

Commit: 2632c071cdf1f6f49c30d243eea4931ee6fcaab2 https://github.com/galaxyproject/galaxy/commit/2632c071cdf1f6f49c30d243eea49... Author: Nuwan Goonasekera 2070605+nuwang@users.noreply.github.com Date: 2018-11-28 (Wed, 28 Nov 2018)

Changed paths: M lib/galaxy/jobs/mapper.py M test/unit/jobs/test_mapper.py M test/unit/jobs/test_rules/10_site.py

Log Message: ----------- Added referrer parameter for dynamic destinations + test

Commit: 6fa0c8f932831fe91db492de09a2bb4b48621738 https://github.com/galaxyproject/galaxy/commit/6fa0c8f932831fe91db492de09a2b... Author: Martin Cech marten@bx.psu.edu Date: 2018-11-28 (Wed, 28 Nov 2018)

Changed paths: M client/galaxy/scripts/layout/menu.js M config/galaxy.yml.sample M doc/source/admin/galaxy_options.rst M lib/galaxy/config.py M lib/galaxy/managers/configuration.py M lib/galaxy/webapps/galaxy/config_schema.yml

Log Message: ----------- add new item to the help menu

Commit: be43693ef05dfae85872412f198d87a31424f486 https://github.com/galaxyproject/galaxy/commit/be43693ef05dfae85872412f198d8... Author: Dannon Baker dannon.baker@gmail.com Date: 2018-11-29 (Thu, 29 Nov 2018)

Changed paths: M scripts/common_startup.sh

Log Message: ----------- Avoid using make for autobuild; reducing necessary dependencies out of the box.

Commit: 77aec5a79dc18e224ca6246659f68a49864a46cf https://github.com/galaxyproject/galaxy/commit/77aec5a79dc18e224ca6246659f68... Author: Dannon Baker dannon.baker@gmail.com Date: 2018-11-29 (Thu, 29 Nov 2018)

Changed paths: M scripts/common_startup.sh

Log Message: ----------- Standardize on spaces in common_startup.sh (tabs were mixed in here)

Commit: 72f5d1a35f0a854a242c0854f670ab82045e95a9 https://github.com/galaxyproject/galaxy/commit/72f5d1a35f0a854a242c0854f670a... Author: Björn Grüning bjoern@gruenings.eu Date: 2018-11-29 (Thu, 29 Nov 2018)

Changed paths: M client/galaxy/scripts/layout/menu.js M config/galaxy.yml.sample M doc/source/admin/galaxy_options.rst M lib/galaxy/config.py M lib/galaxy/managers/configuration.py M lib/galaxy/webapps/galaxy/config_schema.yml

Log Message: ----------- Merge pull request #7054 from martenson/help-menu-item-rel

[18.09] add new item to the help menu

Commit: fa408f485048ee8c7afeb96ac6c9da8dea4661f3 https://github.com/galaxyproject/galaxy/commit/fa408f485048ee8c7afeb96ac6c9d... Author: Dannon Baker dannon.baker@gmail.com Date: 2018-11-29 (Thu, 29 Nov 2018)

Changed paths: M scripts/common_startup.sh

Log Message: ----------- exit with error code (and appropriate message) on either build failure

Commit: 247fd018105ae8d08e7eeb89b5f92dfbe6b8548c https://github.com/galaxyproject/galaxy/commit/247fd018105ae8d08e7eeb89b5f92... Author: Martin Cech marten@bx.psu.edu Date: 2018-11-29 (Thu, 29 Nov 2018)

Changed paths: M client/galaxy/scripts/layout/menu.js M config/galaxy.yml.sample M doc/source/admin/galaxy_options.rst M lib/galaxy/config.py M lib/galaxy/webapps/galaxy/config_schema.yml M static/style/blue/base.css

Log Message: ----------- make the transition non-instrusive

Commit: 4cde6b9b814acae02393c9fc6b432506cb9c429d https://github.com/galaxyproject/galaxy/commit/4cde6b9b814acae02393c9fc6b432... Author: guerler aysam.guerler@gmail.com Date: 2018-11-29 (Thu, 29 Nov 2018)

Changed paths: M client/galaxy/scripts/mvc/tool/tool-form.js

Log Message: ----------- Escape dataset names in job submission success message

Commit: d3679e2541045f25e6007efbaed5d9d11f91a8c4 https://github.com/galaxyproject/galaxy/commit/d3679e2541045f25e6007efbaed5d... Author: Martin Cech marten@bx.psu.edu Date: 2018-11-30 (Fri, 30 Nov 2018)

Changed paths: M static/style/blue/base.css

Log Message: ----------- revert the changes to css, probably remnant from working on dev

Commit: 51afe15f86c0f67e2e51fd0c67ba950a424f0983 https://github.com/galaxyproject/galaxy/commit/51afe15f86c0f67e2e51fd0c67ba9... Author: Nicola Soranzo nicola.soranzo@gmail.com Date: 2018-11-30 (Fri, 30 Nov 2018)

Changed paths: M client/galaxy/scripts/layout/menu.js M config/galaxy.yml.sample M doc/source/admin/galaxy_options.rst M lib/galaxy/config.py M lib/galaxy/webapps/galaxy/config_schema.yml

Log Message: ----------- Merge pull request #7061 from martenson/help-menu-item-rel

[18.09] make the menu transition non-instrusive

Commit: 7183a17efc7cfb598c376eaf0d391efb6848e27d https://github.com/galaxyproject/galaxy/commit/7183a17efc7cfb598c376eaf0d391... Author: Nicola Soranzo nicola.soranzo@earlham.ac.uk Date: 2018-11-30 (Fri, 30 Nov 2018)

Changed paths: M client/galaxy/scripts/layout/menu.js M config/galaxy.yml.sample M doc/source/admin/galaxy_options.rst M lib/galaxy/config.py M lib/galaxy/managers/configuration.py M lib/galaxy/webapps/galaxy/config_schema.yml

Log Message: ----------- Merge branch 'release_18.09' into dev

Commit: 2a3b22cf497055a1afc578a1f7aead35f51a0ba2 https://github.com/galaxyproject/galaxy/commit/2a3b22cf497055a1afc578a1f7aea... Author: Nicola Soranzo nicola.soranzo@earlham.ac.uk Date: 2018-11-30 (Fri, 30 Nov 2018)

Changed paths: M config/galaxy.yml.sample M doc/source/admin/galaxy_options.rst

Log Message: ----------- Update galaxy.yml.sample and galaxy_options.rst

with `make config-rebuild` . Follow-up on https://github.com/galaxyproject/galaxy/pull/6776 .

Commit: 4e1618e754f6bc9b28cbd2fc1dc06c2288b1239f https://github.com/galaxyproject/galaxy/commit/4e1618e754f6bc9b28cbd2fc1dc06... Author: Martin Cech marten@bx.psu.edu Date: 2018-11-30 (Fri, 30 Nov 2018)

Changed paths: M config/galaxy.yml.sample M doc/source/admin/galaxy_options.rst

Log Message: ----------- Merge pull request #7064 from nsoranzo/make_config-rebuild

Update ``galaxy.yml.sample`` and ``galaxy_options.rst``

Commit: 8c8fc364e1ee9c1b91f266c13867d27c6f7cca80 https://github.com/galaxyproject/galaxy/commit/8c8fc364e1ee9c1b91f266c13867d... Author: Martin Cech marten@bx.psu.edu Date: 2018-11-30 (Fri, 30 Nov 2018)

Changed paths: M client/galaxy/scripts/mvc/tool/tool-form.js

Log Message: ----------- Merge pull request #7062 from guerler/escape_select2

Escape dataset names in job submission success message

Commit: 030cf02fc8009cf412a763863756de4b79beba77 https://github.com/galaxyproject/galaxy/commit/030cf02fc8009cf412a763863756d... Author: Martin Cech marten@bx.psu.edu Date: 2018-11-30 (Fri, 30 Nov 2018)

Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-edit-attributes.js M lib/galaxy/webapps/galaxy/controllers/dataset.py

Log Message: ----------- Merge pull request #7018 from qiagu/join1

Add datatype sniff button to edit dataset attributes page

Commit: 6703584714507f129fee6e967df875bfa6027fc0 https://github.com/galaxyproject/galaxy/commit/6703584714507f129fee6e967df87... Author: Sergey Golitsynskiy sgolitsynskiy@gmail.com Date: 2018-11-30 (Fri, 30 Nov 2018)

Changed paths: M doc/source/admin/framework_dependencies.rst

Log Message: ----------- Fix link to requirements.txt

Dependency files rearranged (commit 1b0ccf6, Nov. 1, 2017)

Commit: c679b64272ccbff630fd68d9f201b95d54e75e00 https://github.com/galaxyproject/galaxy/commit/c679b64272ccbff630fd68d9f201b... Author: John Chilton jmchilton@gmail.com Date: 2018-12-02 (Sun, 02 Dec 2018)

Changed paths: M doc/source/admin/framework_dependencies.rst

Log Message: ----------- Merge pull request #7065 from ic4f/dev

Fix link to requirements.txt

Commit: 66fae561b29507a69f5c32690be4791f86f5cdd7 https://github.com/galaxyproject/galaxy/commit/66fae561b29507a69f5c32690be47... Author: Dannon Baker dannon.baker@gmail.com Date: 2018-12-02 (Sun, 02 Dec 2018)

Changed paths: M scripts/common_startup.sh

Log Message: ----------- Don't use pushd/popd

Commit: 118cd15186fc3d8d4784f8847355542ee07a8a5a https://github.com/galaxyproject/galaxy/commit/118cd15186fc3d8d4784f88473555... Author: Martin Cech marten@bx.psu.edu Date: 2018-12-03 (Mon, 03 Dec 2018)

Changed paths: M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt

Log Message: ----------- downgrade bdbag, 1.5.0 requires python:>=2.7.9 which centos7 does not have

Commit: 3931b8ec355df64e780f640d39ac0928d7c8afde https://github.com/galaxyproject/galaxy/commit/3931b8ec355df64e780f640d39ac0... Author: M Bernt m.bernt@ufz.de Date: 2018-12-04 (Tue, 04 Dec 2018)

Changed paths: M lib/galaxy/util/__init__.py

Log Message: ----------- improved parsing of sizes (bytes)

before floats like without byte extension were not recognized (eg 1.0)

Commit: cf25f7dcec6f7f7b13aac93a18ced291d5e74444 https://github.com/galaxyproject/galaxy/commit/cf25f7dcec6f7f7b13aac93a18ced... Author: mvdbeek m.vandenbeek@gmail.com Date: 2018-12-04 (Tue, 04 Dec 2018)

Changed paths: M lib/galaxy/tools/parameters/meta.py

Log Message: ----------- Fix nesting of repeats and error when repeat is provided literally.

This fixex #7048, where in addition to repeat values ('repeat_0|param: some_value') there are also values for the repeat param itself ('repeat': []).

Commit: 3a93fd4f2321bf141b2ccf34ea80c42ee517b33d https://github.com/galaxyproject/galaxy/commit/3a93fd4f2321bf141b2ccf34ea80c... Author: mvdbeek m.vandenbeek@gmail.com Date: 2018-12-04 (Tue, 04 Dec 2018)

Changed paths: M test/unit/tools/test_parameter_parsing.py

Log Message: ----------- Add test for proper nesting in process_keys

and a unit test for https://github.com/galaxyproject/galaxy/issues/7048

Commit: 27cc49d3f785c643b4dcdbf0da09d1bf63ee44f9 https://github.com/galaxyproject/galaxy/commit/27cc49d3f785c643b4dcdbf0da09d... Author: M Bernt m.bernt@ufz.de Date: 2018-12-04 (Tue, 04 Dec 2018)

Changed paths: M lib/galaxy/util/__init__.py

Log Message: ----------- size_to_bytes: use only regex, remove assert, add exceptions

Commit: c90d71dd44794f8499813804290d08d3fdae6a6f https://github.com/galaxyproject/galaxy/commit/c90d71dd44794f8499813804290d0... Author: Nicola Soranzo nicola.soranzo@gmail.com Date: 2018-12-04 (Tue, 04 Dec 2018)

Changed paths: M lib/galaxy/util/__init__.py

Log Message: ----------- Raise ValueError, fix spacing

Commit: df51c468898e6bbc236e5a30a2758de4d06c9642 https://github.com/galaxyproject/galaxy/commit/df51c468898e6bbc236e5a30a2758... Author: Nicola Soranzo nicola.soranzo@gmail.com Date: 2018-12-04 (Tue, 04 Dec 2018)

Changed paths: M lib/galaxy/util/__init__.py

Log Message: ----------- Add missing empty line

Commit: 26a6b1c83381d1c75131f330d8b8f4c23680f1dd https://github.com/galaxyproject/galaxy/commit/26a6b1c83381d1c75131f330d8b8f... Author: Nicola Soranzo nicola.soranzo@gmail.com Date: 2018-12-04 (Tue, 04 Dec 2018)

Changed paths: M lib/galaxy/util/__init__.py

Log Message: ----------- Stricter regexp

Commit: aaa8d1a61cb567b49b2171e27bc623b59c0227fe https://github.com/galaxyproject/galaxy/commit/aaa8d1a61cb567b49b2171e27bc62... Author: Nate Coraor nate@bx.psu.edu Date: 2018-12-04 (Tue, 04 Dec 2018)

Changed paths: M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt

Log Message: ----------- Merge pull request #7070 from martenson/downgrade-bdbag

downgrade bdbag, 1.5.0 requires python:>=2.7.9

Commit: 46ad1992bdbf478495b14780e96e251d00ceb700 https://github.com/galaxyproject/galaxy/commit/46ad1992bdbf478495b14780e96e2... Author: Martin Cech marten@bx.psu.edu Date: 2018-12-04 (Tue, 04 Dec 2018)

Changed paths: M lib/galaxy/tools/parameters/meta.py M test/unit/tools/test_parameter_parsing.py

Log Message: ----------- Merge pull request #7071 from mvdbeek/fix_process_key

[18.09] Fix process key

Commit: ee88806578655fff9d32e72e90468e0ca87c877b https://github.com/galaxyproject/galaxy/commit/ee88806578655fff9d32e72e90468... Author: Nicola Soranzo nicola.soranzo@earlham.ac.uk Date: 2018-12-04 (Tue, 04 Dec 2018)

Changed paths: M lib/galaxy/tools/parameters/meta.py M test/unit/tools/test_parameter_parsing.py

Log Message: ----------- Merge branch 'release_18.09' into dev

Commit: eeffb26423a2b6380087c01af5d3390c2fd9b0df https://github.com/galaxyproject/galaxy/commit/eeffb26423a2b6380087c01af5d33... Author: Helena Rasche hxr@hx42.org Date: 2018-12-04 (Tue, 04 Dec 2018)

Changed paths: M client/galaxy/scripts/mvc/history/history-item-li.js

Log Message: ----------- Implement colourful tags

Commit: e6c4292fd5a3182f01f16dfd445359f5dcb87e0c https://github.com/galaxyproject/galaxy/commit/e6c4292fd5a3182f01f16dfd44535... Author: Helena Rasche hxr@hx42.org Date: 2018-12-04 (Tue, 04 Dec 2018)

Changed paths: M client/galaxy/scripts/mvc/history/history-item-li.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/galaxy/scripts/utils/utils.js

Log Message: ----------- Move to correct location

Commit: 5865fe3513232fe893dd2a638a54218599be11a9 https://github.com/galaxyproject/galaxy/commit/5865fe3513232fe893dd2a638a542... Author: Helena Rasche hxr@hx42.org Date: 2018-12-04 (Tue, 04 Dec 2018)

Changed paths: M client/galaxy/scripts/mvc/history/history-item-li.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/galaxy/scripts/utils/utils.js

Log Message: ----------- Add colorFg function

Commit: 12576ef49477f51137cf0f223600a00c2c7b90e3 https://github.com/galaxyproject/galaxy/commit/12576ef49477f51137cf0f223600a... Author: Helena Rasche hxr@hx42.org Date: 2018-12-04 (Tue, 04 Dec 2018)

Changed paths: M client/galaxy/scripts/mvc/history/history-item-li.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/galaxy/scripts/utils/utils.js

Log Message: ----------- Replace with style function

Commit: 0e7f2b3595a4235b1672205bd13b73153014f139 https://github.com/galaxyproject/galaxy/commit/0e7f2b3595a4235b1672205bd13b7... Author: Helena Rasche hxr@hx42.org Date: 2018-12-04 (Tue, 04 Dec 2018)

Changed paths: M client/galaxy/scripts/utils/utils.js

Log Message: ----------- revert to grey border

Commit: 199cca9417d484b8c4998f66beb4892de69accf3 https://github.com/galaxyproject/galaxy/commit/199cca9417d484b8c4998f66beb48... Author: Nicola Soranzo nicola.soranzo@gmail.com Date: 2018-12-05 (Wed, 05 Dec 2018)

Changed paths: M lib/galaxy/util/__init__.py

Log Message: ----------- Merge pull request #7067 from bernt-matthias/topic/size-parse

Improved parsing of sizes (bytes)

Commit: ad9787ef7050e3747b1b862ba857b1a2557174a0 https://github.com/galaxyproject/galaxy/commit/ad9787ef7050e3747b1b862ba857b... Author: Helena Rasche hxr@hx42.org Date: 2018-12-05 (Wed, 05 Dec 2018)

Changed paths: M client/galaxy/scripts/utils/utils.js

Log Message: ----------- cleanup/docs

Commit: c4dbf8615e98ae8778715e1169b537c8148af3b0 https://github.com/galaxyproject/galaxy/commit/c4dbf8615e98ae8778715e1169b53... Author: Martin Cech marten@bx.psu.edu Date: 2018-12-05 (Wed, 05 Dec 2018)

Changed paths: M client/galaxy/scripts/mvc/history/history-item-li.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/galaxy/scripts/utils/utils.js

Log Message: ----------- Merge pull request #7072 from erasche/colour-tags

Make tags more colourful

Commit: 480143af57163b416f56566153e55d32b90e195b https://github.com/galaxyproject/galaxy/commit/480143af57163b416f56566153e55... Author: Dannon Baker dannon.baker@gmail.com Date: 2018-12-05 (Wed, 05 Dec 2018)

Changed paths: M client/galaxy/scripts/apps/analysis.js

Log Message: ----------- Handle extra cruft sent along by facebook login redirects

Commit: f8ed3e73253e9ad2b893c14409173f9b504f00cc https://github.com/galaxyproject/galaxy/commit/f8ed3e73253e9ad2b893c14409173... Author: Dannon Baker dannon.baker@gmail.com Date: 2018-12-05 (Wed, 05 Dec 2018)

Changed paths: M client/galaxy/scripts/layout/menu.js

Log Message: ----------- Client format.

Commit: f5301c264592f5a6d3f7747b1f930f82384c9495 https://github.com/galaxyproject/galaxy/commit/f5301c264592f5a6d3f7747b1f930... Author: Nicola Soranzo nicola.soranzo@earlham.ac.uk Date: 2018-12-05 (Wed, 05 Dec 2018)

Changed paths: M lib/galaxy/dependencies/pipfiles/default/Pipfile M lib/galaxy/dependencies/pipfiles/default/pinned-dev-requirements.txt M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt

Log Message: ----------- Dependencies fixes, follow up on #7070

Commit: 7eb436cebc39363330e9b0503c36b00cb763dbc5 https://github.com/galaxyproject/galaxy/commit/7eb436cebc39363330e9b0503c36b... Author: Nicola Soranzo nicola.soranzo@earlham.ac.uk Date: 2018-12-05 (Wed, 05 Dec 2018)

Changed paths: M lib/galaxy/dependencies/pipfiles/default/pinned-dev-requirements.txt M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt M lib/galaxy/dependencies/pipfiles/update.sh

Log Message: ----------- Update all dependencies

with `make update-dependencies` using pipenv 2018.11.26 .

Also remove oscillating `python_version < '3.0'` environment marker for `azure-storage-nspkg` package.

Commit: 57459954de189cb1fd9b6ab8654c8f4700241ea2 https://github.com/galaxyproject/galaxy/commit/57459954de189cb1fd9b6ab8654c8... Author: John Chilton jmchilton@gmail.com Date: 2018-12-05 (Wed, 05 Dec 2018)

Changed paths: M scripts/common_startup.sh

Log Message: ----------- Merge pull request #7060 from dannon/no-make-for-autobuild

[18.09] Eliminate dependency on make for automatic client build

Commit: 691fbfe606fba9399f66ffeed916294d3a4e5113 https://github.com/galaxyproject/galaxy/commit/691fbfe606fba9399f66ffeed9162... Author: mvdbeek m.vandenbeek@gmail.com Date: 2018-12-06 (Thu, 06 Dec 2018)

Changed paths: M lib/galaxy/jobs/__init__.py

Log Message: ----------- Fix set_peek method for copied datasets

dataset_assoc is the job to ouptut dataset association that references the HDA created by a job. If the HDA is copied the copies need to be updated as well, so here we need to call `set_peek` on dataset, not dataset_assoc.dataset.

Broken in f4343d876f13e55e92ca228582b4430dcd01e4aa

Thanks for tracking this down @jmchilton!

Commit: 35fd29062587002f70f660e4a7675bd23545fc85 https://github.com/galaxyproject/galaxy/commit/35fd29062587002f70f660e4a7675... Author: jvanbraekel 29703119+jvanbraekel@users.noreply.github.com Date: 2018-12-06 (Thu, 06 Dec 2018)

Changed paths: M templates/admin/tool_shed_repository/manage_repository.mako

Log Message: ----------- Fix Error display

The template display was broken in case of error. 'in_error_state is never defined it should be 'repository.in_error_state' instead. This was leading to some wrong field type display and not displaying the details about the error.

Commit: 4bf27f4642163be0c3b0b7399453833ba1013a8c https://github.com/galaxyproject/galaxy/commit/4bf27f4642163be0c3b0b73994538... Author: Dannon dannon.baker@gmail.com Date: 2018-12-06 (Thu, 06 Dec 2018)

Changed paths: M lib/galaxy/dependencies/pipfiles/default/Pipfile M lib/galaxy/dependencies/pipfiles/default/pinned-dev-requirements.txt M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt M lib/galaxy/dependencies/pipfiles/update.sh

Log Message: ----------- Merge pull request #7079 from nsoranzo/follow-up_on_7070

Follow-up on #7070

Commit: 16f3be66be84ac9827f4c0fa213d9ead9ba30bd2 https://github.com/galaxyproject/galaxy/commit/16f3be66be84ac9827f4c0fa213d9... Author: Nicola Soranzo nicola.soranzo@earlham.ac.uk Date: 2018-12-06 (Thu, 06 Dec 2018)

Changed paths: M scripts/common_startup.sh

Log Message: ----------- Merge branch 'release_18.09' into dev

Commit: b453f531e51c6fc91d44d777de486b31c82cf726 https://github.com/galaxyproject/galaxy/commit/b453f531e51c6fc91d44d777de486... Author: Martin Cech marten@bx.psu.edu Date: 2018-12-06 (Thu, 06 Dec 2018)

Changed paths: M templates/admin/tool_shed_repository/manage_repository.mako

Log Message: ----------- Merge pull request #7080 from jvanbraekel/patch-1

Fix toolshed repository error display

Commit: 4c2f95b1f469d9789e65c4c9be97c4e137014ece https://github.com/galaxyproject/galaxy/commit/4c2f95b1f469d9789e65c4c9be97c... Author: Helena Rasche hxr@hx42.org Date: 2018-12-07 (Fri, 07 Dec 2018)

Changed paths: M client/galaxy/scripts/utils/utils.js

Log Message: ----------- Fix hashing, AND was not the right operation

Commit: bddfe3889031a31ad3efd1dadd8482a6301a9ad9 https://github.com/galaxyproject/galaxy/commit/bddfe3889031a31ad3efd1dadd848... Author: Martin Cech marten@bx.psu.edu Date: 2018-12-07 (Fri, 07 Dec 2018)

Changed paths: M client/galaxy/scripts/utils/utils.js

Log Message: ----------- Merge pull request #7081 from erasche/fix-hash

Fix hashing, AND was not the right operation

Commit: 2de4a0f72e5d51661318e1abeb727fdaa10f7444 https://github.com/galaxyproject/galaxy/commit/2de4a0f72e5d51661318e1abeb727... Author: John Chilton jmchilton@gmail.com Date: 2018-12-07 (Fri, 07 Dec 2018)

Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy_ext/metadata/set_metadata.py

Log Message: ----------- Remove legacy job handling hacks.

These were left in to let Galaxy jobs complete after version upgrades, but the plan was always to remove them eventually.

Commit: 5c384efb8d2ad42d6dfafa84fc09bc02d3f462e8 https://github.com/galaxyproject/galaxy/commit/5c384efb8d2ad42d6dfafa84fc09b... Author: John Chilton jmchilton@gmail.com Date: 2018-12-07 (Fri, 07 Dec 2018)

Changed paths: M lib/galaxy_ext/metadata/set_metadata.py

Log Message: ----------- Fix via refactor set_metadata so more output metadata pruned properly.

Commit: 4894ab9c80ae39f8b5527860618e973daee00a61 https://github.com/galaxyproject/galaxy/commit/4894ab9c80ae39f8b5527860618e9... Author: Dannon Baker dannon.baker@gmail.com Date: 2018-12-07 (Fri, 07 Dec 2018)

Changed paths: M client/galaxy/scripts/mvc/user/user-preferences.js

Log Message: ----------- Add pointer to user permissions interface on finish of make datasets private

Commit: e8d2b334a03c395b8c0abf54208b0e28368d0f81 https://github.com/galaxyproject/galaxy/commit/e8d2b334a03c395b8c0abf54208b0... Author: Nate Coraor nate@bx.psu.edu Date: 2018-12-07 (Fri, 07 Dec 2018)

Changed paths: M client/galaxy/scripts/mvc/history/options-menu.js M client/galaxy/scripts/mvc/user/user-preferences.js M lib/galaxy/webapps/galaxy/controllers/history.py

Log Message: ----------- Merge pull request #6952 from dannon/history_privacy

Quick 'make all datasets private' implementation.

Commit: f09d7b7d93463590dc8434376260248d0f3d4171 https://github.com/galaxyproject/galaxy/commit/f09d7b7d93463590dc84343762602... Author: Martin Cech marten@bx.psu.edu Date: 2018-12-07 (Fri, 07 Dec 2018)

Changed paths: M lib/galaxy_ext/metadata/set_metadata.py

Log Message: ----------- Merge pull request #7084 from jmchilton/fix_set_metadata

Fix via refactor set_metadata so more output metadata pruned properly.

Commit: 1ca77d53ef2bc1067db5c3a3b5d1c36b28aeaa1b https://github.com/galaxyproject/galaxy/commit/1ca77d53ef2bc1067db5c3a3b5d1c... Author: Martin Cech marten@bx.psu.edu Date: 2018-12-07 (Fri, 07 Dec 2018)

Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd

Log Message: ----------- Merge pull request #7049 from bernt-matthias/topic/doc-errors-detection

doc: updated error parsing docs

Commit: ad42f94102048a4c3a3695aaf88a333794aef0f7 https://github.com/galaxyproject/galaxy/commit/ad42f94102048a4c3a3695aaf88a3... Author: Martin Cech marten@bx.psu.edu Date: 2018-12-07 (Fri, 07 Dec 2018)

Changed paths: A client/galaxy/scripts/components/GalaxyLoader.vue

Log Message: ----------- Merge pull request #7052 from inkuzmin/dev

Add styled loader vue component

Commit: 11428a03b8193ff50c35d9dd7069789ca2ba6cc7 https://github.com/galaxyproject/galaxy/commit/11428a03b8193ff50c35d9dd70697... Author: Martin Cech marten@bx.psu.edu Date: 2018-12-07 (Fri, 07 Dec 2018)

Changed paths: M lib/galaxy/managers/workflows.py M lib/galaxy/model/mapping.py A lib/galaxy/model/migrate/versions/0146_workflow_paths.py M lib/galaxy/web/base/controller.py M lib/galaxy/webapps/galaxy/api/workflows.py M test/api/test_workflows.py M test/base/populators.py M test/base/workflow_fixtures.py M test/integration/test_dockerized_jobs.py A test/integration/test_workflow_sync.py

Log Message: ----------- Merge pull request #7019 from jmchilton/path-aware-workflows

File-based Workflow Editor

Commit: 4fbaa161232f1b8e12b23788e258def10e6aa156 https://github.com/galaxyproject/galaxy/commit/4fbaa161232f1b8e12b23788e258d... Author: Dan Fornika dfornika@gmail.com Date: 2018-12-07 (Fri, 07 Dec 2018)

Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py

Log Message: ----------- Add simple stub for mash sketch files

Commit: 4b1d9df4d677a0db7a11f39490671567e95c45be https://github.com/galaxyproject/galaxy/commit/4b1d9df4d677a0db7a11f39490671... Author: Vahid VJalili@users.noreply.github.com Date: 2018-12-07 (Fri, 07 Dec 2018)

Changed paths: M lib/galaxy/webapps/galaxy/api/cloud.py

Log Message: ----------- Replace `credentials` with `authz_id`

on cloud storage get api doc string.

Commit: 7d5a006b01ccd37ad65156be95f5e606dc4ea985 https://github.com/galaxyproject/galaxy/commit/7d5a006b01ccd37ad65156be95f5e... Author: Dan Fornika dfornika@gmail.com Date: 2018-12-07 (Fri, 07 Dec 2018)

Changed paths: M lib/galaxy/datatypes/binary.py

Log Message: ----------- Removed extra whitespace to appease linter

Commit: 27dc7c42c97db9230657a7db86567ac8b253d6b5 https://github.com/galaxyproject/galaxy/commit/27dc7c42c97db9230657a7db86567... Author: Dan Fornika dfornika@gmail.com Date: 2018-12-07 (Fri, 07 Dec 2018)

Changed paths: M lib/galaxy/datatypes/binary.py

Log Message: ----------- Removed extra whitespace to appease linter

Commit: 355b48c361e68a7d9fbe9fe86de7aa2313e5d608 https://github.com/galaxyproject/galaxy/commit/355b48c361e68a7d9fbe9fe86de7a... Author: Nate Coraor nate@bx.psu.edu Date: 2018-12-10 (Mon, 10 Dec 2018)

Changed paths: M lib/galaxy/app.py M lib/galaxy/config.py M lib/galaxy/exceptions/__init__.py M lib/galaxy/exceptions/error_codes.json M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/handler.py M lib/galaxy/jobs/manager.py M lib/galaxy/managers/datasets.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/actions/history_imp_exp.py M lib/galaxy/tools/actions/metadata.py M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/util/handlers.py M lib/galaxy/web/stack/__init__.py M lib/galaxy/web/stack/transport.py M lib/galaxy/webapps/galaxy/api/jobs.py M lib/galaxy/webapps/galaxy/config_schema.yml M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/workflow/scheduling_manager.py M test/unit/jobs/test_job_configuration.py M test/unit/tools/test_actions.py M test/unit/unittest_utils/galaxy_mock.py

Log Message: ----------- Make handler assignment configurable in preparation for new assignment methods.

Commit: 10c45705bca081c336214b08fcc84d209b19b345 https://github.com/galaxyproject/galaxy/commit/10c45705bca081c336214b08fcc84... Author: Nate Coraor nate@bx.psu.edu Date: 2018-12-10 (Mon, 10 Dec 2018)

Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/util/facts.py M lib/galaxy/util/handlers.py M lib/galaxy/web/stack/__init__.py M lib/galaxy/workflow/scheduling_manager.py A test/unit/jobs/handler_template_job_conf.xml M test/unit/jobs/test_job_configuration.py

Log Message: ----------- Unit tests and fixes for bugs discovered while testing.

Commit: 1fb8203a0c1f6f941e0b13fa6357ec04ea677ffb https://github.com/galaxyproject/galaxy/commit/1fb8203a0c1f6f941e0b13fa6357e... Author: Nate Coraor nate@bx.psu.edu Date: 2018-12-10 (Mon, 10 Dec 2018)

Changed paths: M config/galaxy.yml.sample M config/job_conf.xml.sample_advanced M config/workflow_schedulers_conf.xml.sample M doc/source/admin/galaxy_options.rst M doc/source/admin/jobs.md M doc/source/admin/scaling.md M lib/galaxy/jobs/manager.py M lib/galaxy/webapps/galaxy/config_schema.yml

Log Message: ----------- Handler assignment documentation.

Commit: 40f776afde460759b5d682c19ef698fefd2d4388 https://github.com/galaxyproject/galaxy/commit/40f776afde460759b5d682c19ef69... Author: Nate Coraor nate@bx.psu.edu Date: 2018-12-11 (Tue, 11 Dec 2018)

Changed paths: M lib/galaxy/jobs/manager.py M lib/galaxy/util/handlers.py M test/unit/jobs/handler_template_job_conf.xml M test/unit/jobs/test_job_configuration.py

Log Message: ----------- Fix tests broken with changes to job_conf.xml.sample_advanced, fix the broken direct handler assignment method, document the new handler assignment methods for future method authors. Ensure that enqueue does its best to return a handler (if known).

Commit: 4a006335ac4ac84a69b5cb1f851e3e63400443ae https://github.com/galaxyproject/galaxy/commit/4a006335ac4ac84a69b5cb1f851e3... Author: Nate Coraor nate@bx.psu.edu Date: 2018-12-11 (Tue, 11 Dec 2018)

Changed paths: M lib/galaxy/jobs/__init__.py

Log Message: ----------- Fix default job config (no job_conf.xml).

Commit: 10aa953a40e171246bdd1804c74e8019da8e8200 https://github.com/galaxyproject/galaxy/commit/10aa953a40e171246bdd1804c74e8... Author: John Chilton jmchilton@gmail.com Date: 2018-12-11 (Tue, 11 Dec 2018)

Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy_ext/metadata/set_metadata.py

Log Message: ----------- Merge pull request #7082 from jmchilton/legacy_hacks

Remove legacy job handling hacks.

Commit: ece11eaabed2cbc07964e503e6f83179c05a45fd https://github.com/galaxyproject/galaxy/commit/ece11eaabed2cbc07964e503e6f83... Author: John Chilton jmchilton@gmail.com Date: 2018-12-11 (Tue, 11 Dec 2018)

Changed paths: M lib/galaxy/objectstore/__init__.py M lib/galaxy/objectstore/azure_blob.py M lib/galaxy/objectstore/cloud.py M lib/galaxy/objectstore/pithos.py M lib/galaxy/objectstore/s3.py M test/unit/test_objectstore.py

Log Message: ----------- De-couple objectstore abstraction from XML.

- Allow loading objectstores for Python dicts and YAML configurations. - New tests for XML parsing of azure, cloud, pithos, and S3 object stores. - New tests for YAML parsing of all these object stores plus the stock disk and nested ones.

Commit: c7b133b74bfb889cd3b111faa5b1ce17133ca931 https://github.com/galaxyproject/galaxy/commit/c7b133b74bfb889cd3b111faa5b1c... Author: John Chilton jmchilton@gmail.com Date: 2018-12-11 (Tue, 11 Dec 2018)

Changed paths: M lib/galaxy/jobs/__init__.py M test/unit/jobs/test_job_wrapper.py

Log Message: ----------- Localize version strings to the working directory w/predictable path.

new_file_path is awful and we shouldn't be using it.

Commit: c4ab2a0c6bb768fe27b48648d21ab42733133c08 https://github.com/galaxyproject/galaxy/commit/c4ab2a0c6bb768fe27b48648d21ab... Author: Nicola Soranzo nicola.soranzo@earlham.ac.uk Date: 2018-12-11 (Tue, 11 Dec 2018)

Changed paths: M .travis.yml

Log Message: ----------- Add workaround for https://github.com/travis-ci/travis-ci/issues/7940

Commit: 3a1bdd0ea688948db9115a500224c5947c326e99 https://github.com/galaxyproject/galaxy/commit/3a1bdd0ea688948db9115a500224c... Author: John Chilton jmchilton@gmail.com Date: 2018-12-11 (Tue, 11 Dec 2018)

Changed paths: M .travis.yml

Log Message: ----------- Merge pull request #7092 from martenson/boto-workaround

[18.09] boto cfg workaround

Commit: 0e5c96ef3710612bf1171e7094cf7d5427387ecb https://github.com/galaxyproject/galaxy/commit/0e5c96ef3710612bf1171e7094cf7... Author: Nate Coraor nate@bx.psu.edu Date: 2018-12-11 (Tue, 11 Dec 2018)

Changed paths: M scripts/common_startup.sh

Log Message: ----------- Drop "Galaxy pip" in favor of manylinux1 wheels (which are supported in pip >= 8.1).

Commit: b10cfa43ac547eaecbd996cef7201170a0e0da8c https://github.com/galaxyproject/galaxy/commit/b10cfa43ac547eaecbd996cef7201... Author: Nate Coraor nate@bx.psu.edu Date: 2018-12-11 (Tue, 11 Dec 2018)

Changed paths: M scripts/common_startup.sh

Log Message: ----------- Remove unused $GXPIP_VERSION

Commit: efe84751a7bf84b2297df7b77b514b8425fe7c70 https://github.com/galaxyproject/galaxy/commit/efe84751a7bf84b2297df7b77b514... Author: Nicola Soranzo nicola.soranzo@earlham.ac.uk Date: 2018-12-11 (Tue, 11 Dec 2018)

Changed paths: M .travis.yml

Log Message: ----------- Add workaround for https://github.com/travis-ci/travis-ci/issues/7940

Commit: e9aec176fac8bb3681ea533be6178ffd43c3bf4d https://github.com/galaxyproject/galaxy/commit/e9aec176fac8bb3681ea533be6178... Author: Nate Coraor nate@bx.psu.edu Date: 2018-12-11 (Tue, 11 Dec 2018)

Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/workflow/scheduling_manager.py

Log Message: ----------- Fixes for workflow scheduling tests.

Commit: de3b7bb55fd4949456bfb61637cb67b1fd367d6e https://github.com/galaxyproject/galaxy/commit/de3b7bb55fd4949456bfb61637cb6... Author: guerler aysam.guerler@gmail.com Date: 2018-12-11 (Tue, 11 Dec 2018)

Changed paths: A lib/galaxy/webapps/galaxy/api/display_applications.py M lib/galaxy/webapps/galaxy/buildapp.py

Log Message: ----------- Add display applications api endpoint

Commit: 6546e35bff27a60b09bf30ca68c2beb62a61acd4 https://github.com/galaxyproject/galaxy/commit/6546e35bff27a60b09bf30ca68c2b... Author: guerler aysam.guerler@gmail.com Date: 2018-12-11 (Tue, 11 Dec 2018)

Changed paths: M lib/galaxy/webapps/galaxy/api/display_applications.py M lib/galaxy/webapps/galaxy/buildapp.py

Log Message: ----------- Add reload feature to display applications api endpoint

Commit: eb0c0ad9ab204cee83233523c01b11aa040a6388 https://github.com/galaxyproject/galaxy/commit/eb0c0ad9ab204cee83233523c01b1... Author: guerler aysam.guerler@gmail.com Date: 2018-12-11 (Tue, 11 Dec 2018)

Changed paths: M client/galaxy/scripts/apps/admin.js A client/galaxy/scripts/components/admin/DisplayApplications.vue M lib/galaxy/webapps/galaxy/api/display_applications.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin.py

Log Message: ----------- Add display application vue component

Commit: 727ab11480962ec31387cc6934c0fcec14a4ead0 https://github.com/galaxyproject/galaxy/commit/727ab11480962ec31387cc6934c0f... Author: guerler aysam.guerler@gmail.com Date: 2018-12-11 (Tue, 11 Dec 2018)

Changed paths: M client/galaxy/scripts/apps/panels/admin-panel.js

Log Message: ----------- Fix spacing in admin app router

Commit: 35d2cd9bf62a748bc3dd5963a3246b5a5a7e2a18 https://github.com/galaxyproject/galaxy/commit/35d2cd9bf62a748bc3dd5963a3246... Author: guerler aysam.guerler@gmail.com Date: 2018-12-11 (Tue, 11 Dec 2018)

Changed paths: M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/components/admin/DisplayApplications.vue

Log Message: ----------- Load display application data and display number of available applications

Commit: 0b0c0084198d59e5767decb9b79580cc2a3932b2 https://github.com/galaxyproject/galaxy/commit/0b0c0084198d59e5767decb9b7958... Author: Nicola Soranzo nicola.soranzo@earlham.ac.uk Date: 2018-12-12 (Wed, 12 Dec 2018)

Changed paths:

Log Message: ----------- Merge branch 'release_18.09' into dev

Commit: 505e4288eebabf4ff3a317a90785cc6906941e53 https://github.com/galaxyproject/galaxy/commit/505e4288eebabf4ff3a317a90785c... Author: guerler aysam.guerler@gmail.com Date: 2018-12-11 (Tue, 11 Dec 2018)

Changed paths: M client/galaxy/scripts/components/admin/DisplayApplications.vue

Log Message: ----------- Add display application vue component

Commit: 218a02f3dccd8ccb5c6aa3df6c81764cb5e7a793 https://github.com/galaxyproject/galaxy/commit/218a02f3dccd8ccb5c6aa3df6c817... Author: guerler aysam.guerler@gmail.com Date: 2018-12-11 (Tue, 11 Dec 2018)

Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py R templates/webapps/galaxy/admin/view_display_applications.mako

Log Message: ----------- Remove legacy display applications mako and controller endpoints

Commit: e5c9d9673d6d92291b7911f4255cbbafebceed0e https://github.com/galaxyproject/galaxy/commit/e5c9d9673d6d92291b7911f4255cb... Author: Nicola Soranzo nicola.soranzo@earlham.ac.uk Date: 2018-12-12 (Wed, 12 Dec 2018)

Changed paths: M lib/galaxy/util/__init__.py

Log Message: ----------- Fix ``size_to_bytes`` for some float values

Values like `.01` and `1.` were broken in commit 26a6b1c83381d1c75131f330d8b8f4c23680f1dd . The new regexp allows also scientific notation like `1.2E2` .

Commit: 4b097acffe77ab8348b4497cc9032011e2469825 https://github.com/galaxyproject/galaxy/commit/4b097acffe77ab8348b4497cc9032... Author: guerler aysam.guerler@gmail.com Date: 2018-12-11 (Tue, 11 Dec 2018)

Changed paths: M client/galaxy/scripts/components/admin/DisplayApplications.vue M lib/galaxy/webapps/galaxy/api/display_applications.py

Log Message: ----------- Submit reload requests to new display application api endpoint

Commit: b3f4d9b699e7a137dce7d130fe629aa01fc81292 https://github.com/galaxyproject/galaxy/commit/b3f4d9b699e7a137dce7d130fe629... Author: guerler aysam.guerler@gmail.com Date: 2018-12-11 (Tue, 11 Dec 2018)

Changed paths: M lib/galaxy/webapps/galaxy/api/display_applications.py

Log Message: ----------- Remove debug outputs

Commit: e8739a6cf530426bcd6f8c1c3964d7c31fb2a487 https://github.com/galaxyproject/galaxy/commit/e8739a6cf530426bcd6f8c1c3964d... Author: guerler aysam.guerler@gmail.com Date: 2018-12-11 (Tue, 11 Dec 2018)

Changed paths: M client/galaxy/scripts/components/admin/DisplayApplications.vue

Log Message: ----------- Use bootstrap vues table component to render display applications table

Commit: 39870a0d06647cf378ceae8b99065fbb09a8eefb https://github.com/galaxyproject/galaxy/commit/39870a0d06647cf378ceae8b99065... Author: guerler aysam.guerler@gmail.com Date: 2018-12-11 (Tue, 11 Dec 2018)

Changed paths: M client/galaxy/scripts/components/admin/DisplayApplications.vue M lib/galaxy/webapps/galaxy/api/display_applications.py

Log Message: ----------- Highlight reloaded/failed display application rows individually

Commit: f68fa47f295f3d743d7de97521fcf97f78cf0248 https://github.com/galaxyproject/galaxy/commit/f68fa47f295f3d743d7de97521fcf... Author: guerler aysam.guerler@gmail.com Date: 2018-12-11 (Tue, 11 Dec 2018)

Changed paths: M lib/galaxy/webapps/galaxy/api/display_applications.py

Log Message: ----------- Fix linting

Commit: c6fc4dc83a6ac46244ff05d560864cba1de8bf55 https://github.com/galaxyproject/galaxy/commit/c6fc4dc83a6ac46244ff05d560864... Author: John Chilton jmchilton@gmail.com Date: 2018-12-12 (Wed, 12 Dec 2018)

Changed paths: M lib/galaxy/util/__init__.py

Log Message: ----------- Merge pull request #7096 from nsoranzo/followup_on_7067

Fix ``size_to_bytes`` for some float values

Commit: d06718ef24202d2fcaf3d6e8bfaa9a862044f90f https://github.com/galaxyproject/galaxy/commit/d06718ef24202d2fcaf3d6e8bfaa9... Author: John Chilton jmchilton@gmail.com Date: 2018-12-12 (Wed, 12 Dec 2018)

Changed paths: M tools/stats/grouping.py M tools/stats/grouping.xml

Log Message: ----------- Merge pull request #6577 from bernt-matthias/topic/grouping-wreplace

improved grouping tool

Commit: bf550da2afe94ad53aae71e3d930a49cb98558a4 https://github.com/galaxyproject/galaxy/commit/bf550da2afe94ad53aae71e3d930a... Author: John Chilton jmchilton@gmail.com Date: 2018-12-12 (Wed, 12 Dec 2018)

Changed paths: M config/job_resource_params_conf.xml.sample M config/workflow_resource_params_conf.xml.sample M lib/galaxy/tools/parameters/validation.py M lib/galaxy/tools/xsd/galaxy.xsd M test/functional/tools/for_workflows/head.xml M test/unit/tools/test_wrappers.py R tools/data_source/bed_convert.xml M tools/data_source/genbank.xml M tools/data_source/upload.xml M tools/extract/liftOver_wrapper.xml M tools/filters/CreateInterval.xml M tools/filters/bed_to_bigbed.xml M tools/filters/changeCase.xml M tools/filters/fileGrep.xml M tools/filters/fixedValueColumn.xml M tools/filters/gff/gff_filter_by_attribute.xml M tools/filters/gff/gff_filter_by_feature_count.xml M tools/filters/grep.xml M tools/filters/headWrapper.xml M tools/filters/randomlines.xml M tools/filters/remove_beginning.xml M tools/filters/tailWrapper.xml M tools/filters/wig_to_bigwig.xml M tools/maf/vcf_to_maf_customtrack.xml M tools/metag_tools/blat_wrapper.xml M tools/metag_tools/shrimp_color_wrapper.xml M tools/metag_tools/shrimp_wrapper.xml M tools/plotting/bar_chart.xml M tools/plotting/boxplot.xml M tools/solid_tools/maq_cs_wrapper.xml M tools/sr_mapping/PerM.xml M tools/sr_mapping/bfast_wrapper.xml M tools/stats/filtering.xml M tools/stats/gsummary.xml M tools/stats/gsummary.xml.groups

Log Message: ----------- Merge pull request #6684 from nsoranzo/deprecate_param_size

Deprecate `size` attribute of `<param/>` and remove it from tools

Commit: 1fd3fccb216bcfab298e2cfd812f2ec3b3e45afe https://github.com/galaxyproject/galaxy/commit/1fd3fccb216bcfab298e2cfd812f2... Author: John Chilton jmchilton@gmail.com Date: 2018-12-12 (Wed, 12 Dec 2018)

Changed paths: M config/plugins/interactive_environments/neo/config/allowed_images.yml.sample M config/plugins/interactive_environments/neo/config/neo.ini.sample M lib/galaxy/visualization/plugins/interactive_environments.py

Log Message: ----------- Merge pull request #6897 from thobalose/neo4j-ie

Catered for shlex.split(command_inject) and updated Neo4j IE to v3.1.9

Commit: 06184df405c5afa534e358664cfbad2b815b124f https://github.com/galaxyproject/galaxy/commit/06184df405c5afa534e358664cfba... Author: John Chilton jmchilton@gmail.com Date: 2018-12-12 (Wed, 12 Dec 2018)

Changed paths: M .travis.yml A client/galaxy/scripts/components/GalaxyLoader.vue M client/galaxy/scripts/components/HistoryImport.vue M client/galaxy/scripts/components/PluginList.vue M client/galaxy/scripts/components/WorkflowImport.vue M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/dataset/dataset-edit-attributes.js M client/galaxy/scripts/mvc/history/history-item-li.js M client/galaxy/scripts/mvc/history/options-menu.js M client/galaxy/scripts/mvc/tool/tool-form.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/galaxy/scripts/mvc/user/user-preferences.js M client/galaxy/scripts/utils/utils.js M client/galaxy/style/scss/trackster.scss M config/galaxy.yml.sample M config/job_conf.xml.sample_advanced M config/job_resource_params_conf.xml.sample M config/workflow_resource_params_conf.xml.sample M doc/source/admin/framework_dependencies.rst M doc/source/admin/galaxy_options.rst M lib/galaxy/config.py M lib/galaxy/containers/__init__.py M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/pipfiles/default/Pipfile M lib/galaxy/dependencies/pipfiles/default/pinned-dev-requirements.txt M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt M lib/galaxy/dependencies/pipfiles/update.sh M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/handler.py M lib/galaxy/jobs/mapper.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/chronos.py M lib/galaxy/jobs/runners/cli.py M lib/galaxy/jobs/runners/condor.py M lib/galaxy/jobs/runners/drmaa.py M lib/galaxy/jobs/runners/godocker.py M lib/galaxy/jobs/runners/kubernetes.py M lib/galaxy/jobs/runners/local.py M lib/galaxy/jobs/runners/pbs.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/jobs/runners/state_handler_factory.py M lib/galaxy/jobs/runners/state_handlers/resubmit.py M lib/galaxy/jobs/runners/tasks.py A lib/galaxy/jobs/runners/univa.py M lib/galaxy/jobs/runners/util/cli/job/lsf.py M lib/galaxy/jobs/runners/util/job_script/MEMORY_STATEMENT.sh M lib/galaxy/managers/configuration.py M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py M lib/galaxy/model/migrate/versions/0006_change_qual_datatype.py M lib/galaxy/model/migrate/versions/0136_collection_and_workflow_state.py A lib/galaxy/model/migrate/versions/0145_add_workflow_step_input.py A lib/galaxy/model/migrate/versions/0146_workflow_paths.py M lib/galaxy/queue_worker.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/container_resolvers/__init__.py M lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/tools/deps/mulled/mulled_build.py M lib/galaxy/tools/lint.py M lib/galaxy/tools/parameters/meta.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/tools/parameters/validation.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/wrappers.py M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/util/__init__.py M lib/galaxy/util/plugin_config.py M lib/galaxy/util/submodules.py M lib/galaxy/web/base/controller.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/config_schema.yml M lib/galaxy/webapps/galaxy/config_watchers.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/tool_shed/model/__init__.py M lib/galaxy/workflow/extract.py M lib/galaxy/workflow/modules.py M lib/galaxy_ext/metadata/set_metadata.py M lib/tool_shed/util/workflow_util.py M run.sh M run_reports.sh M run_tool_shed.sh M scripts/common_startup.sh M scripts/common_startup_functions.sh M templates/admin/tool_shed_repository/manage_repository.mako M templates/js-app.mako M templates/user/login.mako M templates/user/register.mako M templates/user/reset_password.mako M test/api/test_workflows.py M test/base/populators.py M test/base/workflow_fixtures.py A test/functional/tools/exit_code_from_env.xml M test/functional/tools/for_workflows/head.xml M test/functional/tools/identifier_collection.xml M test/functional/tools/samples_tool_conf.xml A test/integration/chained_dyndest_job_conf.xml A test/integration/chained_dyndest_rules/__init__.py A test/integration/chained_dyndest_rules/module1/__init__.py A test/integration/chained_dyndest_rules/module1/rules.py A test/integration/chained_dyndest_rules/module2/__init__.py A test/integration/chained_dyndest_rules/module2/rules.py A test/integration/chained_dyndest_rules/module3/__init__.py A test/integration/chained_dyndest_rules/module3/rules.py A test/integration/resubmission_tool_detected_always_error_job_conf.xml A test/integration/resubmission_tool_detected_resubmit_job_conf.xml A test/integration/test_chained_dynamic_destinations.py M test/integration/test_dockerized_jobs.py M test/integration/test_job_resubmission.py A test/integration/test_workflow_sync.py M test/unit/jobs/test_mapper.py M test/unit/jobs/test_rules/10_site.py A test/unit/jobs/test_rules_override/10_rule.py A test/unit/jobs/test_rules_override/__init__.py M test/unit/jobs/test_runner_local.py M test/unit/test_galaxy_mapping.py M test/unit/tools/test_parameter_parsing.py M test/unit/tools/test_wrappers.py M test/unit/unittest_utils/galaxy_mock.py M test/unit/workflows/test_modules.py M test/unit/workflows/test_render.py M test/unit/workflows/test_workflow_progress.py M test/unit/workflows/workflow_support.py R tools/data_source/bed_convert.xml M tools/data_source/genbank.xml M tools/data_source/upload.xml M tools/extract/liftOver_wrapper.xml M tools/filters/CreateInterval.xml M tools/filters/bed_to_bigbed.xml M tools/filters/changeCase.xml M tools/filters/fileGrep.xml M tools/filters/fixedValueColumn.xml M tools/filters/gff/gff_filter_by_attribute.xml M tools/filters/gff/gff_filter_by_feature_count.xml M tools/filters/grep.xml M tools/filters/headWrapper.xml M tools/filters/joiner.xml M tools/filters/randomlines.xml M tools/filters/remove_beginning.xml M tools/filters/tailWrapper.xml M tools/filters/wig_to_bigwig.xml M tools/maf/vcf_to_maf_customtrack.xml M tools/metag_tools/blat_wrapper.xml M tools/metag_tools/shrimp_color_wrapper.xml M tools/metag_tools/shrimp_wrapper.xml M tools/plotting/bar_chart.xml M tools/plotting/boxplot.xml M tools/solid_tools/maq_cs_wrapper.xml M tools/sr_mapping/PerM.xml M tools/sr_mapping/bfast_wrapper.xml M tools/stats/filtering.xml M tools/stats/grouping.py M tools/stats/grouping.xml M tools/stats/gsummary.xml M tools/stats/gsummary.xml.groups

Log Message: ----------- Merge remote-tracking branch 'jmchilton/dev' into topic/reclaim_failed

Commit: 7bed9f03180826f7c7f99b12b08bcb265867217b https://github.com/galaxyproject/galaxy/commit/7bed9f03180826f7c7f99b12b08bc... Author: John Chilton jmchilton@gmail.com Date: 2018-12-12 (Wed, 12 Dec 2018)

Changed paths: M config/galaxy.yml.sample M config/job_conf.xml.sample_advanced M config/workflow_schedulers_conf.xml.sample M doc/source/admin/galaxy_options.rst M doc/source/admin/jobs.md M doc/source/admin/scaling.md M lib/galaxy/app.py M lib/galaxy/config.py M lib/galaxy/exceptions/__init__.py M lib/galaxy/exceptions/error_codes.json M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/handler.py M lib/galaxy/jobs/manager.py M lib/galaxy/managers/datasets.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/actions/history_imp_exp.py M lib/galaxy/tools/actions/metadata.py M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/util/facts.py M lib/galaxy/util/handlers.py M lib/galaxy/web/stack/__init__.py M lib/galaxy/web/stack/transport.py M lib/galaxy/webapps/galaxy/api/jobs.py M lib/galaxy/webapps/galaxy/config_schema.yml M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/workflow/scheduling_manager.py A test/unit/jobs/handler_template_job_conf.xml M test/unit/jobs/test_job_configuration.py M test/unit/tools/test_actions.py M test/unit/unittest_utils/galaxy_mock.py

Log Message: ----------- Merge pull request #7091 from natefoo/handler-assignment-fixes

Configurable job/workflow handler assignment methods

Commit: 476be87f9220e63db4aefa5933444c44d608974b https://github.com/galaxyproject/galaxy/commit/476be87f9220e63db4aefa5933444... Author: John Chilton jmchilton@gmail.com Date: 2018-12-12 (Wed, 12 Dec 2018)

Changed paths: M lib/galaxy/jobs/runners/drmaa.py

Log Message: ----------- Merge pull request #6997 from bernt-matthias/topic/drmaa-soft-external-runner

drmaa: soft catch of external runner fails

Commit: 8ccad94bfa87dc4f6260010ac1cce5ce54a321e3 https://github.com/galaxyproject/galaxy/commit/8ccad94bfa87dc4f6260010ac1cce... Author: John Chilton jmchilton@gmail.com Date: 2018-12-12 (Wed, 12 Dec 2018)

Changed paths: M lib/galaxy/webapps/galaxy/api/cloud.py

Log Message: ----------- Merge pull request #7088 from VJalili/patch-5

Replace `credentials` with `authz_id`

Commit: 6db721915fe0565f0ddfb3dcf863cd4ad5c17a57 https://github.com/galaxyproject/galaxy/commit/6db721915fe0565f0ddfb3dcf863c... Author: Björn Grüning bjoern@gruenings.eu Date: 2018-12-12 (Wed, 12 Dec 2018)

Changed paths: M scripts/grt/export.py M scripts/grt/grt.yml.sample

Log Message: ----------- Merge pull request #7041 from erasche/fix-grt

[18.09] GRT: Rip out all parameters, round file sizes

Commit: 4df43adae6fb8e5fb7ab3a7d3c029835a88f3f1a https://github.com/galaxyproject/galaxy/commit/4df43adae6fb8e5fb7ab3a7d3c029... Author: Martin Cech marten@bx.psu.edu Date: 2018-12-12 (Wed, 12 Dec 2018)

Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/layout/menu.js

Log Message: ----------- Merge pull request #7074 from dannon/fix_for_facebook_auth

[18.09] Fix welcome on redirect from facebook auth

Commit: 7dd7d8a5e99d0d4bb0ad4c317d8e9d29c749136d https://github.com/galaxyproject/galaxy/commit/7dd7d8a5e99d0d4bb0ad4c317d8e9... Author: Martin Cech marten@bx.psu.edu Date: 2018-12-12 (Wed, 12 Dec 2018)

Changed paths: M lib/galaxy/jobs/__init__.py

Log Message: ----------- Merge pull request #7078 from mvdbeek/fix_peek_for_running_datasets

[18.09] Fix set_peek method for copied datasets

Commit: 06deee06a48ae263a8ad396aac210ff9093ad6c6 https://github.com/galaxyproject/galaxy/commit/06deee06a48ae263a8ad396aac210... Author: guerler aysam.guerler@gmail.com Date: 2018-12-12 (Wed, 12 Dec 2018)

Changed paths: M client/galaxy/scripts/components/admin/DisplayApplications.vue M test/selenium_tests/test_admin_app.py

Log Message: ----------- Fix selenium test case for display application visibility

Commit: e173bc5fb4bffeac5a4a6cf6503bf05d0423dfa8 https://github.com/galaxyproject/galaxy/commit/e173bc5fb4bffeac5a4a6cf6503bf... Author: Dannon Baker dannon.baker@gmail.com Date: 2018-12-12 (Wed, 12 Dec 2018)

Changed paths: M client/README.md

Log Message: ----------- Client readme updates.

Commit: 91cb172118929cef6c1e5a231a4572efb6b6d865 https://github.com/galaxyproject/galaxy/commit/91cb172118929cef6c1e5a231a457... Author: Dannon Baker dannon.baker@gmail.com Date: 2018-12-12 (Wed, 12 Dec 2018)

Changed paths: M client/README.md

Log Message: ----------- Add note on dependencies being shipped w/ Galaxy, and the autobuilding.

Commit: 97564f140ac37b401616a3a1f1a9a22e7fefd3fd https://github.com/galaxyproject/galaxy/commit/97564f140ac37b401616a3a1f1a9a... Author: Helena Rasche hxr@hx42.org Date: 2018-12-12 (Wed, 12 Dec 2018)

Changed paths: M lib/galaxy/objectstore/__init__.py M lib/galaxy/objectstore/azure_blob.py M lib/galaxy/objectstore/cloud.py M lib/galaxy/objectstore/pithos.py M lib/galaxy/objectstore/s3.py M test/unit/test_objectstore.py

Log Message: ----------- Merge pull request #7085 from jmchilton/objectstore_config

De-couple objectstore abstraction from XML.

Commit: df73d9f2d64d74cd6571ddec7303a1a336f864bf https://github.com/galaxyproject/galaxy/commit/df73d9f2d64d74cd6571ddec7303a... Author: Dannon Baker dannon.baker@gmail.com Date: 2018-12-12 (Wed, 12 Dec 2018)

Changed paths: M client/README.md

Log Message: ----------- Minor tweaks.

Commit: 5dbadf6f35d5dff5520136494583517778f4cbc0 https://github.com/galaxyproject/galaxy/commit/5dbadf6f35d5dff55201364945835... Author: Dannon Baker dannon.baker@gmail.com Date: 2018-12-12 (Wed, 12 Dec 2018)

Changed paths: M client/README.md

Log Message: ----------- Clarify autobuild only works via run.sh/common_startup, and fix one typo.

Commit: 516d05530a5350dc83734b6e283f272ba5346395 https://github.com/galaxyproject/galaxy/commit/516d05530a5350dc83734b6e283f2... Author: Nate Coraor nate@bx.psu.edu Date: 2018-12-12 (Wed, 12 Dec 2018)

Changed paths: M lib/galaxy/jobs/__init__.py M test/unit/jobs/test_job_wrapper.py

Log Message: ----------- Merge pull request #7086 from jmchilton/version_string_local

Localize version strings to the working directory w/predictable path.

Commit: d7bac46638a2652336c7ef43c16d44e2c15a460f https://github.com/galaxyproject/galaxy/commit/d7bac46638a2652336c7ef43c16d4... Author: John Chilton jmchilton@gmail.com Date: 2018-12-12 (Wed, 12 Dec 2018)

Changed paths: M client/README.md

Log Message: ----------- Merge pull request #7102 from dannon/client-readme-updates

Client readme updates.

Commit: 3bc45328f830fe559ceae2aa8703bd4ffb0270ca https://github.com/galaxyproject/galaxy/commit/3bc45328f830fe559ceae2aa8703b... Author: Dannon Baker dannon.baker@gmail.com Date: 2018-12-12 (Wed, 12 Dec 2018)

Changed paths: M lib/galaxy/model/migrate/versions/0146_workflow_paths.py

Log Message: ----------- Fix migration 0146 column selection on downgrade

Commit: 9629c11d0a4557370ea7127276b602dd59f982c5 https://github.com/galaxyproject/galaxy/commit/9629c11d0a4557370ea7127276b60... Author: Dannon Baker dannon.baker@gmail.com Date: 2018-12-12 (Wed, 12 Dec 2018)

Changed paths: M lib/galaxy/model/migrate/versions/0145_add_workflow_step_input.py

Log Message: ----------- Swap order of table drops, avoids conflict w/ constraints by removing stuff in LIFO order

Commit: 586f0ca548c6813e4d2562a47ea9bb5791184e1b https://github.com/galaxyproject/galaxy/commit/586f0ca548c6813e4d2562a47ea9b... Author: Dannon Baker dannon.baker@gmail.com Date: 2018-12-12 (Wed, 12 Dec 2018)

Changed paths: M lib/galaxy/model/migrate/versions/0146_workflow_paths.py

Log Message: ----------- Cleanup, drop of unused methods

Commit: 58dd7e6a458440d057140a2c130b1f9a11a7b879 https://github.com/galaxyproject/galaxy/commit/58dd7e6a458440d057140a2c130b1... Author: Nicola Soranzo nicola.soranzo@gmail.com Date: 2018-12-13 (Thu, 13 Dec 2018)

Changed paths: M lib/galaxy/model/migrate/versions/0145_add_workflow_step_input.py M lib/galaxy/model/migrate/versions/0146_workflow_paths.py

Log Message: ----------- Merge pull request #7103 from dannon/migration_fixes

Fix migration 0146 column selection on downgrade

Commit: 786755ef8ad52acc7cea4805f9376306e3499a99 https://github.com/galaxyproject/galaxy/commit/786755ef8ad52acc7cea4805f9376... Author: mvdbeek m.vandenbeek@gmail.com Date: 2018-12-13 (Thu, 13 Dec 2018)

Changed paths: M lib/galaxy/tools/deps/singularity_util.py

Log Message: ----------- Run singularity in silent mode

The manual says: ``` -s|--silent Only print errors ```

Without this option I'm seeing `WARNING: Not mounting /var/tmp (already mounted in container)` on the stderr.

Commit: eea9528484a3f67bbc90aa8daed88e9967624294 https://github.com/galaxyproject/galaxy/commit/eea9528484a3f67bbc90aa8daed88... Author: John Chilton jmchilton@gmail.com Date: 2018-12-13 (Thu, 13 Dec 2018)

Changed paths: M lib/galaxy/tools/deps/singularity_util.py

Log Message: ----------- Merge pull request #7104 from mvdbeek/silent_flag_singularity

Run singularity in silent mode

Commit: 9883c6cd3703d831e011052096b98718b19fbf9a https://github.com/galaxyproject/galaxy/commit/9883c6cd3703d831e011052096b98... Author: John Chilton jmchilton@gmail.com Date: 2018-12-13 (Thu, 13 Dec 2018)

Changed paths: M lib/galaxy/tools/parameters/output_collect.py

Log Message: ----------- Eliminate unused code block.

Should have been eliminated with 517f248ac49caca3f0933c4b1f48cd4d74cf89fe.

Commit: d3cdf43563c1f3eacfae7cb5f887589a81f2acc6 https://github.com/galaxyproject/galaxy/commit/d3cdf43563c1f3eacfae7cb5f8875... Author: John Chilton jmchilton@gmail.com Date: 2018-12-13 (Thu, 13 Dec 2018)

Changed paths: M lib/galaxy/objectstore/__init__.py M lib/galaxy/objectstore/azure_blob.py M lib/galaxy/objectstore/cloud.py M lib/galaxy/objectstore/pithos.py M lib/galaxy/objectstore/s3.py M test/unit/test_objectstore.py

Log Message: ----------- Add to_dict() to ObjectStores.

Dictify an object store configuration back to its to config_dict description.

Commit: 48436d8efc50a1b7e7424fcc6cdd2a97775e0e01 https://github.com/galaxyproject/galaxy/commit/48436d8efc50a1b7e7424fcc6cdd2... Author: John Chilton jmchilton@gmail.com Date: 2018-12-13 (Thu, 13 Dec 2018)

Changed paths: M lib/galaxy/jobs/__init__.py

Log Message: ----------- Don't write outputs to object store twice.

Broken (?) in 009e2cbf5e9592fd8af782b2cde36d8d1687c003 by that moron @jmchilton

Commit: 1cb21fb55bacd33836a94b7dcd8e95001218c418 https://github.com/galaxyproject/galaxy/commit/1cb21fb55bacd33836a94b7dcd8e9... Author: Martin Cech marten@bx.psu.edu Date: 2018-12-13 (Thu, 13 Dec 2018)

Changed paths: M lib/galaxy/tools/parameters/output_collect.py

Log Message: ----------- Merge pull request #7109 from jmchilton/unused_code_block

Eliminate unused code block in output_collect.

Commit: 5b677cfd52e35e4b325dcd7fe426446c9c695262 https://github.com/galaxyproject/galaxy/commit/5b677cfd52e35e4b325dcd7fe4264... Author: guerler aysam.guerler@gmail.com Date: 2018-12-13 (Thu, 13 Dec 2018)

Changed paths: M client/galaxy/scripts/components/admin/DisplayApplications.vue M test/selenium_tests/test_admin_app.py

Log Message: ----------- Fix selenium test, add missing applications message

Commit: e3ef379674784f766d94c8e126f3744af4f5c9a7 https://github.com/galaxyproject/galaxy/commit/e3ef379674784f766d94c8e126f37... Author: guerler aysam.guerler@gmail.com Date: 2018-12-13 (Thu, 13 Dec 2018)

Changed paths: M client/galaxy/scripts/components/admin/DisplayApplications.vue

Log Message: ----------- Show warning message after requesting display applications

Commit: c6355dfe10040fb0f02e08ed78373b216c7028fb https://github.com/galaxyproject/galaxy/commit/c6355dfe10040fb0f02e08ed78373... Author: Martin Cech marten@bx.psu.edu Date: 2018-12-13 (Thu, 13 Dec 2018)

Changed paths: M lib/galaxy/jobs/__init__.py

Log Message: ----------- Merge pull request #7111 from jmchilton/seems_bad_but_okay

Don't write outputs to object store twice.

Commit: 43a19a05e3efbadca41a0aa38f06973157ce4563 https://github.com/galaxyproject/galaxy/commit/43a19a05e3efbadca41a0aa38f069... Author: Dannon Baker dannon.baker@gmail.com Date: 2018-12-13 (Thu, 13 Dec 2018)

Changed paths: M client/package.json

Log Message: ----------- Client watch referred to an old gulp task that is no longer necessary.

Commit: f5a3ab464743a0d47672c00ce611520d846d6241 https://github.com/galaxyproject/galaxy/commit/f5a3ab464743a0d47672c00ce6115... Author: guerler aysam.guerler@gmail.com Date: 2018-12-13 (Thu, 13 Dec 2018)

Changed paths: A client/galaxy/scripts/components/admin/AdminServices.js M client/galaxy/scripts/components/admin/DisplayApplications.vue

Log Message: ----------- Separate api requests from vue component for admin services

Commit: 255418d158fd0d4a77bd9e56f18c15ec56bac02d https://github.com/galaxyproject/galaxy/commit/255418d158fd0d4a77bd9e56f18c1... Author: guerler aysam.guerler@gmail.com Date: 2018-12-13 (Thu, 13 Dec 2018)

Changed paths: M lib/galaxy/webapps/galaxy/buildapp.py

Log Message: ----------- Fix comment header for display applications api

Commit: 260fa8b6d73f27ed97ebb273b6dfd17134fb8285 https://github.com/galaxyproject/galaxy/commit/260fa8b6d73f27ed97ebb273b6dfd... Author: guerler aysam.guerler@gmail.com Date: 2018-12-13 (Thu, 13 Dec 2018)

Changed paths: M client/galaxy/scripts/mvc/ui/ui-frames.js

Log Message: ----------- Properly escape history names in scratchbook titles

Commit: 7c2a0761de7128fe67258c0d2b842bfec4ced533 https://github.com/galaxyproject/galaxy/commit/7c2a0761de7128fe67258c0d2b842... Author: Martin Cech marten@bx.psu.edu Date: 2018-12-13 (Thu, 13 Dec 2018)

Changed paths: M client/package.json

Log Message: ----------- Merge pull request #7113 from dannon/client-watch-fix

Fix `make client-watch` extra error message.

Commit: fe2b7eb1e690239932b2c49ac9350ee56fe1c5a6 https://github.com/galaxyproject/galaxy/commit/fe2b7eb1e690239932b2c49ac9350... Author: Sergey Golitsynskiy sgolitsynskiy@gmail.com Date: 2018-12-13 (Thu, 13 Dec 2018)

Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js

Log Message: ----------- Enable tagging+annotation of jobs regardless of state

See issue #6330

Commit: 975c8b605fffb968106ec0d3e04569d8d8c70f44 https://github.com/galaxyproject/galaxy/commit/975c8b605fffb968106ec0d3e0456... Author: Nicola Soranzo nicola.soranzo@earlham.ac.uk Date: 2018-12-14 (Fri, 14 Dec 2018)

Changed paths: M scripts/common_startup.sh M scripts/common_startup_functions.sh

Log Message: ----------- Fix activation of ``_galaxy_`` conda env

- Use `conda_activate`, which works also under dash - Run `conda_activate` also when `$GALAXY_CONDA_ENV` already exists - Run `virtualenv` when the conda env is active but `$GALAXY_VIRTUAL_ENV` does not exist - Update the default for `GALAXY_CONDA_ENV` in scripts/common_startup_functions.sh

Follow-up on https://github.com/galaxyproject/galaxy/pull/6975 .

Commit: baa7d7ea8effb41bb04d73e1545e8259630eb9b0 https://github.com/galaxyproject/galaxy/commit/baa7d7ea8effb41bb04d73e1545e8... Author: John Chilton jmchilton@gmail.com Date: 2018-12-14 (Fri, 14 Dec 2018)

Changed paths: M test/unit/tools/test_toolbox.py

Log Message: ----------- Increase timeout on flakey unit test.

Commit: 40acf08a3cd0eda156fe17498ec5a2182a53fa8a https://github.com/galaxyproject/galaxy/commit/40acf08a3cd0eda156fe17498ec5a... Author: John Chilton jmchilton@gmail.com Date: 2018-12-14 (Fri, 14 Dec 2018)

Changed paths: M client/galaxy/scripts/mvc/ui/ui-frames.js

Log Message: ----------- Merge pull request #7114 from guerler/escape_scratchbook_title

Properly escape history names in scratchbook titles

Commit: e7c333a211b45909734ccb2c03105975937254f1 https://github.com/galaxyproject/galaxy/commit/e7c333a211b45909734ccb2c03105... Author: Nicola Soranzo nicola.soranzo@gmail.com Date: 2018-12-14 (Fri, 14 Dec 2018)

Changed paths: M test/unit/tools/test_toolbox.py

Log Message: ----------- Merge pull request #7120 from jmchilton/unit_test_fix

Increase timeout on flakey unit test.

Commit: 1caf7f4bab428a8c7d3d132b60e90b8ce0cb9f86 https://github.com/galaxyproject/galaxy/commit/1caf7f4bab428a8c7d3d132b60e90... Author: John Chilton jmchilton@gmail.com Date: 2018-12-14 (Fri, 14 Dec 2018)

Changed paths: M lib/galaxy/jobs/runners/__init__.py M test/unit/jobs/test_runner_local.py

Log Message: ----------- Merge pull request #6996 from bernt-matthias/topic/reclaim_failed

reclaim ownership for failed jobs

Commit: 9dcb002505a1e2c38604ea8889fef40f41531fdd https://github.com/galaxyproject/galaxy/commit/9dcb002505a1e2c38604ea8889fef... Author: Marius van den Beek m.vandenbeek@gmail.com Date: 2018-12-15 (Sat, 15 Dec 2018)

Changed paths: M scripts/common_startup.sh M scripts/common_startup_functions.sh

Log Message: ----------- Merge pull request #7116 from nsoranzo/followup_on_6975

Fix activation of ``_galaxy_`` conda env

Commit: 8f14121518d1298f5a603e8e52ae5c05212e6360 https://github.com/galaxyproject/galaxy/commit/8f14121518d1298f5a603e8e52ae5... Author: Nicola Soranzo nicola.soranzo@gmail.com Date: 2018-12-16 (Sun, 16 Dec 2018)

Changed paths: M .travis.yml M scripts/common_startup.sh

Log Message: ----------- Merge pull request #7094 from nsoranzo/release_16.01_backport_2383

[16.01] Backport #2383

Commit: 87fa60939696fb4ecbf157e124eacd7afe4c9243 https://github.com/galaxyproject/galaxy/commit/87fa60939696fb4ecbf157e124eac... Author: Nicola Soranzo nicola.soranzo@earlham.ac.uk Date: 2018-12-16 (Sun, 16 Dec 2018)

Changed paths: M .travis.yml M scripts/common_startup.sh

Log Message: ----------- Merge branch 'release_16.01' into release_16.04

Commit: f3c81816db24d7a0b0f3909919c6ca41664fb50d https://github.com/galaxyproject/galaxy/commit/f3c81816db24d7a0b0f3909919c6c... Author: Nicola Soranzo nicola.soranzo@earlham.ac.uk Date: 2018-12-16 (Sun, 16 Dec 2018)

Changed paths: M .travis.yml

Log Message: ----------- Merge branch 'release_16.04' into release_16.07

Commit: a2e70ef67ec9899af50720aac9f3bf16cbc636ac https://github.com/galaxyproject/galaxy/commit/a2e70ef67ec9899af50720aac9f3b... Author: Nicola Soranzo nicola.soranzo@earlham.ac.uk Date: 2018-12-16 (Sun, 16 Dec 2018)

Changed paths: M .travis.yml

Log Message: ----------- Merge branch 'release_16.07' into release_16.10

Commit: 1b30a9a1b98e40befb34eb7c5197610d4eea786f https://github.com/galaxyproject/galaxy/commit/1b30a9a1b98e40befb34eb7c51976... Author: Nicola Soranzo nicola.soranzo@earlham.ac.uk Date: 2018-12-16 (Sun, 16 Dec 2018)

Changed paths: M .travis.yml

Log Message: ----------- Merge branch 'release_16.10' into release_17.01

Commit: 06cfb7e206357718e530c9afa6723c205b664927 https://github.com/galaxyproject/galaxy/commit/06cfb7e206357718e530c9afa6723... Author: Nicola Soranzo nicola.soranzo@earlham.ac.uk Date: 2018-12-16 (Sun, 16 Dec 2018)

Changed paths: M .travis.yml

Log Message: ----------- Merge branch 'release_17.01' into release_17.05

Commit: fdd9a091f86c312c4995a47dc674814609a5519c https://github.com/galaxyproject/galaxy/commit/fdd9a091f86c312c4995a47dc6748... Author: Nicola Soranzo nicola.soranzo@earlham.ac.uk Date: 2018-12-16 (Sun, 16 Dec 2018)

Changed paths: M .travis.yml

Log Message: ----------- Merge branch 'release_17.05' into release_17.09

Commit: 6feef2a2801e15a770997a3dd9556ca46d6c2ca5 https://github.com/galaxyproject/galaxy/commit/6feef2a2801e15a770997a3dd9556... Author: Nicola Soranzo nicola.soranzo@earlham.ac.uk Date: 2018-12-16 (Sun, 16 Dec 2018)

Changed paths: M .travis.yml

Log Message: ----------- Merge branch 'release_17.09' into release_18.01

Commit: bfc634e41536e53fcf05ba97714c48dc8fbcccf4 https://github.com/galaxyproject/galaxy/commit/bfc634e41536e53fcf05ba97714c4... Author: Nicola Soranzo nicola.soranzo@earlham.ac.uk Date: 2018-12-16 (Sun, 16 Dec 2018)

Changed paths: M .travis.yml

Log Message: ----------- Merge branch 'release_18.01' into release_18.05

Commit: 65ca25ed669f4cea983d86460f614666ba3571d1 https://github.com/galaxyproject/galaxy/commit/65ca25ed669f4cea983d86460f614... Author: Nicola Soranzo nicola.soranzo@earlham.ac.uk Date: 2018-12-16 (Sun, 16 Dec 2018)

Changed paths:

Log Message: ----------- Merge branch 'release_18.05' into release_18.09

Commit: b22b7e58680fce07ce57440951ec581a74faa463 https://github.com/galaxyproject/galaxy/commit/b22b7e58680fce07ce57440951ec5... Author: Nicola Soranzo nicola.soranzo@earlham.ac.uk Date: 2018-12-16 (Sun, 16 Dec 2018)

Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/layout/menu.js M lib/galaxy/jobs/__init__.py M scripts/grt/export.py M scripts/grt/grt.yml.sample

Log Message: ----------- Merge branch 'release_18.09' into dev

Commit: 0fdb89a1b447d33ea0c62c47f56d0a06a1d0d1bf https://github.com/galaxyproject/galaxy/commit/0fdb89a1b447d33ea0c62c47f56d0... Author: Dannon Baker dannon.baker@gmail.com Date: 2018-12-17 (Mon, 17 Dec 2018)

Changed paths: M client/galaxy/scripts/components/GalaxyLoader.vue M client/galaxy/scripts/mvc/collection/collection-li.js M client/galaxy/scripts/mvc/collection/collection-view.js M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/history/hdca-li.js M client/galaxy/scripts/mvc/history/history-item-li.js M client/galaxy/scripts/mvc/list/list-item.js M client/galaxy/scripts/mvc/list/list-view.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/galaxy/scripts/utils/utils.js

Log Message: ----------- Fixes state-change animations causing 'block' display appearing in various places due to collection job state fetches. Includes some import/export refactoring and general client cleanup.

Commit: f5b7553fea0f08c1bb37ce43172b91feed15bb44 https://github.com/galaxyproject/galaxy/commit/f5b7553fea0f08c1bb37ce43172b9... Author: guerler aysam.guerler@gmail.com Date: 2018-12-17 (Mon, 17 Dec 2018)

Changed paths: M lib/galaxy/webapps/galaxy/api/display_applications.py

Log Message: ----------- Add require admin to display applications api

Commit: dd5e3c6c68077268d3d551857e508d914ed1d3f9 https://github.com/galaxyproject/galaxy/commit/dd5e3c6c68077268d3d551857e508... Author: guerler aysam.guerler@gmail.com Date: 2018-12-17 (Mon, 17 Dec 2018)

Changed paths: M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin.py

Log Message: ----------- Move error stack controller endpoint to tools api

Commit: d7539d07eb426dbf7176f67434715671ccda63d7 https://github.com/galaxyproject/galaxy/commit/d7539d07eb426dbf7176f67434715... Author: Aysam Guerler aysam.guerler@gmail.com Date: 2018-12-17 (Mon, 17 Dec 2018)

Changed paths: M client/galaxy/scripts/components/GalaxyLoader.vue M client/galaxy/scripts/mvc/collection/collection-li.js M client/galaxy/scripts/mvc/collection/collection-view.js M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/history/hdca-li.js M client/galaxy/scripts/mvc/history/history-item-li.js M client/galaxy/scripts/mvc/list/list-item.js M client/galaxy/scripts/mvc/list/list-view.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/galaxy/scripts/utils/utils.js

Log Message: ----------- Merge pull request #7122 from dannon/collection_jobstate_animation_fix

Fixes state-change animations causing 'block' display

Commit: 3665ef056d377960edd92b558fcf903f9280a204 https://github.com/galaxyproject/galaxy/commit/3665ef056d377960edd92b558fcf9... Author: guerler aysam.guerler@gmail.com Date: 2018-12-17 (Mon, 17 Dec 2018)

Changed paths: M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/panels/admin-panel.js A client/galaxy/scripts/components/admin/AdminServices.js A client/galaxy/scripts/components/admin/ErrorStack.vue M lib/galaxy/webapps/galaxy/buildapp.py

Log Message: ----------- Add error stack vue component and client side routes

Commit: 8eceb76ee1e36ae14403ccfbaf082ed6395451b6 https://github.com/galaxyproject/galaxy/commit/8eceb76ee1e36ae14403ccfbaf082... Author: guerler aysam.guerler@gmail.com Date: 2018-12-17 (Mon, 17 Dec 2018)

Changed paths: R templates/admin/tool_errors.mako

Log Message: ----------- Remove legacy tool error mako file

Commit: 481243c3ed0a31ebde7a4ed85592e7068e5e4b45 https://github.com/galaxyproject/galaxy/commit/481243c3ed0a31ebde7a4ed85592e... Author: guerler aysam.guerler@gmail.com Date: 2018-12-17 (Mon, 17 Dec 2018)

Changed paths: M client/galaxy/scripts/components/admin/ErrorStack.vue

Log Message: ----------- Remove unused attribute

Commit: 462303043d47437486fb0d6df5b65d43f8235790 https://github.com/galaxyproject/galaxy/commit/462303043d47437486fb0d6df5b65... Author: guerler aysam.guerler@gmail.com Date: 2018-12-17 (Mon, 17 Dec 2018)

Changed paths: M client/galaxy/scripts/components/admin/ErrorStack.vue

Log Message: ----------- Remove unused tag in vue component

Commit: 8a439cfb0f81e2ca8a7ab8c2526452c27a875046 https://github.com/galaxyproject/galaxy/commit/8a439cfb0f81e2ca8a7ab8c252645... Author: guerler aysam.guerler@gmail.com Date: 2018-12-17 (Mon, 17 Dec 2018)

Changed paths: M client/galaxy/scripts/components/admin/ErrorStack.vue

Log Message: ----------- Allow sorting by file name in error log table

Commit: fe349ef334f643faf08fe35b4f1da87e82fa1bbf https://github.com/galaxyproject/galaxy/commit/fe349ef334f643faf08fe35b4f1da... Author: John Chilton jmchilton@gmail.com Date: 2018-12-17 (Mon, 17 Dec 2018)

Changed paths: M lib/galaxy/jobs/__init__.py

Log Message: ----------- Remove __collected_datasets__ from hook dict.

Added for Tool subclass hooks in ca8cc1420ef80bd2fef17fa9bb21dbb0714b4a88 but doesn't seem to be used in any tool implementation hooks.

Commit: 30d5baf90978f79b57fbd7f8008a76c05fe5c11d https://github.com/galaxyproject/galaxy/commit/30d5baf90978f79b57fbd7f8008a7... Author: guerler aysam.guerler@gmail.com Date: 2018-12-17 (Mon, 17 Dec 2018)

Changed paths: M lib/galaxy/webapps/galaxy/api/tools.py

Log Message: ----------- Fix comment section of error stack api endpoint

Commit: faec3dc0589189ce12522f2466cb62b0c80c8ccf https://github.com/galaxyproject/galaxy/commit/faec3dc0589189ce12522f2466cb6... Author: Dannon dannon.baker@gmail.com Date: 2018-12-17 (Mon, 17 Dec 2018)

Changed paths: M lib/galaxy/jobs/__init__.py

Log Message: ----------- Merge pull request #7123 from jmchilton/collected_remove

Remove unused __collected_datasets__ from tool hook dict.

Commit: 22e1350f7a9eeddd53ffa5b6febb492ceefb004c https://github.com/galaxyproject/galaxy/commit/22e1350f7a9eeddd53ffa5b6febb4... Author: pvanheus pvh@sanbi.ac.za Date: 2018-12-18 (Tue, 18 Dec 2018)

Changed paths: M lib/galaxy/tools/filter_from_file.xml

Log Message: ----------- Update help text as per suggestion from CWunder

This [thread](https://help.galaxyproject.org/t/clearer-documentation-for-filter-list/231) suggests that the help text for this tool is not clear. This PR attempts to address that weakness.

Commit: a00d013fd14ecc1eca59b8d572c1ec5a673bce74 https://github.com/galaxyproject/galaxy/commit/a00d013fd14ecc1eca59b8d572c1e... Author: guerler aysam.guerler@gmail.com Date: 2018-12-18 (Tue, 18 Dec 2018)

Changed paths: M lib/galaxy/webapps/galaxy/api/display_applications.py

Log Message: ----------- Remove admin requirment from index endpoint of display applications

Commit: b7bb1df769e683f1b5e23b04de3194f6cb1d5545 https://github.com/galaxyproject/galaxy/commit/b7bb1df769e683f1b5e23b04de319... Author: Martin Cech marten@bx.psu.edu Date: 2018-12-18 (Tue, 18 Dec 2018)

Changed paths: M lib/galaxy/tools/filter_from_file.xml

Log Message: ----------- Merge pull request #7127 from pvanheus/patch-10

Update help text as per suggestion from CWunder

Commit: 548d0cb2c9e38594f747c17e57939eca2344353f https://github.com/galaxyproject/galaxy/commit/548d0cb2c9e38594f747c17e57939... Author: Nate Coraor nate@bx.psu.edu Date: 2018-12-18 (Tue, 18 Dec 2018)

Changed paths: M lib/galaxy/jobs/handler.py M lib/galaxy/util/handlers.py

Log Message: ----------- WIP job assignment using database transaction isolation

Commit: b067fd194b2a3a28c23900eb45ace726aa842d78 https://github.com/galaxyproject/galaxy/commit/b067fd194b2a3a28c23900eb45ace... Author: Nate Coraor nate@bx.psu.edu Date: 2018-12-18 (Tue, 18 Dec 2018)

Changed paths: M lib/galaxy/config.py M lib/galaxy/jobs/handler.py

Log Message: ----------- Rename job assigner to job grabber and clean up, also add support for (preferable) FOR UPDATE ... SKIP LOCKED

Commit: 34eb8a45c1e4e069ca6d91965aa1985eb444da83 https://github.com/galaxyproject/galaxy/commit/34eb8a45c1e4e069ca6d91965aa19... Author: Nate Coraor nate@bx.psu.edu Date: 2018-12-18 (Tue, 18 Dec 2018)

Changed paths: M lib/galaxy/config.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/handler.py M lib/galaxy/util/handlers.py M lib/galaxy/workflow/scheduling_manager.py

Log Message: ----------- Integrate DB serialization methods with new handler assignment process

Commit: 473210714e719f4c36d77b49281a82567b294c8e https://github.com/galaxyproject/galaxy/commit/473210714e719f4c36d77b49281a8... Author: Nate Coraor nate@bx.psu.edu Date: 2018-12-18 (Tue, 18 Dec 2018)

Changed paths: M lib/galaxy/config.py M lib/galaxy/util/handlers.py M lib/galaxy/web/stack/__init__.py M lib/galaxy/workflow/scheduling_manager.py M scripts/galaxy-main

Log Message: ----------- Add support for dynamic handlers when using DB serialization handler assignment

Commit: 602b86ef9ee0efddb3614f03c19d5772ab5bdf0d https://github.com/galaxyproject/galaxy/commit/602b86ef9ee0efddb3614f03c19d5... Author: Nate Coraor nate@bx.psu.edu Date: 2018-12-18 (Tue, 18 Dec 2018)

Changed paths: M lib/galaxy/jobs/handler.py

Log Message: ----------- SQLAlchemize the grabber query and fold grabber directly into JobHandlerQueue

Commit: 2c73ac3e22f608a3049f5bafc477b1a199d25c33 https://github.com/galaxyproject/galaxy/commit/2c73ac3e22f608a3049f5bafc477b... Author: Nate Coraor nate@bx.psu.edu Date: 2018-12-18 (Tue, 18 Dec 2018)

Changed paths: M lib/galaxy/jobs/handler.py

Log Message: ----------- No longer using trace logging

Commit: d4c69218627dc8afc83fc4b6fa9e65c47bdd7897 https://github.com/galaxyproject/galaxy/commit/d4c69218627dc8afc83fc4b6fa9e6... Author: Nate Coraor nate@bx.psu.edu Date: 2018-12-18 (Tue, 18 Dec 2018)

Changed paths: M lib/galaxy/jobs/runners/slurm.py

Log Message: ----------- Fix for use of `log.trace` in Slurm runner

Commit: e1e32cdcc6e3a300f5534ca961d2459634142367 https://github.com/galaxyproject/galaxy/commit/e1e32cdcc6e3a300f5534ca961d24... Author: John Chilton jmchilton@gmail.com Date: 2018-12-18 (Tue, 18 Dec 2018)

Changed paths: M test/functional/tools/samples_tool_conf.xml A test/functional/tools/tool_provided_metadata_10.xml

Log Message: ----------- Test for 'metadata' in newer style discovered primary datasets.

Commit: 62a7c40ba4f29293bc921e81bd90ea59a570319b https://github.com/galaxyproject/galaxy/commit/62a7c40ba4f29293bc921e81bd90e... Author: John Chilton jmchilton@gmail.com Date: 2018-12-18 (Tue, 18 Dec 2018)

Changed paths: M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/tools/verify/__init__.py

Log Message: ----------- Fix for testing extra files in tool tests.

Wouldn't be testing if primary file didn't specify a filename to test against.

Commit: 953730d61ca81e79f898312b526ab8fa0680c9e0 https://github.com/galaxyproject/galaxy/commit/953730d61ca81e79f898312b526ab... Author: John Chilton jmchilton@gmail.com Date: 2018-12-18 (Tue, 18 Dec 2018)

Changed paths: M test/functional/tools/samples_tool_conf.xml A test/functional/tools/tool_provided_metadata_11.xml A test/functional/tools/tool_provided_metadata_12.xml

Log Message: ----------- Tests for tool provided metadata specifing extra files.

Commit: e31274b7f58dec15c45874acebdf82ae35e39999 https://github.com/galaxyproject/galaxy/commit/e31274b7f58dec15c45874acebdf8... Author: Martin Cech marten@bx.psu.edu Date: 2018-12-18 (Tue, 18 Dec 2018)

Changed paths: M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/tools/verify/__init__.py M test/functional/tools/samples_tool_conf.xml A test/functional/tools/tool_provided_metadata_10.xml A test/functional/tools/tool_provided_metadata_11.xml A test/functional/tools/tool_provided_metadata_12.xml

Log Message: ----------- Merge pull request #7131 from jmchilton/extra_files_3

Fixes and tests for collecting extra files for discovered datasets.

Commit: a3d1c6872b558d470b1a2f2667e6abffd920d856 https://github.com/galaxyproject/galaxy/commit/a3d1c6872b558d470b1a2f2667e6a... Author: Dannon Baker dannon.baker@gmail.com Date: 2018-12-18 (Tue, 18 Dec 2018)

Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js

Log Message: ----------- Minor formatting; tabstop=4

Commit: 5a666eb656093cd3df5332ca78c617cb3d547b8c https://github.com/galaxyproject/galaxy/commit/5a666eb656093cd3df5332ca78c61... Author: Dannon Baker dannon.baker@gmail.com Date: 2018-12-18 (Tue, 18 Dec 2018)

Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js

Log Message: ----------- Avoid using underscore where there's a vanilla alternative.

Commit: 1854c934cb23131662dfb5a903ad5cae98a93662 https://github.com/galaxyproject/galaxy/commit/1854c934cb23131662dfb5a903ad5... Author: Dannon dannon.baker@gmail.com Date: 2018-12-19 (Wed, 19 Dec 2018)

Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js

Log Message: ----------- Merge pull request #7115 from ic4f/feature_i6330

[WIP] Enable tagging+annotation of jobs regardless of state

Commit: e237bcfd16d6a72e78afe1405e4eaeb05a91af20 https://github.com/galaxyproject/galaxy/commit/e237bcfd16d6a72e78afe1405e4ea... Author: guerler aysam.guerler@gmail.com Date: 2018-12-19 (Wed, 19 Dec 2018)

Changed paths: M client/galaxy/scripts/components/admin/DisplayApplications.vue

Log Message: ----------- Use b-alert instead of basic bootstrap alert messages

Commit: 558aca71d69ea81746013489be52ee5813ecc43c https://github.com/galaxyproject/galaxy/commit/558aca71d69ea81746013489be52e... Author: guerler aysam.guerler@gmail.com Date: 2018-12-19 (Wed, 19 Dec 2018)

Changed paths: M client/galaxy/scripts/components/admin/DisplayApplications.vue

Log Message: ----------- Replace default links with bootstrap vue buttons

Commit: 9bbdb34fb6f0676675851691280f261a3f37bb9e https://github.com/galaxyproject/galaxy/commit/9bbdb34fb6f0676675851691280f2... Author: John Chilton jmchilton@gmail.com Date: 2018-12-19 (Wed, 19 Dec 2018)

Changed paths: M lib/galaxy/tools/parameters/output_collect.py

Log Message: ----------- Remove unneeded session flushes and adds when collecting primary datasets.

Commit: bc695f898c3f7098cc6cef1acb68bcbec2c77f0b https://github.com/galaxyproject/galaxy/commit/bc695f898c3f7098cc6cef1acb68b... Author: guerler aysam.guerler@gmail.com Date: 2018-12-19 (Wed, 19 Dec 2018)

Changed paths: M client/galaxy/scripts/components/admin/ErrorStack.vue

Log Message: ----------- Use bootstrap vue message alerts

Commit: 6f669dd79b3ed7ad51658ef4f9b56fad834c2390 https://github.com/galaxyproject/galaxy/commit/6f669dd79b3ed7ad51658ef4f9b56... Author: Mason nerdinacan@gmail.com Date: 2018-12-19 (Wed, 19 Dec 2018)

Changed paths: M client/galaxy/scripts/app/singleton.js M client/galaxy/scripts/layout/panel.js

Log Message: ----------- 7132 Updated singleton to address cors issue in toolshed frames

Commit: 60146ec89be41aec9a8d6216e96908b9095e6054 https://github.com/galaxyproject/galaxy/commit/60146ec89be41aec9a8d6216e9690... Author: Mason nerdinacan@gmail.com Date: 2018-12-19 (Wed, 19 Dec 2018)

Changed paths: M client/galaxy/scripts/layout/panel.js

Log Message: ----------- Replaced test code with real code

Commit: 1edb7489a16775ef2e3810e675c8182762d92540 https://github.com/galaxyproject/galaxy/commit/1edb7489a16775ef2e3810e675c81... Author: mvdbeek m.vandenbeek@gmail.com Date: 2018-12-20 (Thu, 20 Dec 2018)

Changed paths: M config/tool_conf.xml.sample

Log Message: ----------- Drop tools without installable dependencies

These seem to be beyond legacy, and since their not installable let's drop them from the default config. I left them in tool_conf.xml.main, since they appear to be installed on main.

Commit: 6a0a6ec1d1ee638731eb456da7abdee8b5582853 https://github.com/galaxyproject/galaxy/commit/6a0a6ec1d1ee638731eb456da7abd... Author: John Chilton jmchilton@gmail.com Date: 2018-12-20 (Thu, 20 Dec 2018)

Changed paths: M config/tool_conf.xml.sample

Log Message: ----------- Merge pull request #7136 from mvdbeek/remove_tools_without_deps

Drop tools without installable dependencies

Commit: 34ada99915c63943bac4630ebb461b54c37b9838 https://github.com/galaxyproject/galaxy/commit/34ada99915c63943bac4630ebb461... Author: guerler aysam.guerler@gmail.com Date: 2018-12-20 (Thu, 20 Dec 2018)

Changed paths: M client/galaxy/scripts/utils/uploadbox.js

Log Message: ----------- Use regular js-event handling instead of jquery for uploader

Commit: 8f10178e43d1ca001a0a02291ef7b01c3891cc30 https://github.com/galaxyproject/galaxy/commit/8f10178e43d1ca001a0a02291ef7b... Author: guerler aysam.guerler@gmail.com Date: 2018-12-20 (Thu, 20 Dec 2018)

Changed paths: M client/galaxy/scripts/mvc/upload/composite/composite-row.js M client/galaxy/style/scss/upload.scss

Log Message: ----------- Fix dragover highlighting for composite dataset uploader

Commit: 2f8a62344e66194e3a8d37a8539a8540abbbb494 https://github.com/galaxyproject/galaxy/commit/2f8a62344e66194e3a8d37a8539a8... Author: guerler aysam.guerler@gmail.com Date: 2018-12-20 (Thu, 20 Dec 2018)

Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-content.js

Log Message: ----------- Use default js to handle drop events in tool form

Commit: cf7f1b0745482c5e7cd75fa9d8e91e95124fcfac https://github.com/galaxyproject/galaxy/commit/cf7f1b0745482c5e7cd75fa9d8e91... Author: Dannon Baker dannon.baker@gmail.com Date: 2018-12-20 (Thu, 20 Dec 2018)

Changed paths: M client/galaxy/scripts/layout/panel.js

Log Message: ----------- Client formatting.

Commit: 7eca9baf5ae5c2a43e54d9dd9e76797fe2406568 https://github.com/galaxyproject/galaxy/commit/7eca9baf5ae5c2a43e54d9dd9e767... Author: Dannon Baker dannon.baker@gmail.com Date: 2018-12-20 (Thu, 20 Dec 2018)

Changed paths: M client/galaxy/scripts/app/singleton.js M client/galaxy/scripts/layout/panel.js

Log Message: ----------- Merge branch '7132_fix_cors_singleton_storage' into dev

Commit: 1c82d08ab5c216ad568ec1d51d3398ffb0214c18 https://github.com/galaxyproject/galaxy/commit/1c82d08ab5c216ad568ec1d51d339... Author: anilthanki thanki.anil@gmail.com Date: 2018-12-20 (Thu, 20 Dec 2018)

Changed paths: A config/plugins/visualizations/aequatus/README.md A config/plugins/visualizations/aequatus/config/aequatus.xml A config/plugins/visualizations/aequatus/static/aequatus-vis/LICENSE A config/plugins/visualizations/aequatus/static/aequatus-vis/README.md A config/plugins/visualizations/aequatus/static/aequatus-vis/_config.yml A config/plugins/visualizations/aequatus/static/aequatus-vis/scripts/cigarUtils.js A config/plugins/visualizations/aequatus/static/aequatus-vis/scripts/d3_tree.js A config/plugins/visualizations/aequatus/static/aequatus-vis/scripts/drawCIGARs.js A config/plugins/visualizations/aequatus/static/aequatus-vis/scripts/drawGene.js A config/plugins/visualizations/aequatus/static/aequatus-vis/scripts/drawGeneExonOnly.js A config/plugins/visualizations/aequatus/static/aequatus-vis/scripts/geneView.js A config/plugins/visualizations/aequatus/static/aequatus-vis/scripts/init.js A config/plugins/visualizations/aequatus/static/aequatus-vis/scripts/jquery/jquery-ui-1.12.1.min.css A config/plugins/visualizations/aequatus/static/aequatus-vis/scripts/jquery/jquery.svg.css A config/plugins/visualizations/aequatus/static/aequatus-vis/scripts/jquery/js/jquery-3.3.1.min.js A config/plugins/visualizations/aequatus/static/aequatus-vis/scripts/jquery/js/jquery-migrate-1.4.1.min.js A config/plugins/visualizations/aequatus/static/aequatus-vis/scripts/jquery/js/jquery-ui-1.12.1.min.js A config/plugins/visualizations/aequatus/static/aequatus-vis/scripts/jquery/js/jquery.cookie.js A config/plugins/visualizations/aequatus/static/aequatus-vis/scripts/jquery/js/jquery.svg.js A config/plugins/visualizations/aequatus/static/aequatus-vis/scripts/newick.js A config/plugins/visualizations/aequatus/static/aequatus-vis/scripts/scriptaculous/prototype.js A config/plugins/visualizations/aequatus/static/aequatus-vis/scripts/util.js A config/plugins/visualizations/aequatus/static/aequatus-vis/styles/font-awesome-5.6.1/css/fontawesome.min.css A config/plugins/visualizations/aequatus/static/aequatus-vis/styles/font-awesome-5.6.1/css/solid.min.css A config/plugins/visualizations/aequatus/static/aequatus-vis/styles/font-awesome-5.6.1/webfonts/FontAwesome.otf A config/plugins/visualizations/aequatus/static/aequatus-vis/styles/font-awesome-5.6.1/webfonts/fa-solid-900.eot A config/plugins/visualizations/aequatus/static/aequatus-vis/styles/font-awesome-5.6.1/webfonts/fa-solid-900.svg A config/plugins/visualizations/aequatus/static/aequatus-vis/styles/font-awesome-5.6.1/webfonts/fa-solid-900.ttf A config/plugins/visualizations/aequatus/static/aequatus-vis/styles/font-awesome-5.6.1/webfonts/fa-solid-900.woff A config/plugins/visualizations/aequatus/static/aequatus-vis/styles/font-awesome-5.6.1/webfonts/fa-solid-900.woff2 A config/plugins/visualizations/aequatus/static/aequatus-vis/styles/font-awesome-5.6.1/webfonts/fontawesome-webfont.eot A config/plugins/visualizations/aequatus/static/aequatus-vis/styles/font-awesome-5.6.1/webfonts/fontawesome-webfont.svg A config/plugins/visualizations/aequatus/static/aequatus-vis/styles/font-awesome-5.6.1/webfonts/fontawesome-webfont.ttf A config/plugins/visualizations/aequatus/static/aequatus-vis/styles/font-awesome-5.6.1/webfonts/fontawesome-webfont.woff A config/plugins/visualizations/aequatus/static/aequatus-vis/styles/style.css A config/plugins/visualizations/aequatus/static/scripts/controls.js A config/plugins/visualizations/aequatus/static/scripts/popup.js A config/plugins/visualizations/aequatus/static/scripts/readSQLite.js A config/plugins/visualizations/aequatus/static/scripts/sql.js A config/plugins/visualizations/aequatus/static/scripts/worker.js A config/plugins/visualizations/aequatus/static/scripts/worker.sql.js A config/plugins/visualizations/aequatus/static/styles/aequatus.css A config/plugins/visualizations/aequatus/templates/aequatus.mako M lib/galaxy/datatypes/binary.py

Log Message: ----------- adds Aequatus visualisation plugin

updates Aequatus control panel-settings font size

Update README.md

fix path to aequatus static scripts

updates with upstream

removes console

removes installation guide

removes demo

removes duplicates

removes d3.js

removes bootstrap

prunes font-awesome

removes less of font-awesome

removes scss of font-awesome

uses font-swesome min

removes bootstrap

removes leftandright css class

updates jQuery and changes css class for popup

updates jQuery

updates fontawesome to 5.6.1

restore galaxy.yml.sample

add missing resource

update paths after updating font

remove console log

switch to minified jquery ui

Commit: 288453d4d017425f1f6121552e132fe8030624aa https://github.com/galaxyproject/galaxy/commit/288453d4d017425f1f6121552e132... Author: Martin Cech marten@bx.psu.edu Date: 2018-12-20 (Thu, 20 Dec 2018)

Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py

Log Message: ----------- Merge pull request #7087 from dfornika/mash-sketch-datatype

Add datatype for Mash Sketch files.

Commit: ab8fd9bc95b3e40eb3efc294408330954aa0220a https://github.com/galaxyproject/galaxy/commit/ab8fd9bc95b3e40eb3efc29440833... Author: Dannon Baker dannon.baker@gmail.com Date: 2018-12-20 (Thu, 20 Dec 2018)

Changed paths: M client/galaxy/style/scss/base.scss M templates/base/base_panels.mako M templates/webapps/reports/base_panels.mako M templates/webapps/reports/index.mako M templates/webapps/tool_shed/admin/index.mako M templates/webapps/tool_shed/base_panels.mako M templates/webapps/tool_shed/group/index.mako M templates/webapps/tool_shed/index.mako

Log Message: ----------- Fixes toolshed and reports styling that was previously applied at the mako template level. We'll want to update the look here, I think, but this is an incremental step that correctly uses the background image, bundled via webpack.

Commit: cd119d641ad59a9da008875b5c32f20127bcbd65 https://github.com/galaxyproject/galaxy/commit/cd119d641ad59a9da008875b5c32f... Author: John Chilton jmchilton@gmail.com Date: 2018-12-21 (Fri, 21 Dec 2018)

Changed paths: M client/README.md M client/galaxy/scripts/app/singleton.js M client/galaxy/scripts/apps/analysis.js A client/galaxy/scripts/components/GalaxyLoader.vue M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/panel.js M client/galaxy/scripts/mvc/collection/collection-li.js M client/galaxy/scripts/mvc/collection/collection-view.js M client/galaxy/scripts/mvc/dataset/dataset-edit-attributes.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/history/hdca-li.js M client/galaxy/scripts/mvc/history/history-item-li.js M client/galaxy/scripts/mvc/history/options-menu.js M client/galaxy/scripts/mvc/list/list-item.js M client/galaxy/scripts/mvc/list/list-view.js M client/galaxy/scripts/mvc/tool/tool-form.js M client/galaxy/scripts/mvc/ui/ui-frames.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/galaxy/scripts/mvc/user/user-preferences.js M client/galaxy/scripts/utils/utils.js M client/package.json M config/datatypes_conf.xml.sample M config/galaxy.yml.sample M config/job_conf.xml.sample_advanced M config/job_resource_params_conf.xml.sample M config/plugins/interactive_environments/neo/config/allowed_images.yml.sample M config/plugins/interactive_environments/neo/config/neo.ini.sample M config/tool_conf.xml.sample M config/workflow_resource_params_conf.xml.sample M config/workflow_schedulers_conf.xml.sample M doc/source/admin/framework_dependencies.rst M doc/source/admin/galaxy_options.rst M doc/source/admin/jobs.md M doc/source/admin/scaling.md M lib/galaxy/app.py M lib/galaxy/config.py M lib/galaxy/datatypes/binary.py M lib/galaxy/dependencies/pipfiles/default/Pipfile M lib/galaxy/dependencies/pipfiles/default/pinned-dev-requirements.txt M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt M lib/galaxy/dependencies/pipfiles/update.sh M lib/galaxy/exceptions/__init__.py M lib/galaxy/exceptions/error_codes.json M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/handler.py M lib/galaxy/jobs/manager.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/drmaa.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/managers/configuration.py M lib/galaxy/managers/datasets.py M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py M lib/galaxy/model/migrate/versions/0145_add_workflow_step_input.py A lib/galaxy/model/migrate/versions/0146_workflow_paths.py M lib/galaxy/objectstore/__init__.py M lib/galaxy/objectstore/azure_blob.py M lib/galaxy/objectstore/cloud.py M lib/galaxy/objectstore/pithos.py M lib/galaxy/objectstore/s3.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/actions/history_imp_exp.py M lib/galaxy/tools/actions/metadata.py M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/tools/deps/singularity_util.py M lib/galaxy/tools/filter_from_file.xml M lib/galaxy/tools/parameters/meta.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/tools/parameters/validation.py M lib/galaxy/tools/verify/__init__.py M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/util/__init__.py M lib/galaxy/util/facts.py M lib/galaxy/util/handlers.py M lib/galaxy/visualization/plugins/interactive_environments.py M lib/galaxy/web/base/controller.py M lib/galaxy/web/stack/__init__.py M lib/galaxy/web/stack/transport.py M lib/galaxy/webapps/galaxy/api/cloud.py M lib/galaxy/webapps/galaxy/api/jobs.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/config_schema.yml M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/workflow/scheduling_manager.py M lib/galaxy_ext/metadata/set_metadata.py M scripts/common_startup.sh M scripts/common_startup_functions.sh M scripts/grt/export.py M scripts/grt/grt.yml.sample M templates/admin/tool_shed_repository/manage_repository.mako M test/api/test_workflows.py M test/base/populators.py M test/base/workflow_fixtures.py M test/functional/tools/for_workflows/head.xml M test/functional/tools/samples_tool_conf.xml A test/functional/tools/tool_provided_metadata_10.xml A test/functional/tools/tool_provided_metadata_11.xml A test/functional/tools/tool_provided_metadata_12.xml M test/integration/test_dockerized_jobs.py A test/integration/test_workflow_sync.py A test/unit/jobs/handler_template_job_conf.xml M test/unit/jobs/test_job_configuration.py M test/unit/jobs/test_job_wrapper.py M test/unit/jobs/test_runner_local.py M test/unit/test_objectstore.py M test/unit/tools/test_actions.py M test/unit/tools/test_parameter_parsing.py M test/unit/tools/test_toolbox.py M test/unit/tools/test_wrappers.py M test/unit/unittest_utils/galaxy_mock.py R tools/data_source/bed_convert.xml M tools/data_source/genbank.xml M tools/data_source/upload.xml M tools/extract/liftOver_wrapper.xml M tools/filters/CreateInterval.xml M tools/filters/bed_to_bigbed.xml M tools/filters/changeCase.xml M tools/filters/fileGrep.xml M tools/filters/fixedValueColumn.xml M tools/filters/gff/gff_filter_by_attribute.xml M tools/filters/gff/gff_filter_by_feature_count.xml M tools/filters/grep.xml M tools/filters/headWrapper.xml M tools/filters/randomlines.xml M tools/filters/remove_beginning.xml M tools/filters/tailWrapper.xml M tools/filters/wig_to_bigwig.xml M tools/maf/vcf_to_maf_customtrack.xml M tools/metag_tools/blat_wrapper.xml M tools/metag_tools/shrimp_color_wrapper.xml M tools/metag_tools/shrimp_wrapper.xml M tools/plotting/bar_chart.xml M tools/plotting/boxplot.xml M tools/solid_tools/maq_cs_wrapper.xml M tools/sr_mapping/PerM.xml M tools/sr_mapping/bfast_wrapper.xml M tools/stats/filtering.xml M tools/stats/grouping.py M tools/stats/grouping.xml M tools/stats/gsummary.xml M tools/stats/gsummary.xml.groups

Log Message: ----------- Merge remote-tracking branch 'jmchilton/dev' into pulsar_resubmit

Commit: 0727f17ade3bb964a260907860a7ab0aee39a4b3 https://github.com/galaxyproject/galaxy/commit/0727f17ade3bb964a260907860a7a... Author: John Chilton jmchilton@gmail.com Date: 2018-12-21 (Fri, 21 Dec 2018)

Changed paths: M lib/galaxy/jobs/runners/pulsar.py M test/integration/resubmission_pulsar_job_conf.xml

Log Message: ----------- Fixes for Pulsar error handling.

More uniform error hanlding to fix test. Simplify test case of resubmission to test just jobs resubmit properly (no need to test Pulsar-to-Pulsar resubmission in particular here I don't think, maybe as a second test - but not a first?).

Commit: 5d8e0bb049a5ffdc0197a1e8436f358d4352ce09 https://github.com/galaxyproject/galaxy/commit/5d8e0bb049a5ffdc0197a1e8436f3... Author: Sergey Golitsynskiy sgolitsynskiy@gmail.com Date: 2018-12-21 (Fri, 21 Dec 2018)

Changed paths: M doc/source/dev/build_a_job_runner.rst

Log Message: ----------- Correct code error in 'build job runner' tutorial

When __init__ is called, **kwargs (most likely) will not contain the 'runner_param_specs' key. And if so, calling update() on kwargs['runner_param_specs'] will cause an error. Check if key exists, then update or create.

Commit: 0bd861aec759edb86a86e5e599e5b208dec48e43 https://github.com/galaxyproject/galaxy/commit/0bd861aec759edb86a86e5e599e5b... Author: Sergey Golitsynskiy sgolitsynskiy@gmail.com Date: 2018-12-21 (Fri, 21 Dec 2018)

Changed paths: M doc/source/dev/build_a_job_runner.rst

Log Message: ----------- Code style improvement to previous commit

Commit: 38687ff15a092477a798891eed572c7680e4d037 https://github.com/galaxyproject/galaxy/commit/38687ff15a092477a798891eed572... Author: Dannon dannon.baker@gmail.com Date: 2018-12-21 (Fri, 21 Dec 2018)

Changed paths: M doc/source/dev/build_a_job_runner.rst

Log Message: ----------- Merge pull request #7148 from ic4f/dev

Correct code error in 'build job runner' tutorial

Commit: fbf67196fff08a8c7a04d23703082cd77893e815 https://github.com/galaxyproject/galaxy/commit/fbf67196fff08a8c7a04d23703082... Author: Mason nerdinacan@gmail.com Date: 2018-12-21 (Fri, 21 Dec 2018)

Changed paths: M client/galaxy/scripts/apps/extended.js

Log Message: ----------- added store library to exported libs in bundleEntries

Commit: 3c2858ab0c9d79de18e28abfcef89de789e2c70c https://github.com/galaxyproject/galaxy/commit/3c2858ab0c9d79de18e28abfcef89... Author: Dannon dannon.baker@gmail.com Date: 2018-12-21 (Fri, 21 Dec 2018)

Changed paths: M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/panels/admin-panel.js A client/galaxy/scripts/components/admin/AdminServices.js A client/galaxy/scripts/components/admin/DisplayApplications.vue A lib/galaxy/webapps/galaxy/api/display_applications.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin.py R templates/webapps/galaxy/admin/view_display_applications.mako M test/selenium_tests/test_admin_app.py

Log Message: ----------- Merge pull request #7097 from guerler/display_applications

Replace display applications mako with vue component

Commit: 3af7a5c1a754a72c3dab94fde0eb1cc3476405fe https://github.com/galaxyproject/galaxy/commit/3af7a5c1a754a72c3dab94fde0eb1... Author: Dannon Baker dannon.baker@gmail.com Date: 2018-12-21 (Fri, 21 Dec 2018)

Changed paths: M client/galaxy/scripts/components/admin/AdminServices.js M client/galaxy/scripts/components/admin/DisplayApplications.vue

Log Message: ----------- Client format I intended to lump into display applications merge.

Commit: 9de86adc06dc3fa0d071d84252fd9c9b4befd2a0 https://github.com/galaxyproject/galaxy/commit/9de86adc06dc3fa0d071d84252fd9... Author: Dannon dannon.baker@gmail.com Date: 2018-12-21 (Fri, 21 Dec 2018)

Changed paths: M lib/galaxy/tools/parameters/output_collect.py

Log Message: ----------- Merge pull request #7134 from jmchilton/remove_flushes

Remove unneeded session flushes and adds when discovering outputs.

Commit: e8d95fba71a44b128dd873c336d95b7e551607a7 https://github.com/galaxyproject/galaxy/commit/e8d95fba71a44b128dd873c336d95... Author: Dannon dannon.baker@gmail.com Date: 2018-12-21 (Fri, 21 Dec 2018)

Changed paths: M client/galaxy/scripts/apps/extended.js

Log Message: ----------- Merge pull request #7149 from Nerdinacan/include_store_in_bundleEntries

added store library to exported libs in bundleEntries

Commit: d53e33cf9f814700d14743d8addd4e059b380ebd https://github.com/galaxyproject/galaxy/commit/d53e33cf9f814700d14743d8addd4... Author: guerler aysam.guerler@gmail.com Date: 2018-12-21 (Fri, 21 Dec 2018)

Changed paths: M client/galaxy/scripts/app/singleton.js M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/extended.js M client/galaxy/scripts/apps/panels/admin-panel.js M client/galaxy/scripts/components/GalaxyLoader.vue M client/galaxy/scripts/components/admin/AdminServices.js A client/galaxy/scripts/components/admin/DisplayApplications.vue M client/galaxy/scripts/layout/panel.js M client/galaxy/scripts/mvc/collection/collection-li.js M client/galaxy/scripts/mvc/collection/collection-view.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/history/hdca-li.js M client/galaxy/scripts/mvc/history/history-item-li.js M client/galaxy/scripts/mvc/list/list-item.js M client/galaxy/scripts/mvc/list/list-view.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/galaxy/scripts/utils/utils.js M config/datatypes_conf.xml.sample M config/tool_conf.xml.sample M doc/source/dev/build_a_job_runner.rst M lib/galaxy/datatypes/binary.py M lib/galaxy/jobs/__init__.py M lib/galaxy/tools/filter_from_file.xml M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/tools/verify/__init__.py A lib/galaxy/webapps/galaxy/api/display_applications.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin.py R templates/webapps/galaxy/admin/view_display_applications.mako M test/functional/tools/samples_tool_conf.xml A test/functional/tools/tool_provided_metadata_10.xml A test/functional/tools/tool_provided_metadata_11.xml A test/functional/tools/tool_provided_metadata_12.xml M test/selenium_tests/test_admin_app.py

Log Message: ----------- Merge branch 'dev' into admin_error_log

Commit: d385be993a4939f5741c54296a041ab994731f50 https://github.com/galaxyproject/galaxy/commit/d385be993a4939f5741c54296a041... Author: guerler aysam.guerler@gmail.com Date: 2018-12-21 (Fri, 21 Dec 2018)

Changed paths: M client/galaxy/scripts/components/admin/ErrorStack.vue

Log Message: ----------- Fix consistency of parameter naming to in error stack component

Commit: e4e2d9c09a45375faeb3e52d16beac87d4df1f99 https://github.com/galaxyproject/galaxy/commit/e4e2d9c09a45375faeb3e52d16bea... Author: Dannon dannon.baker@gmail.com Date: 2018-12-21 (Fri, 21 Dec 2018)

Changed paths: A config/plugins/visualizations/aequatus/README.md A config/plugins/visualizations/aequatus/config/aequatus.xml A config/plugins/visualizations/aequatus/static/aequatus-vis/LICENSE A config/plugins/visualizations/aequatus/static/aequatus-vis/README.md A config/plugins/visualizations/aequatus/static/aequatus-vis/_config.yml A config/plugins/visualizations/aequatus/static/aequatus-vis/scripts/cigarUtils.js A config/plugins/visualizations/aequatus/static/aequatus-vis/scripts/d3_tree.js A config/plugins/visualizations/aequatus/static/aequatus-vis/scripts/drawCIGARs.js A config/plugins/visualizations/aequatus/static/aequatus-vis/scripts/drawGene.js A config/plugins/visualizations/aequatus/static/aequatus-vis/scripts/drawGeneExonOnly.js A config/plugins/visualizations/aequatus/static/aequatus-vis/scripts/geneView.js A config/plugins/visualizations/aequatus/static/aequatus-vis/scripts/init.js A config/plugins/visualizations/aequatus/static/aequatus-vis/scripts/jquery/jquery-ui-1.12.1.min.css A config/plugins/visualizations/aequatus/static/aequatus-vis/scripts/jquery/jquery.svg.css A config/plugins/visualizations/aequatus/static/aequatus-vis/scripts/jquery/js/jquery-3.3.1.min.js A config/plugins/visualizations/aequatus/static/aequatus-vis/scripts/jquery/js/jquery-migrate-1.4.1.min.js A config/plugins/visualizations/aequatus/static/aequatus-vis/scripts/jquery/js/jquery-ui-1.12.1.min.js A config/plugins/visualizations/aequatus/static/aequatus-vis/scripts/jquery/js/jquery.cookie.js A config/plugins/visualizations/aequatus/static/aequatus-vis/scripts/jquery/js/jquery.svg.js A config/plugins/visualizations/aequatus/static/aequatus-vis/scripts/newick.js A config/plugins/visualizations/aequatus/static/aequatus-vis/scripts/scriptaculous/prototype.js A config/plugins/visualizations/aequatus/static/aequatus-vis/scripts/util.js A config/plugins/visualizations/aequatus/static/aequatus-vis/styles/font-awesome-5.6.1/css/fontawesome.min.css A config/plugins/visualizations/aequatus/static/aequatus-vis/styles/font-awesome-5.6.1/css/solid.min.css A config/plugins/visualizations/aequatus/static/aequatus-vis/styles/font-awesome-5.6.1/webfonts/FontAwesome.otf A config/plugins/visualizations/aequatus/static/aequatus-vis/styles/font-awesome-5.6.1/webfonts/fa-solid-900.eot A config/plugins/visualizations/aequatus/static/aequatus-vis/styles/font-awesome-5.6.1/webfonts/fa-solid-900.svg A config/plugins/visualizations/aequatus/static/aequatus-vis/styles/font-awesome-5.6.1/webfonts/fa-solid-900.ttf A config/plugins/visualizations/aequatus/static/aequatus-vis/styles/font-awesome-5.6.1/webfonts/fa-solid-900.woff A config/plugins/visualizations/aequatus/static/aequatus-vis/styles/font-awesome-5.6.1/webfonts/fa-solid-900.woff2 A config/plugins/visualizations/aequatus/static/aequatus-vis/styles/font-awesome-5.6.1/webfonts/fontawesome-webfont.eot A config/plugins/visualizations/aequatus/static/aequatus-vis/styles/font-awesome-5.6.1/webfonts/fontawesome-webfont.svg A config/plugins/visualizations/aequatus/static/aequatus-vis/styles/font-awesome-5.6.1/webfonts/fontawesome-webfont.ttf A config/plugins/visualizations/aequatus/static/aequatus-vis/styles/font-awesome-5.6.1/webfonts/fontawesome-webfont.woff A config/plugins/visualizations/aequatus/static/aequatus-vis/styles/style.css A config/plugins/visualizations/aequatus/static/scripts/controls.js A config/plugins/visualizations/aequatus/static/scripts/popup.js A config/plugins/visualizations/aequatus/static/scripts/readSQLite.js A config/plugins/visualizations/aequatus/static/scripts/sql.js A config/plugins/visualizations/aequatus/static/scripts/worker.js A config/plugins/visualizations/aequatus/static/scripts/worker.sql.js A config/plugins/visualizations/aequatus/static/styles/aequatus.css A config/plugins/visualizations/aequatus/templates/aequatus.mako M lib/galaxy/datatypes/binary.py

Log Message: ----------- Merge pull request #6484 from anilthanki/aequatus-vis

Adds Aequatus visualisation plugin

Commit: abf98be7833f1df15ad292b453f5b79899e8412f https://github.com/galaxyproject/galaxy/commit/abf98be7833f1df15ad292b453f5b... Author: John Chilton jmchilton@gmail.com Date: 2018-12-21 (Fri, 21 Dec 2018)

Changed paths: M lib/galaxy/jobs/runners/pulsar.py

Log Message: ----------- lint fix

Commit: 26c950f569111ccd61621849c0fc7aecbf70e76b https://github.com/galaxyproject/galaxy/commit/26c950f569111ccd61621849c0fc7... Author: John Chilton jmchilton@gmail.com Date: 2018-12-21 (Fri, 21 Dec 2018)

Changed paths: M lib/galaxy/jobs/mapper.py M lib/galaxy/jobs/runners/pulsar.py A test/integration/resubmission_pulsar_job_conf.xml M test/integration/test_job_resubmission.py M test/unit/jobs/test_mapper.py M test/unit/jobs/test_rules/10_site.py

Log Message: ----------- Merge pull request #7053 from nuwang/pulsar_resubmit

Added resubmit handlers on Pulsar connection failures

Commit: c8b6fa0ead77a707d839a8e03c286fcefedb7d52 https://github.com/galaxyproject/galaxy/commit/c8b6fa0ead77a707d839a8e03c286... Author: guerler aysam.guerler@gmail.com Date: 2018-12-23 (Sun, 23 Dec 2018)

Changed paths: M client/galaxy/scripts/mvc/form/form-data.js M client/galaxy/scripts/mvc/form/form-input.js

Log Message: ----------- Fix connected value handling in workflow editor

Commit: fd205ebfbe25f9ba8f19da20ae2e2a20b0cd600a https://github.com/galaxyproject/galaxy/commit/fd205ebfbe25f9ba8f19da20ae2e2... Author: guerler aysam.guerler@gmail.com Date: 2018-12-23 (Sun, 23 Dec 2018)

Changed paths: M client/galaxy/style/scss/ui.scss

Log Message: ----------- Remove pointer from inactive collapsible title

Commit: f0b88169334f695e957029357d759cb841df2499 https://github.com/galaxyproject/galaxy/commit/f0b88169334f695e957029357d759... Author: guerler aysam.guerler@gmail.com Date: 2018-12-23 (Sun, 23 Dec 2018)

Changed paths: M client/galaxy/scripts/mvc/form/form-input.js

Log Message: ----------- Fix tooltip update for collapsible and connected input parameters in workflow editor

Commit: 04623376d76db8086625a4d0fa4cbd9549fbae99 https://github.com/galaxyproject/galaxy/commit/04623376d76db8086625a4d0fa4cb... Author: guerler aysam.guerler@gmail.com Date: 2018-12-23 (Sun, 23 Dec 2018)

Changed paths: M client/galaxy/scripts/mvc/form/form-input.js

Log Message: ----------- Fix logic for collapsible options

Commit: bbe86fb2cc9a01dbc53995ec823b1f3a9ca4c460 https://github.com/galaxyproject/galaxy/commit/bbe86fb2cc9a01dbc53995ec823b1... Author: guerler aysam.guerler@gmail.com Date: 2018-12-23 (Sun, 23 Dec 2018)

Changed paths: M client/galaxy/scripts/mvc/form/form-input.js

Log Message: ----------- Fix type in form input wrapper related to connected modules

Commit: 0f8db20c8e12bbb35804a911ae0dd7b1bfa4f55c https://github.com/galaxyproject/galaxy/commit/0f8db20c8e12bbb35804a911ae0dd... Author: guerler aysam.guerler@gmail.com Date: 2018-12-23 (Sun, 23 Dec 2018)

Changed paths: M client/galaxy/scripts/mvc/form/form-input.js

Log Message: ----------- Remove show call to connected/collapsible tooltip, not required for refresh

Commit: 460c0ac014016837f4d64f3f46f5cec79ca37f24 https://github.com/galaxyproject/galaxy/commit/460c0ac014016837f4d64f3f46f5c... Author: guerler aysam.guerler@gmail.com Date: 2018-12-23 (Sun, 23 Dec 2018)

Changed paths: M client/galaxy/style/scss/ui.scss

Log Message: ----------- Remove fixed width from parameter option icons

Commit: 1dad09fc92c0d14479d6c58a36c28e46971aaf5c https://github.com/galaxyproject/galaxy/commit/1dad09fc92c0d14479d6c58a36c28... Author: guerler aysam.guerler@gmail.com Date: 2018-12-23 (Sun, 23 Dec 2018)

Changed paths: M client/galaxy/scripts/mvc/form/form-input.js

Log Message: ----------- Add connected check directly to associated value

Commit: 647479f40ae1c5e4c1569b173c7cc0ae8c029c93 https://github.com/galaxyproject/galaxy/commit/647479f40ae1c5e4c1569b173c7cc... Author: John Chilton jmchilton@gmail.com Date: 2018-12-26 (Wed, 26 Dec 2018)

Changed paths: M lib/galaxy/tools/parser/yaml.py A test/functional/tools/collection_creates_pair_y.yml M test/unit/tools/test_parsing.py

Log Message: ----------- Fix for parsing collection outputs for YAML/dictified tools.

Commit: 3d373827b3b1d59dd166ad6db1b95dedcb256004 https://github.com/galaxyproject/galaxy/commit/3d373827b3b1d59dd166ad6db1b95... Author: John Chilton jmchilton@gmail.com Date: 2018-12-26 (Wed, 26 Dec 2018)

Changed paths: M lib/galaxy/tools/parser/output_collection_def.py M lib/galaxy/tools/parser/util.py M lib/galaxy/tools/parser/yaml.py M test/unit/tools/test_collect_primary_datasets.py

Log Message: ----------- Fix dataset discovery for YAML/dictified tools.

Commit: 234d3ee8a6c4979aeeea4bbd9a07d875c379f0be https://github.com/galaxyproject/galaxy/commit/234d3ee8a6c4979aeeea4bbd9a07d... Author: John Chilton jmchilton@gmail.com Date: 2018-12-26 (Wed, 26 Dec 2018)

Changed paths: M lib/galaxy/jobs/__init__.py

Log Message: ----------- Remove redundant Task code.

get_job is overridden in Task, that should be sufficient I suspect.

Commit: 47d8fedfa4d4b84ef47fcebd2b0f5536b919c353 https://github.com/galaxyproject/galaxy/commit/47d8fedfa4d4b84ef47fcebd2b0f5... Author: John Chilton jmchilton@gmail.com Date: 2018-12-26 (Wed, 26 Dec 2018)

Changed paths: M lib/galaxy/jobs/__init__.py

Log Message: ----------- Reuse get_param_dict in job wrapper.

There is a comment to this, listen to the smart comment and then delete.

Commit: c5dbd78af6ae4c7738a05708ffb01e444ee92a2b https://github.com/galaxyproject/galaxy/commit/c5dbd78af6ae4c7738a05708ffb01... Author: guerler aysam.guerler@gmail.com Date: 2018-12-26 (Wed, 26 Dec 2018)

Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js

Log Message: ----------- Do not use default value in workflow execution form for runtime values

Commit: 471d54c27af26699be234155585bc488b5d16f65 https://github.com/galaxyproject/galaxy/commit/471d54c27af26699be234155585bc... Author: John Chilton jmchilton@gmail.com Date: 2018-12-27 (Thu, 27 Dec 2018)

Changed paths: M lib/galaxy/jobs/__init__.py

Log Message: ----------- Merge pull request #7155 from jmchilton/reuse_get_params

Small de-duplication cleanups to galaxy.jobs

Commit: 7b911c6fcd4b6fca661275afee13c247b766c169 https://github.com/galaxyproject/galaxy/commit/7b911c6fcd4b6fca661275afee13c... Author: Björn Grüning bjoern@gruenings.eu Date: 2018-12-29 (Sat, 29 Dec 2018)

Changed paths: M lib/galaxy/tools/parser/yaml.py A test/functional/tools/collection_creates_pair_y.yml M test/unit/tools/test_parsing.py

Log Message: ----------- Merge pull request #7153 from jmchilton/fix_output_collection_yaml

Fix for parsing collection outputs for YAML/dictified tools.

Commit: 4c741ef00ef0fcde5af1b2e270acc0f0f2f407ec https://github.com/galaxyproject/galaxy/commit/4c741ef00ef0fcde5af1b2e270acc... Author: Björn Grüning bjoern@gruenings.eu Date: 2018-12-29 (Sat, 29 Dec 2018)

Changed paths: M lib/galaxy/tools/parser/output_collection_def.py M lib/galaxy/tools/parser/util.py M lib/galaxy/tools/parser/yaml.py M test/unit/tools/test_collect_primary_datasets.py

Log Message: ----------- Merge pull request #7152 from jmchilton/fix_yaml_discovery

Fix dataset discovery for YAML/dictified tools.

Commit: 0d28c65c3d1ce504850a3ba94b99099abb68cd92 https://github.com/galaxyproject/galaxy/commit/0d28c65c3d1ce504850a3ba94b990... Author: mvdbeek m.vandenbeek@gmail.com Date: 2018-12-31 (Mon, 31 Dec 2018)

Changed paths: M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/buildapp.py M test/api/test_tools.py

Log Message: ----------- Allow anonymous downloading of test-data files

Commit: 6791f3b99905ac0db0a8e2c23f38a4bce8b1d3c8 https://github.com/galaxyproject/galaxy/commit/6791f3b99905ac0db0a8e2c23f38a... Author: mvdbeek m.vandenbeek@gmail.com Date: 2018-12-31 (Mon, 31 Dec 2018)

Changed paths: M lib/galaxy/tools/verify/__init__.py M lib/galaxy/tools/verify/interactor.py M lib/galaxy/tools/verify/test_data.py M lib/galaxy/webapps/galaxy/api/tools.py M test/api/test_tools.py

Log Message: ----------- Also allow downloading test-data directories

This is (apparently ...) used by tools that create/test directories in the extra_files_path.

Commit: e30ff62b0e1069d4316e15660d130df87e6c6217 https://github.com/galaxyproject/galaxy/commit/e30ff62b0e1069d4316e15660d130... Author: mvdbeek m.vandenbeek@gmail.com Date: 2018-12-31 (Mon, 31 Dec 2018)

Changed paths: M lib/galaxy/util/streamball.py M lib/galaxy/webapps/galaxy/api/tools.py

Log Message: ----------- Move stream_archive to galaxy.util.streamball

Commit: 5490a6db7c5fa5db431c64b51998f923110106a6 https://github.com/galaxyproject/galaxy/commit/5490a6db7c5fa5db431c64b51998f... Author: mvdbeek m.vandenbeek@gmail.com Date: 2018-12-31 (Mon, 31 Dec 2018)

Changed paths: M test/functional/tools/composite_output_tests.xml

Log Message: ----------- Add `extra_files type="directory"` test

Commit: 95f866d77c4adbe2055b28f37808b709658a9903 https://github.com/galaxyproject/galaxy/commit/95f866d77c4adbe2055b28f37808b... Author: mvdbeek m.vandenbeek@gmail.com Date: 2018-12-31 (Mon, 31 Dec 2018)

Changed paths: M lib/galaxy/tools/verify/__init__.py M lib/galaxy/tools/verify/interactor.py

Log Message: ----------- Make type="directory" remote compatible

We download an archive containing the specified directory for tests.

Commit: f1acff02ded73df1014316f276b7e89d9decec37 https://github.com/galaxyproject/galaxy/commit/f1acff02ded73df1014316f276b7e... Author: mvdbeek m.vandenbeek@gmail.com Date: 2018-12-31 (Mon, 31 Dec 2018)

Changed paths: M test/functional/tools/composite_output_tests.xml

Log Message: ----------- Quote remaining parametera

Commit: 9c08b416dbdbac16106f7dbd5b7eaf805d2ec996 https://github.com/galaxyproject/galaxy/commit/9c08b416dbdbac16106f7dbd5b7ea... Author: John Chilton jmchilton@gmail.com Date: 2019-01-01 (Tue, 01 Jan 2019)

Changed paths: M lib/galaxy/objectstore/__init__.py M lib/galaxy/objectstore/azure_blob.py M lib/galaxy/objectstore/cloud.py M lib/galaxy/objectstore/pithos.py M lib/galaxy/objectstore/s3.py M test/unit/test_objectstore.py

Log Message: ----------- Merge pull request #7110 from jmchilton/os_to_dict

Add to_dict() to ObjectStores.

Commit: 4877bfafa6cd5b8af419c9dad0615bcd39e9559e https://github.com/galaxyproject/galaxy/commit/4877bfafa6cd5b8af419c9dad0615... Author: mvdbeek m.vandenbeek@gmail.com Date: 2019-01-01 (Tue, 01 Jan 2019)

Changed paths: M test/api/test_tools.py

Log Message: ----------- Test that test-data paths outside of test-data folder cannot be downloaded

Commit: 0eb96a63f59f3def6e82df045357e61d2e4e6196 https://github.com/galaxyproject/galaxy/commit/0eb96a63f59f3def6e82df045357e... Author: M Bernt m.bernt@ufz.de Date: 2019-01-02 (Wed, 02 Jan 2019)

Changed paths: M doc/source/admin/cluster.md

Log Message: ----------- doc: added missing docs for new UNIVA runner

Commit: 6869883309bbef76d36b62d388c604e989734cc6 https://github.com/galaxyproject/galaxy/commit/6869883309bbef76d36b62d388c60... Author: John Chilton jmchilton@gmail.com Date: 2019-01-02 (Wed, 02 Jan 2019)

Changed paths: M doc/source/admin/cluster.md

Log Message: ----------- Merge pull request #7161 from bernt-matthias/topic/univa-doc

doc: added missing docs for new UNIVA runner

Commit: e87e1561e336bb187ac5e40f55a107614bc38686 https://github.com/galaxyproject/galaxy/commit/e87e1561e336bb187ac5e40f55a10... Author: John Chilton jmchilton@gmail.com Date: 2019-01-02 (Wed, 02 Jan 2019)

Changed paths: M lib/galaxy/tools/verify/__init__.py M lib/galaxy/tools/verify/interactor.py M lib/galaxy/tools/verify/test_data.py M lib/galaxy/util/streamball.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/buildapp.py M test/api/test_tools.py M test/functional/tools/composite_output_tests.xml

Log Message: ----------- Merge pull request #7160 from mvdbeek/unprivileged_remote_tool_tests

Unprivileged remote tool tests

Commit: a8944f5a039aee937b1d31855a4f00d2e84a1c64 https://github.com/galaxyproject/galaxy/commit/a8944f5a039aee937b1d31855a4f0... Author: John Chilton jmchilton@gmail.com Date: 2019-01-02 (Wed, 02 Jan 2019)

Changed paths: M client/galaxy/scripts/mvc/form/form-data.js M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/style/scss/ui.scss

Log Message: ----------- Merge pull request #7150 from guerler/connected_value

Follow-up on handling connectable and collapsible parameters in workflows

Commit: 65419bd3763dcfc78d92808a6a323ed10ee014ef https://github.com/galaxyproject/galaxy/commit/65419bd3763dcfc78d92808a6a323... Author: John Chilton jmchilton@gmail.com Date: 2019-01-02 (Wed, 02 Jan 2019)

Changed paths: M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/panels/admin-panel.js M client/galaxy/scripts/components/admin/AdminServices.js A client/galaxy/scripts/components/admin/ErrorStack.vue M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin.py R templates/admin/tool_errors.mako

Log Message: ----------- Merge pull request #7124 from guerler/admin_error_log

Adds a vue component to display tool errors in the admin panel

Commit: e906ca1ffdd92f2b7709373b0e82c84a5218b077 https://github.com/galaxyproject/galaxy/commit/e906ca1ffdd92f2b7709373b0e82c... Author: John Chilton jmchilton@gmail.com Date: 2019-01-02 (Wed, 02 Jan 2019)

Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-content.js M client/galaxy/scripts/mvc/upload/composite/composite-row.js M client/galaxy/scripts/utils/uploadbox.js M client/galaxy/style/scss/upload.scss

Log Message: ----------- Merge pull request #7145 from guerler/fix_drop

Use regular js-event handling instead of jquery for uploader

Commit: aae7c9bb8457da24e45790b17464db0656b08746 https://github.com/galaxyproject/galaxy/commit/aae7c9bb8457da24e45790b17464d... Author: mvdbeek m.vandenbeek@gmail.com Date: 2019-01-02 (Wed, 02 Jan 2019)

Changed paths: M lib/galaxy/tools/verify/test_data.py

Log Message: ----------- Fix TestDataResolver.get_filecontent

Commit: 9e7fa2f0e98afc252bda91852063ee2b38e276a4 https://github.com/galaxyproject/galaxy/commit/9e7fa2f0e98afc252bda91852063e... Author: Marcus Christie machrist@iu.edu Date: 2019-01-02 (Wed, 02 Jan 2019)

Changed paths: M lib/galaxy/authnz/managers.py

Log Message: ----------- Lower provider name

The keys of the oidc_backends_config dict are created by lowercasing the provider names in oidc_backends_config.xml file so we need to lower the provider name given in the request in order to find the backend config.

Commit: 14ed1e78377b1945eebd967d08537bc931cf79e1 https://github.com/galaxyproject/galaxy/commit/14ed1e78377b1945eebd967d08537... Author: John Chilton jmchilton@gmail.com Date: 2019-01-02 (Wed, 02 Jan 2019)

Changed paths: M lib/galaxy/tools/verify/test_data.py

Log Message: ----------- Merge pull request #7165 from mvdbeek/remote_test_data_followup

Fix TestDataResolver.get_filecontent

Commit: cf01e9e7ac8722d2e90fd5a6a6534b654aa89f0a https://github.com/galaxyproject/galaxy/commit/cf01e9e7ac8722d2e90fd5a6a6534... Author: Martin Cech marten@bx.psu.edu Date: 2019-01-02 (Wed, 02 Jan 2019)

Changed paths: M client/galaxy/style/scss/base.scss M templates/base/base_panels.mako M templates/webapps/reports/base_panels.mako M templates/webapps/reports/index.mako M templates/webapps/tool_shed/admin/index.mako M templates/webapps/tool_shed/base_panels.mako M templates/webapps/tool_shed/group/index.mako M templates/webapps/tool_shed/index.mako

Log Message: ----------- Merge pull request #7146 from dannon/fix_toolshed_styles

Fixes toolshed and reports styling that was previously applied at the…

Commit: 97bf8b7d738b0f40725cc5abcf5d1b783eb820cb https://github.com/galaxyproject/galaxy/commit/97bf8b7d738b0f40725cc5abcf5d1... Author: Nicola Soranzo nicola.soranzo@earlham.ac.uk Date: 2019-01-03 (Thu, 03 Jan 2019)

Changed paths: M lib/tool_shed/util/repository_util.py

Log Message: ----------- Remove unnecessary split

Commit: c242842b7e0e5032b08532fedd362c30a7f00866 https://github.com/galaxyproject/galaxy/commit/c242842b7e0e5032b08532fedd362... Author: Nicola Soranzo nicola.soranzo@earlham.ac.uk Date: 2019-01-04 (Fri, 04 Jan 2019)

Changed paths: M lib/galaxy/tools/parameters/meta.py

Log Message: ----------- Use dict ``setdefault()``

Commit: 5a6f489276d9c5d3732948f7050b080004b84c11 https://github.com/galaxyproject/galaxy/commit/5a6f489276d9c5d3732948f7050b0... Author: Nicola Soranzo nicola.soranzo@earlham.ac.uk Date: 2019-01-04 (Fri, 04 Jan 2019)

Changed paths: M lib/galaxy/tools/errors.py

Log Message: ----------- Remove mailto link from error reports

`email_str` is often not a simple email address.

Commit: cd8b129b8e462eaf281ea0ef5cbd02d50dc32e66 https://github.com/galaxyproject/galaxy/commit/cd8b129b8e462eaf281ea0ef5cbd0... Author: mvdbeek m.vandenbeek@gmail.com Date: 2019-01-04 (Fri, 04 Jan 2019)

Changed paths: M test/api/test_tools.py

Log Message: ----------- Fix test_test_data_download

This contains 5 items after https://github.com/galaxyproject/galaxy-test-data/pull/2 had been merged.

Commit: 0d221b33e6b86611d09da8fa275d1e087dcf0c78 https://github.com/galaxyproject/galaxy/commit/0d221b33e6b86611d09da8fa275d1... Author: Marius van den Beek m.vandenbeek@gmail.com Date: 2019-01-04 (Fri, 04 Jan 2019)

Changed paths: M lib/galaxy/tools/errors.py M lib/galaxy/tools/parameters/meta.py M lib/tool_shed/util/repository_util.py

Log Message: ----------- Merge pull request #7168 from nsoranzo/misc

Misc fixes

Commit: 403d0a9361ca5fcc400eed6500415d288bf04903 https://github.com/galaxyproject/galaxy/commit/403d0a9361ca5fcc400eed6500415... Author: Nicola Soranzo nicola.soranzo@earlham.ac.uk Date: 2019-01-04 (Fri, 04 Jan 2019)

Changed paths: M test/unit/tools/test_parameter_parsing.py

Log Message: ----------- Stricter ``process_key`` tests

Commit: 31e5fced00778cf469b98dc05eb5f3221fc0caa6 https://github.com/galaxyproject/galaxy/commit/31e5fced00778cf469b98dc05eb5f... Author: mvdbeek m.vandenbeek@gmail.com Date: 2019-01-04 (Fri, 04 Jan 2019)

Changed paths: M lib/galaxy/tools/parameters/meta.py M test/unit/tools/test_parameter_parsing.py

Log Message: ----------- Fix nesting and test

Commit: b0691089eafd303cc0a31b589f465f552a90c40a https://github.com/galaxyproject/galaxy/commit/b0691089eafd303cc0a31b589f465... Author: Nate Coraor nate@bx.psu.edu Date: 2019-01-04 (Fri, 04 Jan 2019)

Changed paths: M test/unit/jobs/test_job_configuration.py

Log Message: ----------- Unit tests for new DB serialization handler assignment methods

Commit: 55e539d1e943805634ec290eadb412e86a27571a https://github.com/galaxyproject/galaxy/commit/55e539d1e943805634ec290eadb41... Author: Nicola Soranzo nicola.soranzo@gmail.com Date: 2019-01-04 (Fri, 04 Jan 2019)

Changed paths: M test/api/test_tools.py

Log Message: ----------- Merge pull request #7171 from mvdbeek/fix_test_data_download_api_test

Fix test_test_data_download

Commit: b8f445556abf8469b022afd9b59fa0a14b45dad9 https://github.com/galaxyproject/galaxy/commit/b8f445556abf8469b022afd9b59fa... Author: Nicola Soranzo nicola.soranzo@gmail.com Date: 2019-01-04 (Fri, 04 Jan 2019)

Changed paths: M lib/galaxy/tools/parameters/meta.py M test/unit/tools/test_parameter_parsing.py

Log Message: ----------- Merge pull request #7169 from mvdbeek/fix_process_key_unordered_elements

Fix process_key test and deal with unordered repeat elements

Commit: df7f8b425d16ddb54d4acb181f9a4ee415b510ea https://github.com/galaxyproject/galaxy/commit/df7f8b425d16ddb54d4acb181f9a4... Author: Nate Coraor nate@bx.psu.edu Date: 2019-01-04 (Fri, 04 Jan 2019)

Changed paths: M test/base/integration_util.py A test/integration/handler_template_job_conf.xml A test/integration/test_handler_assignment_methods.py M test/integration/test_scripts.py

Log Message: ----------- Integration tests for handler assignment methods

Commit: fa071b3c4fca24caed2d9a258e31ae87851a0da2 https://github.com/galaxyproject/galaxy/commit/fa071b3c4fca24caed2d9a258e31a... Author: Björn Grüning bjoern@gruenings.eu Date: 2019-01-05 (Sat, 05 Jan 2019)

Changed paths: M lib/galaxy/authnz/managers.py

Log Message: ----------- Merge pull request #7166 from machristie/lower-provider-name

Lower provider name

Commit: 1222f80ae99da18f6361bbad6234bfba65e278f5 https://github.com/galaxyproject/galaxy/commit/1222f80ae99da18f6361bbad6234b... Author: John Chilton jmchilton@gmail.com Date: 2019-01-05 (Sat, 05 Jan 2019)

Changed paths: M lib/galaxy/config.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/handler.py M lib/galaxy/util/handlers.py M lib/galaxy/web/stack/__init__.py M lib/galaxy/workflow/scheduling_manager.py M scripts/galaxy-main M test/base/integration_util.py A test/integration/handler_template_job_conf.xml A test/integration/test_handler_assignment_methods.py M test/integration/test_scripts.py M test/unit/jobs/test_job_configuration.py

Log Message: ----------- Merge pull request #7129 from natefoo/serializable-job-assignment

Perform job assignment using DB serialization techniques

Commit: cbcd3627f3833ada31b58863d5504666bb98b956 https://github.com/galaxyproject/galaxy/commit/cbcd3627f3833ada31b58863d5504... Author: mvdbeek m.vandenbeek@gmail.com Date: 2019-01-06 (Sun, 06 Jan 2019)

Changed paths: M lib/galaxy/tools/deps/container_resolvers/__init__.py M lib/galaxy/tools/deps/container_resolvers/explicit.py M lib/galaxy/tools/deps/container_resolvers/mulled.py

Log Message: ----------- Allow passing unused keywords to container resolver

Commit: 8f8642aa33e4c25e9f3bdff28b37a334af97b89c https://github.com/galaxyproject/galaxy/commit/8f8642aa33e4c25e9f3bdff28b37a... Author: mvdbeek m.vandenbeek@gmail.com Date: 2019-01-06 (Sun, 06 Jan 2019)

Changed paths: M lib/galaxy/config.py

Log Message: ----------- Merge container resolver with high-level dependency manager

Commit: b505fe37eac6b0331c20b26b7a0cddc49942a38a https://github.com/galaxyproject/galaxy/commit/b505fe37eac6b0331c20b26b7a0cd... Author: mvdbeek m.vandenbeek@gmail.com Date: 2019-01-06 (Sun, 06 Jan 2019)

Changed paths: M lib/galaxy/tools/deps/resolvers/__init__.py

Log Message: ----------- Introduce a ContainerDependency class

Commit: 360e605be965be5c414ca9ead34c536dd4003fd9 https://github.com/galaxyproject/galaxy/commit/360e605be965be5c414ca9ead34c5... Author: mvdbeek m.vandenbeek@gmail.com Date: 2019-01-06 (Sun, 06 Jan 2019)

Changed paths: M lib/galaxy/tools/deps/__init__.py

Log Message: ----------- Adjust _requirements_to_dependencies_dict to also report available containers in the manage dependencies menu

Commit: 40d8a38108fca6c21efc72f66660b3a1a7c42caa https://github.com/galaxyproject/galaxy/commit/40d8a38108fca6c21efc72f66660b... Author: mvdbeek m.vandenbeek@gmail.com Date: 2019-01-06 (Sun, 06 Jan 2019)

Changed paths: M lib/galaxy/tools/deps/__init__.py

Log Message: ----------- Augment NullDependency with version

and always record incoming null dependencies, since the container resolvers don't return NullDependency objects.

Commit: f2128692a4f42da2254a53b69cbf1931e74c10dc https://github.com/galaxyproject/galaxy/commit/f2128692a4f42da2254a53b69cbf1... Author: mvdbeek m.vandenbeek@gmail.com Date: 2019-01-06 (Sun, 06 Jan 2019)

Changed paths: M lib/galaxy/tools/deps/container_resolvers/mulled.py

Log Message: ----------- Fix matching single package mulled docker containers

An image like `quay.io/biocontainers/ucsc-liftover:357--1` would otherwise have the package name `quay.io/biocontainers/ucsc-liftover` instead of `ucsc-liftover`

Commit: fa6cca0224fd2b0239160df565a58507b05ac00f https://github.com/galaxyproject/galaxy/commit/fa6cca0224fd2b0239160df565a58... Author: mvdbeek m.vandenbeek@gmail.com Date: 2019-01-06 (Sun, 06 Jan 2019)

Changed paths: M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/containers.py M lib/galaxy/tools/deps/views.py

Log Message: ----------- Only walk through enabled container resolvers

Commit: 541f0ebf3d754f5a8eb4a3d8a56d0c197c29c5cb https://github.com/galaxyproject/galaxy/commit/541f0ebf3d754f5a8eb4a3d8a56d0... Author: mvdbeek m.vandenbeek@gmail.com Date: 2019-01-06 (Sun, 06 Jan 2019)

Changed paths: M lib/galaxy/config.py M lib/galaxy/jobs/rule_helper.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/containers.py M lib/galaxy/tools/deps/dependencies.py

Log Message: ----------- Avoid circular imports

by moving {App,Job,Tool} Info classes to dependencies.py

Commit: 3b4b510ad01f48253587db1bcd87400237709673 https://github.com/galaxyproject/galaxy/commit/3b4b510ad01f48253587db1bcd874... Author: mvdbeek m.vandenbeek@gmail.com Date: 2019-01-06 (Sun, 06 Jan 2019)

Changed paths: M lib/galaxy/tools/deps/container_resolvers/__init__.py

Log Message: ----------- Add `can_uninstall_dependencies` attribute to ContainerResolver

Commit: a4f18d8f601c83826a451d63af2fa67d319f58a7 https://github.com/galaxyproject/galaxy/commit/a4f18d8f601c83826a451d63af2fa... Author: mvdbeek m.vandenbeek@gmail.com Date: 2019-01-06 (Sun, 06 Jan 2019)

Changed paths: M lib/galaxy/config.py M lib/galaxy/tools/deps/__init__.py A lib/galaxy/tools/deps/container_classes.py M lib/galaxy/tools/deps/views.py

Log Message: ----------- Make DependencyManager container & destination-aware

This will allow us to use the proper parameters when pulling containers.

Commit: 2d3ab4ce1205aec24664225d74b2a851cb94b2b0 https://github.com/galaxyproject/galaxy/commit/2d3ab4ce1205aec24664225d74b2a... Author: mvdbeek m.vandenbeek@gmail.com Date: 2019-01-06 (Sun, 06 Jan 2019)

Changed paths: M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/views.py M lib/galaxy/webapps/galaxy/api/tools.py

Log Message: ----------- Allow specifying resolver index and resolver_type when installing dependencies via tools API

Commit: 7ca17e2b83d45e3c5a63643cc59785f6162803c5 https://github.com/galaxyproject/galaxy/commit/7ca17e2b83d45e3c5a63643cc5978... Author: mvdbeek m.vandenbeek@gmail.com Date: 2019-01-06 (Sun, 06 Jan 2019)

Changed paths: M lib/galaxy/tools/deps/__init__.py

Log Message: ----------- Drop NullDependency only when not skipping resolver

Commit: 59c56b8f563fd4298d37d40af0b0f429761c4392 https://github.com/galaxyproject/galaxy/commit/59c56b8f563fd4298d37d40af0b0f... Author: mvdbeek m.vandenbeek@gmail.com Date: 2019-01-06 (Sun, 06 Jan 2019)

Changed paths: M lib/galaxy/webapps/galaxy/api/tools.py

Log Message: ----------- Mention index and resolver_type in API docstring

Commit: 2aab490807245c30935389001605c170bbebbf98 https://github.com/galaxyproject/galaxy/commit/2aab490807245c30935389001605c... Author: mvdbeek m.vandenbeek@gmail.com Date: 2019-01-06 (Sun, 06 Jan 2019)

Changed paths: M lib/galaxy/tools/deps/container_classes.py M lib/galaxy/tools/deps/containers.py M lib/galaxy/tools/deps/dockerfiles.py

Log Message: ----------- Move Container classes into container_classes to avoid circular imports

Commit: 55f989c23650e94e1f28a3ac60d10931dfd70076 https://github.com/galaxyproject/galaxy/commit/55f989c23650e94e1f28a3ac60d10... Author: mvdbeek m.vandenbeek@gmail.com Date: 2019-01-06 (Sun, 06 Jan 2019)

Changed paths: M lib/galaxy/tools/deps/container_resolvers/mulled.py

Log Message: ----------- Make mulled docker containers installable

Commit: 19bc4985c91c14295d7c2048355a0bf71d4ec1cd https://github.com/galaxyproject/galaxy/commit/19bc4985c91c14295d7c2048355a0... Author: mvdbeek m.vandenbeek@gmail.com Date: 2019-01-06 (Sun, 06 Jan 2019)

Changed paths: M lib/galaxy/tools/deps/views.py M lib/galaxy/webapps/galaxy/api/tools.py

Log Message: ----------- Allow selecting resolver when uninstalling through tools API

Commit: 50d8e3079d873fe4161149b00365cf0d5702eb56 https://github.com/galaxyproject/galaxy/commit/50d8e3079d873fe4161149b00365c... Author: mvdbeek m.vandenbeek@gmail.com Date: 2019-01-06 (Sun, 06 Jan 2019)

Changed paths: M test/integration/test_resolvers.py

Log Message: ----------- Add integration test for un/install with resolver_type

Commit: 66a3f556abeb410fd59f1b408efae94f168699d8 https://github.com/galaxyproject/galaxy/commit/66a3f556abeb410fd59f1b408efae... Author: mvdbeek m.vandenbeek@gmail.com Date: 2019-01-06 (Sun, 06 Jan 2019)

Changed paths: M lib/galaxy/tools/deps/container_classes.py M lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/tools/deps/containers.py M lib/galaxy/tools/deps/singularity_util.py

Log Message: ----------- Use singularity build with biocontainers

This makes it possible to pull a container from quay.io/biocontainers and to convert it to singularity format for later execution (via the CachedMulledSingularityContainerResolver).

This is nicely integrated with the DependencyManager view, so you can (as for conda or docker) do: ``` requests.post(galaxy_url+'/api/tools/deseq2/dependencies', {'key': API_KEY, 'resolver_type': 'mulled_singularity'}) ```

This is quite lightweight, the resulting image is significantly smaller than the conda env (since it is compressed), and the install process is much faster.

Commit: 1fcbd971c8aa743b3e035ddc27a4ea78e01bac0a https://github.com/galaxyproject/galaxy/commit/1fcbd971c8aa743b3e035ddc27a4e... Author: mvdbeek m.vandenbeek@gmail.com Date: 2019-01-06 (Sun, 06 Jan 2019)

Changed paths: M config/container_resolvers_conf.xml.sample M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/containers.py

Log Message: ----------- Try cached resolver before non-cached

Commit: b41d969d681e3d427fd9f42ca9502c91634f061d https://github.com/galaxyproject/galaxy/commit/b41d969d681e3d427fd9f42ca9502... Author: mvdbeek m.vandenbeek@gmail.com Date: 2019-01-06 (Sun, 06 Jan 2019)

Changed paths: M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/tools/deps/singularity_util.py A test/integration/singularity_job_conf.xml A test/integration/test_containerized_jobs.py R test/integration/test_dockerized_jobs.py

Log Message: ----------- Add integration test for singularity resolution

Commit: fd4b009089d226e05a6191c3067fad560c5a77c8 https://github.com/galaxyproject/galaxy/commit/fd4b009089d226e05a6191c3067fa... Author: mvdbeek m.vandenbeek@gmail.com Date: 2019-01-06 (Sun, 06 Jan 2019)

Changed paths: M test/base/integration_util.py M test/integration/test_containerized_jobs.py

Log Message: ----------- Skip singualrity integration tests if singularity not available

Commit: 2d6863067554f38ac05625bee1b81663a7973a1a https://github.com/galaxyproject/galaxy/commit/2d6863067554f38ac05625bee1b81... Author: mvdbeek m.vandenbeek@gmail.com Date: 2019-01-06 (Sun, 06 Jan 2019)

Changed paths: M lib/galaxy/tools/deps/container_resolvers/mulled.py

Log Message: ----------- Add MulledSingularityContainerResolver to __all__

Otherwise speicifying the resolver in containers_conf.xml fails.

Commit: 337bddfd4841d51291f940effc99a4622f10649a https://github.com/galaxyproject/galaxy/commit/337bddfd4841d51291f940effc99a... Author: mvdbeek m.vandenbeek@gmail.com Date: 2019-01-06 (Sun, 06 Jan 2019)

Changed paths: M lib/galaxy/webapps/galaxy/api/tools.py

Log Message: ----------- Pass in user, fixes dependency install for data manager tools

Commit: 83473f075d9e8cce04dc775d37b44b87baca9931 https://github.com/galaxyproject/galaxy/commit/83473f075d9e8cce04dc775d37b44... Author: mvdbeek m.vandenbeek@gmail.com Date: 2019-01-06 (Sun, 06 Jan 2019)

Changed paths: M test/docker/base/Dockerfile M test/docker/base/run_test_wrapper.sh R test/docker/base/start_mysql.sh

Log Message: ----------- Update testing docker image; drop mysql tests, add singularity

Commit: 6b25cace916de7a694b0e83ee640d7170c24cd10 https://github.com/galaxyproject/galaxy/commit/6b25cace916de7a694b0e83ee640d... Author: mvdbeek m.vandenbeek@gmail.com Date: 2019-01-06 (Sun, 06 Jan 2019)

Changed paths: M lib/galaxy/tools/deps/__init__.py

Log Message: ----------- Do run through build_mulled resolver if install is set

Commit: 0d86c9098c032742b091d4691634ada81da980f0 https://github.com/galaxyproject/galaxy/commit/0d86c9098c032742b091d4691634a... Author: mvdbeek m.vandenbeek@gmail.com Date: 2019-01-06 (Sun, 06 Jan 2019)

Changed paths: M lib/galaxy/tools/deps/__init__.py

Log Message: ----------- Make NullDependencyManager a class with empty non-container dependencies

Commit: 13592e5e85195cb0c457457fb1a350fa8df213d4 https://github.com/galaxyproject/galaxy/commit/13592e5e85195cb0c457457fb1a35... Author: mvdbeek m.vandenbeek@gmail.com Date: 2019-01-06 (Sun, 06 Jan 2019)

Changed paths: M lib/galaxy/tools/deps/container_resolvers/mulled.py

Log Message: ----------- Fix __str__ for BuildSingularityContainerResolver

Commit: ccb8429a84e8d4a63f57e320510b5de2524eb5e6 https://github.com/galaxyproject/galaxy/commit/ccb8429a84e8d4a63f57e320510b5... Author: mvdbeek m.vandenbeek@gmail.com Date: 2019-01-06 (Sun, 06 Jan 2019)

Changed paths: M lib/galaxy/tools/deps/mulled/mulled_build.py

Log Message: ----------- Download a binary that works on OSX

Commit: 4ef3460c041f210b0c0513a3786b186bac7a05e9 https://github.com/galaxyproject/galaxy/commit/4ef3460c041f210b0c0513a3786b1... Author: mvdbeek m.vandenbeek@gmail.com Date: 2019-01-06 (Sun, 06 Jan 2019)

Changed paths: M lib/galaxy/tools/deps/__init__.py

Log Message: ----------- DependencyManager lint fix

Commit: ac5e7d994912b292fb3d3464e4e5e58859070bc9 https://github.com/galaxyproject/galaxy/commit/ac5e7d994912b292fb3d3464e4e5e... Author: mvdbeek m.vandenbeek@gmail.com Date: 2019-01-06 (Sun, 06 Jan 2019)

Changed paths: M lib/galaxy/config.py M lib/galaxy/tools/deps/container_resolvers/mulled.py

Log Message: ----------- Make `resolver` methods respect enabled_container_types

Commit: 62863e8991728a1fe4b92cf42cd9d1e825ff1a02 https://github.com/galaxyproject/galaxy/commit/62863e8991728a1fe4b92cf42cd9d... Author: mvdbeek m.vandenbeek@gmail.com Date: 2019-01-06 (Sun, 06 Jan 2019)

Changed paths: M lib/galaxy/tools/deps/mulled/mulled_build.py

Log Message: ----------- Don't fail if build exists and also don't remove build dir if it already exists

Commit: 4a307ac5bea000d097e8488017f437e678a97a7f https://github.com/galaxyproject/galaxy/commit/4a307ac5bea000d097e8488017f43... Author: mvdbeek m.vandenbeek@gmail.com Date: 2019-01-06 (Sun, 06 Jan 2019)

Changed paths: M lib/galaxy/tools/deps/container_resolvers/explicit.py M lib/galaxy/tools/deps/containers.py

Log Message: ----------- Add ExplicitSingularityContainerResolver

Commit: a6a186a64251f206294f2fd3416fb08db4234f47 https://github.com/galaxyproject/galaxy/commit/a6a186a64251f206294f2fd3416fb... Author: mvdbeek m.vandenbeek@gmail.com Date: 2019-01-06 (Sun, 06 Jan 2019)

Changed paths: M lib/galaxy/tools/deps/requirements.py

Log Message: ----------- Make containers list, map can only be iterated once

Commit: 44d73f72c8967b114114d662ddb42098514026ee https://github.com/galaxyproject/galaxy/commit/44d73f72c8967b114114d662ddb42... Author: mvdbeek m.vandenbeek@gmail.com Date: 2019-01-06 (Sun, 06 Jan 2019)

Changed paths: M run_tests.sh M test/docker/base/Dockerfile M test/docker/base/run_test_wrapper.sh

Log Message: ----------- Update Dockefile and run_test_wrapper.sh

We use the Galaxy users' home dir for HOME. Otherwise os.environ.get('HOME') would return '/home/galaxy', but jobs run would see /galaxy.

Commit: c0b63a18c7a2fa7d7fb45ffbddfcef5aa4c00c67 https://github.com/galaxyproject/galaxy/commit/c0b63a18c7a2fa7d7fb45ffbddfce... Author: mvdbeek m.vandenbeek@gmail.com Date: 2019-01-06 (Sun, 06 Jan 2019)

Changed paths: M test/functional/tools/job_environment_default.xml M test/functional/tools/job_environment_default_legacy.xml M test/integration/test_containerized_jobs.py

Log Message: ----------- Fix container integration tests

Commit: a0bd7072adf7f03a82adfddf3216b15ce7105c87 https://github.com/galaxyproject/galaxy/commit/a0bd7072adf7f03a82adfddf3216b... Author: mvdbeek m.vandenbeek@gmail.com Date: 2019-01-06 (Sun, 06 Jan 2019)

Changed paths: M lib/galaxy/tools/deps/container_resolvers/mulled.py

Log Message: ----------- Use bash for mulled ContainerDescriptions

The base mulled container contains bash, and unfortunately bashisms such as <(cat bla) are very common in widely used Galaxy wrappers. So I think it makes sense to default to bash here.

Commit: 99a0ab03e90d2f9355c130403b1a0f5cb1ca5706 https://github.com/galaxyproject/galaxy/commit/99a0ab03e90d2f9355c130403b1a0... Author: mvdbeek m.vandenbeek@gmail.com Date: 2019-01-06 (Sun, 06 Jan 2019)

Changed paths: M run_tests.sh

Log Message: ----------- Temporarily test from mvdbeek/testing-base

Commit: a056f1746069a38b43bd0cc62bbe12d96aaa5145 https://github.com/galaxyproject/galaxy/commit/a056f1746069a38b43bd0cc62bbe1... Author: mvdbeek m.vandenbeek@gmail.com Date: 2019-01-06 (Sun, 06 Jan 2019)

Changed paths: M config/galaxy.yml.sample M doc/source/admin/galaxy_options.rst M lib/galaxy/config.py M lib/galaxy/tools/deps/dependencies.py M lib/galaxy/webapps/galaxy/config_schema.yml

Log Message: ----------- Document and use mulled_channels option

Commit: 93622f026bacef4328e2415aad72f521d92192c9 https://github.com/galaxyproject/galaxy/commit/93622f026bacef4328e2415aad72f... Author: mvdbeek m.vandenbeek@gmail.com Date: 2019-01-06 (Sun, 06 Jan 2019)

Changed paths: M lib/galaxy/tools/deps/container_resolvers/mulled.py

Log Message: ----------- Only parse build if build in name

Otherwise this fails with ``` Traceback (most recent call last): File "lib/galaxy/web/framework/decorators.py", line 277, in decorator rval = func(self, trans, *args, **kwargs) File "lib/galaxy/web/framework/decorators.py", line 101, in decorator return func(self, trans, *args, **kwargs) File "lib/galaxy/webapps/galaxy/api/tools.py", line 239, in install_dependencies tool._view.install_dependencies(tool.requirements, **kwds) File "lib/galaxy/tools/deps/views.py", line 107, in install_dependencies return self._dependency_manager._requirements_to_dependencies_dict(requirements, **kwds) File "lib/galaxy/tools/deps/__init__.py", line 190, in _requirements_to_dependencies_dict **kwds) File "lib/galaxy/tools/deps/container_resolvers/mulled.py", line 343, in resolve name = targets_to_mulled_name(targets=targets, hash_func=self.hash_func, namespace=self.namespace) File "lib/galaxy/tools/deps/container_resolvers/mulled.py", line 278, in targets_to_mulled_name version, build = split_tag(tag) File "lib/galaxy/tools/deps/mulled/util.py", line 69, in split_tag build = tag.split('--', 1)[1] IndexError: list index out of range ``` if a single-target image was build with a build_mulled resolver.

Commit: b3af5176d35b0a1e818975c263018fb7ea800bcd https://github.com/galaxyproject/galaxy/commit/b3af5176d35b0a1e818975c263018... Author: mvdbeek m.vandenbeek@gmail.com Date: 2019-01-06 (Sun, 06 Jan 2019)

Changed paths: M lib/galaxy/tools/deps/mulled/invfile.lua M lib/galaxy/tools/deps/mulled/mulled_build.py

Log Message: ----------- Replace deprecated singularity import with build

And upgrade singularity build image to 2.4.6 (latest on biocontainers). Overall this is necessary because singularity import 2.3X doesn't work behind proxies. The change from `Singularity` to `Singularity.def` is necessary because the script uses the `file` command if the Singularity file doesn't end in .def or is not exactly Singularity (it is `/import/Singularity` in our case). `file` isn't available in the biocontainers image.

Commit: 5f389dd11ea3da935b382871305bf0a7c1e2d3d4 https://github.com/galaxyproject/galaxy/commit/5f389dd11ea3da935b382871305bf... Author: Nicola Soranzo nicola.soranzo@gmail.com Date: 2019-01-06 (Sun, 06 Jan 2019)

Changed paths: M config/container_resolvers_conf.xml.sample M config/galaxy.yml.sample M doc/source/admin/galaxy_options.rst M lib/galaxy/webapps/galaxy/config_schema.yml

Log Message: ----------- Fix spelling in resolver docs

Co-Authored-By: mvdbeek m.vandenbeek@gmail.com

Commit: 0343d3d87f438bdb669959bc5141030169cc01ba https://github.com/galaxyproject/galaxy/commit/0343d3d87f438bdb669959bc51410... Author: mvdbeek m.vandenbeek@gmail.com Date: 2019-01-06 (Sun, 06 Jan 2019)

Changed paths: M lib/galaxy/tools/deps/mulled/util.py

Log Message: ----------- Cache requests to mulled registry for 5 minutes

When going through the resolvers we can easily exceed the allowed API request rate.

Commit: 9051c10cba8360bc5a4ee199ff01657c3fda3b20 https://github.com/galaxyproject/galaxy/commit/9051c10cba8360bc5a4ee199ff016... Author: mvdbeek m.vandenbeek@gmail.com Date: 2019-01-06 (Sun, 06 Jan 2019)

Changed paths: M run_tests.sh

Log Message: ----------- More docker debug

Commit: a03f8bdffd272e0195a6bf88931fb17b6e428d13 https://github.com/galaxyproject/galaxy/commit/a03f8bdffd272e0195a6bf88931fb... Author: mvdbeek m.vandenbeek@gmail.com Date: 2019-01-06 (Sun, 06 Jan 2019)

Changed paths: M run_tests.sh M test/docker/base/run_test_wrapper.sh

Log Message: ----------- Test singularity exec as Galaxy user

Commit: 658816264a8e84bacfdf83e9c9029338b2e1f85d https://github.com/galaxyproject/galaxy/commit/658816264a8e84bacfdf83e9c9029... Author: mvdbeek m.vandenbeek@gmail.com Date: 2019-01-06 (Sun, 06 Jan 2019)

Changed paths: M lib/galaxy/tools/deps/singularity_util.py

Log Message: ----------- Explicitly pass home dir to singularity command

Commit: 06f5abe1bc16eccf750baf7a754d48dfdedaaf5a https://github.com/galaxyproject/galaxy/commit/06f5abe1bc16eccf750baf7a754d4... Author: mvdbeek m.vandenbeek@gmail.com Date: 2019-01-06 (Sun, 06 Jan 2019)

Changed paths: M test/docker/base/Dockerfile

Log Message: ----------- Install singularity 3.0.1 from source

Commit: bed8b54af604a2caf9161a5265953c90ae5a6c8a https://github.com/galaxyproject/galaxy/commit/bed8b54af604a2caf9161a5265953... Author: mvdbeek m.vandenbeek@gmail.com Date: 2019-01-06 (Sun, 06 Jan 2019)

Changed paths: M .ci/jenkins/integration-py3/run_tests.sh M .ci/jenkins/integration/run_tests.sh M run_tests.sh M test/docker/base/run_test_wrapper.sh

Log Message: ----------- Only run integration tests with --privileged

Commit: 9517871b4af27c9647436d84ea2bfe76bb242ca8 https://github.com/galaxyproject/galaxy/commit/9517871b4af27c9647436d84ea2bf... Author: mvdbeek m.vandenbeek@gmail.com Date: 2019-01-06 (Sun, 06 Jan 2019)

Changed paths: M run_tests.sh

Log Message: ----------- Bump image to use

Commit: 6b3af3b2ffa8d90946a6b2d9b803779df35e19fd https://github.com/galaxyproject/galaxy/commit/6b3af3b2ffa8d90946a6b2d9b8037... Author: mvdbeek m.vandenbeek@gmail.com Date: 2019-01-06 (Sun, 06 Jan 2019)

Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/command_factory.py

Log Message: ----------- Make dependency_shell_commands a property

If we know we use a container we don't need to pass through the dependency resolver.

Commit: 8a34101089085c6203cdd11468de4a0866922534 https://github.com/galaxyproject/galaxy/commit/8a34101089085c6203cdd11468de4... Author: mvdbeek m.vandenbeek@gmail.com Date: 2019-01-06 (Sun, 06 Jan 2019)

Changed paths: M config/container_resolvers_conf.xml.sample M lib/galaxy/tools/deps/container_resolvers/mulled.py

Log Message: ----------- Introduce `auto_install` ContainerResolver flag

If set to True (thats's the default), the container resolvers that can pull or build images will do that, if they are enabled. You can set this to `False` and instead pass through the DependencyManager to use these resolvers to pull or build images.

Commit: 128af8f9ba21a56f3021791affc2a539f74fc1fb https://github.com/galaxyproject/galaxy/commit/128af8f9ba21a56f3021791affc2a... Author: John Chilton jmchilton@gmail.com Date: 2019-01-06 (Sun, 06 Jan 2019)

Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js

Log Message: ----------- Merge pull request #7157 from guerler/workflow_runtime_default_value

Do not use default values for runtime values in workflow execution form

Commit: 7ca7394c7d1e19ec5a42dae526b5bc20f33c3ac9 https://github.com/galaxyproject/galaxy/commit/7ca7394c7d1e19ec5a42dae526b5b... Author: Nicola Soranzo nicola.soranzo@earlham.ac.uk Date: 2019-01-07 (Mon, 07 Jan 2019)

Changed paths: M config/galaxy.yml.sample M config/tool_shed.yml.sample M doc/source/admin/galaxy_options.rst M lib/galaxy/webapps/galaxy/config_schema.yml M lib/galaxy/webapps/tool_shed/config_schema.yml

Log Message: ----------- Document ``message_box_class`` option

Reported by @vazovn

Commit: 952af6b6fde107c9769f3393beb44032f36e9827 https://github.com/galaxyproject/galaxy/commit/952af6b6fde107c9769f3393beb44... Author: Dannon dannon.baker@gmail.com Date: 2019-01-07 (Mon, 07 Jan 2019)

Changed paths: M config/galaxy.yml.sample M config/tool_shed.yml.sample M doc/source/admin/galaxy_options.rst M lib/galaxy/webapps/galaxy/config_schema.yml M lib/galaxy/webapps/tool_shed/config_schema.yml

Log Message: ----------- Merge pull request #7174 from nsoranzo/message_box_class

Document ``message_box_class`` option

Commit: 03b363a1ef92e696ba07050e2a4832c15c8a8964 https://github.com/galaxyproject/galaxy/commit/03b363a1ef92e696ba07050e2a483... Author: John Chilton jmchilton@gmail.com Date: 2019-01-07 (Mon, 07 Jan 2019)

Changed paths: M .ci/jenkins/integration-py3/run_tests.sh M .ci/jenkins/integration/run_tests.sh M config/container_resolvers_conf.xml.sample M config/galaxy.yml.sample M doc/source/admin/galaxy_options.rst M lib/galaxy/config.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/command_factory.py M lib/galaxy/jobs/rule_helper.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/tools/deps/__init__.py A lib/galaxy/tools/deps/container_classes.py M lib/galaxy/tools/deps/container_resolvers/__init__.py M lib/galaxy/tools/deps/container_resolvers/explicit.py M lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/tools/deps/containers.py M lib/galaxy/tools/deps/dependencies.py M lib/galaxy/tools/deps/dockerfiles.py M lib/galaxy/tools/deps/mulled/invfile.lua M lib/galaxy/tools/deps/mulled/mulled_build.py M lib/galaxy/tools/deps/mulled/util.py M lib/galaxy/tools/deps/requirements.py M lib/galaxy/tools/deps/resolvers/__init__.py M lib/galaxy/tools/deps/singularity_util.py M lib/galaxy/tools/deps/views.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/config_schema.yml M run_tests.sh M test/base/integration_util.py M test/docker/base/Dockerfile M test/docker/base/run_test_wrapper.sh R test/docker/base/start_mysql.sh M test/functional/tools/job_environment_default.xml M test/functional/tools/job_environment_default_legacy.xml A test/integration/singularity_job_conf.xml A test/integration/test_containerized_jobs.py R test/integration/test_dockerized_jobs.py M test/integration/test_resolvers.py

Log Message: ----------- Merge pull request #7125 from mvdbeek/MulledSingularityContainerResolver

Use singularity build / exec with biocontainers

Commit: 07ed1a90df388a348d06a285a57683ef08bf4c25 https://github.com/galaxyproject/galaxy/commit/07ed1a90df388a348d06a285a5768... Author: John Chilton jmchilton@gmail.com Date: 2019-01-07 (Mon, 07 Jan 2019)

Changed paths: M lib/galaxy/version.py

Log Message: ----------- Update version to 19.01.rc1

Commit: 998eb858560b075da3c0ef5acc2b079743c09162 https://github.com/galaxyproject/galaxy/commit/998eb858560b075da3c0ef5acc2b0... Author: Dannon Baker dannon.baker@gmail.com Date: 2019-01-07 (Mon, 07 Jan 2019)

Changed paths: M lib/galaxy/webapps/galaxy/controllers/page.py

Log Message: ----------- Fix hda accessibility check in Page's renderForSave name fetching

Commit: 2a17860fad4c3ee7f40ed4d85cc3854407a8c3d7 https://github.com/galaxyproject/galaxy/commit/2a17860fad4c3ee7f40ed4d85cc38... Author: Dannon dannon.baker@gmail.com Date: 2019-01-07 (Mon, 07 Jan 2019)

Changed paths: M lib/galaxy/jobs/runners/slurm.py

Log Message: ----------- Merge pull request #7128 from natefoo/slurm-trace-log-fix

[18.05] Fix for use of `log.trace` in Slurm runner

Commit: 37a9f2bcea99ea55f7b36b94aa481558702ca897 https://github.com/galaxyproject/galaxy/commit/37a9f2bcea99ea55f7b36b94aa481... Author: Nate Coraor nate@bx.psu.edu Date: 2019-01-07 (Mon, 07 Jan 2019)

Changed paths: M doc/Makefile M doc/source/admin/config_logging.rst

Log Message: ----------- Update logging config docs:

- The example for split file logging was invalid (referenced the nonexistent "generic" formatter)

- Switch YAML dicts from 4- to 2-space indent to match the indentation style in galaxy.yml.sample

- Document setting the message format with the YAML config

- Reword a few things to hopefully be a bit clearer

Commit: 36a9f3bc4358f4382f152d0aebfef3b497ed0a4b https://github.com/galaxyproject/galaxy/commit/36a9f3bc4358f4382f152d0aebfef... Author: Nicola Soranzo nicola.soranzo@gmail.com Date: 2019-01-08 (Tue, 08 Jan 2019)

Changed paths: M lib/galaxy/version.py

Log Message: ----------- Merge pull request #7176 from jmchilton/version-19.01

Update version to 19.01.rc1

Commit: 3ecb0a1a08d4a3e8370c34596e066972ec2cd642 https://github.com/galaxyproject/galaxy/commit/3ecb0a1a08d4a3e8370c34596e066... Author: John Chilton jmchilton@gmail.com Date: 2019-01-08 (Tue, 08 Jan 2019)

Changed paths: M test/selenium_tests/test_workflow_run.py

Log Message: ----------- Fix workflow parameter test case?

Commit: 240633b3739ca4f9b2159940f0d285c7ecaed45c https://github.com/galaxyproject/galaxy/commit/240633b3739ca4f9b2159940f0d28... Author: Nicola Soranzo nicola.soranzo@gmail.com Date: 2019-01-08 (Tue, 08 Jan 2019)

Changed paths: M test/selenium_tests/test_workflow_run.py

Log Message: ----------- Comment out unused line

Commit: 7fb4ba8f3c35066e7213a22f215d062b674aef49 https://github.com/galaxyproject/galaxy/commit/7fb4ba8f3c35066e7213a22f215d0... Author: Simon Bray 32272674+simonbray@users.noreply.github.com Date: 2019-01-08 (Tue, 08 Jan 2019)

Changed paths: M config/datatypes_conf.xml.sample

Log Message: ----------- adding itp and mdp datatypes (for gromacs)

Resubmitting an old PR which somehow got lost: https://github.com/galaxyproject/galaxy/pull/6812/

Commit: f6b978be8cce63bc954e0457e7c0d681617ec43c https://github.com/galaxyproject/galaxy/commit/f6b978be8cce63bc954e0457e7c0d... Author: Martin Cech marten@bx.psu.edu Date: 2019-01-08 (Tue, 08 Jan 2019)

Changed paths: M lib/galaxy/webapps/tool_shed/controllers/repository.py M test/shed_functional/functional/test_0000_basic_repository_features.py M test/shed_functional/functional/test_0420_citable_urls_for_repositories.py

Log Message: ----------- prevent XSS on toolshed when browsing repo changeset

fix invalid changeset ts test, fix flake8

Revert "fix invalid changeset ts test, fix flake8"

This reverts commit 84864fe82a9f3b9ffa1cd5ef272f979e867e2002.

tweak the invalid changeset test and add a new one

Commit: 6b0c214875a9f645ea26db354c21e7b73a0d538c https://github.com/galaxyproject/galaxy/commit/6b0c214875a9f645ea26db354c21e... Author: Aysam Guerler aysam.guerler@gmail.com Date: 2019-01-08 (Tue, 08 Jan 2019)

Changed paths: M test/selenium_tests/test_workflow_run.py

Log Message: ----------- Merge pull request #7188 from jmchilton/fix_wf_parameters

[19.01] Fix workflow parameter test case?

Commit: 2e82b7f8c03bb94d424618f812ff943b3ec22fc3 https://github.com/galaxyproject/galaxy/commit/2e82b7f8c03bb94d424618f812ff9... Author: Martin Cech marten@bx.psu.edu Date: 2019-01-08 (Tue, 08 Jan 2019)

Changed paths: M lib/galaxy/webapps/galaxy/api/library_datasets.py

Log Message: ----------- fix library dataset permission API

broken in refactoring

Commit: 5e3ebb13c0ad37fe499eb20a644a2821e6ac109d https://github.com/galaxyproject/galaxy/commit/5e3ebb13c0ad37fe499eb20a644a2... Author: Martin Cech marten@bx.psu.edu Date: 2019-01-08 (Tue, 08 Jan 2019)

Changed paths: M lib/galaxy/webapps/galaxy/api/library_datasets.py

Log Message: ----------- fix import ordering, thanks @nsoranzo

Commit: 29abf8f437af63681a5170e590582a10bf5a173a https://github.com/galaxyproject/galaxy/commit/29abf8f437af63681a5170e590582... Author: Martin Cech marten@bx.psu.edu Date: 2019-01-08 (Tue, 08 Jan 2019)

Changed paths: M lib/galaxy/managers/library_datasets.py M lib/galaxy/webapps/galaxy/api/library_datasets.py

Log Message: ----------- refactor approach so the method is inherited to ldda

Commit: 193f5eae6ea33053d70e57268d832635eb873945 https://github.com/galaxyproject/galaxy/commit/193f5eae6ea33053d70e57268d832... Author: Martin Cech marten@bx.psu.edu Date: 2019-01-08 (Tue, 08 Jan 2019)

Changed paths: M lib/galaxy/webapps/galaxy/api/datasets.py

Log Message: ----------- call the method through the proper manager

Commit: 6256ac0f119cbe9b3f5b49d80647c89f4c8baa3a https://github.com/galaxyproject/galaxy/commit/6256ac0f119cbe9b3f5b49d80647c... Author: John Chilton jmchilton@gmail.com Date: 2019-01-09 (Wed, 09 Jan 2019)

Changed paths: M lib/galaxy/managers/library_datasets.py M lib/galaxy/webapps/galaxy/api/datasets.py M lib/galaxy/webapps/galaxy/api/library_datasets.py

Log Message: ----------- Merge pull request #7190 from martenson/fix-permission-api

[18.09] fix library dataset permission API

Commit: ce1a1ee778df99359c291bd53cda6fe0485cc8b5 https://github.com/galaxyproject/galaxy/commit/ce1a1ee778df99359c291bd53cda6... Author: Dannon dannon.baker@gmail.com Date: 2019-01-09 (Wed, 09 Jan 2019)

Changed paths: M lib/galaxy/webapps/tool_shed/controllers/repository.py M test/shed_functional/functional/test_0000_basic_repository_features.py M test/shed_functional/functional/test_0420_citable_urls_for_repositories.py

Log Message: ----------- Merge pull request #7180 from martenson/security-ts

[18.09] Prevent XSS on toolshed when browsing repo changeset

Commit: 79672df45221e4417d2c363bb262c19a2eb48b1f https://github.com/galaxyproject/galaxy/commit/79672df45221e4417d2c363bb262c... Author: Nate Coraor nate@bx.psu.edu Date: 2019-01-09 (Wed, 09 Jan 2019)

Changed paths: M config/job_conf.xml.sample_advanced M doc/source/admin/scaling.md

Log Message: ----------- Update documentation for handler assignment method configurability and remove some legacy stuff.

Commit: e9773f17335bea2d9106aa364d29f1f53454c883 https://github.com/galaxyproject/galaxy/commit/e9773f17335bea2d9106aa364d29f... Author: Dannon Baker dannon.baker@gmail.com Date: 2019-01-09 (Wed, 09 Jan 2019)

Changed paths: M doc/source/admin/config_logging.rst

Log Message: ----------- Minor spello

Commit: 35c60489e8d52a47e82ae4462dfd7af5ced26f2b https://github.com/galaxyproject/galaxy/commit/35c60489e8d52a47e82ae4462dfd7... Author: Nate Coraor nate@bx.psu.edu Date: 2019-01-09 (Wed, 09 Jan 2019)

Changed paths: M doc/source/admin/apache.md M doc/source/admin/nginx.md

Log Message: ----------- Fixed link to proxy_package_layout in proxy docs

Commit: c4ad6b9e4b3e80a1aa9d5f16712e3133b224fd02 https://github.com/galaxyproject/galaxy/commit/c4ad6b9e4b3e80a1aa9d5f16712e3... Author: Nicola Soranzo nicola.soranzo@earlham.ac.uk Date: 2019-01-09 (Wed, 09 Jan 2019)

Changed paths: M lib/galaxy/jobs/runners/slurm.py

Log Message: ----------- Merge branch 'release_18.05' into release_18.09

Commit: d16a2348c5dcc6ef764e0a45086c5a84262a1862 https://github.com/galaxyproject/galaxy/commit/d16a2348c5dcc6ef764e0a45086c5... Author: Nicola Soranzo nicola.soranzo@earlham.ac.uk Date: 2019-01-09 (Wed, 09 Jan 2019)

Changed paths: M lib/galaxy/jobs/runners/slurm.py M lib/galaxy/managers/library_datasets.py M lib/galaxy/webapps/galaxy/api/datasets.py M lib/galaxy/webapps/galaxy/api/library_datasets.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M test/shed_functional/functional/test_0000_basic_repository_features.py M test/shed_functional/functional/test_0420_citable_urls_for_repositories.py

Log Message: ----------- Merge branch 'release_18.09' into release_19.01

Commit: 0f04e4f045a53a947f0c07df469a96f99131248a https://github.com/galaxyproject/galaxy/commit/0f04e4f045a53a947f0c07df469a9... Author: Dannon Baker dannon.baker@gmail.com Date: 2019-01-09 (Wed, 09 Jan 2019)

Changed paths: M client/gulpfile.js M client/package.json M client/yarn.lock

Log Message: ----------- Re-enable gulp task transpiling/staging some galaxy code, pending a more thorough review of external accessors. This fixes (at minimum) IE launching.

Commit: 6a983284e4aaf3ec8f9f46ef05f5b63a501b6671 https://github.com/galaxyproject/galaxy/commit/6a983284e4aaf3ec8f9f46ef05f5b... Author: Dannon Baker dannon.baker@gmail.com Date: 2019-01-09 (Wed, 09 Jan 2019)

Changed paths: M client/gulpfile.js

Log Message: ----------- Uglify staged scripts used by external accessors.

Commit: c7703a531d8ad0ca802c35026902fe9d842c8332 https://github.com/galaxyproject/galaxy/commit/c7703a531d8ad0ca802c35026902f... Author: Dannon Baker dannon.baker@gmail.com Date: 2019-01-09 (Wed, 09 Jan 2019)

Changed paths: M client/gulpfile.js

Log Message: ----------- Leave TODO for removing these particular tasks prior to 19.05

Commit: ae565883ce9fef6e56baf2b032c23cf2a8698cd4 https://github.com/galaxyproject/galaxy/commit/ae565883ce9fef6e56baf2b032c23... Author: Dannon Baker dannon.baker@gmail.com Date: 2019-01-09 (Wed, 09 Jan 2019)

Changed paths: A static/style/largespinner.gif

Log Message: ----------- Re-stage largespinner, since there are external accessors...

Commit: 75bf2bcb320ccbc9e40bbc8681809365736ba098 https://github.com/galaxyproject/galaxy/commit/75bf2bcb320ccbc9e40bbc8681809... Author: Dannon Baker dannon.baker@gmail.com Date: 2019-01-09 (Wed, 09 Jan 2019)

Changed paths: M client/galaxy/scripts/galaxy.interactive_environments.js M client/galaxy/style/scss/base.scss R static/style/largespinner.gif

Log Message: ----------- Since base.css (packed) is available, use those styles instead of staging manually.

Commit: eea4aee8ccc1cc1a92ec65163b85e5f87bb68393 https://github.com/galaxyproject/galaxy/commit/eea4aee8ccc1cc1a92ec65163b85e... Author: James Taylor james@jamestaylor.org Date: 2019-01-09 (Wed, 09 Jan 2019)

Changed paths: M client/galaxy/scripts/galaxy.interactive_environments.js M client/galaxy/style/scss/base.scss M client/gulpfile.js M client/package.json M client/yarn.lock

Log Message: ----------- Merge pull request #7196 from dannon/restage_scripts

[19.01] Re-enable script staging

Commit: c960924e892c44d91436a618bd8169a60ef74142 https://github.com/galaxyproject/galaxy/commit/c960924e892c44d91436a618bd816... Author: mvdbeek m.vandenbeek@gmail.com Date: 2019-01-10 (Thu, 10 Jan 2019)

Changed paths: M lib/galaxy/tools/verify/interactor.py

Log Message: ----------- Allow passing test_history in verify_tool func

Commit: 4b920afba2e0b2ad24bbe00511a51297e60a2f06 https://github.com/galaxyproject/galaxy/commit/4b920afba2e0b2ad24bbe00511a51... Author: mvdbeek m.vandenbeek@gmail.com Date: 2019-01-10 (Thu, 10 Jan 2019)

Changed paths: M lib/galaxy/tools/verify/interactor.py A test/api/test_galaxy_interactor.py

Log Message: ----------- Make interactor changes backwards compatible

Commit: 338020f2a5203afad239e3a1b6e0becf7edad22b https://github.com/galaxyproject/galaxy/commit/338020f2a5203afad239e3a1b6e0b... Author: mvdbeek m.vandenbeek@gmail.com Date: 2019-01-10 (Thu, 10 Jan 2019)

Changed paths: M lib/galaxy/webapps/tool_shed/controllers/repository.py

Log Message: ----------- Fix error in view_tool_metadata (https://sentry.galaxyproject.org/sentry/toolshed/issues/294272/)

Commit: 141c2a1ef37ae29b4c6e481337c6efd3a41fcd1d https://github.com/galaxyproject/galaxy/commit/141c2a1ef37ae29b4c6e481337c6e... Author: Nicola Soranzo nicola.soranzo@earlham.ac.uk Date: 2019-01-10 (Thu, 10 Jan 2019)

Changed paths: M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/tool_shed/tools/tool_validator.py

Log Message: ----------- Fix indentation

Broken in commit cf2645f9a658c5e122fea0309bf73a1f64590c39 .

Commit: 72bb23fc2df3e00d55e59259d4a995e5ad939eb8 https://github.com/galaxyproject/galaxy/commit/72bb23fc2df3e00d55e59259d4a99... Author: Dannon dannon.baker@gmail.com Date: 2019-01-10 (Thu, 10 Jan 2019)

Changed paths: M lib/galaxy/tools/verify/interactor.py A test/api/test_galaxy_interactor.py

Log Message: ----------- Merge pull request #7199 from mvdbeek/backport_interactor_improvements

[19.01] Backport #7167 - interactor improvements

Commit: c17c20b8cf7c74dc7ae225a812f4faaa6fc8f40a https://github.com/galaxyproject/galaxy/commit/c17c20b8cf7c74dc7ae225a812f4f... Author: Martin Cech marten@bx.psu.edu Date: 2019-01-10 (Thu, 10 Jan 2019)

Changed paths: M lib/galaxy/webapps/galaxy/controllers/page.py

Log Message: ----------- Merge pull request #7181 from dannon/page_save_history_fix

[18.05] Fix hda accessibility check in Page's renderForSave name fetching

Commit: a7ae52159712f61b3ac65cd194126b274308fa23 https://github.com/galaxyproject/galaxy/commit/a7ae52159712f61b3ac65cd194126... Author: Martin Cech marten@bx.psu.edu Date: 2019-01-10 (Thu, 10 Jan 2019)

Changed paths: M lib/galaxy/webapps/galaxy/controllers/page.py

Log Message: ----------- Merge branch 'release_18.05' into release_18.09

Commit: 2aa8ed4efbcf1224d335593e9d64966b8b173bac https://github.com/galaxyproject/galaxy/commit/2aa8ed4efbcf1224d335593e9d649... Author: Anthony Bretaudeau anthony.bretaudeau@inria.fr Date: 2019-01-11 (Fri, 11 Jan 2019)

Changed paths: M lib/galaxy/webapps/galaxy/api/library_contents.py

Log Message: ----------- fix tag_using_filenames not converted to bool

Commit: 105a1d8a61ef6ec79992017d2cff3a18decab113 https://github.com/galaxyproject/galaxy/commit/105a1d8a61ef6ec79992017d2cff3... Author: Dannon dannon.baker@gmail.com Date: 2019-01-11 (Fri, 11 Jan 2019)

Changed paths: M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/tool_shed/tools/tool_validator.py

Log Message: ----------- Merge pull request #7201 from mvdbeek/fix_view_metadata_error

[18.09] Fix error in view_tool_metadata

Commit: b6d5675f5da1e91aece2df4af5d037072e897185 https://github.com/galaxyproject/galaxy/commit/b6d5675f5da1e91aece2df4af5d03... Author: mvdbeek m.vandenbeek@gmail.com Date: 2019-01-15 (Tue, 15 Jan 2019)

Changed paths: M config/galaxy.yml.sample M config/reports.yml.sample M config/tool_shed.yml.sample M doc/source/admin/galaxy_options.rst M lib/galaxy/webapps/config_manage.py M lib/galaxy/webapps/galaxy/config_schema.yml

Log Message: ----------- Update galaxy.yml.sample for prefix config

Commit: af21a8fa58fcd6945786cc307a5a258775854fe5 https://github.com/galaxyproject/galaxy/commit/af21a8fa58fcd6945786cc307a5a2... Author: Nicola Soranzo nicola.soranzo@earlham.ac.uk Date: 2019-01-15 (Tue, 15 Jan 2019)

Changed paths: M lib/galaxy/webapps/galaxy/controllers/page.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/tool_shed/tools/tool_validator.py

Log Message: ----------- Merge branch 'release_18.09' into release_19.01

Commit: 3fa43dfecea37a5f56e3675afad0bd65d3196f56 https://github.com/galaxyproject/galaxy/commit/3fa43dfecea37a5f56e3675afad0b... Author: Dannon Baker dannon.baker@gmail.com Date: 2019-01-15 (Tue, 15 Jan 2019)

Changed paths: M client/galaxy/scripts/mvc/history/history-view-edit.js

Log Message: ----------- Swap to normal event bindings for multipanel drop. get(0) isn't great, but we'll overhaul this more in the future.

Commit: 7c13cdf006733182b4bfb07ced24df729600e670 https://github.com/galaxyproject/galaxy/commit/7c13cdf006733182b4bfb07ced24d... Author: John Chilton jmchilton@gmail.com Date: 2019-01-15 (Tue, 15 Jan 2019)

Changed paths: M client/galaxy/scripts/mvc/history/history-view-edit.js

Log Message: ----------- Merge pull request #7218 from dannon/fix_multipanel_drop

[19.01] Swap to normal event bindings for multipanel drag/drop.

Commit: 54aecb3f31812c86d370034cf557537780efbcdf https://github.com/galaxyproject/galaxy/commit/54aecb3f31812c86d370034cf5575... Author: mvdbeek m.vandenbeek@gmail.com Date: 2019-01-17 (Thu, 17 Jan 2019)

Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-manager.js M lib/galaxy/exceptions/__init__.py M lib/galaxy/managers/workflows.py M lib/galaxy/workflow/modules.py

Log Message: ----------- Properly deal with missing tools in subworkflows

If a subworkflow is missing tools the entire parent workflow couldn't be loaded into the editor, because we raised an exception. This is now only logged as an error. On the user side we now prevent running and saving such workflows by actually implementing the `get_errors` method for the SubWorkflowModule class.

This should fix https://github.com/galaxyproject/galaxy/issues/7140.

Commit: 6ff84684bd577ea4610d63213cc090b86d983aa8 https://github.com/galaxyproject/galaxy/commit/6ff84684bd577ea4610d63213cc09... Author: mvdbeek m.vandenbeek@gmail.com Date: 2019-01-17 (Thu, 17 Jan 2019)

Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/tool_shed/controllers/repository.py

Log Message: ----------- Fix displaying tool help images on python 3

Commit: ab8ea1ee40c2a7de3a7cc6e6aaafba95f451a6c6 https://github.com/galaxyproject/galaxy/commit/ab8ea1ee40c2a7de3a7cc6e6aaafb... Author: guerler aysam.guerler@gmail.com Date: 2019-01-17 (Thu, 17 Jan 2019)

Changed paths: M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/ui/ui-slider.js

Log Message: ----------- Add error listener for input elements, utilize to highlight numeric value range adjustments

Commit: 48c2807e2ebecf7fd01bd56e102ccaaa25947a29 https://github.com/galaxyproject/galaxy/commit/48c2807e2ebecf7fd01bd56e102cc... Author: guerler aysam.guerler@gmail.com Date: 2019-01-17 (Thu, 17 Jan 2019)

Changed paths: M client/galaxy/scripts/mvc/form/form-section.js

Log Message: ----------- Fix name of error handler helper function

Commit: d20c6f6d8c1cfdd677afa04ad70c10e11c7228f4 https://github.com/galaxyproject/galaxy/commit/d20c6f6d8c1cfdd677afa04ad70c1... Author: guerler aysam.guerler@gmail.com Date: 2019-01-17 (Thu, 17 Jan 2019)

Changed paths: M client/galaxy/scripts/mvc/form/form-section.js

Log Message: ----------- Remove unused default error message

Commit: ef02c60f792a8aeadcaa58d8e0a4ac71d65aa42b https://github.com/galaxyproject/galaxy/commit/ef02c60f792a8aeadcaa58d8e0a4a... Author: guerler aysam.guerler@gmail.com Date: 2019-01-17 (Thu, 17 Jan 2019)

Changed paths: M client/galaxy/scripts/mvc/ui/ui-slider.js

Log Message: ----------- Move local slider helper variables into score/statement

Commit: 8534ef5d5cef95bad2dbb882b8285a44deb0dca6 https://github.com/galaxyproject/galaxy/commit/8534ef5d5cef95bad2dbb882b8285... Author: guerler aysam.guerler@gmail.com Date: 2019-01-17 (Thu, 17 Jan 2019)

Changed paths: M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/ui/ui-slider.js

Log Message: ----------- Move field error binding to input element wrapper

Commit: 48811d4c0c79b5dfdba2e51471f71d9d9fa0b34e https://github.com/galaxyproject/galaxy/commit/48811d4c0c79b5dfdba2e51471f71... Author: guerler aysam.guerler@gmail.com Date: 2019-01-17 (Thu, 17 Jan 2019)

Changed paths: M client/galaxy/scripts/mvc/form/form-input.js

Log Message: ----------- Use listento caller to bind input element error listener

Commit: 97651462212b2a08a18b67b9fe2d731732b3d1c3 https://github.com/galaxyproject/galaxy/commit/97651462212b2a08a18b67b9fe2d7... Author: guerler aysam.guerler@gmail.com Date: 2019-01-17 (Thu, 17 Jan 2019)

Changed paths: M client/galaxy/scripts/mvc/ui/ui-slider.js

Log Message: ----------- Add additional validation to slider out-of-range error detection

Commit: b1b1d848d35816cfa344aeb687c78c7a0c93e66f https://github.com/galaxyproject/galaxy/commit/b1b1d848d35816cfa344aeb687c78... Author: mvdbeek m.vandenbeek@gmail.com Date: 2019-01-17 (Thu, 17 Jan 2019)

Changed paths: M lib/galaxy/workflow/modules.py

Log Message: ----------- Fix loading subworkflows

Commit: 24f97f6917da606f8b9c1fc1fb4faef5c54f1933 https://github.com/galaxyproject/galaxy/commit/24f97f6917da606f8b9c1fc1fb4fa... Author: mvdbeek m.vandenbeek@gmail.com Date: 2019-01-17 (Thu, 17 Jan 2019)

Changed paths: M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/genetics.py M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/webapps/galaxy/api/datasets.py M lib/galaxy/webapps/galaxy/api/library_datasets.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/root.py

Log Message: ----------- Open files in binary mode when sending data

Commit: 7a9422600c76ad49515844d582bf6d5f507076e8 https://github.com/galaxyproject/galaxy/commit/7a9422600c76ad49515844d582bf6... Author: Nicola Soranzo nicola.soranzo@earlham.ac.uk Date: 2019-01-17 (Thu, 17 Jan 2019)

Changed paths: M test/api/test_galaxy_interactor.py

Log Message: ----------- Fix ``GalaxyInteractorBackwardCompatTestCase.test_local_test_data_download`` API test

Broken in commit bf851269c30996876c0614e7a5b57da495c44ac9 .

Commit: d460d218ad898242046c2422aa211fe6a4830462 https://github.com/galaxyproject/galaxy/commit/d460d218ad898242046c2422aa211... Author: Dannon dannon.baker@gmail.com Date: 2019-01-17 (Thu, 17 Jan 2019)

Changed paths: M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/ui/ui-slider.js

Log Message: ----------- Merge pull request #7229 from mvdbeek/backport_sliding_validator

[19.01] Backport #7183 input element listener

Commit: ed6011755cf7cf5c7232bd43365dd01ab0b12af5 https://github.com/galaxyproject/galaxy/commit/ed6011755cf7cf5c7232bd43365dd... Author: John Chilton jmchilton@gmail.com Date: 2019-01-17 (Thu, 17 Jan 2019)

Changed paths: M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/genetics.py M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/webapps/galaxy/api/datasets.py M lib/galaxy/webapps/galaxy/api/library_datasets.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M test/api/test_galaxy_interactor.py

Log Message: ----------- Merge pull request #7228 from mvdbeek/fix_image_display_py3

[19.01] Fix displaying tool help images on python 3

Commit: 06aa30ffdca0fe092fa2d094aa23da34b10a1667 https://github.com/galaxyproject/galaxy/commit/06aa30ffdca0fe092fa2d094aa23d... Author: Anthony Bretaudeau anthony.bretaudeau@inria.fr Date: 2019-01-18 (Fri, 18 Jan 2019)

Changed paths: M lib/galaxy/actions/library.py

Log Message: ----------- disable tag_using_filenames by default (consistent with #5115)

Commit: 8d99791afb6a699e987bd1e25aaea8582f7f7065 https://github.com/galaxyproject/galaxy/commit/8d99791afb6a699e987bd1e25aaea... Author: mvdbeek m.vandenbeek@gmail.com Date: 2019-01-18 (Fri, 18 Jan 2019)

Changed paths: M tools/data_source/data_source.py

Log Message: ----------- Fix data_source tools on python 3

Commit: b0b5fb44d282b52391becdac1b190ebbd075168d https://github.com/galaxyproject/galaxy/commit/b0b5fb44d282b52391becdac1b190... Author: Nicola Soranzo nicola.soranzo@gmail.com Date: 2019-01-18 (Fri, 18 Jan 2019)

Changed paths: M lib/galaxy/actions/library.py M lib/galaxy/webapps/galaxy/api/library_contents.py

Log Message: ----------- Merge pull request #7204 from abretaud/tag_fn

[19.01] Data library: fix tag_using_filenames not properly converted to bool

Commit: 7b14c3099876d5991ebdea85ff18c027de434be8 https://github.com/galaxyproject/galaxy/commit/7b14c3099876d5991ebdea85ff18c... Author: mvdbeek m.vandenbeek@gmail.com Date: 2019-01-18 (Fri, 18 Jan 2019)

Changed paths: M lib/galaxy/datatypes/sniff.py

Log Message: ----------- Reduce duplicated code

Commit: e92e978ca179870d586e08f16a0542b9dd499a2a https://github.com/galaxyproject/galaxy/commit/e92e978ca179870d586e08f16a054... Author: mvdbeek m.vandenbeek@gmail.com Date: 2019-01-18 (Fri, 18 Jan 2019)

Changed paths: M lib/galaxy/datatypes/interval.py

Log Message: ----------- Drop use of col1_startswith

Contigs may start with whatever sequence you like. Luckily this isn't essential to the datatypes.

Leaving data.col1_startswith in case toolshed datatypes import this.

Commit: 6f861dec7e897bbc06b2cffbb33b2fdd9e6ac11a https://github.com/galaxyproject/galaxy/commit/6f861dec7e897bbc06b2cffbb33b2... Author: mvdbeek m.vandenbeek@gmail.com Date: 2019-01-18 (Fri, 18 Jan 2019)

Changed paths: M lib/galaxy/exceptions/__init__.py

Log Message: ----------- Overridde __init__ for ToolMissingException

Commit: d2d87625f0a5989c40c40a8d50857efb5dc21c36 https://github.com/galaxyproject/galaxy/commit/d2d87625f0a5989c40c40a8d50857... Author: John Chilton jmchilton@gmail.com Date: 2019-01-18 (Fri, 18 Jan 2019)

Changed paths: M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/sniff.py

Log Message: ----------- Merge pull request #7237 from mvdbeek/datatype_fixes

[19.01] Interval datatype fixes

Commit: 9467d0261cab5712d15dfcfa7ca5d7cdb765f631 https://github.com/galaxyproject/galaxy/commit/9467d0261cab5712d15dfcfa7ca5d... Author: John Chilton jmchilton@gmail.com Date: 2019-01-18 (Fri, 18 Jan 2019)

Changed paths: M tools/data_source/data_source.py

Log Message: ----------- Merge pull request #7236 from mvdbeek/data_source_fix

[19.01] Fix data_source tools on python 3

Commit: 889c1026c0893636b4fc6375443408c0ec2b4a8a https://github.com/galaxyproject/galaxy/commit/889c1026c0893636b4fc637544340... Author: John Chilton jmchilton@gmail.com Date: 2019-01-18 (Fri, 18 Jan 2019)

Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-manager.js M lib/galaxy/exceptions/__init__.py M lib/galaxy/managers/workflows.py M lib/galaxy/workflow/modules.py

Log Message: ----------- Merge pull request #7227 from mvdbeek/fix_workflow_loading_saving

[18.09] Properly deal with missing tools in workflows

Commit: a10d2c51d3e29ceef17b056992f04f98b0f8472c https://github.com/galaxyproject/galaxy/commit/a10d2c51d3e29ceef17b056992f04... Author: Dannon Baker dannon.baker@gmail.com Date: 2019-01-18 (Fri, 18 Jan 2019)

Changed paths: M scripts/common_startup.sh

Log Message: ----------- Add/pin configurable node version to 18.09. Backport/tweak of https://github.com/galaxyproject/galaxy/pull/7220)

Commit: 5c90e02d3665caec50369baf0918e58f043af6e4 https://github.com/galaxyproject/galaxy/commit/5c90e02d3665caec50369baf0918e... Author: mvdbeek m.vandenbeek@gmail.com Date: 2019-01-21 (Mon, 21 Jan 2019)

Changed paths: M lib/galaxy/webapps/galaxy/controllers/workflow.py

Log Message: ----------- Fix workflow save_as functionality

Fixes https://github.com/galaxyproject/galaxy/issues/7240, broken in https://github.com/galaxyproject/galaxy/pull/7019, where it was renamed from `build_workflow_from_dict` to `build_workflow_from_raw_description`.

Commit: 8862b9311b000b83a733ed216130f0a7cfe7d4ba https://github.com/galaxyproject/galaxy/commit/8862b9311b000b83a733ed216130f... Author: Nicola Soranzo nicola.soranzo@gmail.com Date: 2019-01-21 (Mon, 21 Jan 2019)

Changed paths: M lib/galaxy/webapps/galaxy/controllers/workflow.py

Log Message: ----------- Use update_workflow_from_raw_description method

not build_workflow_from_raw_description

Co-Authored-By: mvdbeek m.vandenbeek@gmail.com

Commit: b4e450cff021b68831337a8e0bf12c892f54eb8c https://github.com/galaxyproject/galaxy/commit/b4e450cff021b68831337a8e0bf12... Author: Nicola Soranzo nicola.soranzo@earlham.ac.uk Date: 2019-01-21 (Mon, 21 Jan 2019)

Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-manager.js M lib/galaxy/exceptions/__init__.py M lib/galaxy/managers/workflows.py M lib/galaxy/workflow/modules.py

Log Message: ----------- Merge branch 'release_18.09' into release_19.01

Commit: f24176d95060288a0973ef78dab43bf552efb3ba https://github.com/galaxyproject/galaxy/commit/f24176d95060288a0973ef78dab43... Author: Nicola Soranzo nicola.soranzo@gmail.com Date: 2019-01-21 (Mon, 21 Jan 2019)

Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-manager.js M lib/galaxy/exceptions/__init__.py M lib/galaxy/managers/workflows.py M lib/galaxy/workflow/modules.py

Log Message: ----------- Merge pull request #7245 from nsoranzo/release_19.01

Merge branch 'release_18.09' into release_19.01

Commit: bdd340cf1c2e31a5a8c82995bad26d07c7ed5adb https://github.com/galaxyproject/galaxy/commit/bdd340cf1c2e31a5a8c82995bad26... Author: Nicola Soranzo nicola.soranzo@gmail.com Date: 2019-01-21 (Mon, 21 Jan 2019)

Changed paths: M lib/galaxy/webapps/galaxy/controllers/workflow.py

Log Message: ----------- Merge pull request #7241 from mvdbeek/fix_workflow_save_as

[19.01] Fix workflow save_as functionality

Commit: 31c71fbd6fb65cc4a4358e8b415d48885e73e7de https://github.com/galaxyproject/galaxy/commit/31c71fbd6fb65cc4a4358e8b415d4... Author: mvdbeek m.vandenbeek@gmail.com Date: 2019-01-22 (Tue, 22 Jan 2019)

Changed paths: M lib/galaxy/util/__init__.py M test/unit/test_utils.py

Log Message: ----------- strip() text when loading xml

Should fix https://github.com/galaxyproject/galaxy/issues/7250.

Commit: 920f07369dc553a31a848fe044b563b83bd0f2dc https://github.com/galaxyproject/galaxy/commit/920f07369dc553a31a848fe044b56... Author: John Chilton jmchilton@gmail.com Date: 2019-01-22 (Tue, 22 Jan 2019)

Changed paths: M lib/galaxy/util/__init__.py M test/unit/test_utils.py

Log Message: ----------- Merge pull request #7252 from mvdbeek/fix_shed_tool_conf_parsing

[18.09] strip() text when parsing xml

Commit: eb406cc210b556a9218d778383451916d7cd1ecf https://github.com/galaxyproject/galaxy/commit/eb406cc210b556a9218d778383451... Author: mvdbeek m.vandenbeek@gmail.com Date: 2019-01-22 (Tue, 22 Jan 2019)

Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py

Log Message: ----------- Fix install operation in installed_repository_grid

The incoming url keywords look like this: ``` operation=install&id=ebfb8f50c6abde6d?async=false&sort=name&page=1&show_item_checkboxes=true&advanced_search=false&operation=install&id=ebfb8f50c6abde6d ``` and the id parameter gets parsed into a list: ``` ['ebfb8f50c6abde6d?async=false', 'ebfb8f50c6abde6d'] ```

Obviously there's something wrong in the grid or mako, but this works fine.

Fixes https://github.com/galaxyproject/galaxy/issues/5619

Commit: 35fe3bf716e4f527755f75ebb99b9dbdb777e37d https://github.com/galaxyproject/galaxy/commit/35fe3bf716e4f527755f75ebb99b9... Author: mvdbeek m.vandenbeek@gmail.com Date: 2019-01-23 (Wed, 23 Jan 2019)

Changed paths: M lib/galaxy/workflow/modules.py

Log Message: ----------- Not all workflow outputs have a UUID

Commit: f2a454c776bea547967c867e47a827a9a969f67c https://github.com/galaxyproject/galaxy/commit/f2a454c776bea547967c867e47a82... Author: mvdbeek m.vandenbeek@gmail.com Date: 2019-01-24 (Thu, 24 Jan 2019)

Changed paths: M lib/galaxy/workflow/modules.py

Log Message: ----------- Fix output uuid comparison

Commit: 5adfa81a8b6366467d003a9e7b2a551255fdfb20 https://github.com/galaxyproject/galaxy/commit/5adfa81a8b6366467d003a9e7b2a5... Author: Nicola Soranzo nicola.soranzo@earlham.ac.uk Date: 2019-01-24 (Thu, 24 Jan 2019)

Changed paths: M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt

Log Message: ----------- Update sqlalchemy-migrate requirement to 0.12.0

Fix https://github.com/galaxyproject/galaxy/issues/7159

Commit: 1a4c1ec514024bb5ee71997afe54158083ca5222 https://github.com/galaxyproject/galaxy/commit/1a4c1ec514024bb5ee71997afe541... Author: Nicola Soranzo nicola.soranzo@gmail.com Date: 2019-01-24 (Thu, 24 Jan 2019)

Changed paths: M lib/galaxy/workflow/modules.py

Log Message: ----------- Merge pull request #7258 from mvdbeek/fix_workflow_uuid_access

[18.09] Not all workflow outputs have a UUID

Commit: f9ca90a2288acbbc7de5d5e3b903d143519f1174 https://github.com/galaxyproject/galaxy/commit/f9ca90a2288acbbc7de5d5e3b903d... Author: Nicola Soranzo nicola.soranzo@earlham.ac.uk Date: 2019-01-24 (Thu, 24 Jan 2019)

Changed paths: M lib/galaxy/util/__init__.py M lib/galaxy/workflow/modules.py M test/unit/test_utils.py

Log Message: ----------- Merge branch 'release_18.09' into release_19.01

Commit: f0bd2df6d4f314c449937dff6878720e83d060bb https://github.com/galaxyproject/galaxy/commit/f0bd2df6d4f314c449937dff68787... Author: Dannon dannon.baker@gmail.com Date: 2019-01-24 (Thu, 24 Jan 2019)

Changed paths: M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt

Log Message: ----------- Merge pull request #7265 from nsoranzo/release_18.09_sqlalchemy-migrate_0.12.0

[18.09] Update sqlalchemy-migrate requirement to 0.12.0

Commit: 7b08e98ffce50a1f99fca392ac6e1462fd97ed7e https://github.com/galaxyproject/galaxy/commit/7b08e98ffce50a1f99fca392ac6e1... Author: Nicola Soranzo nicola.soranzo@earlham.ac.uk Date: 2019-01-24 (Thu, 24 Jan 2019)

Changed paths: M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt

Log Message: ----------- Merge branch 'release_18.09' into release_19.01

Commit: 6a660e9893b6fc5eb9bb0f3225fdeb9fb9ad763f https://github.com/galaxyproject/galaxy/commit/6a660e9893b6fc5eb9bb0f3225fde... Author: Dannon dannon.baker@gmail.com Date: 2019-01-24 (Thu, 24 Jan 2019)

Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py

Log Message: ----------- Merge pull request #7253 from mvdbeek/fix_install_in_manage_tools_grid

[18.09] Fix install operation in installed_repository_grid

Commit: dc6ec1ed3dec5663aeb127b85bb4b1aa724afb9f https://github.com/galaxyproject/galaxy/commit/dc6ec1ed3dec5663aeb127b85bb4b... Author: Dannon Baker dannon.baker@gmail.com Date: 2019-01-24 (Thu, 24 Jan 2019)

Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py

Log Message: ----------- Merge remote-tracking branch 'upstream/release_18.09' into release_19.01

Commit: 12128ad49d763ad725e5861ff0e1cd5aaeb5461e https://github.com/galaxyproject/galaxy/commit/12128ad49d763ad725e5861ff0e1c... Author: Dannon Baker dannon.baker@gmail.com Date: 2019-01-24 (Thu, 24 Jan 2019)

Changed paths: M client/galaxy/scripts/toolshed/groups/group-detail-view.js

Log Message: ----------- Fix _.escape typo in toolshed group detail view

Commit: 8c93a914d86071968075a551ed307633ea68fbff https://github.com/galaxyproject/galaxy/commit/8c93a914d86071968075a551ed307... Author: Nicola Soranzo nicola.soranzo@gmail.com Date: 2019-01-24 (Thu, 24 Jan 2019)

Changed paths: M client/galaxy/scripts/toolshed/groups/group-detail-view.js

Log Message: ----------- Merge pull request #7267 from dannon/toolshed-roup-detail-view-typo

[19.01] Fix _.escape typo in toolshed group detail view

Commit: d83db6a53796137c8ccc96efe3b40f3f3f88f694 https://github.com/galaxyproject/galaxy/commit/d83db6a53796137c8ccc96efe3b40... Author: John Chilton jmchilton@gmail.com Date: 2019-01-27 (Sun, 27 Jan 2019)

Changed paths: M config/galaxy.yml.sample M doc/source/admin/galaxy_options.rst M lib/galaxy/config.py M lib/galaxy/webapps/galaxy/config_schema.yml

Log Message: ----------- Stop with tool migrations by default, they are not needed in modern Galaxies...

... and even problematic in some ways.

Commit: 7061f2a2af6ae7335b918dc4115ee8170efd7f67 https://github.com/galaxyproject/galaxy/commit/7061f2a2af6ae7335b918dc4115ee... Author: mvdbeek m.vandenbeek@gmail.com Date: 2019-01-28 (Mon, 28 Jan 2019)

Changed paths: M lib/galaxy/webapps/galaxy/api/toolshed.py

Log Message: ----------- Fix installing tools via tool_id

Commit: c8b3d5e4c415514ef626b2009791476d51f9cf9b https://github.com/galaxyproject/galaxy/commit/c8b3d5e4c415514ef626b20097914... Author: Marius van den Beek m.vandenbeek@gmail.com Date: 2019-01-29 (Tue, 29 Jan 2019)

Changed paths: M config/galaxy.yml.sample M doc/source/admin/galaxy_options.rst M lib/galaxy/config.py M lib/galaxy/webapps/galaxy/config_schema.yml

Log Message: ----------- Merge pull request #7275 from jmchilton/1901_migrate_tools

[18.09] Stop tool migrations checking by default...

Commit: 152e0012c7c1cb037894b1b32ee040b619642863 https://github.com/galaxyproject/galaxy/commit/152e0012c7c1cb037894b1b32ee04... Author: Nicola Soranzo nicola.soranzo@earlham.ac.uk Date: 2019-01-29 (Tue, 29 Jan 2019)

Changed paths: M config/galaxy.yml.sample M doc/source/admin/galaxy_options.rst M lib/galaxy/config.py M lib/galaxy/webapps/galaxy/config_schema.yml

Log Message: ----------- Merge branch 'release_18.09' into release_19.01

Commit: 6cdca798ef62a85d4fa1a4f402f58521e3c57249 https://github.com/galaxyproject/galaxy/commit/6cdca798ef62a85d4fa1a4f402f58... Author: John Chilton jmchilton@gmail.com Date: 2019-01-30 (Wed, 30 Jan 2019)

Changed paths: M lib/galaxy/webapps/galaxy/api/toolshed.py

Log Message: ----------- Merge pull request #7277 from mvdbeek/fix_install_via_tool_id

[19.01] Fix installing tools via tool_id

Commit: bdc6243a78b0fcf1e0d0a89670ec19dcb3aa9479 https://github.com/galaxyproject/galaxy/commit/bdc6243a78b0fcf1e0d0a89670ec1... Author: Helena Rasche hxr@hx42.org Date: 2019-02-01 (Fri, 01 Feb 2019)

Changed paths: M client/galaxy/style/scss/base.scss

Log Message: ----------- Darker tool form in workflow editor

Commit: 038d1a1d83fac689e0d00f85cb59057bfe79bfcc https://github.com/galaxyproject/galaxy/commit/038d1a1d83fac689e0d00f85cb590... Author: Helena Rasche hxr@hx42.org Date: 2019-02-01 (Fri, 01 Feb 2019)

Changed paths: M client/galaxy/style/scss/base.scss

Log Message: ----------- Revert "Darker tool form in workflow editor"

This reverts commit bdc6243a78b0fcf1e0d0a89670ec19dcb3aa9479.

Commit: 9a133e91f84d31e0c4e39c36301a368d66c48508 https://github.com/galaxyproject/galaxy/commit/9a133e91f84d31e0c4e39c36301a3... Author: Nicola Soranzo nicola.soranzo@gmail.com Date: 2019-02-01 (Fri, 01 Feb 2019)

Changed paths: M doc/source/admin/scaling.md

Log Message: ----------- Remove spurious characters

Co-Authored-By: natefoo nate@bx.psu.edu

Commit: 74fcf12fa0968ef448fecb3f0ff9bd4736f91cd2 https://github.com/galaxyproject/galaxy/commit/74fcf12fa0968ef448fecb3f0ff9b... Author: Nate Coraor nate@bx.psu.edu Date: 2019-02-01 (Fri, 01 Feb 2019)

Changed paths: M doc/source/admin/scaling.md

Log Message: ----------- Incorporate suggestions from @nsoranzo

Commit: 49cbad5debb649013e142134b3b4ad8361125914 https://github.com/galaxyproject/galaxy/commit/49cbad5debb649013e142134b3b4a... Author: Daniel Blankenberg dan.blankenberg@gmail.com Date: 2019-02-02 (Sat, 02 Feb 2019)

Changed paths: M config/job_conf.xml.sample_advanced M doc/Makefile M doc/source/admin/apache.md M doc/source/admin/config_logging.rst M doc/source/admin/nginx.md M doc/source/admin/scaling.md

Log Message: ----------- Merge pull request #7191 from natefoo/admin-docs-19.01

[19.01] Properly document handler assignment method configuration and fix logging configuration docs

Commit: 428c6632f0196ebd45a42d1c61776ac3402e985f https://github.com/galaxyproject/galaxy/commit/428c6632f0196ebd45a42d1c61776... Author: Daniel Blankenberg dan.blankenberg@gmail.com Date: 2019-02-04 (Mon, 04 Feb 2019)

Changed paths: M tool-data/intermine_simple_display.loc.sample

Log Message: ----------- Remove errant space in intermine_simple_display.loc.sample

Commit: 526bebbb2817376b4c4e131890d75d1ea76b0e85 https://github.com/galaxyproject/galaxy/commit/526bebbb2817376b4c4e131890d75... Author: Martin Cech marten@bx.psu.edu Date: 2019-02-04 (Mon, 04 Feb 2019)

Changed paths: M tool-data/intermine_simple_display.loc.sample

Log Message: ----------- Merge pull request #7298 from blankenberg/intermine-loc-fix-19.01

[19.01] Remove errant space in intermine_simple_display.loc.sample

Commit: 9f501bb2b0bfa5193cd908d5f43bdca9a4bc5a2d https://github.com/galaxyproject/galaxy/commit/9f501bb2b0bfa5193cd908d5f43bd... Author: Matt Chambers matt.chambers42@gmail.com Date: 2019-02-04 (Mon, 04 Feb 2019)

Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py A lib/galaxy/datatypes/test/brukerbaf.d.tar

Log Message: ----------- Add datatypes and sniffers for several directory-based mass spectrometry formats: Bruker BAF, Agilent/Bruker YEP, Bruker TDF, Agilent MassHunter, and Waters MassLynx

Commit: 68a66f462e007fdbcf8e966fc5cc1a7ea06a8527 https://github.com/galaxyproject/galaxy/commit/68a66f462e007fdbcf8e966fc5cc1... Author: Bjoern Gruening bjoern.gruening@gmail.com Date: 2019-02-05 (Tue, 05 Feb 2019)

Changed paths: M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt

Log Message: ----------- update h5py dependency

Commit: d79514b823371c36c12dcbb6aef25a4490cd50ca https://github.com/galaxyproject/galaxy/commit/d79514b823371c36c12dcbb6aef25... Author: Bjoern Gruening bjoern.gruening@gmail.com Date: 2019-02-05 (Tue, 05 Feb 2019)

Changed paths: M lib/galaxy/tools/verify/asserts/__init__.py

Log Message: ----------- allow assertions on binary inputs

Commit: e37036af04ac34dd7c865f5f11ccaa0ee4e17e9a https://github.com/galaxyproject/galaxy/commit/e37036af04ac34dd7c865f5f11cca... Author: Bjoern Gruening bjoern.gruening@gmail.com Date: 2019-02-05 (Tue, 05 Feb 2019)

Changed paths: A lib/galaxy/tools/verify/asserts/hdf5.py

Log Message: ----------- add hdf5 assert tests

Commit: db2987b2b21fefad9feb2af0bd4f93b7d490361f https://github.com/galaxyproject/galaxy/commit/db2987b2b21fefad9feb2af0bd4f9... Author: Bjoern Gruening bjoern.gruening@gmail.com Date: 2019-02-05 (Tue, 05 Feb 2019)

Changed paths: A test/functional/tools/validation_hdf5.xml

Log Message: ----------- add test tool for new assertions

Commit: d4420b75662b7667d430f78be67b09e69037a77b https://github.com/galaxyproject/galaxy/commit/d4420b75662b7667d430f78be67b0... Author: Bjoern Gruening bjoern.gruening@gmail.com Date: 2019-02-05 (Tue, 05 Feb 2019)

Changed paths: M test/functional/tools/samples_tool_conf.xml

Log Message: ----------- register new test tool

Commit: a00fd508b758fc73aeb537ca98156fff1c7ac14d https://github.com/galaxyproject/galaxy/commit/a00fd508b758fc73aeb537ca98156... Author: Bjoern Gruening bjoern.gruening@gmail.com Date: 2019-02-05 (Tue, 05 Feb 2019)

Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd

Log Message: ----------- adopt XSD for new syntax

Commit: cb13e56e6bd00a932e9594241fe043f845d4f815 https://github.com/galaxyproject/galaxy/commit/cb13e56e6bd00a932e9594241fe04... Author: Bjoern Gruening bjoern.gruening@gmail.com Date: 2019-02-05 (Tue, 05 Feb 2019)

Changed paths: A test-data/matrix.cool

Log Message: ----------- add test-data for new hdf5 based tool test

Commit: e9f40f2f95a611f0fab6d81bb225cf409b86f353 https://github.com/galaxyproject/galaxy/commit/e9f40f2f95a611f0fab6d81bb225c... Author: Bjoern Gruening bjoern.gruening@gmail.com Date: 2019-02-05 (Tue, 05 Feb 2019)

Changed paths: M lib/galaxy/tools/verify/asserts/hdf5.py

Log Message: ----------- fix pep8

Commit: 4df1de38ba390ee6513bc85fbb0643e6e152bd25 https://github.com/galaxyproject/galaxy/commit/4df1de38ba390ee6513bc85fbb064... Author: mvdbeek m.vandenbeek@gmail.com Date: 2019-02-05 (Tue, 05 Feb 2019)

Changed paths: M lib/galaxy/workflow/modules.py

Log Message: ----------- Map over multiple=true in workflow run

There is some unfortunate divergence between the mapping over code in tool runs vs workflow runs. Without this patch a list:list input to a multiple="true" data input would get fully reduced in workflow, while tool runs would just reduce the inner collection (and I think that's the correct behavior).

Commit: cf68cbe907729283a8a359d9a8dbcb0013ebcee5 https://github.com/galaxyproject/galaxy/commit/cf68cbe907729283a8a359d9a8dbc... Author: mvdbeek m.vandenbeek@gmail.com Date: 2019-02-05 (Tue, 05 Feb 2019)

Changed paths: M test/api/test_workflows.py

Log Message: ----------- Verify that list:list will be reduced to list in multi data input

Commit: 2a97f726cc86d44610738d04755622e8e4b8342a https://github.com/galaxyproject/galaxy/commit/2a97f726cc86d44610738d0475562... Author: John Chilton jmchilton@gmail.com Date: 2019-02-05 (Tue, 05 Feb 2019)

Changed paths: M lib/galaxy/tools/verify/asserts/hdf5.py M lib/galaxy/tools/xsd/galaxy.xsd M test/functional/tools/validation_hdf5.xml

Log Message: ----------- Tweaks to hdf5 testing.

- This is in galaxy-lib so h5py import should probably be conditional. - Namespace very generic test functions a bit by adding h5 into the names. - Stricter validation of XSD (the other assertions don't have this but that is problematic on their part), I'm not sure if the docs will render unevenly now though - we may want to revisit that and do this for all the assertions.

Commit: ae8bf6f793edda9211b59c68d6c029b9fa74154a https://github.com/galaxyproject/galaxy/commit/ae8bf6f793edda9211b59c68d6c02... Author: John Chilton jmchilton@gmail.com Date: 2019-02-05 (Tue, 05 Feb 2019)

Changed paths: A doc/source/releases/19.01.rst M doc/source/releases/19.01_announce.rst A doc/source/releases/19.05_announce.rst

Log Message: ----------- Release notes raw.

Commit: a36b56e6940cf8e406ebca90114e2a9974e50e0d https://github.com/galaxyproject/galaxy/commit/a36b56e6940cf8e406ebca90114e2... Author: mvdbeek m.vandenbeek@gmail.com Date: 2019-02-05 (Tue, 05 Feb 2019)

Changed paths: M test/api/test_workflows.py

Log Message: ----------- Drop redundant wait for history

wait_for_invocation_and_jobs does that already, thx @nsoranzo.

Commit: 3d4ff4fc372bc6b44b384af944b548915427fda4 https://github.com/galaxyproject/galaxy/commit/3d4ff4fc372bc6b44b384af944b54... Author: Björn Grüning bjoern@gruenings.eu Date: 2019-02-05 (Tue, 05 Feb 2019)

Changed paths: M lib/galaxy/tools/verify/asserts/hdf5.py M lib/galaxy/tools/xsd/galaxy.xsd M test/functional/tools/validation_hdf5.xml

Log Message: ----------- Merge pull request #41 from jmchilton/hdf5_tests

Tweaks to hdf5 testing.

Commit: 365ac400ae629b415b8ec11a364ec0e4465d1c7f https://github.com/galaxyproject/galaxy/commit/365ac400ae629b415b8ec11a364ec... Author: Matt Chambers matt.chambers42@gmail.com Date: 2019-02-05 (Tue, 05 Feb 2019)

Changed paths: M lib/galaxy/datatypes/binary.py

Log Message: ----------- Fix lint errors

Commit: 413af14bb55d890ca053d08877cee98ab440008f https://github.com/galaxyproject/galaxy/commit/413af14bb55d890ca053d08877cee... Author: Matt Chambers matt.chambers42@gmail.com Date: 2019-02-05 (Tue, 05 Feb 2019)

Changed paths: M lib/galaxy/datatypes/binary.py

Log Message: ----------- Fix lint errors

Commit: c4fbe94bcfeef2acc5edf516a625578c7578feff https://github.com/galaxyproject/galaxy/commit/c4fbe94bcfeef2acc5edf516a6255... Author: Nicola Soranzo nicola.soranzo@gmail.com Date: 2019-02-05 (Tue, 05 Feb 2019)

Changed paths: M lib/galaxy/workflow/modules.py M test/api/test_workflows.py

Log Message: ----------- Merge pull request #7302 from mvdbeek/dont_reduce_list_list_in_multi_data_input_workflow_step

[19.01] Don't reduce list:list in multi data input workflow step

Commit: d30852b286b9baba5cf6faffa389db8ec2837114 https://github.com/galaxyproject/galaxy/commit/d30852b286b9baba5cf6faffa389d... Author: Matt Chambers matt.chambers42@gmail.com Date: 2019-02-05 (Tue, 05 Feb 2019)

Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py A lib/galaxy/datatypes/test/some.wiff.tar

Log Message: ----------- Add wiff.tar extension and sniffer

Commit: b5713ca170cfeb574063a2ec9dca8adbee1f7d74 https://github.com/galaxyproject/galaxy/commit/b5713ca170cfeb574063a2ec9dca8... Author: John Chilton jmchilton@gmail.com Date: 2019-02-05 (Tue, 05 Feb 2019)

Changed paths: M doc/source/releases/19.01.rst M doc/source/releases/19.01_announce.rst M doc/source/releases/index.rst

Log Message: ----------- Progress on 19.01 release notes...

Commit: 0a7583b6de024d02b7063fa3f59c7febe63df5f5 https://github.com/galaxyproject/galaxy/commit/0a7583b6de024d02b7063fa3f59c7... Author: Helena Rasche hxr@hx42.org Date: 2019-02-06 (Wed, 06 Feb 2019)

Changed paths: M client/galaxy/style/scss/base.scss M client/galaxy/style/scss/theme/blue.scss

Log Message: ----------- More contrast

Commit: 87c82595771438b0e8244b32885430e4fe1bab6e https://github.com/galaxyproject/galaxy/commit/87c82595771438b0e8244b3288543... Author: Helena Rasche hxr@hx42.org Date: 2019-02-06 (Wed, 06 Feb 2019)

Changed paths: M client/galaxy/style/scss/base.scss

Log Message: ----------- Add box-shadow

Commit: 12fde52494541d73da42a41d026c8a0217d7533c https://github.com/galaxyproject/galaxy/commit/12fde52494541d73da42a41d026c8... Author: Helena Rasche hxr@hx42.org Date: 2019-02-06 (Wed, 06 Feb 2019)

Changed paths: M client/galaxy/style/scss/theme/blue.scss

Log Message: ----------- remove inaccurate comment

Commit: dc303f004fc5254f6de14bc29084532d3db98912 https://github.com/galaxyproject/galaxy/commit/dc303f004fc5254f6de14bc290845... Author: Matt Chambers matt.chambers42@gmail.com Date: 2019-02-06 (Wed, 06 Feb 2019)

Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py

Log Message: ----------- Remove try/except in sniffers Add .d/.raw to file_ext

Commit: d36cf51f6b63407fd96e49918fe6092d993275a9 https://github.com/galaxyproject/galaxy/commit/d36cf51f6b63407fd96e49918fe60... Author: Bjoern Gruening bjoern.gruening@gmail.com Date: 2019-02-06 (Wed, 06 Feb 2019)

Changed paths: M lib/galaxy/tools/verify/asserts/hdf5.py M lib/galaxy/tools/xsd/galaxy.xsd M test/functional/tools/validation_hdf5.xml

Log Message: ----------- change "name" to "key"

Commit: b59d76eb4a928af8866275cb91afd583a82fee99 https://github.com/galaxyproject/galaxy/commit/b59d76eb4a928af8866275cb91afd... Author: Helena Rasche hxr@hx42.org Date: 2019-02-06 (Wed, 06 Feb 2019)

Changed paths: M lib/galaxy/util/__init__.py

Log Message: ----------- Fix emoji tags

Commit: dd917099ba43b3d9638c16623ca45bc13edfc9c5 https://github.com/galaxyproject/galaxy/commit/dd917099ba43b3d9638c16623ca45... Author: Marius van den Beek m.vandenbeek@gmail.com Date: 2019-02-06 (Wed, 06 Feb 2019)

Changed paths: M lib/galaxy/util/__init__.py

Log Message: ----------- Only block the single category of C characters that is problematic

Co-Authored-By: erasche hxr@hx42.org

Commit: e3f1234b2c1359e4d5353ba0e0b56834a964bb28 https://github.com/galaxyproject/galaxy/commit/e3f1234b2c1359e4d5353ba0e0b56... Author: Martin Cech marten@bx.psu.edu Date: 2019-02-06 (Wed, 06 Feb 2019)

Changed paths: M lib/galaxy/util/__init__.py

Log Message: ----------- Merge pull request #7310 from erasche/fix-emoji-tags

[19.01] Fix emoji tags

Commit: 23d4af5dafbb768ba61c6cf8849cd17087f31520 https://github.com/galaxyproject/galaxy/commit/23d4af5dafbb768ba61c6cf8849cd... Author: Helena Rasche hxr@hx42.org Date: 2019-02-06 (Wed, 06 Feb 2019)

Changed paths: M client/galaxy/style/scss/base.scss

Log Message: ----------- Revert "Add box-shadow"

This reverts commit 87c82595771438b0e8244b32885430e4fe1bab6e.

Commit: 8f7263a1dcce4a2d3e5c251e4253dece2998e61d https://github.com/galaxyproject/galaxy/commit/8f7263a1dcce4a2d3e5c251e4253d... Author: John Chilton jmchilton@gmail.com Date: 2019-02-07 (Thu, 07 Feb 2019)

Changed paths: M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt M lib/galaxy/tools/verify/asserts/__init__.py A lib/galaxy/tools/verify/asserts/hdf5.py M lib/galaxy/tools/xsd/galaxy.xsd A test-data/matrix.cool M test/functional/tools/samples_tool_conf.xml A test/functional/tools/validation_hdf5.xml

Log Message: ----------- Merge pull request #7301 from bgruening/hdf5_tests

Add new test syntax specific for HDF5 files

Commit: d710bb860b5802a64420eb3d5e1ebac6ac88d4ea https://github.com/galaxyproject/galaxy/commit/d710bb860b5802a64420eb3d5e1eb... Author: mvdbeek m.vandenbeek@gmail.com Date: 2019-02-07 (Thu, 07 Feb 2019)

Changed paths: M lib/galaxy/tools/data_manager/manager.py M lib/galaxy/tools/loader_directory.py

Log Message: ----------- Discriminate data managers and allow managed testing

I am not a big fan of the heuristic in which we fall back to loading the data manager tool relative to the data_manager_conf.xml file, but I don't really see a better way here.

Commit: f0026962219ebad2177f57ebee5ae9b837882e60 https://github.com/galaxyproject/galaxy/commit/f0026962219ebad2177f57ebee5ae... Author: Nate Coraor nate@bx.psu.edu Date: 2019-02-07 (Thu, 07 Feb 2019)

Changed paths: M client/galaxy/style/scss/base.scss M client/galaxy/style/scss/theme/blue.scss

Log Message: ----------- Merge pull request #7309 from erasche/more-contrast

[19.01] More contrast in CSS

Commit: f7322d85a317614de1a745da57d5e394b5eb8041 https://github.com/galaxyproject/galaxy/commit/f7322d85a317614de1a745da57d5e... Author: Björn Grüning bjoern@gruenings.eu Date: 2019-02-09 (Sat, 09 Feb 2019)

Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py A lib/galaxy/datatypes/test/brukerbaf.d.tar A lib/galaxy/datatypes/test/some.wiff.tar

Log Message: ----------- Merge pull request #7299 from chambm/feature/rawtar-datatypes

Add datatypes and sniffers for tar archives of directory-based MS formats and WIFF/SCAN pairs

Commit: 9c9c8a5d50d7c8ae68f34712d0e9b053aed33ea2 https://github.com/galaxyproject/galaxy/commit/9c9c8a5d50d7c8ae68f34712d0e9b... Author: Martin Cech marten@bx.psu.edu Date: 2019-02-11 (Mon, 11 Feb 2019)

Changed paths: M scripts/common_startup.sh

Log Message: ----------- Merge pull request #7239 from dannon/node_ver_pin_18.09

[18.09] Add/pin configurable node version

Commit: b33b06440ffdd7e58b6172315df1e015e4ac0e52 https://github.com/galaxyproject/galaxy/commit/b33b06440ffdd7e58b6172315df1e... Author: Nicola Soranzo nicola.soranzo@earlham.ac.uk Date: 2019-02-12 (Tue, 12 Feb 2019)

Changed paths: M scripts/common_startup.sh

Log Message: ----------- Merge branch 'release_18.09' into release_19.01

Commit: 06d1e5a8b22072bd1de9961bcfcf051a86b90f5f https://github.com/galaxyproject/galaxy/commit/06d1e5a8b22072bd1de9961bcfcf0... Author: Bjoern Gruening bjoern.gruening@gmail.com Date: 2019-02-12 (Tue, 12 Feb 2019)

Changed paths: M lib/galaxy/tools/verify/__init__.py

Log Message: ----------- fix the name of presevered test-data

Commit: 740fc8594edf6e15fdecdc3d1f30be259dc7dea2 https://github.com/galaxyproject/galaxy/commit/740fc8594edf6e15fdecdc3d1f30b... Author: Bjoern Gruening bjoern.gruening@gmail.com Date: 2019-02-12 (Tue, 12 Feb 2019)

Changed paths: M lib/galaxy/tools/verify/interactor.py

Log Message: ----------- improve test error message

Commit: f311ebd1e2c237f7dc5b10f67f20aea28921877c https://github.com/galaxyproject/galaxy/commit/f311ebd1e2c237f7dc5b10f67f20a... Author: Bjoern Gruening bjoern.gruening@gmail.com Date: 2019-02-12 (Tue, 12 Feb 2019)

Changed paths: M lib/galaxy/tools/verify/interactor.py

Log Message: ----------- mention planemo explicitly

Commit: f3208503f69bae63ef48e18deb85e7aa974e20c5 https://github.com/galaxyproject/galaxy/commit/f3208503f69bae63ef48e18deb85e... Author: Dannon Baker dannon.baker@gmail.com Date: 2019-02-12 (Tue, 12 Feb 2019)

Changed paths: M client/galaxy/scripts/layout/communication-server-view.js

Log Message: ----------- Drop 'fade in' classes on iframe; prefer static display without extra animations and fixes opacity issue from biostar.

Commit: bfeb2727573a6c1c77551369bf46acf93d78190b https://github.com/galaxyproject/galaxy/commit/bfeb2727573a6c1c77551369bf46a... Author: Dannon Baker dannon.baker@gmail.com Date: 2019-02-12 (Tue, 12 Feb 2019)

Changed paths: M client/galaxy/scripts/layout/communication-server-view.js M client/galaxy/style/scss/base.scss

Log Message: ----------- drop redundant communication server frame styles.

Commit: b29b8b5c17f4126b0af597c0bccac850767f5aff https://github.com/galaxyproject/galaxy/commit/b29b8b5c17f4126b0af597c0bccac... Author: Dannon Baker dannon.baker@gmail.com Date: 2019-02-12 (Tue, 12 Feb 2019)

Changed paths: M client/galaxy/scripts/layout/communication-server-view.js

Log Message: ----------- Use standard bootstrap classes for sizing here since it's only used in one spot.

Commit: 62d8d808eb096daa4c99bdefd3c0aabaa3a59e56 https://github.com/galaxyproject/galaxy/commit/62d8d808eb096daa4c99bdefd3c0a... Author: John Chilton jmchilton@gmail.com Date: 2019-02-13 (Wed, 13 Feb 2019)

Changed paths: M lib/galaxy/tools/data_manager/manager.py M lib/galaxy/tools/loader_directory.py

Log Message: ----------- Merge pull request #7331 from mvdbeek/test_data_managers

[19.01] Discriminate data managers and allow managed testing

Commit: 45d06acbc8f31bdeab7b895d3fadf71d4a9aaa84 https://github.com/galaxyproject/galaxy/commit/45d06acbc8f31bdeab7b895d3fadf... Author: John Chilton jmchilton@gmail.com Date: 2019-02-13 (Wed, 13 Feb 2019)

Changed paths: M client/galaxy/scripts/layout/communication-server-view.js M client/galaxy/style/scss/base.scss

Log Message: ----------- Merge pull request #7354 from dannon/comm_server_fixes

[19.01] Communication Server Display Fixes

Commit: 728ff2075de24fc2386ae925efd8fde885d959db https://github.com/galaxyproject/galaxy/commit/728ff2075de24fc2386ae925efd8f... Author: John Chilton jmchilton@gmail.com Date: 2019-02-14 (Thu, 14 Feb 2019)

Changed paths: M lib/galaxy/tools/verify/__init__.py

Log Message: ----------- Merge pull request #7352 from bgruening/test_data_fix

fix the filename of saved test-data

Commit: b67dc2ba24ec0c712db693cb8859e6eb703d724e https://github.com/galaxyproject/galaxy/commit/b67dc2ba24ec0c712db693cb8859e... Author: Dannon dannon.baker@gmail.com Date: 2019-02-14 (Thu, 14 Feb 2019)

Changed paths: M lib/galaxy/tools/verify/interactor.py

Log Message: ----------- Merge pull request #7353 from bgruening/improve_err_message

Improve error message during tool testing

Commit: 16af73423f2c5a1181b016dcc01955c1c2ab037a https://github.com/galaxyproject/galaxy/commit/16af73423f2c5a1181b016dcc0195... Author: Marius van den Beek m.vandenbeek@gmail.com Date: 2019-02-18 (Mon, 18 Feb 2019)

Changed paths: M doc/source/releases/19.01.rst

Log Message: ----------- Update doc/source/releases/19.01.rst

Co-Authored-By: jmchilton jmchilton@gmail.com

Commit: 072b8d73eca68201bcf691c7dc9fa22272433ac3 https://github.com/galaxyproject/galaxy/commit/072b8d73eca68201bcf691c7dc9fa... Author: Marius van den Beek m.vandenbeek@gmail.com Date: 2019-02-18 (Mon, 18 Feb 2019)

Changed paths: M doc/source/releases/19.01.rst

Log Message: ----------- Update doc/source/releases/19.01.rst

Co-Authored-By: jmchilton jmchilton@gmail.com

Commit: 2a3555d9d73e4a9f72b003a319698f7e8fb01d3c https://github.com/galaxyproject/galaxy/commit/2a3555d9d73e4a9f72b003a319698... Author: John Chilton jmchilton@gmail.com Date: 2019-02-18 (Mon, 18 Feb 2019)

Changed paths: M doc/source/releases/19.01.rst M doc/source/releases/19.01_announce.rst

Log Message: ----------- Better Singularity summary thanks to @mvdbeek.

Commit: 94bcb8d00f3fc8817cdca5ef3ab383e705b950d6 https://github.com/galaxyproject/galaxy/commit/94bcb8d00f3fc8817cdca5ef3ab38... Author: John Chilton jmchilton@gmail.com Date: 2019-02-18 (Mon, 18 Feb 2019)

Changed paths: M doc/source/releases/19.01.rst

Log Message: ----------- More fixes to 19.01 release notes.

Commit: ca4acf78df6cfc89f76b0f09143d0301aac234b4 https://github.com/galaxyproject/galaxy/commit/ca4acf78df6cfc89f76b0f09143d0... Author: Nicola Soranzo nicola.soranzo@gmail.com Date: 2019-02-18 (Mon, 18 Feb 2019)

Changed paths: M doc/source/releases/19.01_announce.rst

Log Message: ----------- Sort PR numbers

Small fixes.

Commit: 37a93972d59459ffd50d340d53c5f278b3e15dae https://github.com/galaxyproject/galaxy/commit/37a93972d59459ffd50d340d53c5f... Author: Nicola Soranzo nicola.soranzo@gmail.com Date: 2019-02-18 (Mon, 18 Feb 2019)

Changed paths: M doc/source/releases/19.01.rst

Log Message: ----------- Fix PR link

Commit: 203353597671ec7c3daa02791705ebb921fb28ad https://github.com/galaxyproject/galaxy/commit/203353597671ec7c3daa02791705e... Author: John Chilton jmchilton@gmail.com Date: 2019-02-18 (Mon, 18 Feb 2019)

Changed paths: M doc/parse_gx_xsd.py M lib/galaxy/tools/xsd/galaxy.xsd

Log Message: ----------- Fix HDF5 test assert docs

Alternative to https://github.com/galaxyproject/galaxy/pull/7382, fix documentation without giving up better validation one gets with actual types for assertion XML elements.

Commit: 7abd448cbe64e64758e476d0e78921288663abd4 https://github.com/galaxyproject/galaxy/commit/7abd448cbe64e64758e476d0e7892... Author: Daniel Blankenberg dan.blankenberg@gmail.com Date: 2019-02-18 (Mon, 18 Feb 2019)

Changed paths: M config/datatypes_conf.xml.sample A lib/galaxy/datatypes/anvio.py

Log Message: ----------- Add datatypes for Anvi'o

Commit: 948cdb251a500a41b8b6c81891868e0b0bbec070 https://github.com/galaxyproject/galaxy/commit/948cdb251a500a41b8b6c81891868... Author: Daniel Blankenberg dan.blankenberg@gmail.com Date: 2019-02-18 (Mon, 18 Feb 2019)

Changed paths: M lib/galaxy/datatypes/anvio.py

Log Message: ----------- cleanup anvio.py

Commit: cf31e330e8575ccc6635dfd1c9c2c1cc95454e1f https://github.com/galaxyproject/galaxy/commit/cf31e330e8575ccc6635dfd1c9c2c... Author: Daniel Blankenberg dan.blankenberg@gmail.com Date: 2019-02-18 (Mon, 18 Feb 2019)

Changed paths: M lib/galaxy/datatypes/anvio.py

Log Message: ----------- Decrease readability.

Commit: 51280fbf7d345deb6d2cc0aefd4f0bbe598a92c1 https://github.com/galaxyproject/galaxy/commit/51280fbf7d345deb6d2cc0aefd4f0... Author: Daniel Blankenberg dan.blankenberg@gmail.com Date: 2019-02-18 (Mon, 18 Feb 2019)

Changed paths: M lib/galaxy/datatypes/anvio.py

Log Message: ----------- flip a line

Commit: 737bae8f9b920ec9bed43a2d25378b19ace12f58 https://github.com/galaxyproject/galaxy/commit/737bae8f9b920ec9bed43a2d25378... Author: Nicola Soranzo nicola.soranzo@earlham.ac.uk Date: 2019-02-19 (Tue, 19 Feb 2019)

Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd

Log Message: ----------- Reword HDF5 attribute test docs

Commit: 35529a05fb9210bd2f7fce3f91418cdf95cebb2f https://github.com/galaxyproject/galaxy/commit/35529a05fb9210bd2f7fce3f91418... Author: Björn Grüning bjoern@gruenings.eu Date: 2019-02-19 (Tue, 19 Feb 2019)

Changed paths: M doc/parse_gx_xsd.py M lib/galaxy/tools/xsd/galaxy.xsd

Log Message: ----------- Merge pull request #7384 from jmchilton/fix_h5_assertion_docs

[19.01] Fix HDF5 test assert docs

Commit: d72f82de98f464ace59db312fe9db398793c3494 https://github.com/galaxyproject/galaxy/commit/d72f82de98f464ace59db312fe9db... Author: Martin Cech marten@bx.psu.edu Date: 2019-02-19 (Tue, 19 Feb 2019)

Changed paths: M config/galaxy.yml.sample M config/reports.yml.sample M config/tool_shed.yml.sample M doc/source/admin/galaxy_options.rst M lib/galaxy/webapps/config_manage.py M lib/galaxy/webapps/galaxy/config_schema.yml

Log Message: ----------- remove Paste config option, reword URL prefix

Commit: 6d24026ba59fbe3e534067cd8dce76d4e6a2f38f https://github.com/galaxyproject/galaxy/commit/6d24026ba59fbe3e534067cd8dce7... Author: Marius van den Beek m.vandenbeek@gmail.com Date: 2019-02-19 (Tue, 19 Feb 2019)

Changed paths: M config/galaxy.yml.sample M config/reports.yml.sample M config/tool_shed.yml.sample M doc/source/admin/galaxy_options.rst M lib/galaxy/webapps/config_manage.py M lib/galaxy/webapps/galaxy/config_schema.yml

Log Message: ----------- Merge pull request #11 from martenson/fix_galaxy_yml_prefix_comments

remove Paste config option, reword URL prefix

Commit: ac9b300df66bc696a7e2c3a2093ded02222ac1e4 https://github.com/galaxyproject/galaxy/commit/ac9b300df66bc696a7e2c3a2093de... Author: Martin Cech marten@bx.psu.edu Date: 2019-02-19 (Tue, 19 Feb 2019)

Changed paths: M config/datatypes_conf.xml.sample A lib/galaxy/datatypes/anvio.py

Log Message: ----------- Merge pull request #7385 from blankenberg/19.01-anvio-datatypes

[19.01] Add datatypes for Anvi'o

Commit: b4fc7c19a80c38b595cb08f05fd6765a07f95920 https://github.com/galaxyproject/galaxy/commit/b4fc7c19a80c38b595cb08f05fd67... Author: mvdbeek m.vandenbeek@gmail.com Date: 2019-02-20 (Wed, 20 Feb 2019)

Changed paths: M lib/galaxy/tools/__init__.py

Log Message: ----------- Report line number mismatch in sort collection tool

Otherwise this would just fail because sorted_elements is undefined. I don't think there can be a HDA without metadata, so I've dropped that check.

Commit: 015ce5cedc21c1a318d6455534f52f8acc3d36ca https://github.com/galaxyproject/galaxy/commit/015ce5cedc21c1a318d6455534f52... Author: Martin Cech marten@bx.psu.edu Date: 2019-02-20 (Wed, 20 Feb 2019)

Changed paths: A doc/source/releases/19.01.rst M doc/source/releases/19.01_announce.rst A doc/source/releases/19.05_announce.rst M doc/source/releases/index.rst

Log Message: ----------- Merge pull request #7308 from jmchilton/19.01_release_notes

[19.01] Release notes for 19.01.

Commit: 648d01685bf26c9dcb5231cc61755d95a4696928 https://github.com/galaxyproject/galaxy/commit/648d01685bf26c9dcb5231cc61755... Author: Martin Cech marten@bx.psu.edu Date: 2019-02-20 (Wed, 20 Feb 2019)

Changed paths: M lib/galaxy/tools/__init__.py

Log Message: ----------- Merge pull request #7390 from mvdbeek/more_useful_error_message

[19.01] Report line number mismatch in sort collection tool

Commit: 8c9c27b7f6bd14581af870b0d38339d90501e464 https://github.com/galaxyproject/galaxy/commit/8c9c27b7f6bd14581af870b0d3833... Author: mvdbeek m.vandenbeek@gmail.com Date: 2019-02-21 (Thu, 21 Feb 2019)

Changed paths: M config/galaxy.yml.sample M doc/source/admin/galaxy_options.rst

Log Message: ----------- Drop filter-with from docs / .sample

Commit: 726ad9a0f68d134d7bc2ffa37ad3f369787d19da https://github.com/galaxyproject/galaxy/commit/726ad9a0f68d134d7bc2ffa37ad3f... Author: Dannon Baker dannon.baker@gmail.com Date: 2019-02-21 (Thu, 21 Feb 2019)

Changed paths: M Makefile M scripts/common_startup.sh

Log Message: ----------- Bump yarn's network timeout from 2 minutes to 5 minutes.

Commit: 4ad4fe59be7bbcc1917d3a1e039fa3f3a8367709 https://github.com/galaxyproject/galaxy/commit/4ad4fe59be7bbcc1917d3a1e039fa... Author: Martin Cech marten@bx.psu.edu Date: 2019-02-21 (Thu, 21 Feb 2019)

Changed paths: M Makefile M scripts/common_startup.sh

Log Message: ----------- Merge pull request #7399 from dannon/bump_yarn_network_tolerance

[19.01] Bump yarn network tolerance

Commit: 1a0f067590d8dcd88857e38d58f62b95a467c641 https://github.com/galaxyproject/galaxy/commit/1a0f067590d8dcd88857e38d58f62... Author: Martin Cech marten@bx.psu.edu Date: 2019-02-21 (Thu, 21 Feb 2019)

Changed paths: M config/galaxy.yml.sample M doc/source/admin/galaxy_options.rst M lib/galaxy/webapps/galaxy/config_schema.yml

Log Message: ----------- change config schema to reflect removing paste options

Commit: 351c188830793946ce6fa71dfaab95fe3af7cf7a https://github.com/galaxyproject/galaxy/commit/351c188830793946ce6fa71dfaab9... Author: Nicola Soranzo nicola.soranzo@earlham.ac.uk Date: 2019-02-22 (Fri, 22 Feb 2019)

Changed paths: M config/galaxy.yml.sample M config/reports.yml.sample M config/tool_shed.yml.sample M doc/source/admin/galaxy_options.rst M doc/source/admin/reports_options.rst M lib/galaxy/webapps/galaxy/config_schema.yml M lib/galaxy/webapps/reports/config_schema.yml M lib/galaxy/webapps/tool_shed/config_schema.yml

Log Message: ----------- Remove ``filter-with`` and update ``cookie_path`` options also for Tool Shed and Reports

Commit: a83eb67775442f37b22ff20203b88a234ab11bec https://github.com/galaxyproject/galaxy/commit/a83eb67775442f37b22ff20203b88... Author: Nate Coraor nate@bx.psu.edu Date: 2019-02-22 (Fri, 22 Feb 2019)

Changed paths: M config/galaxy.yml.sample M config/reports.yml.sample M config/tool_shed.yml.sample M doc/source/admin/galaxy_options.rst M doc/source/admin/reports_options.rst M lib/galaxy/webapps/galaxy/config_schema.yml M lib/galaxy/webapps/reports/config_schema.yml M lib/galaxy/webapps/tool_shed/config_schema.yml

Log Message: ----------- Slight rewording of the cookie_path option description, and corrections to file_path and new_file_path descriptions.

Commit: 5fc5b4aaab373d344f6d286e9dab4b2ce78f98eb https://github.com/galaxyproject/galaxy/commit/5fc5b4aaab373d344f6d286e9dab4... Author: Marius van den Beek m.vandenbeek@gmail.com Date: 2019-02-22 (Fri, 22 Feb 2019)

Changed paths: M config/galaxy.yml.sample M config/reports.yml.sample M config/tool_shed.yml.sample M doc/source/admin/galaxy_options.rst M doc/source/admin/reports_options.rst M lib/galaxy/webapps/galaxy/config_schema.yml M lib/galaxy/webapps/reports/config_schema.yml M lib/galaxy/webapps/tool_shed/config_schema.yml

Log Message: ----------- Merge pull request #12 from natefoo/mvdbeek-fix_galaxy_yml_prefix_comments

Slight rewording of the cookie_path option description, and corrections to file_path and new_file_path descriptions

Commit: 656b3c2f87a0dfd49284e113d7df6f2b88b43464 https://github.com/galaxyproject/galaxy/commit/656b3c2f87a0dfd49284e113d7df6... Author: John Chilton jmchilton@gmail.com Date: 2019-02-22 (Fri, 22 Feb 2019)

Changed paths: M lib/galaxy/webapps/galaxy/controllers/dataset.py

Log Message: ----------- Refactor dataset fetching in get/set dataset method in web controller.

Commit: 1529758ecb781a8bcbfe727acad9e7f2209c824b https://github.com/galaxyproject/galaxy/commit/1529758ecb781a8bcbfe727acad9e... Author: John Chilton jmchilton@gmail.com Date: 2019-02-22 (Fri, 22 Feb 2019)

Changed paths: M lib/galaxy/webapps/galaxy/controllers/dataset.py

Log Message: ----------- Merge branch 'release_18.01' into release_18.05

Commit: 2f973ac7fa7726ff309a8a8893962fbcd58ffded https://github.com/galaxyproject/galaxy/commit/2f973ac7fa7726ff309a8a8893962... Author: John Chilton jmchilton@gmail.com Date: 2019-02-22 (Fri, 22 Feb 2019)

Changed paths: M lib/galaxy/webapps/galaxy/controllers/dataset.py

Log Message: ----------- Merge branch 'release_18.05' into release_18.09

Commit: 8651e1eea3779233c1dff3c28ae7b4a0c3fb9735 https://github.com/galaxyproject/galaxy/commit/8651e1eea3779233c1dff3c28ae7b... Author: John Chilton jmchilton@gmail.com Date: 2019-02-22 (Fri, 22 Feb 2019)

Changed paths: M lib/galaxy/webapps/galaxy/controllers/dataset.py

Log Message: ----------- Merge branch 'release_18.09' into release_19.01

Commit: 9b72f5a880e39d1a3fd99d8aa6b1509f4e8d6ad1 https://github.com/galaxyproject/galaxy/commit/9b72f5a880e39d1a3fd99d8aa6b15... Author: Nicola Soranzo nicola.soranzo@gmail.com Date: 2019-02-22 (Fri, 22 Feb 2019)

Changed paths: M config/galaxy.yml.sample M config/reports.yml.sample M config/tool_shed.yml.sample M doc/source/admin/galaxy_options.rst M doc/source/admin/reports_options.rst M lib/galaxy/webapps/config_manage.py M lib/galaxy/webapps/galaxy/config_schema.yml M lib/galaxy/webapps/reports/config_schema.yml M lib/galaxy/webapps/tool_shed/config_schema.yml

Log Message: ----------- Merge pull request #7216 from mvdbeek/fix_galaxy_yml_prefix_comments

[18.09] Update configuration samples

Commit: 808aa5bef7fb5e0aa24818cc4bd9da647ccd3f01 https://github.com/galaxyproject/galaxy/commit/808aa5bef7fb5e0aa24818cc4bd9d... Author: Nate Coraor nate@bx.psu.edu Date: 2019-02-22 (Fri, 22 Feb 2019)

Changed paths: M config/galaxy.yml.sample M config/reports.yml.sample M config/tool_shed.yml.sample M doc/source/admin/galaxy_options.rst M doc/source/admin/reports_options.rst M lib/galaxy/webapps/config_manage.py M lib/galaxy/webapps/galaxy/config_schema.yml M lib/galaxy/webapps/reports/config_schema.yml M lib/galaxy/webapps/tool_shed/config_schema.yml

Log Message: ----------- Merge remote-tracking branch 'upstream/release_18.09' into release_19.01

Commit: 47ed81feb95c092587c68deb07e247c3a4d29bff https://github.com/galaxyproject/galaxy/commit/47ed81feb95c092587c68deb07e24... Author: mvdbeek m.vandenbeek@gmail.com Date: 2019-02-26 (Tue, 26 Feb 2019)

Changed paths: M tools/data_source/upload.py

Log Message: ----------- Remove unreachable print statement

I don't think an exception could ever occur here.

Commit: ed375993ebc43112e03f58779d7c8c104e67956a https://github.com/galaxyproject/galaxy/commit/ed375993ebc43112e03f58779d7c8... Author: mvdbeek m.vandenbeek@gmail.com Date: 2019-02-26 (Tue, 26 Feb 2019)

Changed paths: M lib/galaxy/datatypes/proteomics.py

Log Message: ----------- Fix analyze75 hdr file upload when convert newlines is on

Commit: bd25ff919c2f94dea446e656a757c61f8237db89 https://github.com/galaxyproject/galaxy/commit/bd25ff919c2f94dea446e656a757c... Author: Martin Cech marten@bx.psu.edu Date: 2019-02-26 (Tue, 26 Feb 2019)

Changed paths: M lib/galaxy/datatypes/proteomics.py M tools/data_source/upload.py

Log Message: ----------- Merge pull request #7414 from mvdbeek/fix_analyze_75

[19.01] Fix analyze 75 datatype upload

Commit: 14f3ce3b5092467e3d9dde9bd94fdab5f6b604b2 https://github.com/galaxyproject/galaxy/commit/14f3ce3b5092467e3d9dde9bd94fd... Author: Dannon Baker dannon.baker@gmail.com Date: 2019-02-26 (Tue, 26 Feb 2019)

Changed paths: M client/galaxy/scripts/mvc/workflow/workflow.js

Log Message: ----------- Fix workflow interface drop to import

Commit: 1583eecfdb338aae17fbb199160f7937e3b0ec01 https://github.com/galaxyproject/galaxy/commit/1583eecfdb338aae17fbb199160f7... Author: Dannon Baker dannon.baker@gmail.com Date: 2019-02-26 (Tue, 26 Feb 2019)

Changed paths: M client/galaxy/scripts/apps/extended.js M client/galaxy/scripts/components/admin/ErrorStack.vue M client/galaxy/scripts/galaxy.interactive_environments.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/workflow/workflow.js M client/galaxy/style/scss/base.scss

Log Message: ----------- Client formatting sync for 19.01

Commit: 7553326ba1af32e50c3695cbb67795fc11f0ecdc https://github.com/galaxyproject/galaxy/commit/7553326ba1af32e50c3695cbb6779... Author: John Chilton jmchilton@gmail.com Date: 2019-02-26 (Tue, 26 Feb 2019)

Changed paths: M client/galaxy/scripts/apps/extended.js M client/galaxy/scripts/components/admin/ErrorStack.vue M client/galaxy/scripts/galaxy.interactive_environments.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/workflow/workflow.js M client/galaxy/style/scss/base.scss

Log Message: ----------- Merge pull request #7415 from dannon/fix-workflow-drop-hack

[19.01] Fix workflow list drop-to-upload

Commit: fdb18045b76220b847163857e6e58acc19cef347 https://github.com/galaxyproject/galaxy/commit/fdb18045b76220b847163857e6e58... Author: John Chilton jmchilton@gmail.com Date: 2019-02-26 (Tue, 26 Feb 2019)

Changed paths: M lib/galaxy/version.py

Log Message: ----------- Update version to 19.01

Commit: 8ac4de222dd6921fa2feb89b8f2aaa0ded4f0c0f https://github.com/galaxyproject/galaxy/commit/8ac4de222dd6921fa2feb89b8f2aa... Author: John Chilton jmchilton@gmail.com Date: 2019-02-26 (Tue, 26 Feb 2019)

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test/integration/chained_dyndest_rules/module3/rules.py A test/integration/handler_template_job_conf.xml A test/integration/resubmission_pulsar_job_conf.xml A test/integration/resubmission_tool_detected_always_error_job_conf.xml A test/integration/resubmission_tool_detected_resubmit_job_conf.xml A test/integration/singularity_job_conf.xml A test/integration/test_chained_dynamic_destinations.py M test/integration/test_cli_runners.py A test/integration/test_containerized_jobs.py A test/integration/test_datatype_upload.py R test/integration/test_dockerized_jobs.py A test/integration/test_handler_assignment_methods.py M test/integration/test_job_environments.py M test/integration/test_job_resubmission.py M test/integration/test_resolvers.py M test/integration/test_scripts.py M test/integration/test_upload_configuration_options.py A test/integration/test_workflow_sync.py M test/manual/workflows_scaling.py M test/selenium_tests/framework.py M test/selenium_tests/test_admin_app.py M 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M tools/sr_mapping/PerM.xml M tools/sr_mapping/bfast_wrapper.xml M tools/stats/aggregate_scores_in_intervals.py M tools/stats/filtering.py M tools/stats/filtering.xml M tools/stats/grouping.py M tools/stats/grouping.xml M tools/stats/gsummary.py M tools/stats/gsummary.xml M tools/stats/gsummary.xml.groups

Log Message: ----------- Merge branch 'release_19.01'

Compare: https://github.com/galaxyproject/galaxy/compare/c228760e1f06...8ac4de222dd6