Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy 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 client/galaxy/images/light_gray_grid.gif A client/galaxy/images/mag_glass.png A client/galaxy/images/masthead_bg.png A client/galaxy/images/menu_bg.png A client/galaxy/images/mutation_visualization_example.png A client/galaxy/images/ok_bg.png A client/galaxy/images/ok_icon.svg A client/galaxy/images/ok_large.png A client/galaxy/images/ok_small.png A client/galaxy/images/overview_arrows.png A client/galaxy/images/panel_header_bg.png A client/galaxy/images/pearson.png A client/galaxy/images/popupmenu_callout_top.png A client/galaxy/images/question-balloon.png A client/galaxy/images/question-octagon-frame.png A client/galaxy/images/resizable.png A client/galaxy/images/scatter.png A client/galaxy/images/scatterplot.png A client/galaxy/images/select2-spinner.gif A client/galaxy/images/select2.png A client/galaxy/images/select2x2.png A client/galaxy/images/silk/add.png A client/galaxy/images/silk/book.png A client/galaxy/images/silk/book_open.png A client/galaxy/images/silk/chart_curve.png A client/galaxy/images/silk/folder.png A client/galaxy/images/silk/folder_page.png A client/galaxy/images/silk/link.png A client/galaxy/images/silk/link_break.png A client/galaxy/images/silk/page_white.png A client/galaxy/images/silk/page_white_compressed.png A client/galaxy/images/silk/resultset_bottom.png A client/galaxy/images/silk/resultset_next.png A client/galaxy/images/silk/resultset_previous.png A client/galaxy/images/solid_qual.png A client/galaxy/images/spearman.png A client/galaxy/images/sprite-fugue.png A client/galaxy/images/sprite-history-buttons.png A client/galaxy/images/sprite-history-states.png A client/galaxy/images/star.gif A client/galaxy/images/thumbtack_icon.png A client/galaxy/images/thumbtack_icon_dark.png A client/galaxy/images/tiny_arrow_left.png A client/galaxy/images/tiny_arrow_right.png A client/galaxy/images/tipsy.gif A client/galaxy/images/tracks/block.png A client/galaxy/images/tracks/close_btn.gif A client/galaxy/images/tracks/diag_bg.gif A client/galaxy/images/tracks/go_btn.gif A client/galaxy/images/tracks/handle-left.gif A client/galaxy/images/tracks/handle-right.gif A client/galaxy/images/tracks/pan_left.gif A client/galaxy/images/tracks/pan_right.gif A client/galaxy/images/tracks/show_history.gif A client/galaxy/images/tracks/zoom_in.gif A client/galaxy/images/tracks/zoom_in_full.gif A client/galaxy/images/tracks/zoom_out.gif A client/galaxy/images/tracks/zoom_out_full.gif A client/galaxy/images/visualization/draggable_horizontal.png A client/galaxy/images/visualization/draggable_vertical.png A client/galaxy/images/visualization/strand_left.png A client/galaxy/images/visualization/strand_left_inv.png A client/galaxy/images/visualization/strand_right.png A client/galaxy/images/visualization/strand_right_inv.png A client/galaxy/images/wait_icon.svg A client/galaxy/images/wait_large.png A client/galaxy/images/wait_small.png A client/galaxy/images/warn_bg.png A client/galaxy/images/warn_icon.svg A client/galaxy/images/warn_large.png A client/galaxy/images/warn_message_icon.png A client/galaxy/images/warn_small.png A client/galaxy/images/workflow_circle_drag.png A client/galaxy/images/workflow_circle_green.png A client/galaxy/images/workflow_circle_open.png A client/galaxy/jsconfig.json M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/apps/chart.js M client/galaxy/scripts/apps/extended.js M client/galaxy/scripts/apps/login.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/galaxy/scripts/galaxy.js A client/galaxy/scripts/galaxy.monitor.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/panel.js M client/galaxy/scripts/layout/router.js M client/galaxy/scripts/layout/scratchbook.js A client/galaxy/scripts/libs/jquery.custom.js M client/galaxy/scripts/mvc/base-mvc.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/list-of-pairs-collection-creator.js M client/galaxy/scripts/mvc/dataset/data.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.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/rules/rule-definitions.js M client/galaxy/scripts/mvc/tool/tools.js M client/galaxy/scripts/mvc/tours.js M client/galaxy/scripts/mvc/ui/ui-rules-edit.js M client/galaxy/scripts/mvc/ui/ui-slider.js M client/galaxy/scripts/mvc/user/user-model.js M client/galaxy/scripts/mvc/workflow/workflow-node.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M client/galaxy/scripts/nls/zh/locale.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/polyfills.js M client/galaxy/scripts/qunit/assets/base.css M client/galaxy/scripts/qunit/tests/galaxy_app_base_tests.js M client/galaxy/scripts/qunit/tests/page_tests.js M client/galaxy/scripts/reports/run_stats.js A client/galaxy/scripts/sample.test.js A client/galaxy/scripts/style.js M client/galaxy/scripts/ui/editable-text.js M client/galaxy/scripts/ui/fa-icon-button.js A client/galaxy/scripts/unitTestBundle.js M client/galaxy/scripts/utils/config.js A client/galaxy/scripts/utils/installMonitor.js A client/galaxy/scripts/utils/mock.js A client/galaxy/scripts/utils/serverPath.js M client/galaxy/scripts/viz/phyloviz.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/galaxy/style/scss/autocomplete_tagging.scss M client/galaxy/style/scss/base.scss M client/galaxy/style/scss/collection.scss M client/galaxy/style/scss/history.scss M client/galaxy/style/scss/iconic_stroke.scss A client/galaxy/style/scss/jquery.rating.scss M client/galaxy/style/scss/jstree.scss M client/galaxy/style/scss/list-item.scss M client/galaxy/style/scss/select2.scss A client/galaxy/style/scss/sprite-fugue.scss A client/galaxy/style/scss/sprite-history-buttons.scss A client/galaxy/style/scss/sprite-history-states.scss M client/galaxy/style/scss/trackster.scss M client/galaxy/style/scss/ui.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 M client/gulpfile.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/webpack.config.js M client/yarn.lock A config/container_resolvers_conf.xml.sample M config/containers_conf.yml.sample M config/datatypes_conf.xml.sample M config/galaxy.yml.sample M config/migrated_tools_conf.xml.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/common/templates/chart_entry_point.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 config/plugins/webhooks/demo/tour_generator/config.yml A config/plugins/webhooks/demo/tour_generator/package.json M config/plugins/webhooks/demo/tour_generator/script.js A config/plugins/webhooks/demo/tour_generator/tour_generator.js M config/shed_tool_conf.xml.sample M config/tool_conf.xml.main M config/tool_conf.xml.sample M doc/source/admin/conda_faq.rst M doc/source/admin/dependency_resolvers.rst 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 doc/source/admin/special_topics/bug_reports.rst M doc/source/admin/special_topics/interactive_environments.rst M doc/source/admin/tool_panel.rst M doc/source/dev/faq.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 doc/source/releases/index.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/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 A lib/galaxy/datatypes/converters/tar_to_directory.xml 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/neo4j.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 A lib/galaxy/datatypes/test/0.txt 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 A lib/galaxy/datatypes/test/1.json M lib/galaxy/datatypes/test/1.owl A lib/galaxy/datatypes/test/1.qname_sorted.bam 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/diamond.rma6 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/datatypes/util/gff_util.py M lib/galaxy/datatypes/xml.py M lib/galaxy/dependencies/conda-file.sh 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/exceptions/__init__.py M lib/galaxy/exceptions/error_codes.json M lib/galaxy/jobs/__init__.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/__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/jobs/runners/util/cli/shell/local.py M lib/galaxy/jobs/runners/util/cli/shell/rsh.py M lib/galaxy/managers/base.py M lib/galaxy/managers/cloud.py M lib/galaxy/managers/collections.py M lib/galaxy/managers/context.py M lib/galaxy/managers/datasets.py M lib/galaxy/managers/folders.py M lib/galaxy/managers/libraries.py M lib/galaxy/managers/library_datasets.py M lib/galaxy/managers/rbac_secured.py M lib/galaxy/managers/sharable.py M lib/galaxy/managers/tags.py M lib/galaxy/managers/users.py M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/model/custom_types.py M lib/galaxy/model/mapping.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/model/search.py M lib/galaxy/objectstore/cloud.py M lib/galaxy/security/__init__.py M lib/galaxy/security/validate_user_input.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/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/data/__init__.py M lib/galaxy/tools/deps/brew_exts.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/containers.py M lib/galaxy/tools/deps/docker_util.py M lib/galaxy/tools/deps/mulled/mulled_build.py M lib/galaxy/tools/deps/mulled/mulled_build_channel.py M lib/galaxy/tools/deps/resolvers/conda.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/execute.py 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/dynamic_options.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/tools/parameters/history_query.py M lib/galaxy/tools/parser/cwl.py M lib/galaxy/tools/parser/xml.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/verify/asserts/__init__.py M lib/galaxy/tools/verify/interactor.py M lib/galaxy/tools/verify/test_data.py M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/util/__init__.py M lib/galaxy/util/checkers.py M lib/galaxy/util/compression_utils.py M lib/galaxy/util/inflection.py M lib/galaxy/util/json.py M lib/galaxy/util/monitors.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/decorators.py M lib/galaxy/web/framework/middleware/batch.py M lib/galaxy/webapps/galaxy/api/cloud.py M lib/galaxy/webapps/galaxy/api/cloudauthz.py M lib/galaxy/webapps/galaxy/api/configuration.py M lib/galaxy/webapps/galaxy/api/datasets.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/uploads.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/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/data_manager.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/forms.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/page.py M lib/galaxy/webapps/galaxy/controllers/tool_runner.py M lib/galaxy/webapps/galaxy/controllers/user.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/api/tools.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/upload.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/capsule/capsule_manager.py M lib/tool_shed/galaxy_install/migrate/check.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/managers/groups.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/common_util.py M lib/tool_shed/util/hg_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 run_tests.sh M scripts/bootstrap_history.py M scripts/check_python.py M scripts/cleanup_datasets/pgcleanup.py M scripts/get_uwsgi_args.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 R static/GruntFile.js R static/images/Armitagep_manhattan.png R static/images/Armitagep_qqplot.png R static/images/add_icon.png R static/images/add_icon_dark.png R static/images/aggregate_history1.png R static/images/aggregate_history2.png R static/images/bar_chart.png R static/images/bed_warn.png R static/images/closebox.png R static/images/dat_points_table_brows_1.png R static/images/ddarrowsplit.png R static/images/delete.gif A static/images/delete_tag_icon_gray.png R static/images/delete_tag_icon_gray.png R static/images/delete_tag_icon_white.png R static/images/documents-stack-faded.png R static/images/documents-stack.png R static/images/dropdownarrow.png R static/images/fetchTax.png A static/images/fugue R static/images/fugue/application-dock-270-bw.png R 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/hatch-023858.png R static/images/histogram.png R static/images/histogram2.png R static/images/jstree/32px.png R static/images/jstree/40px.png R static/images/jstree/throbber.gif R static/images/kendall.png R static/images/light_gray_grid.gif R static/images/mag_glass.png R static/images/mutation_visualization_example.png R static/images/overview_arrows.png R static/images/pearson.png R static/images/resizable.png R static/images/scatter.png R static/images/scatterplot.png R static/images/select2-spinner.gif R static/images/select2.png R static/images/select2x2.png R static/images/silk/add.png R static/images/silk/book.png R static/images/silk/book_open.png R static/images/silk/chart_curve.png R static/images/silk/folder.png R static/images/silk/folder_page.png R static/images/silk/link.png R static/images/silk/link_break.png R static/images/silk/page_white.png R static/images/silk/page_white_compressed.png R static/images/silk/resultset_bottom.png R static/images/silk/resultset_next.png R static/images/silk/resultset_previous.png R static/images/solid_qual.png R static/images/spearman.png R static/images/star.gif R static/images/thumbtack_icon.png R static/images/thumbtack_icon_dark.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 A static/images/visualization R static/images/visualization/draggable_horizontal.png R static/images/visualization/draggable_vertical.png R static/images/visualization/strand_left.png R static/images/visualization/strand_left_inv.png R static/images/visualization/strand_right.png R static/images/visualization/strand_right_inv.png M static/style/base.css A static/style/blue/base.css R static/style/blue/base.css R static/style/blue/base_bg.png R static/style/blue/button_bar_bg_light.png R static/style/blue/data_empty.png R static/style/blue/data_error.png R static/style/blue/data_ok.png R static/style/blue/data_queued.png R static/style/blue/done_message_icon.png R static/style/blue/error_bg.png R static/style/blue/error_large.png R static/style/blue/error_message_icon.png R static/style/blue/error_small.png R static/style/blue/footer_title_bg.png R static/style/blue/form_body_bg.png R static/style/blue/form_title_bg.png R static/style/blue/fugue.png R static/style/blue/gray_bg.png R static/style/blue/hgrad.png R static/style/blue/hgrad_over.png R static/style/blue/history-buttons.png R static/style/blue/history-states.png A static/style/blue/info_icon.svg R static/style/blue/info_large.png R static/style/blue/info_message_icon.png R static/style/blue/info_small.png R static/style/blue/largespinner.gif R static/style/blue/layout_callout_top.png R static/style/blue/masthead_bg.png R static/style/blue/menu_bg.png R static/style/blue/ok_bg.png R static/style/blue/ok_large.png A static/style/blue/ok_small.png R static/style/blue/ok_small.png R static/style/blue/panel_header_bg.png R static/style/blue/popupmenu_callout_top.png R static/style/blue/question-balloon.png A static/style/blue/question-octagon-frame.png R static/style/blue/question-octagon-frame.png R static/style/blue/tiny_arrow_left.png R static/style/blue/tiny_arrow_right.png M static/style/blue/trackster.css R static/style/blue/wait_large.png R static/style/blue/wait_small.png R static/style/blue/warn_bg.png R static/style/blue/warn_large.png R 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/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/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/show_params.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 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 templates/webapps/galaxy/galaxy.masthead.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/common/repository_actions_menu.mako M templates/webapps/tool_shed/common/reset_metadata_on_selected_repositories.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 M templates/webapps/tool_shed/role/role.mako M templates/webapps/tool_shed/user/username.mako A test-data/MTBLS6.zip 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/driver_util.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 M test/functional/tools/disambiguate_cond.xml 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/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/navigates_galaxy.py M test/galaxy_selenium/navigation.yml A test/integration/test_cli_runners.py A test/integration/test_datatype_upload.py M test/integration/test_job_environments.py M test/integration/test_upload_configuration_options.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_library_contents.py M test/selenium_tests/test_uploads.py M test/shed_functional/base/twilltestcase.py M test/shed_functional/functional/test_1460_data_managers.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/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 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_filters.py M test/unit/web/framework/test_webapp.py M test/unit/workflows/test_extract_summary.py M test/unit/workflows/test_workflow_progress.py A tools/cloud/send.py A tools/cloud/send.xml 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 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: 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: 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: 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: 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: 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 Compare: https://github.com/galaxyproject/galaxy/compare/3ed0ce862bf9...cfacaae8b50c **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.