Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 77c34446728f414491dd7a14fc5992800d9ae32a https://github.com/galaxyproject/galaxy/commit/77c34446728f414491dd7a14fc599... Author: vjalili <jalili.vahid@gmail.com> Date: 2018-05-07 (Mon, 07 May 2018) Changed paths: M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Add webapp mapper for cloud upload API. Commit: 92830a1c155450a68bdd5d214d3f432f00056a1c https://github.com/galaxyproject/galaxy/commit/92830a1c155450a68bdd5d214d3f4... Author: vjalili <jalili.vahid@gmail.com> Date: 2018-05-07 (Mon, 07 May 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/cloud.py Log Message: ----------- Implement cloud upload API. Commit: 4e23c5e67dbc57ff03512f65549d6ea097a70deb https://github.com/galaxyproject/galaxy/commit/4e23c5e67dbc57ff03512f65549d6... Author: vjalili <jalili.vahid@gmail.com> Date: 2018-05-07 (Mon, 07 May 2018) Changed paths: M lib/galaxy/managers/cloud.py Log Message: ----------- Implement logic of uploading dataset(s) to cloud in the cloud manager. Commit: 62d67c9c401c2c5c1547457fe82229cf97e7e0ff https://github.com/galaxyproject/galaxy/commit/62d67c9c401c2c5c1547457fe8222... Author: vjalili <jalili.vahid@gmail.com> Date: 2018-05-07 (Mon, 07 May 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/cloud.py Log Message: ----------- Check for missing arguments from payload in cloud upload api. Commit: 63be2dba410c1d1cc17e6e4a1030d100bf5eaf6b https://github.com/galaxyproject/galaxy/commit/63be2dba410c1d1cc17e6e4a1030d... Author: vjalili <jalili.vahid@gmail.com> Date: 2018-05-07 (Mon, 07 May 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/cloud.py Log Message: ----------- Assert the validity of provided history ID in cloud upload API. Commit: 6a9ce39a2147b0b2449e4eaf73fb6e54399b5976 https://github.com/galaxyproject/galaxy/commit/6a9ce39a2147b0b2449e4eaf73fb6... Author: vjalili <jalili.vahid@gmail.com> Date: 2018-05-07 (Mon, 07 May 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/cloud.py Log Message: ----------- Assert the validity of provided dataset ID(s). Commit: ff42cc7b0684c47191a94e4d1a016dcbc7ef21b1 https://github.com/galaxyproject/galaxy/commit/ff42cc7b0684c47191a94e4d1a016... Author: vjalili <jalili.vahid@gmail.com> Date: 2018-05-07 (Mon, 07 May 2018) Changed paths: M lib/galaxy/managers/cloud.py M lib/galaxy/webapps/galaxy/api/cloud.py Log Message: ----------- In cloud upload API, handle overwriting an existing object. Commit: f1b9a23c939f20718b430916e5e5fdd4d9b2a330 https://github.com/galaxyproject/galaxy/commit/f1b9a23c939f20718b430916e5e5f... Author: vjalili <jalili.vahid@gmail.com> Date: 2018-05-07 (Mon, 07 May 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/cloud.py Log Message: ----------- Use named arguments in cloud upload API when calling its manager. Commit: 35a30219f652741e20f6810b42c21dbf3e74e0c0 https://github.com/galaxyproject/galaxy/commit/35a30219f652741e20f6810b42c21... Author: vjalili <jalili.vahid@gmail.com> Date: 2018-05-07 (Mon, 07 May 2018) Changed paths: M lib/galaxy/managers/cloud.py Log Message: ----------- Fix a bug in cloud upload API. Commit: 17ab3e8d2dff82996264a3404fda800a707b8487 https://github.com/galaxyproject/galaxy/commit/17ab3e8d2dff82996264a3404fda8... Author: vjalili <jalili.vahid@gmail.com> Date: 2018-05-07 (Mon, 07 May 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/cloud.py Log Message: ----------- Update cloud upload API description. Commit: 0ed19ad7b0402c7be544a358386b80377d63d85c https://github.com/galaxyproject/galaxy/commit/0ed19ad7b0402c7be544a358386b8... Author: vjalili <jalili.vahid@gmail.com> Date: 2018-05-07 (Mon, 07 May 2018) Changed paths: M lib/galaxy/managers/cloud.py M lib/galaxy/webapps/galaxy/api/cloud.py Log Message: ----------- Update cloud upload API description. Commit: 3b74bd899c323f99135362a23f64726cd09ee331 https://github.com/galaxyproject/galaxy/commit/3b74bd899c323f99135362a23f647... Author: vjalili <jalili.vahid@gmail.com> Date: 2018-05-07 (Mon, 07 May 2018) Changed paths: M lib/galaxy/managers/cloud.py Log Message: ----------- Fix bugs related to import order and boolean assert in cloud upload API. Commit: c7c7691c98b2ef2cdeee5bf7661b9415e6eebf86 https://github.com/galaxyproject/galaxy/commit/c7c7691c98b2ef2cdeee5bf7661b9... Author: vjalili <jalili.vahid@gmail.com> Date: 2018-07-12 (Thu, 12 Jul 2018) Changed paths: M .ci/flake8_blacklist.txt M .ci/jenkins/selenium/run_tests.sh M .gitignore M .travis.yml M Makefile M client/GruntFile.js M client/bower.json A 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 A client/galaxy/docs/galaxy-tables.md A client/galaxy/docs/galaxy-tabs.md 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/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/HistoryImport.vue M client/galaxy/scripts/components/HistoryView.vue M client/galaxy/scripts/components/PluginList.vue M client/galaxy/scripts/components/RuleCollectionBuilder.vue A client/galaxy/scripts/components/RulesDisplay.vue A client/galaxy/scripts/components/Sharing.vue A client/galaxy/scripts/components/WorkflowImport.vue M client/galaxy/scripts/components/admin/DataTablesGrid.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/communication-server-view.js A client/galaxy/scripts/layout/data.js R client/galaxy/scripts/layout/generic-nav-view.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/legacy/grid/grid-view.js R client/galaxy/scripts/libs/bootstrap-tour.js R client/galaxy/scripts/libs/bootstrap.js A client/galaxy/scripts/mocha/test.js A client/galaxy/scripts/mocha/tests/rules_dsl_spec.yml A client/galaxy/scripts/mocha/tests/rules_tests.js M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M client/galaxy/scripts/mvc/collection/pair-collection-creator.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-parameters.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/form/form-wrapper.js M client/galaxy/scripts/mvc/grid/grid-model.js M client/galaxy/scripts/mvc/grid/grid-shared.js M client/galaxy/scripts/mvc/grid/grid-template.js M client/galaxy/scripts/mvc/grid/grid-view.js M client/galaxy/scripts/mvc/history/hdca-li-edit.js M client/galaxy/scripts/mvc/history/history-contents.js M client/galaxy/scripts/mvc/history/history-item-li.js M client/galaxy/scripts/mvc/history/history-list.js M client/galaxy/scripts/mvc/history/history-model.js R client/galaxy/scripts/mvc/history/history-structure-view.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/history/multi-panel.js M client/galaxy/scripts/mvc/history/options-menu.js M client/galaxy/scripts/mvc/library/library-dataset-view.js M client/galaxy/scripts/mvc/library/library-folder-view.js M client/galaxy/scripts/mvc/library/library-folderlist-view.js M client/galaxy/scripts/mvc/library/library-folderrow-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/library/library-library-view.js M client/galaxy/scripts/mvc/library/library-librarylist-view.js M client/galaxy/scripts/mvc/library/library-libraryrow-view.js M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js M client/galaxy/scripts/mvc/list/list-view.js A client/galaxy/scripts/mvc/rules/rule-definitions.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/tools.js M client/galaxy/scripts/mvc/tours.js M client/galaxy/scripts/mvc/ui/error-modal.js M client/galaxy/scripts/mvc/ui/ui-buttons.js M client/galaxy/scripts/mvc/ui/ui-drilldown.js M client/galaxy/scripts/mvc/ui/ui-frames.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-modal.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 A 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-library.js M client/galaxy/scripts/mvc/ui/ui-select.js M client/galaxy/scripts/mvc/ui/ui-tabs.js M 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/rules-input-view.js M client/galaxy/scripts/mvc/upload/composite/composite-row.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-button.js M client/galaxy/scripts/mvc/upload/upload-ftp.js M client/galaxy/scripts/mvc/user/user-quotameter.js M client/galaxy/scripts/mvc/visualization/chart/components/model.js M client/galaxy/scripts/mvc/visualization/chart/components/screenshot.js M client/galaxy/scripts/mvc/visualization/chart/utilities/jobs.js M client/galaxy/scripts/mvc/visualization/chart/utilities/series.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-node.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/qunit/test-app.js M client/galaxy/scripts/qunit/tests/form_tests.js M client/galaxy/scripts/qunit/tests/masthead_tests.js M client/galaxy/scripts/qunit/tests/ui_tests.js M client/galaxy/scripts/reports/run_stats.js M client/galaxy/scripts/toolshed/groups/group-detail-view.js M client/galaxy/scripts/toolshed/groups/group-list-view.js M client/galaxy/scripts/ui/filter-control.js M client/galaxy/scripts/utils/async-save-text.js M client/galaxy/scripts/utils/config.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/sweepster.js M client/galaxy/scripts/viz/trackster.js M client/galaxy/scripts/viz/trackster/painters.js M client/galaxy/scripts/viz/trackster/tracks.js M client/galaxy/scripts/viz/visualization.js R client/galaxy/style/less/autocomplete_tagging.less R client/galaxy/style/less/base.less R client/galaxy/style/less/bootstrap.less R client/galaxy/style/less/bootstrap/alerts.less R client/galaxy/style/less/bootstrap/badges.less R client/galaxy/style/less/bootstrap/bootstrap.less R client/galaxy/style/less/bootstrap/breadcrumbs.less R client/galaxy/style/less/bootstrap/button-groups.less R client/galaxy/style/less/bootstrap/buttons.less R client/galaxy/style/less/bootstrap/carousel.less R client/galaxy/style/less/bootstrap/close.less R client/galaxy/style/less/bootstrap/code.less R client/galaxy/style/less/bootstrap/component-animations.less R client/galaxy/style/less/bootstrap/dropdowns.less R client/galaxy/style/less/bootstrap/forms.less R client/galaxy/style/less/bootstrap/glyphicons.less R client/galaxy/style/less/bootstrap/grid.less R client/galaxy/style/less/bootstrap/input-groups.less R client/galaxy/style/less/bootstrap/jumbotron.less R client/galaxy/style/less/bootstrap/labels.less R client/galaxy/style/less/bootstrap/list-group.less R client/galaxy/style/less/bootstrap/media.less R client/galaxy/style/less/bootstrap/mixins.less R client/galaxy/style/less/bootstrap/modals.less R client/galaxy/style/less/bootstrap/navbar.less R client/galaxy/style/less/bootstrap/navs.less R client/galaxy/style/less/bootstrap/normalize.less R client/galaxy/style/less/bootstrap/pager.less R client/galaxy/style/less/bootstrap/pagination.less R client/galaxy/style/less/bootstrap/panels.less R client/galaxy/style/less/bootstrap/popovers.less R client/galaxy/style/less/bootstrap/print.less R client/galaxy/style/less/bootstrap/progress-bars.less R client/galaxy/style/less/bootstrap/responsive-utilities.less R client/galaxy/style/less/bootstrap/scaffolding.less R client/galaxy/style/less/bootstrap/tables.less R client/galaxy/style/less/bootstrap/theme.less R client/galaxy/style/less/bootstrap/thumbnails.less R client/galaxy/style/less/bootstrap/tooltip.less R client/galaxy/style/less/bootstrap/type.less R client/galaxy/style/less/bootstrap/utilities.less R client/galaxy/style/less/bootstrap/variables.less R client/galaxy/style/less/bootstrap/wells.less R client/galaxy/style/less/charts.less R client/galaxy/style/less/circster.less R client/galaxy/style/less/collection.less R client/galaxy/style/less/dataset.less R client/galaxy/style/less/embed_item.less R client/galaxy/style/less/flex.less R client/galaxy/style/less/fontawesome/bordered-pulled.less R client/galaxy/style/less/fontawesome/core.less R client/galaxy/style/less/fontawesome/fixed-width.less R client/galaxy/style/less/fontawesome/font-awesome.less R client/galaxy/style/less/fontawesome/icons.less R client/galaxy/style/less/fontawesome/larger.less R client/galaxy/style/less/fontawesome/list.less R client/galaxy/style/less/fontawesome/mixins.less R client/galaxy/style/less/fontawesome/path.less R client/galaxy/style/less/fontawesome/rotated-flipped.less R client/galaxy/style/less/fontawesome/spinning.less R client/galaxy/style/less/fontawesome/stacked.less R client/galaxy/style/less/fontawesome/variables.less R client/galaxy/style/less/frame.less R client/galaxy/style/less/galaxy_bootstrap.less R client/galaxy/style/less/galaxy_bootstrap/overrides.less R client/galaxy/style/less/galaxy_bootstrap/variables.less R client/galaxy/style/less/galaxy_variables.less R client/galaxy/style/less/history.less R client/galaxy/style/less/iconic_stroke.less R client/galaxy/style/less/job.less R client/galaxy/style/less/jstree.less R client/galaxy/style/less/library.less R client/galaxy/style/less/list-item.less R client/galaxy/style/less/reports.less R client/galaxy/style/less/select2.less R client/galaxy/style/less/theme/blue.less R client/galaxy/style/less/theme/plain.less R client/galaxy/style/less/toastr.less R client/galaxy/style/less/tour.less R client/galaxy/style/less/trackster.less R client/galaxy/style/less/ui.less R client/galaxy/style/less/ui/dataset-choice.less R client/galaxy/style/less/ui/error-modal.less R client/galaxy/style/less/ui/icon-btn.less R client/galaxy/style/less/ui/pagination.less R client/galaxy/style/less/ui/paired-collection-creator.less R client/galaxy/style/less/ui/peek-column-selector.less R client/galaxy/style/less/ui/search-input.less R client/galaxy/style/less/upload.less A client/galaxy/style/scss/autocomplete_tagging.scss A client/galaxy/style/scss/base.scss A client/galaxy/style/scss/charts.scss A client/galaxy/style/scss/circster.scss A client/galaxy/style/scss/collection.scss A client/galaxy/style/scss/dataset.scss A client/galaxy/style/scss/embed_item.scss A client/galaxy/style/scss/flex.scss A client/galaxy/style/scss/frame.scss A client/galaxy/style/scss/galaxy_bootstrap/overrides.scss A client/galaxy/style/scss/galaxy_bootstrap/variables.scss A client/galaxy/style/scss/galaxy_variables.scss A client/galaxy/style/scss/history.scss A client/galaxy/style/scss/iconic_stroke.scss A client/galaxy/style/scss/job.scss A client/galaxy/style/scss/jstree.scss A client/galaxy/style/scss/library.scss A client/galaxy/style/scss/list-item.scss A client/galaxy/style/scss/reports.scss A client/galaxy/style/scss/select2.scss A client/galaxy/style/scss/theme/blue.scss A client/galaxy/style/scss/theme/plain.scss A client/galaxy/style/scss/toastr.scss A client/galaxy/style/scss/tour.scss A client/galaxy/style/scss/trackster.scss A client/galaxy/style/scss/ui.scss A client/galaxy/style/scss/ui/dataset-choice.scss A client/galaxy/style/scss/ui/error-modal.scss A client/galaxy/style/scss/ui/icon-btn.scss A client/galaxy/style/scss/ui/pagination.scss A client/galaxy/style/scss/ui/paired-collection-creator.scss A client/galaxy/style/scss/ui/peek-column-selector.scss A client/galaxy/style/scss/ui/search-input.scss A client/galaxy/style/scss/upload.scss R client/grunt-tasks/style.js M client/gulpfile.js M client/karma.config.js M client/package.json A client/styleguide.config.js M client/webpack.config.js M client/yarn.lock M config/containers_conf.yml.sample M config/datatypes_conf.xml.sample M config/galaxy.yml.sample M config/job_conf.xml.sample_advanced M config/job_conf.xml.sample_basic M config/job_metrics_conf.xml.sample M config/local_conda_mapping.yml.sample A config/oidc_backends_config.xml.sample A config/oidc_config.xml.sample M config/plugins/interactive_environments/common/templates/ie.mako M config/plugins/interactive_environments/jupyter/static/js/jupyter.js M config/plugins/interactive_environments/jupyter/templates/jupyter.mako M config/plugins/tours/core.scratchbook.yaml M config/plugins/visualizations/common/templates/chart_entry_point.mako M config/plugins/visualizations/csg/templates/csg.mako M config/plugins/visualizations/cytoscape/config/cytoscape.xml M config/plugins/visualizations/drawrna/config/drawrna.xml M config/plugins/visualizations/example/config/example.xml M config/plugins/visualizations/graphviz/templates/graphviz.mako M config/plugins/visualizations/heatmap/heatmap_cluster/config/heatmap_cluster.xml M config/plugins/visualizations/heatmap/heatmap_default/config/heatmap_default.xml M config/plugins/visualizations/heatmap/heatmap_default/src/script.js M config/plugins/visualizations/heatmap/heatmap_default/static/script.js A config/plugins/visualizations/hivtrace/config/hivtrace.xml A config/plugins/visualizations/hivtrace/static/448c34a56d699c29117adc64c43affeb.woff2 A config/plugins/visualizations/hivtrace/static/674f50d287a8c48dc19ba404d20fe713.eot A config/plugins/visualizations/hivtrace/static/89889688147bd7575d6327160d64e760.svg A config/plugins/visualizations/hivtrace/static/912ec66d7572ff821749319396470bde.svg A config/plugins/visualizations/hivtrace/static/af7ae505a9eed503f8b8e6982036873e.woff2 A config/plugins/visualizations/hivtrace/static/b06871f281fee6b241d60582ae9369b9.ttf A config/plugins/visualizations/hivtrace/static/e18bbf611f2a2e43afc071aa2f4e1512.ttf A config/plugins/visualizations/hivtrace/static/f4769f9bdb7466be65088239c12046d1.eot A config/plugins/visualizations/hivtrace/static/fa2772327f55d8198301fdb8bcfc8158.woff A config/plugins/visualizations/hivtrace/static/fee66e712a8a08eef5805a46892932ad.woff A config/plugins/visualizations/hivtrace/static/hivtrace.css A config/plugins/visualizations/hivtrace/static/hivtrace.css.map A config/plugins/visualizations/hivtrace/static/hivtrace.js A config/plugins/visualizations/hivtrace/static/hivtrace.js.map A config/plugins/visualizations/hivtrace/static/logo.png A config/plugins/visualizations/hivtrace/static/vendor.js A config/plugins/visualizations/hivtrace/static/vendor.js.map A config/plugins/visualizations/hivtrace/templates/index.mako M config/plugins/visualizations/jqplot/jqplot_bar/config/jqplot_bar.xml M config/plugins/visualizations/jqplot/jqplot_bar/src/script.js M config/plugins/visualizations/jqplot/jqplot_bar/static/script.css M config/plugins/visualizations/jqplot/jqplot_bar/static/script.js M config/plugins/visualizations/jqplot/jqplot_box/config/jqplot_box.xml M config/plugins/visualizations/jqplot/jqplot_histogram/config/jqplot_histogram.xml M config/plugins/visualizations/jqplot/jqplot_line/config/jqplot_line.xml M config/plugins/visualizations/jqplot/jqplot_scatter/config/jqplot_scatter.xml M config/plugins/visualizations/msa/config/msa.xml M config/plugins/visualizations/ngl/config/ngl.xml M config/plugins/visualizations/nvd3/nvd3_bar/config/nvd3_bar.xml M config/plugins/visualizations/nvd3/nvd3_bar_stacked/config/nvd3_bar_stacked.xml M config/plugins/visualizations/nvd3/nvd3_histogram/config/nvd3_histogram.xml M config/plugins/visualizations/nvd3/nvd3_histogram_discrete/config/nvd3_histogram_discrete.xml M config/plugins/visualizations/nvd3/nvd3_horizontal/config/nvd3_horizontal.xml M config/plugins/visualizations/nvd3/nvd3_horizontal_stacked/config/nvd3_horizontal_stacked.xml M config/plugins/visualizations/nvd3/nvd3_line/config/nvd3_line.xml M config/plugins/visualizations/nvd3/nvd3_line_focus/config/nvd3_line_focus.xml M config/plugins/visualizations/nvd3/nvd3_pie/config/nvd3_pie.xml M config/plugins/visualizations/nvd3/nvd3_scatter/config/nvd3_scatter.xml M config/plugins/visualizations/nvd3/nvd3_stackedarea/config/nvd3_stackedarea.xml M config/plugins/visualizations/nvd3/nvd3_stackedarea_full/config/nvd3_stackedarea_full.xml M config/plugins/visualizations/nvd3/nvd3_stackedarea_stream/config/nvd3_stackedarea_stream.xml M config/plugins/visualizations/phylocanvas/config/phylocanvas.xml M config/plugins/visualizations/pv/config/pv.xml M config/plugins/visualizations/scatterplot/templates/scatterplot.mako M config/plugins/visualizations/unipept/templates/unipept.mako M config/plugins/visualizations/venn/config/venn.xml M config/plugins/webhooks/demo/search/script.js M config/reports.yml.sample M config/tool_conf.xml.main M config/tool_conf.xml.sample M config/tool_data_table_conf.xml.sample M config/tool_destinations.yml.sample M config/tool_shed.yml.sample M create_db.sh M display_applications/igb/bam.xml M display_applications/igb/bb.xml M display_applications/igb/bed.xml M display_applications/igb/bedgraph.xml M display_applications/igb/bigwig.xml M display_applications/igb/gtf.xml M display_applications/igb/wig.xml A display_applications/intermine/intermine_simple.xml M doc/parse_gx_xsd.py M doc/source/admin/authentication.md M doc/source/admin/cluster.md M doc/source/admin/framework_dependencies.rst M doc/source/admin/galaxy_options.rst M doc/source/admin/jobs.md M doc/source/admin/reports_options.rst M doc/source/admin/scaling.md M doc/source/admin/special_topics/bug_reports.rst A doc/source/admin/special_topics/gdpr_compliance.rst M doc/source/admin/special_topics/index.rst M doc/source/admin/special_topics/performance_tracking.rst M doc/source/conf.versioning.py M doc/source/lib/galaxy.web.framework.middleware.rst M doc/source/project/organization.rst A doc/source/releases/18.05.rst M doc/source/releases/18.05_announce.rst M doc/source/releases/index.rst M extract_dataset_parts.sh M lib/galaxy/app.py M lib/galaxy/auth/__init__.py M lib/galaxy/auth/providers/alwaysreject.py M lib/galaxy/auth/providers/ldap_ad.py M lib/galaxy/auth/providers/localdb.py M lib/galaxy/auth/providers/pam_auth.py A lib/galaxy/authnz/__init__.py A lib/galaxy/authnz/managers.py A lib/galaxy/authnz/psa_authnz.py M lib/galaxy/config.py M lib/galaxy/containers/__init__.py M lib/galaxy/containers/docker.py M lib/galaxy/containers/docker_model.py M lib/galaxy/containers/docker_swarm.py R lib/galaxy/containers/docker_swarm_manager.py M lib/galaxy/dataset_collections/structure.py M lib/galaxy/dataset_collections/subcollections.py M lib/galaxy/dataset_collections/type_description.py M lib/galaxy/datatypes/annotation.py M lib/galaxy/datatypes/assembly.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/blast.py M lib/galaxy/datatypes/constructive_solid_geometry.py A lib/galaxy/datatypes/converters/bam_to_bai.xml M lib/galaxy/datatypes/converters/bam_to_bigwig_converter.xml M lib/galaxy/datatypes/converters/bed_gff_or_vcf_to_bigwig_converter.xml M lib/galaxy/datatypes/converters/bedgraph_to_bigwig_converter.xml A lib/galaxy/datatypes/converters/bz2_to_uncompressed.xml M lib/galaxy/datatypes/converters/fasta_to_2bit.xml M lib/galaxy/datatypes/converters/fasta_to_fai.xml R lib/galaxy/datatypes/converters/fastagz_to_fasta.xml R lib/galaxy/datatypes/converters/fastqbz2_to_fastq.xml R lib/galaxy/datatypes/converters/fastqcssangerbz2_to_fastqcssanger.xml R lib/galaxy/datatypes/converters/fastqcssangergz_to_fastqcssanger.xml R lib/galaxy/datatypes/converters/fastqgz_to_fastq.xml R lib/galaxy/datatypes/converters/fastqilluminabz2_to_fastqillumina.xml R lib/galaxy/datatypes/converters/fastqilluminagz_to_fastqillumina.xml R lib/galaxy/datatypes/converters/fastqsangerbz2_to_fastqsanger.xml R lib/galaxy/datatypes/converters/fastqsangergz_to_fastqsanger.xml R lib/galaxy/datatypes/converters/fastqsolexabz2_to_fastqsolexa.xml R lib/galaxy/datatypes/converters/fastqsolexagz_to_fastqsolexa.xml R lib/galaxy/datatypes/converters/genbankgz_to_genbank.xml A lib/galaxy/datatypes/converters/gz_to_uncompressed.xml M lib/galaxy/datatypes/converters/interval_to_bigwig_converter.xml M lib/galaxy/datatypes/converters/sam_to_bigwig_converter.xml M lib/galaxy/datatypes/converters/wig_to_bigwig_converter.xml M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/display_applications/util.py M lib/galaxy/datatypes/genetics.py M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/molecules.py M lib/galaxy/datatypes/mothur.py M lib/galaxy/datatypes/msa.py M lib/galaxy/datatypes/phylip.py M lib/galaxy/datatypes/plant_tribes.py M lib/galaxy/datatypes/proteomics.py M lib/galaxy/datatypes/qualityscore.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/1.afg A lib/galaxy/datatypes/test/1.arff A lib/galaxy/datatypes/test/1.fastqsanger.bz2 A lib/galaxy/datatypes/test/1.fastqsanger.gz A lib/galaxy/datatypes/test/1.hdt A lib/galaxy/datatypes/test/1.obo A lib/galaxy/datatypes/test/1.owl A lib/galaxy/datatypes/test/1.phyloxml A lib/galaxy/datatypes/test/1.stockholm A lib/galaxy/datatypes/test/1.tiff A lib/galaxy/datatypes/test/1.ttl A lib/galaxy/datatypes/test/1.xmfa A lib/galaxy/datatypes/test/2.tabular A lib/galaxy/datatypes/test/2.txt A lib/galaxy/datatypes/test/3.txt A lib/galaxy/datatypes/test/Acanium.hmm A lib/galaxy/datatypes/test/diamond.daa A lib/galaxy/datatypes/test/empty.txt M lib/galaxy/datatypes/test/example.iqtree A lib/galaxy/datatypes/test/test.blib M lib/galaxy/datatypes/text.py M lib/galaxy/datatypes/triples.py M lib/galaxy/datatypes/upload_util.py M lib/galaxy/datatypes/xml.py M lib/galaxy/dependencies/__init__.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-requirements.txt M lib/galaxy/dependencies/pipfiles/develop/Pipfile R lib/galaxy/dependencies/pipfiles/develop/Pipfile.lock M lib/galaxy/dependencies/pipfiles/develop/pinned-requirements.txt R lib/galaxy/dependencies/pipfiles/flake8/Pipfile.lock M lib/galaxy/dependencies/pipfiles/flake8/pinned-requirements.txt M lib/galaxy/dependencies/pipfiles/update.sh A lib/galaxy/dependencies/requirements.txt M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/actions/post.py M lib/galaxy/jobs/dynamic_tool_destination.py R lib/galaxy/jobs/error_level.py M lib/galaxy/jobs/handler.py M lib/galaxy/jobs/mapper.py M lib/galaxy/jobs/metrics/instrumenters/cgroup.py M lib/galaxy/jobs/metrics/instrumenters/collectl.py M lib/galaxy/jobs/metrics/instrumenters/core.py M lib/galaxy/jobs/metrics/instrumenters/cpuinfo.py M lib/galaxy/jobs/metrics/instrumenters/env.py A lib/galaxy/jobs/metrics/instrumenters/hostname.py M lib/galaxy/jobs/metrics/instrumenters/meminfo.py M lib/galaxy/jobs/metrics/instrumenters/uname.py M lib/galaxy/jobs/output_checker.py M lib/galaxy/jobs/rule_helper.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/chronos.py M lib/galaxy/jobs/runners/drmaa.py M lib/galaxy/jobs/runners/kubernetes.py M lib/galaxy/jobs/runners/local.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/jobs/runners/slurm.py M lib/galaxy/jobs/runners/util/cli/job/slurm.py M lib/galaxy/jobs/runners/util/cli/job/torque.py M lib/galaxy/jobs/runners/util/cli/shell/rsh.py R lib/galaxy/jobs/runners/util/drmaa/__init__.py M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh M lib/galaxy/jobs/runners/util/job_script/__init__.py R lib/galaxy/jobs/runners/util/retry.py M lib/galaxy/managers/base.py M lib/galaxy/managers/citations.py M lib/galaxy/managers/cloud.py M lib/galaxy/managers/collections.py M lib/galaxy/managers/collections_util.py M lib/galaxy/managers/configuration.py M lib/galaxy/managers/histories.py M lib/galaxy/managers/pages.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/0136_collection_and_workflow_state.py A lib/galaxy/model/migrate/versions/0141_add_oidc_tables.py A lib/galaxy/model/migrate/versions/0142_change_numeric_metric_precision.py M lib/galaxy/model/orm/scripts.py M lib/galaxy/queue_worker.py M lib/galaxy/security/__init__.py M lib/galaxy/security/passwords.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/actions/upload.py A lib/galaxy/tools/apply_rules.xml M lib/galaxy/tools/data/__init__.py M lib/galaxy/tools/data_fetch.py M lib/galaxy/tools/data_manager/manager.py M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/tools/deps/containers.py M lib/galaxy/tools/deps/docker_util.py M lib/galaxy/tools/deps/resolvers/default_conda_mapping.yml 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/json.py M lib/galaxy/tools/error_reports/plugins/sentry.py M lib/galaxy/tools/errors.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/execute.py A lib/galaxy/tools/filter_empty_collection.xml M lib/galaxy/tools/filter_failed_collection.xml M lib/galaxy/tools/linters/general.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/dataset_matcher.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/parameters/output_collect.py M lib/galaxy/tools/parameters/wrapped_json.py M lib/galaxy/tools/parser/cwl.py A lib/galaxy/tools/parser/error_level.py M lib/galaxy/tools/parser/interface.py M lib/galaxy/tools/parser/output_actions.py M lib/galaxy/tools/parser/output_collection_def.py M lib/galaxy/tools/parser/output_objects.py M lib/galaxy/tools/parser/util.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/relabel_from_file.xml M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/util/maf_utilities.py M lib/galaxy/tools/verify/__init__.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/checkers.py M lib/galaxy/util/compression_utils.py M lib/galaxy/util/create_history_template.py M lib/galaxy/util/json.py M lib/galaxy/util/path/__init__.py M lib/galaxy/util/permutations.py A lib/galaxy/util/rules_dsl.py A lib/galaxy/util/watcher.py M lib/galaxy/version.py M lib/galaxy/visualization/data_providers/phyloviz/__init__.py M lib/galaxy/visualization/plugins/interactive_environments.py M lib/galaxy/visualization/plugins/plugin.py M lib/galaxy/web/base/controller.py M lib/galaxy/web/framework/decorators.py M lib/galaxy/web/framework/helpers/grids.py R lib/galaxy/web/framework/middleware/graphite.py M lib/galaxy/web/framework/middleware/sentry.py M lib/galaxy/web/framework/middleware/statsd.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/web/proxy/__init__.py M lib/galaxy/web/security/__init__.py M lib/galaxy/web/stack/__init__.py M lib/galaxy/webapps/config_manage.py M lib/galaxy/webapps/galaxy/api/cloud.py M lib/galaxy/webapps/galaxy/api/datatypes.py M lib/galaxy/webapps/galaxy/api/histories.py M lib/galaxy/webapps/galaxy/api/history_contents.py M lib/galaxy/webapps/galaxy/api/jobs.py M lib/galaxy/webapps/galaxy/api/library_datasets.py M lib/galaxy/webapps/galaxy/api/pages.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/api/users.py M lib/galaxy/webapps/galaxy/api/visualizations.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/config_schema.yml M lib/galaxy/webapps/galaxy/config_watchers.py M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py A lib/galaxy/webapps/galaxy/controllers/authnz.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/interactive_environments.py M lib/galaxy/webapps/galaxy/controllers/page.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/webapps/reports/config.py M lib/galaxy/webapps/reports/config_schema.yml M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/api/repository_revisions.py M lib/galaxy/webapps/tool_shed/config.py M lib/galaxy/webapps/tool_shed/config_schema.yml M lib/galaxy/webapps/tool_shed/controllers/admin.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/model/__init__.py M lib/galaxy/workflow/modules.py M lib/galaxy_ext/metadata/set_metadata.py M lib/tool_shed/capsule/capsule_manager.py M lib/tool_shed/dependencies/attribute_handlers.py M lib/tool_shed/dependencies/repository/relation_builder.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py M lib/tool_shed/grids/repository_grids.py M lib/tool_shed/grids/repository_review_grids.py M lib/tool_shed/grids/util.py M lib/tool_shed/metadata/metadata_generator.py M lib/tool_shed/metadata/repository_metadata_manager.py M lib/tool_shed/repository_registry.py M lib/tool_shed/repository_types/metadata.py M lib/tool_shed/repository_types/repository_suite_definition.py M lib/tool_shed/repository_types/tool_dependency_definition.py M lib/tool_shed/tools/data_table_manager.py M lib/tool_shed/tools/tool_validator.py M lib/tool_shed/tools/tool_version_manager.py M lib/tool_shed/util/admin_util.py M lib/tool_shed/util/commit_util.py M lib/tool_shed/util/common_util.py M lib/tool_shed/util/encoding_util.py M lib/tool_shed/util/hg_util.py M lib/tool_shed/util/metadata_util.py M lib/tool_shed/util/readme_util.py M lib/tool_shed/util/repository_content_util.py M lib/tool_shed/util/repository_util.py M lib/tool_shed/util/review_util.py M lib/tool_shed/util/shed_util_common.py M lib/tool_shed/util/web_util.py M manage_db.sh M run.sh M run_reports.sh M run_tests.sh M run_tool_shed.sh M scripts/api/common.py M scripts/bootstrap_history.py M scripts/check_python.py M scripts/cleanup_datasets/delete_datasets.sh M scripts/cleanup_datasets/delete_userless_histories.sh M scripts/cleanup_datasets/purge_datasets.sh M scripts/cleanup_datasets/purge_folders.sh M scripts/cleanup_datasets/purge_histories.sh M scripts/cleanup_datasets/purge_libraries.sh M scripts/common_startup.sh M scripts/common_startup_functions.sh R scripts/common_startup_variables.sh A scripts/docker_swarm_manager.py M scripts/get_uwsgi_args.py M scripts/grt/export.py M scripts/grt/grt.yml.sample M scripts/grt/upload.py M scripts/maintenance.sh A scripts/plugin_staging.py A static/images/fonts/FontAwesome.otf M static/images/fonts/fontawesome-webfont.eot A static/images/fonts/fontawesome-webfont.svg M static/images/fonts/fontawesome-webfont.ttf M static/images/fonts/fontawesome-webfont.woff A static/images/fonts/fontawesome-webfont.woff2 M static/style/blue/autocomplete_tagging.css M static/style/blue/base.css M static/style/blue/circster.css M static/style/blue/embed_item.css M static/style/blue/library.css M static/style/blue/reports.css M static/style/blue/trackster.css M static/welcome.html.sample R templates/admin/impersonate.mako R templates/admin/view_data_tables_registry.mako R templates/admin/view_datatypes_registry.mako M templates/base/base_panels.mako M templates/display_common.mako M templates/ind_share_base.mako R templates/sharing_base.mako M templates/show_params.mako M templates/tagging_common.mako M templates/user/login.mako M templates/webapps/galaxy/admin/center.mako M templates/webapps/galaxy/admin/view_display_applications.mako M templates/webapps/galaxy/data_manager/index.mako M templates/webapps/galaxy/dataset/copy_view.mako M templates/webapps/galaxy/galaxy.panels.mako R templates/webapps/galaxy/history/structure.mako M templates/webapps/galaxy/workflow/editor.mako M templates/webapps/reports/index.mako M templates/webapps/tool_shed/base_panels.mako M templates/webapps/tool_shed/common/grid_common.mako M templates/webapps/tool_shed/repository/manage_repository.mako M templates/webapps/tool_shed/repository/view_repository.mako M templates/webapps/tool_shed/user/manage_email_alerts.mako A test-data/1.tiff A test-data/filter1_in6.bed A test-data/filter1_test6.bed A test-data/rules/treated1fb.txt A test-data/rules/treated2fb.txt A test-data/rules/treated3fb.txt M test-data/rules/uniprot.json A test-data/rules/untreated1fb.txt A test-data/rules/untreated2fb.txt A test-data/rules/untreated3fb.txt A test-data/rules/untreated4fb.txt A test-data/sort_out1.bed A test-data/sort_out2.bed A test-data/sort_out3.tab A test-data/sort_out4.sam M test/api/test_jobs.py M test/api/test_libraries.py M test/api/test_tools.py M test/api/test_tools_upload.py M test/api/test_workflows.py A test/base/data/rules_dsl_spec.yml M test/base/populators.py A test/base/rules_test_data.py A test/base/workflow_fixtures.py M test/base/workflows_format_2/main.py M test/docker/base/Dockerfile M test/docker/base/ansible_vars.yml M test/docker/base/run_test_wrapper.sh M test/functional/test_data_managers.py M test/functional/test_toolbox.py A test/functional/tools/collection_paired_conditional_structured_like.xml A test/functional/tools/collection_paired_structured_like.xml A test/functional/tools/collection_type_source_map_over.xml A test/functional/tools/empty_select.xml M test/functional/tools/for_workflows/cat_collection.xml A test/functional/tools/identifier_single_in_repeat.xml A test/functional/tools/inputs_as_json_with_paths.xml M test/functional/tools/job_properties.xml M test/functional/tools/multi_data_optional.xml A test/functional/tools/output_action_change_format_paired.xml R test/functional/tools/paired_collection_map_over_structured_like.xml M test/functional/tools/sample_datatypes_conf.xml M test/functional/tools/samples_tool_conf.xml M test/galaxy_selenium/components.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 M test/integration/test_scripts.py M test/integration/test_upload_configuration_options.py R test/selenium_tests/_workflow_fixtures.py M test/selenium_tests/framework.py A test/selenium_tests/test_admin_app.py M test/selenium_tests/test_library_landing.py M test/selenium_tests/test_registration.py M test/selenium_tests/test_saved_histories.py M test/selenium_tests/test_tool_form.py M test/selenium_tests/test_uploads.py M test/selenium_tests/test_workflow_editor.py M test/selenium_tests/test_workflow_management.py M test/selenium_tests/test_workflow_run.py M test/unit/config/1607_root_filters/config/galaxy.ini M test/unit/config/1607_root_samples/config/galaxy.ini M test/unit/datatypes/dataproviders/test_base_dataproviders.py M test/unit/datatypes/test_bam.py A test/unit/datatypes/test_datatypes_registry.py M test/unit/jobs/test_job_output_checker.py M test/unit/jobs/test_runner_params.py M test/unit/test_galaxy_mapping.py M test/unit/test_remote_shell.py A test/unit/test_rule_utils.py M test/unit/test_security_helper.py A test/unit/test_security_passwords.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_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/unittest_utils/galaxy_mock.py M test/unit/unittest_utils/tempfilecache.py M test/unit/visualizations/plugins/test_VisualizationPlugin.py M test/unit/visualizations/plugins/test_VisualizationsRegistry.py M test/unit/web/framework/test_webapp.py M test/unit/workflows/test_extract_summary.py M test/unit/workflows/test_modules.py A tool-data/intermine_simple_display.loc.sample A tools/data_source/intermine.xml M tools/data_source/upload.py M tools/evolution/codingSnps.xml M tools/extract/extract_genomic_dna.xml M tools/extract/liftOver_wrapper.xml M tools/filters/bed_to_bigbed.xml M tools/filters/cutWrapper.pl M tools/filters/sorter.py M tools/filters/sorter.xml M tools/filters/wig_to_bigwig.xml M tools/phenotype_association/gpass.xml M tools/phenotype_association/lps.xml M tools/phenotype_association/master2gd_snp.xml M tools/phenotype_association/master2pg.xml M tools/sr_mapping/bfast_wrapper.xml M tools/stats/filtering.py M tools/stats/filtering.xml M tox.ini Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into upload_to_cloud Commit: 5b1b4314a3ac140779146286f4dc2cfd5fad6807 https://github.com/galaxyproject/galaxy/commit/5b1b4314a3ac140779146286f4dc2... Author: vjalili <jalili.vahid@gmail.com> Date: 2018-07-12 (Thu, 12 Jul 2018) Changed paths: M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Refactor the API end point from `upload` to `copy_to`. Commit: 97fd2088faa0eda1275448d7552a47c801ab9a4b https://github.com/galaxyproject/galaxy/commit/97fd2088faa0eda1275448d7552a4... Author: vjalili <jalili.vahid@gmail.com> Date: 2018-07-12 (Thu, 12 Jul 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/cloud.py Log Message: ----------- Add cloud storage `copy_to` API. Commit: 7e8be2ff53e9f6f781618c2182d9b3d58675c47e https://github.com/galaxyproject/galaxy/commit/7e8be2ff53e9f6f781618c2182d9b... Author: vjalili <jalili.vahid@gmail.com> Date: 2018-07-12 (Thu, 12 Jul 2018) Changed paths: M lib/galaxy/managers/cloud.py Log Message: ----------- Add cloud-based storage `copy-to` manager. Commit: b3f1a7cf9cdc29bcc52a6d7f5c35fc6ecfa02878 https://github.com/galaxyproject/galaxy/commit/b3f1a7cf9cdc29bcc52a6d7f5c35f... Author: Enis Afgan <afgane@gmail.com> Date: 2018-07-12 (Thu, 12 Jul 2018) Changed paths: M lib/galaxy/managers/cloud.py M lib/galaxy/webapps/galaxy/api/cloud.py Log Message: ----------- Doc style updates; copy-to return dict with copied datasets Commit: 4a8857e4f9daf15101270724375dad14c4897e6c https://github.com/galaxyproject/galaxy/commit/4a8857e4f9daf15101270724375da... Author: Enis Afgan <afgane@gmail.com> Date: 2018-07-12 (Thu, 12 Jul 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 #6078 from VJalili/upload_to_cloud Upload data to a cloud-based storage Compare: https://github.com/galaxyproject/galaxy/compare/2abb01b6cbb1...4a8857e4f9da **NOTE:** This service 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.