Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 571fedf00654c36ee60115abff50d4d4d4031a5b https://github.com/galaxyproject/galaxy/commit/571fedf00654c36ee60115abff50d... Author: guerler <aysam.guerler@gmail.com> Date: 2018-02-28 (Wed, 28 Feb 2018) Changed paths: M client/galaxy/scripts/layout/menu.js M lib/galaxy/visualization/plugins/registry.py M lib/galaxy/webapps/galaxy/buildapp.py M static/style/blue/base.css Log Message: ----------- Remove menu options from visualization tab, shift tab to workflows Commit: 0bd98c320ee0ca8c998dfbfc8f84a174066969a7 https://github.com/galaxyproject/galaxy/commit/0bd98c320ee0ca8c998dfbfc8f84a... Author: guerler <aysam.guerler@gmail.com> Date: 2018-02-28 (Wed, 28 Feb 2018) Changed paths: A lib/galaxy/webapps/galaxy/api/plugins.py Log Message: ----------- Add plugins endpoint Commit: cc3e5244d603e13afcf4501aefc88868e971fe50 https://github.com/galaxyproject/galaxy/commit/cc3e5244d603e13afcf4501aefc88... Author: guerler <aysam.guerler@gmail.com> Date: 2018-02-28 (Wed, 28 Feb 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/plugins.py Log Message: ----------- Remove unused imports from plugins api endpoint Commit: 1ca6499ea10c35d1647898d50dfac442055fa1cc https://github.com/galaxyproject/galaxy/commit/1ca6499ea10c35d1647898d50dfac... Author: guerler <aysam.guerler@gmail.com> Date: 2018-02-28 (Wed, 28 Feb 2018) Changed paths: M client/galaxy/scripts/apps/analysis.js A client/galaxy/scripts/components/PluginList.vue M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Add vue list for plugins Commit: f4e52caab6027a50b631331ad3cd02fd3ca2a0a8 https://github.com/galaxyproject/galaxy/commit/f4e52caab6027a50b631331ad3cd0... Author: guerler <aysam.guerler@gmail.com> Date: 2018-02-28 (Wed, 28 Feb 2018) Changed paths: M client/galaxy/scripts/components/PluginList.vue Log Message: ----------- Remove id from header value Commit: 82e58d9086e7e0da86aab270d07bf8ff442cb2e4 https://github.com/galaxyproject/galaxy/commit/82e58d9086e7e0da86aab270d07bf... Author: guerler <aysam.guerler@gmail.com> Date: 2018-02-28 (Wed, 28 Feb 2018) Changed paths: M client/galaxy/scripts/layout/menu.js Log Message: ----------- Redirect to list of plugins Commit: fbead2daa5ea1da1974ed60e3740a2530165996c https://github.com/galaxyproject/galaxy/commit/fbead2daa5ea1da1974ed60e3740a... Author: guerler <aysam.guerler@gmail.com> Date: 2018-03-01 (Thu, 01 Mar 2018) Changed paths: M client/galaxy/scripts/components/PluginList.vue M lib/galaxy/visualization/plugins/config_parser.py M lib/galaxy/visualization/plugins/plugin.py Log Message: ----------- Add select field to thumbnail view to allow dataset selection Commit: d5d60e95aa749c6f14dbc9ae01dcf3e515ce0c2f https://github.com/galaxyproject/galaxy/commit/d5d60e95aa749c6f14dbc9ae01dcf... Author: guerler <aysam.guerler@gmail.com> Date: 2018-03-01 (Thu, 01 Mar 2018) Changed paths: M client/galaxy/scripts/components/PluginList.vue M lib/galaxy/visualization/plugins/plugin.py Log Message: ----------- Remove comment and debug output Commit: 15636fa6f144f4a2203b76df0b47cd7d70d03ada https://github.com/galaxyproject/galaxy/commit/15636fa6f144f4a2203b76df0b47c... Author: guerler <aysam.guerler@gmail.com> Date: 2018-03-01 (Thu, 01 Mar 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/plugins.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Revise resource mapping, add show action to plugins endpoint Commit: a8daf446eab87cffb5483a6d96b5f8d244d8286c https://github.com/galaxyproject/galaxy/commit/a8daf446eab87cffb5483a6d96b5f... Author: guerler <aysam.guerler@gmail.com> Date: 2018-03-01 (Thu, 01 Mar 2018) Changed paths: M client/galaxy/scripts/components/PluginList.vue M lib/galaxy/webapps/galaxy/api/plugins.py Log Message: ----------- Add error handlers, populate select list with applicable datasets Commit: b6ad62c0e09d3c67951849cdaeb340e9bc9f11a0 https://github.com/galaxyproject/galaxy/commit/b6ad62c0e09d3c67951849cdaeb34... Author: guerler <aysam.guerler@gmail.com> Date: 2018-03-01 (Thu, 01 Mar 2018) Changed paths: M client/galaxy/scripts/components/PluginList.vue M client/galaxy/scripts/layout/menu.js Log Message: ----------- Add event handler for create button Commit: a1f9cdcf45ccb448341d60f5eed6e32303244a39 https://github.com/galaxyproject/galaxy/commit/a1f9cdcf45ccb448341d60f5eed6e... Author: guerler <aysam.guerler@gmail.com> Date: 2018-03-01 (Thu, 01 Mar 2018) Changed paths: M client/galaxy/scripts/layout/menu.js Log Message: ----------- Restore sub menu options for visualization tab Commit: 8763a2c25fb0237e1dc23b06845e249ca1bc687a https://github.com/galaxyproject/galaxy/commit/8763a2c25fb0237e1dc23b06845e2... Author: guerler <aysam.guerler@gmail.com> Date: 2018-03-01 (Thu, 01 Mar 2018) Changed paths: M client/galaxy/scripts/components/PluginList.vue Log Message: ----------- Add simple filter search Commit: 923286612d7e31ffaf474a60392960f36345895f https://github.com/galaxyproject/galaxy/commit/923286612d7e31ffaf474a6039296... Author: guerler <aysam.guerler@gmail.com> Date: 2018-03-01 (Thu, 01 Mar 2018) Changed paths: M client/galaxy/scripts/components/PluginList.vue Log Message: ----------- Revise dataset selection label Commit: a077f45ba9830136f2869e39e50680e7dfc41c5b https://github.com/galaxyproject/galaxy/commit/a077f45ba9830136f2869e39e5068... Author: guerler <aysam.guerler@gmail.com> Date: 2018-03-01 (Thu, 01 Mar 2018) Changed paths: M client/galaxy/scripts/components/PluginList.vue Log Message: ----------- Match search word with description Commit: 980f2b9708cb9e95bbacf0ae0decb42f7cd0da6c https://github.com/galaxyproject/galaxy/commit/980f2b9708cb9e95bbacf0ae0decb... Author: guerler <aysam.guerler@gmail.com> Date: 2018-03-05 (Mon, 05 Mar 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.js Log Message: ----------- Partial fix for internal scatterplot Commit: a6559248c9e877911ed86b08135f7aae6408fb0b https://github.com/galaxyproject/galaxy/commit/a6559248c9e877911ed86b08135f7... Author: guerler <aysam.guerler@gmail.com> Date: 2018-03-05 (Mon, 05 Mar 2018) Changed paths: M config/plugins/visualizations/scatterplot/src/scatterplot.js Log Message: ----------- Remove comments Commit: 044ca897d53c08939508935c003c5e3d665ba769 https://github.com/galaxyproject/galaxy/commit/044ca897d53c08939508935c003c5... Author: guerler <aysam.guerler@gmail.com> Date: 2018-03-05 (Mon, 05 Mar 2018) Changed paths: M config/plugins/visualizations/nvd3/nvd3_histogram/config/nvd3_histogram.xml Log Message: ----------- Add confirm option Commit: 58f0afe23b9c9590bd8cda1dd4d7c3b731fb0969 https://github.com/galaxyproject/galaxy/commit/58f0afe23b9c9590bd8cda1dd4d7c... Author: guerler <aysam.guerler@gmail.com> Date: 2018-03-05 (Mon, 05 Mar 2018) Changed paths: M client/galaxy/scripts/components/PluginList.vue Log Message: ----------- Hide grid if error occurs Commit: eec8bf47036c0057f9a21578159199b6c036acbb https://github.com/galaxyproject/galaxy/commit/eec8bf47036c0057f9a2157815919... Author: guerler <aysam.guerler@gmail.com> Date: 2018-03-05 (Mon, 05 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-buttons.js M client/galaxy/scripts/mvc/visualization/chart/components/model.js M client/galaxy/scripts/mvc/visualization/chart/views/menu.js M client/galaxy/scripts/mvc/visualization/chart/views/viewer.js Log Message: ----------- Augment button model with visibile attribute Commit: 7f342c340e7739854a1cd7fda375d947aa8addb2 https://github.com/galaxyproject/galaxy/commit/7f342c340e7739854a1cd7fda375d... Author: guerler <aysam.guerler@gmail.com> Date: 2018-03-05 (Mon, 05 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-buttons.js M client/galaxy/scripts/mvc/visualization/chart/views/menu.js M client/galaxy/style/less/charts.less M static/style/blue/base.css Log Message: ----------- Fix default inline handler, fix fullscreen switch Commit: 4f4c8967c0de717f27b5057aaeaef8e3b4d0da98 https://github.com/galaxyproject/galaxy/commit/4f4c8967c0de717f27b5057aaeaef... Author: guerler <aysam.guerler@gmail.com> Date: 2018-03-05 (Mon, 05 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/visualization/chart/components/model.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/viewer.js 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/config/heatmap_shared.xml 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/nvd3/nvd3_histogram_discrete/config/nvd3_histogram_discrete.xml Log Message: ----------- Fix modified handler Commit: f47b88730b2dba31daeeba76f76b06aea44fdbc6 https://github.com/galaxyproject/galaxy/commit/f47b88730b2dba31daeeba76f76b0... Author: guerler <aysam.guerler@gmail.com> Date: 2018-03-05 (Mon, 05 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/visualization/chart/components/model.js Log Message: ----------- Remove unused variable Commit: bebc022d6f6c6a0dff627381c7c435fffbdbe3e0 https://github.com/galaxyproject/galaxy/commit/bebc022d6f6c6a0dff627381c7c43... Author: guerler <aysam.guerler@gmail.com> Date: 2018-03-05 (Mon, 05 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/visualization/chart/views/viewer.js Log Message: ----------- Add info notification for visualizations which require additional confirmation Commit: 5e98958c22dba2665f762052e4d017145a243395 https://github.com/galaxyproject/galaxy/commit/5e98958c22dba2665f762052e4d01... Author: guerler <aysam.guerler@gmail.com> Date: 2018-03-05 (Mon, 05 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/visualization/chart/views/menu.js M client/galaxy/scripts/mvc/visualization/chart/views/viewer.js M client/galaxy/style/less/charts.less M static/style/blue/base.css Log Message: ----------- Highlight check button to confirm settings Commit: eadeb0f91717e24464279b4d694bf0725710048b https://github.com/galaxyproject/galaxy/commit/eadeb0f91717e24464279b4d694bf... Author: guerler <aysam.guerler@gmail.com> Date: 2018-03-05 (Mon, 05 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/visualization/chart/utilities/datasets.js M config/plugins/visualizations/venn/src/script.js M config/plugins/visualizations/venn/static/script.js Log Message: ----------- Add additional data validation Commit: e01d1a0049ebc2ca7c05b0439d461afa9a38ea70 https://github.com/galaxyproject/galaxy/commit/e01d1a0049ebc2ca7c05b0439d461... Author: guerler <aysam.guerler@gmail.com> Date: 2018-03-05 (Mon, 05 Mar 2018) Changed paths: M config/plugins/visualizations/nvd3/nvd3_bar/src/nvd3.js M config/plugins/visualizations/nvd3/nvd3_bar/static/nvd3.js Log Message: ----------- Fix data validation for pie charts Commit: 88be6acf911333f1a54d7eef6b564971150cbdff https://github.com/galaxyproject/galaxy/commit/88be6acf911333f1a54d7eef6b564... Author: guerler <aysam.guerler@gmail.com> Date: 2018-03-06 (Tue, 06 Mar 2018) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/apps/extended.js A client/galaxy/scripts/components/DisplayStructured.vue A client/galaxy/scripts/components/HistoryView.vue M client/galaxy/scripts/layout/page.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/history-list.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/list/list-view.js M client/galaxy/scripts/mvc/tool/tool-genomespace.js M client/galaxy/scripts/mvc/workflow/workflow.js M client/galaxy/scripts/ui/loading-indicator.js M client/galaxy/scripts/utils/utils.js M config/datatypes_conf.xml.sample M lib/galaxy/actions/library.py M lib/galaxy/datatypes/assembly.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/blast.py R lib/galaxy/datatypes/converters/bam_native_to_bam_converter.xml M lib/galaxy/datatypes/converters/bed_to_gff_converter.py M lib/galaxy/datatypes/converters/fasta_to_len.py M lib/galaxy/datatypes/converters/fastqsolexa_to_fasta_converter.py M lib/galaxy/datatypes/converters/fastqsolexa_to_qual_converter.py M lib/galaxy/datatypes/converters/gff_to_bed_converter.py M lib/galaxy/datatypes/converters/interval_to_bed_converter.py M lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.py M lib/galaxy/datatypes/converters/interval_to_coverage.py M lib/galaxy/datatypes/converters/interval_to_fli.py M lib/galaxy/datatypes/converters/lped_to_fped_converter.py M lib/galaxy/datatypes/converters/maf_to_fasta_converter.py M lib/galaxy/datatypes/converters/maf_to_interval_converter.py M lib/galaxy/datatypes/converters/picard_interval_list_to_bed6_converter.py M lib/galaxy/datatypes/converters/ref_to_seq_taxonomy_converter.py M lib/galaxy/datatypes/converters/sam_to_bam.py M lib/galaxy/datatypes/converters/sam_to_bam_native.xml A lib/galaxy/datatypes/converters/to_coordinate_sorted_bam.xml A lib/galaxy/datatypes/converters/to_qname_sorted_bam.xml M lib/galaxy/datatypes/converters/wiggle_to_simple_converter.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/images.py M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/molecules.py M lib/galaxy/datatypes/msa.py M lib/galaxy/datatypes/qualityscore.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/text.py M lib/galaxy/datatypes/xml.py M lib/galaxy/exceptions/__init__.py M lib/galaxy/jobs/dynamic_tool_destination.py M lib/galaxy/jobs/handler.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/managers/containers.py M lib/galaxy/model/__init__.py M lib/galaxy/model/item_attrs.py M lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py M lib/galaxy/model/migrate/versions/0137_add_copied_from_job_id_column.py M lib/galaxy/security/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/upload.py M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/tools/cwl/util.py M lib/galaxy/tools/data/__init__.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/container_resolvers/__init__.py M lib/galaxy/tools/deps/containers.py M lib/galaxy/tools/deps/mulled/util.py M lib/galaxy/tools/deps/resolvers/__init__.py M lib/galaxy/tools/deps/resolvers/brewed_tool_shed_packages.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/deps/resolvers/galaxy_packages.py M lib/galaxy/tools/deps/resolvers/homebrew.py M lib/galaxy/tools/deps/resolvers/lmod.py M lib/galaxy/tools/deps/resolvers/modules.py M lib/galaxy/tools/deps/resolvers/resolver_mixins.py M lib/galaxy/tools/deps/resolvers/tool_shed_packages.py M lib/galaxy/tools/deps/resolvers/unlinked_tool_shed_packages.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/tools/parser/output_objects.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/integrated_panel.py M lib/galaxy/tools/toolbox/lineages/interface.py M lib/galaxy/tools/toolbox/panel.py M lib/galaxy/tools/verify/test_data.py M lib/galaxy/tools/wrappers.py M lib/galaxy/tools/xsd/galaxy.xsd A lib/galaxy/util/create_history_template.py M lib/galaxy/util/inflection.py M lib/galaxy/util/monitors.py M lib/galaxy/util/none_like.py M lib/galaxy/util/path/__init__.py M lib/galaxy/visualization/data_providers/genome.py M lib/galaxy/web/base/controller.py M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/webapps/galaxy/api/remote_files.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/tag.py M lib/galaxy/webapps/reports/controllers/query.py M lib/galaxy/webapps/tool_shed/security/__init__.py M lib/galaxy/workflow/scheduling_manager.py M scripts/migrate_tools/migrate_tools.py R templates/webapps/galaxy/history/display_structured.mako R templates/webapps/galaxy/history/view.mako A test-data/qname_sorted.bam M test/functional/tools/multi_output_recurse.xml M test/functional/tools/sam_to_bam_native.xml M test/functional/tools/sample_datatypes_conf.xml M test/unit/tools/test_toolbox.py M tools/data_source/upload.xml Log Message: ----------- Merge branch 'dev' into visualization_header Commit: 04bfefb7dae2a0d035d76f57a6c552facee8bd19 https://github.com/galaxyproject/galaxy/commit/04bfefb7dae2a0d035d76f57a6c55... Author: guerler <aysam.guerler@gmail.com> Date: 2018-03-08 (Thu, 08 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-genomespace.js M client/galaxy/style/less/ui.less M config/galaxy.yml.sample M config/plugins/webhooks/demo/tour_generator/__init__.py M doc/source/admin/galaxy_options.rst M lib/galaxy/app.py M lib/galaxy/config.py M lib/galaxy/datatypes/binary.py M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt M lib/galaxy/managers/workflows.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/mulled/mulled_build.py M lib/galaxy/tools/parser/interface.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/parser/yaml.py M lib/galaxy/tools/test.py M lib/galaxy/tools/verify/asserts/__init__.py A lib/galaxy/tools/verify/interactor.py A lib/galaxy/tools/verify/script.py M lib/galaxy/tools/verify/test_data.py M lib/galaxy/util/path/__init__.py M lib/galaxy/util/sanitize_html.py M lib/galaxy/util/validation.py M lib/galaxy/visualization/plugins/resource_parser.py M lib/galaxy/web/base/controller.py M lib/galaxy/webapps/galaxy/api/annotations.py M lib/galaxy/webapps/galaxy/api/folder_contents.py M lib/galaxy/webapps/galaxy/api/page_revisions.py M lib/galaxy/webapps/galaxy/api/pages.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/api/visualizations.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/config_schema.yml M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/page.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/tool_shed/util/workflow_util.py R scripts/microbes/BeautifulSoup.py M scripts/microbes/harvest_bacteria.py M static/style/blue/base.css M test/api/test_tools.py M test/base/api.py M test/base/driver_util.py M test/base/interactor.py M test/base/testcase.py R test/base/tool_shed_util.py M test/functional/test_data_managers.py M test/functional/test_toolbox.py M test/functional/twilltestcase.py M test/integration/test_data_manager_table_reload.py A test/integration/test_shed_tool_tests.py A test/integration/uses_shed.py M test/shed_functional/base/twilltestcase.py M test/unit/tools/test_parsing.py M tools/genomespace/genomespace_exporter.xml M tools/genomespace/genomespace_importer.xml M tools/genomespace/genomespace_push.xml Log Message: ----------- Merge branch 'dev' into visualization_header Commit: e57136523c5e5674c1091cfcec601a5b65fc3fd3 https://github.com/galaxyproject/galaxy/commit/e57136523c5e5674c1091cfcec601... Author: guerler <aysam.guerler@gmail.com> Date: 2018-03-08 (Thu, 08 Mar 2018) Changed paths: 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 Log Message: ----------- Fix trackster urls Commit: 840ad914c5a3ce7ad7b8fd2f4c4f5bf051543c95 https://github.com/galaxyproject/galaxy/commit/840ad914c5a3ce7ad7b8fd2f4c4f5... Author: guerler <aysam.guerler@gmail.com> Date: 2018-03-08 (Thu, 08 Mar 2018) Changed paths: M client/galaxy/scripts/components/PluginList.vue M lib/galaxy/visualization/plugins/plugin.py M lib/galaxy/visualization/plugins/registry.py M lib/galaxy/webapps/galaxy/controllers/visualization.py Log Message: ----------- Move url creation to plugins Commit: f3eb82208971e151399ac2c7d7539d7d8ca1630b https://github.com/galaxyproject/galaxy/commit/f3eb82208971e151399ac2c7d7539... Author: guerler <aysam.guerler@gmail.com> Date: 2018-03-09 (Fri, 09 Mar 2018) Changed paths: M lib/galaxy/visualization/plugins/plugin.py M lib/galaxy/visualization/plugins/registry.py Log Message: ----------- Revise url generator Commit: 4c49af552787bcf89e363323dc6eda5dfb12d8cf https://github.com/galaxyproject/galaxy/commit/4c49af552787bcf89e363323dc6ed... Author: guerler <aysam.guerler@gmail.com> Date: 2018-03-09 (Fri, 09 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/visualization/visualization-view.js Log Message: ----------- Client parses url parameters Commit: b42960951af3b438050751f208c5452421f60a80 https://github.com/galaxyproject/galaxy/commit/b42960951af3b438050751f208c54... Author: guerler <aysam.guerler@gmail.com> Date: 2018-03-09 (Fri, 09 Mar 2018) Changed paths: M lib/galaxy/visualization/plugins/plugin.py M lib/galaxy/visualization/plugins/registry.py M lib/galaxy/webapps/galaxy/controllers/visualization.py Log Message: ----------- Restore built-in location Commit: b35a4dfe017b43b49400090e662c9eebb8e62dfa https://github.com/galaxyproject/galaxy/commit/b35a4dfe017b43b49400090e662c9... Author: guerler <aysam.guerler@gmail.com> Date: 2018-03-09 (Fri, 09 Mar 2018) Changed paths: M config/plugins/visualizations/csg/config/csg.xml A config/plugins/visualizations/csg/static/logo.png M config/plugins/visualizations/phyloviz/config/phyloviz.xml A config/plugins/visualizations/phyloviz/static/logo.png M config/plugins/visualizations/trackster/config/trackster.xml A config/plugins/visualizations/trackster/static/logo.png Log Message: ----------- Add description for trackster and other visualizations Commit: dc3cd003549cd9f54e7a955af8e7ecec355c2a44 https://github.com/galaxyproject/galaxy/commit/dc3cd003549cd9f54e7a955af8e7e... Author: guerler <aysam.guerler@gmail.com> Date: 2018-03-09 (Fri, 09 Mar 2018) Changed paths: M config/plugins/visualizations/graphviz/config/graphviz.xml M config/plugins/visualizations/unipept/config/unipept.xml Log Message: ----------- Add additional descriptions Commit: ace94178c8af8cbd8d098229d96a7a27104da798 https://github.com/galaxyproject/galaxy/commit/ace94178c8af8cbd8d098229d96a7... Author: guerler <aysam.guerler@gmail.com> Date: 2018-03-09 (Fri, 09 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/visualization/chart/components/model.js M client/galaxy/scripts/mvc/visualization/chart/utilities/jobs.js Log Message: ----------- Revise data submission tool Commit: 553474ddfd32229787630989099127e8029dd4f9 https://github.com/galaxyproject/galaxy/commit/553474ddfd3222978763098909912... Author: guerler <aysam.guerler@gmail.com> Date: 2018-03-09 (Fri, 09 Mar 2018) Changed paths: M config/plugins/visualizations/example/config/example.xml Log Message: ----------- Hide example plugin Commit: f08223bc7a7ac7e9827543601707009c2ac8a0f1 https://github.com/galaxyproject/galaxy/commit/f08223bc7a7ac7e98275436017070... Author: guerler <aysam.guerler@gmail.com> Date: 2018-03-09 (Fri, 09 Mar 2018) Changed paths: M lib/galaxy/visualization/plugins/registry.py Log Message: ----------- Sort plugins by display name Commit: 7d95d28d7c729ff25fe8f9f21e9bd7fcad183cbe https://github.com/galaxyproject/galaxy/commit/7d95d28d7c729ff25fe8f9f21e9bd... Author: guerler <aysam.guerler@gmail.com> Date: 2018-03-09 (Fri, 09 Mar 2018) Changed paths: M config/plugins/visualizations/trackster/config/trackster.xml Log Message: ----------- Increase priority for trackster Commit: e0c25f42668f3956ee152843057fda74cdea79a4 https://github.com/galaxyproject/galaxy/commit/e0c25f42668f3956ee152843057fd... Author: guerler <aysam.guerler@gmail.com> Date: 2018-03-09 (Fri, 09 Mar 2018) Changed paths: M config/plugins/visualizations/example/config/example.xml Log Message: ----------- Enable example Commit: 1aa5f8283eaaf5f03b929215ffd49982a74febc2 https://github.com/galaxyproject/galaxy/commit/1aa5f8283eaaf5f03b929215ffd49... Author: guerler <aysam.guerler@gmail.com> Date: 2018-03-09 (Fri, 09 Mar 2018) Changed paths: M lib/galaxy/visualization/plugins/registry.py Log Message: ----------- Fix lint Commit: 7afecf9d1ab0b5d6ad5c34a180ff599b318bc0a1 https://github.com/galaxyproject/galaxy/commit/7afecf9d1ab0b5d6ad5c34a180ff5... Author: guerler <aysam.guerler@gmail.com> Date: 2018-03-09 (Fri, 09 Mar 2018) Changed paths: M test/unit/unittest_utils/galaxy_mock.py M test/unit/visualizations/plugins/test_VisualizationsRegistry.py Log Message: ----------- Fix test cases Commit: 00f282ccaab220d290a298f28fe8d9b113cf908b https://github.com/galaxyproject/galaxy/commit/00f282ccaab220d290a298f28fe8d... Author: guerler <aysam.guerler@gmail.com> Date: 2018-03-09 (Fri, 09 Mar 2018) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/components/PluginList.vue M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M lib/galaxy/visualization/plugins/registry.py M lib/galaxy/webapps/galaxy/api/plugins.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Use vue instead of backbone view Commit: cb9ecb63f533dfc648af1b016975f89cb2591bfe https://github.com/galaxyproject/galaxy/commit/cb9ecb63f533dfc648af1b016975f... Author: guerler <aysam.guerler@gmail.com> Date: 2018-03-09 (Fri, 09 Mar 2018) Changed paths: R client/galaxy/scripts/mvc/visualization/visualization-view.js Log Message: ----------- Remove backbone visualization selector Commit: b325e086f20f241bc2c2a39a705b7d12bda5e06d https://github.com/galaxyproject/galaxy/commit/b325e086f20f241bc2c2a39a705b7... Author: guerler <aysam.guerler@gmail.com> Date: 2018-03-09 (Fri, 09 Mar 2018) Changed paths: M client/galaxy/scripts/apps/analysis.js Log Message: ----------- Remove unused import Commit: 9f52c391229d07687dfa792fa525cb8c781e3b93 https://github.com/galaxyproject/galaxy/commit/9f52c391229d07687dfa792fa525c... Author: guerler <aysam.guerler@gmail.com> Date: 2018-03-09 (Fri, 09 Mar 2018) Changed paths: M client/galaxy/scripts/components/PluginList.vue Log Message: ----------- Use parsed dataset id in visualization selector instead of showing select field Commit: 21aa7462875f064766be2e5a6e7b35f7de7dc2b0 https://github.com/galaxyproject/galaxy/commit/21aa7462875f064766be2e5a6e7b3... Author: guerler <aysam.guerler@gmail.com> Date: 2018-03-09 (Fri, 09 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-buttons.js Log Message: ----------- Fix button inline style Commit: c14ed8732f76cab4e72371878fd770fc01c7bfb0 https://github.com/galaxyproject/galaxy/commit/c14ed8732f76cab4e72371878fd77... Author: guerler <aysam.guerler@gmail.com> Date: 2018-03-09 (Fri, 09 Mar 2018) Changed paths: M client/galaxy/scripts/components/HistoryImport.vue M client/galaxy/scripts/components/PluginList.vue Log Message: ----------- Temporary use of style section in vue component Commit: 9bb1e48aba4bd5de3d0b59b113d8dce2d047612b https://github.com/galaxyproject/galaxy/commit/9bb1e48aba4bd5de3d0b59b113d8d... Author: guerler <aysam.guerler@gmail.com> Date: 2018-03-09 (Fri, 09 Mar 2018) Changed paths: M config/job_metrics_conf.xml.sample M lib/galaxy/actions/library.py M lib/galaxy/app.py M lib/galaxy/datatypes/sniff.py A lib/galaxy/datatypes/upload_util.py M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/jobs/__init__.py A lib/galaxy/jobs/metrics/instrumenters/cgroup.py M lib/galaxy/managers/collections.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/upload.py M lib/galaxy/tools/actions/upload_common.py A lib/galaxy/tools/data_fetch.py A lib/galaxy/tools/data_fetch.xml M lib/galaxy/tools/execute.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/tools/special_tools.py M lib/galaxy/util/compression_utils.py A lib/galaxy/webapps/galaxy/api/_fetch_util.py M lib/galaxy/webapps/galaxy/api/library_contents.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/workflow/modules.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py A scripts/api/fetch_to_library.py A scripts/api/fetch_to_library_example.yml A test-data/1.csv A test-data/example-bag.zip A test-data/testdir1.zip M test/api/test_dataset_collections.py M test/api/test_libraries.py M test/api/test_tools_upload.py M test/base/driver_util.py M test/base/integration_util.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 Log Message: ----------- Merge branch 'dev' into visualization_header Commit: a706929bd6fe7f9d502e756cc592806a79480147 https://github.com/galaxyproject/galaxy/commit/a706929bd6fe7f9d502e756cc5928... Author: guerler <aysam.guerler@gmail.com> Date: 2018-03-12 (Mon, 12 Mar 2018) Changed paths: M client/galaxy/scripts/utils/config.js M client/galaxy/scripts/viz/trackster.js M client/galaxy/scripts/viz/trackster/filters.js M client/galaxy/scripts/viz/trackster/painters.js M client/galaxy/scripts/viz/trackster/slotting.js M client/galaxy/scripts/viz/trackster/tracks.js M client/galaxy/scripts/viz/visualization.js M config/datatypes_conf.xml.sample A doc/source/releases/18.01.rst M doc/source/releases/18.01_announce.rst A doc/source/releases/18.05_announce.rst M doc/source/releases/index.rst M lib/galaxy/containers/docker_model.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/converters/bam_to_bigwig_converter.xml R lib/galaxy/datatypes/converters/sam_to_bam_native.xml A lib/galaxy/datatypes/converters/sam_to_unsorted_bam.xml M lib/galaxy/datatypes/converters/to_coordinate_sorted_bam.xml M lib/galaxy/datatypes/converters/to_qname_sorted_bam.xml M lib/galaxy/datatypes/sniff.py M lib/galaxy/tools/toolbox/filters/__init__.py M lib/galaxy/tools/verify/interactor.py M lib/galaxy/tools/verify/script.py M lib/galaxy/visualization/plugins/interactive_environments.py M lib/galaxy/visualization/plugins/plugin.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/tool_shed/util/tool_util.py M test/functional/test_toolbox.py R test/functional/tools/sam_to_bam_native.xml A test/functional/tools/sam_to_unsorted_bam.xml M test/functional/tools/sample_datatypes_conf.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge branch 'dev' into visualization_header Commit: ef619f5905820d635f068a5c372b4167dec121bd https://github.com/galaxyproject/galaxy/commit/ef619f5905820d635f068a5c372b4... Author: guerler <aysam.guerler@gmail.com> Date: 2018-03-13 (Tue, 13 Mar 2018) Changed paths: M doc/source/releases/18.01_announce.rst M lib/galaxy/managers/libraries.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/workflow/run_request.py M scripts/common_startup.sh M test/api/test_workflows.py Log Message: ----------- Merge branch 'dev' into visualization_header Commit: c07c17e93dbd137947320b417082733a8a34345e https://github.com/galaxyproject/galaxy/commit/c07c17e93dbd137947320b4170827... Author: guerler <aysam.guerler@gmail.com> Date: 2018-03-13 (Tue, 13 Mar 2018) Changed paths: M config/plugins/visualizations/msa/static/script.js Log Message: ----------- Restore missing src for msa Commit: f58507880e26693a3142c94023e1f010e668b126 https://github.com/galaxyproject/galaxy/commit/f58507880e26693a3142c94023e1f... Author: guerler <aysam.guerler@gmail.com> Date: 2018-03-13 (Tue, 13 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/form/form-data.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/style/less/ui.less M static/style/blue/base.css Log Message: ----------- Merge branch 'dev' into visualization_header Commit: bf30a02f1e03f6058c755489a9aa1503463cf8c3 https://github.com/galaxyproject/galaxy/commit/bf30a02f1e03f6058c755489a9aa1... Author: guerler <aysam.guerler@gmail.com> Date: 2018-03-14 (Wed, 14 Mar 2018) Changed paths: M client/galaxy/scripts/apps/panels/tool-panel.js M client/galaxy/scripts/mvc/grid/grid-template.js M client/galaxy/scripts/mvc/upload/collection/collection-view.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-view.js M client/galaxy/scripts/utils/uploadbox.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/tools/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/web/framework/decorators.py A lib/galaxy/webapps/galaxy/api/uploads.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/config_schema.yml M lib/galaxy/webapps/galaxy/controllers/root.py M test/base/driver_util.py Log Message: ----------- Merge branch 'dev' into visualization_header Commit: df5838e6c1924e2f0303c675e0262736ece52238 https://github.com/galaxyproject/galaxy/commit/df5838e6c1924e2f0303c675e0262... Author: guerler <aysam.guerler@gmail.com> Date: 2018-03-14 (Wed, 14 Mar 2018) Changed paths: M client/galaxy/scripts/viz/trackster.js Log Message: ----------- Fix trackster link Commit: 7c3c36e7626769c653b9b3b8f6208c861c60a24d https://github.com/galaxyproject/galaxy/commit/7c3c36e7626769c653b9b3b8f6208... Author: guerler <aysam.guerler@gmail.com> Date: 2018-03-22 (Thu, 22 Mar 2018) Changed paths: A config/plugins/visualizations/scatterplot/static/logo.png Log Message: ----------- Add logo for scatterplot Commit: 0e150b4051b9ff567e5c5a26fb213d36d42ebdf9 https://github.com/galaxyproject/galaxy/commit/0e150b4051b9ff567e5c5a26fb213... Author: guerler <aysam.guerler@gmail.com> Date: 2018-03-22 (Thu, 22 Mar 2018) Changed paths: M client/galaxy/scripts/layout/menu.js Log Message: ----------- Rename tab to Visualize Commit: e0572e104fb4589c58415bb3d5f99ffe996b2f9c https://github.com/galaxyproject/galaxy/commit/e0572e104fb4589c58415bb3d5f99... Author: guerler <aysam.guerler@gmail.com> Date: 2018-03-22 (Thu, 22 Mar 2018) Changed paths: M Makefile M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/collection/collection-model.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-error.js M client/galaxy/scripts/mvc/dataset/dataset-model.js M client/galaxy/scripts/mvc/form/form-wrapper.js M client/galaxy/scripts/mvc/grid/grid-shared.js M client/galaxy/scripts/mvc/history/history-list.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/ui/ui-misc.js M client/galaxy/scripts/mvc/ui/ui-select-content.js M client/galaxy/scripts/mvc/upload/default/default-row.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/visualization-model.js M client/galaxy/scripts/mvc/workflow/workflow.js M client/galaxy/scripts/ui/pagination.js M client/galaxy/scripts/ui/peek-column-selector.js M client/package.json M config/datatypes_conf.xml.sample M config/galaxy.yml.sample M config/job_conf.xml.sample_advanced A config/plugins/visualizations/scatterplot/.babelrc M config/plugins/visualizations/scatterplot/package.json A config/plugins/visualizations/scatterplot/src/jqglobals.js M config/plugins/visualizations/scatterplot/src/scatterplot.js M config/plugins/visualizations/scatterplot/static/scatterplot.js M config/plugins/visualizations/scatterplot/templates/scatterplot.mako M config/reports.yml.sample M config/tool_conf.xml.main M config/tool_conf.xml.sample M config/tool_shed.yml.sample A config/workflow_resource_mapper_conf.yml.sample A config/workflow_resource_params_conf.xml.sample M doc/source/admin/cluster.md M doc/source/admin/nginx.md M doc/source/admin/scaling.md M doc/source/releases/18.01_announce.rst M lib/galaxy/config.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/genetics.py M lib/galaxy/datatypes/ngsindex.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/dynamic_tool_destination.py M lib/galaxy/jobs/mapper.py M lib/galaxy/jobs/runners/util/job_script/MEMORY_STATEMENT.sh M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/model/orm/engine_factory.py M lib/galaxy/objectstore/__init__.py M lib/galaxy/security/__init__.py M lib/galaxy/security/passwords.py M lib/galaxy/security/validate_user_input.py M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/tools/data_fetch.py M lib/galaxy/tools/execute.py M lib/galaxy/tools/loader_directory.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/tools/verify/interactor.py M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/util/__init__.py M lib/galaxy/util/checkers.py M lib/galaxy/webapps/config_manage.py M lib/galaxy/webapps/galaxy/api/_fetch_util.py M lib/galaxy/webapps/galaxy/api/remote_files.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/config_schema.yml M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/workflow/modules.py A lib/galaxy/workflow/resources/__init__.py A lib/galaxy/workflow/resources/example.py.sample M lib/galaxy/workflow/run_request.py M lib/galaxy_ext/metadata/set_metadata.py M lib/tool_shed/util/hg_util.py M lib/tool_shed/util/shed_util_common.py M lib/tool_shed/util/tool_util.py M run_tests.sh A scripts/apply_tags.py M scripts/bootstrap_history.py M scripts/cleanup_datasets/admin_cleanup_datasets.py M scripts/cleanup_datasets/update_dataset_size.py M test/api/test_libraries.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/galaxy_selenium/navigates_galaxy.py M test/integration/test_upload_configuration_options.py M test/selenium_tests/framework.py M test/selenium_tests/test_collection_builders.py M test/selenium_tests/test_jupyter.py M test/selenium_tests/test_library_to_collections.py M test/selenium_tests/test_tool_form.py M test/shed_functional/test_data/emboss/datatypes/datatypes_conf.xml A test/unit/jobs/dynamic_tool_destination/data/job_conf.xml M test/unit/jobs/dynamic_tool_destination/data/priority_tool_destination.yml M test/unit/jobs/dynamic_tool_destination/data/test_no_verbose.yml M test/unit/jobs/dynamic_tool_destination/data/test_num_input_datasets.yml M test/unit/jobs/dynamic_tool_destination/data/tool_destination.yml M test/unit/jobs/dynamic_tool_destination/mockGalaxy.py M test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py M test/unit/jobs/dynamic_tool_destination/ymltests.py M tools/data_source/upload.py M tools/data_source/upload.xml Log Message: ----------- Merge branch 'dev' into visualization_header Commit: 8b5c0b223ef9092420b9912b153b0d257fe5a1a5 https://github.com/galaxyproject/galaxy/commit/8b5c0b223ef9092420b9912b153b0... Author: guerler <aysam.guerler@gmail.com> Date: 2018-03-27 (Tue, 27 Mar 2018) Changed paths: M client/galaxy/scripts/components/PluginList.vue Log Message: ----------- Allow target top rendering for visualizations Commit: 0cdd9b9ecd235a34ba6018542156f9780bf22f77 https://github.com/galaxyproject/galaxy/commit/0cdd9b9ecd235a34ba6018542156f... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-03-27 (Tue, 27 Mar 2018) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/components/PluginList.vue M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/form/form-wrapper.js M client/galaxy/scripts/mvc/grid/grid-shared.js M client/galaxy/scripts/mvc/history/history-list.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/ui/ui-buttons.js M client/galaxy/scripts/mvc/ui/ui-misc.js M client/galaxy/scripts/mvc/visualization/chart/views/menu.js M client/galaxy/scripts/mvc/visualization/chart/views/viewer.js Log Message: ----------- Client formatting Commit: 2b2fd9289857b258f7e63f64668d776c49a54ec8 https://github.com/galaxyproject/galaxy/commit/2b2fd9289857b258f7e63f64668d7... Author: guerler <aysam.guerler@gmail.com> Date: 2018-03-27 (Tue, 27 Mar 2018) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/layout/menu.js M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Use visualizations route to link to plugins Commit: 38c2a895009c03204026ca7d74af70f92dd29f4e https://github.com/galaxyproject/galaxy/commit/38c2a895009c03204026ca7d74af7... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-03-27 (Tue, 27 Mar 2018) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/layout/menu.js M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Merge branch 'visualization_header' of github.com:guerler/galaxy into visualization_header Commit: c5beedef6b9f4498e4df0adfb39ddc519715f997 https://github.com/galaxyproject/galaxy/commit/c5beedef6b9f4498e4df0adfb39dd... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-03-27 (Tue, 27 Mar 2018) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/components/HistoryImport.vue A client/galaxy/scripts/components/PluginList.vue M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/form/form-wrapper.js M client/galaxy/scripts/mvc/grid/grid-shared.js M client/galaxy/scripts/mvc/history/history-list.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/ui/ui-buttons.js M client/galaxy/scripts/mvc/ui/ui-misc.js M client/galaxy/scripts/mvc/visualization/chart/components/model.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/groups.js M client/galaxy/scripts/mvc/visualization/chart/views/menu.js M client/galaxy/scripts/mvc/visualization/chart/views/viewer.js R client/galaxy/scripts/mvc/visualization/visualization-view.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/style/less/charts.less M config/plugins/visualizations/csg/config/csg.xml A config/plugins/visualizations/csg/static/logo.png M config/plugins/visualizations/graphviz/config/graphviz.xml 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/config/heatmap_shared.xml 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/msa/static/script.js M config/plugins/visualizations/nvd3/nvd3_bar/src/nvd3.js M config/plugins/visualizations/nvd3/nvd3_bar/static/nvd3.js 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/phyloviz/config/phyloviz.xml A config/plugins/visualizations/phyloviz/static/logo.png M config/plugins/visualizations/scatterplot/src/scatterplot.js A config/plugins/visualizations/scatterplot/static/logo.png M config/plugins/visualizations/scatterplot/static/scatterplot.js M config/plugins/visualizations/trackster/config/trackster.xml A config/plugins/visualizations/trackster/static/logo.png M config/plugins/visualizations/unipept/config/unipept.xml M config/plugins/visualizations/venn/src/script.js M config/plugins/visualizations/venn/static/script.js M lib/galaxy/visualization/plugins/config_parser.py M lib/galaxy/visualization/plugins/plugin.py M lib/galaxy/visualization/plugins/registry.py A lib/galaxy/webapps/galaxy/api/plugins.py M lib/galaxy/webapps/galaxy/buildapp.py M static/style/blue/base.css M test/unit/unittest_utils/galaxy_mock.py M test/unit/visualizations/plugins/test_VisualizationsRegistry.py Log Message: ----------- Merge branch 'visualization_header' into dev Compare: https://github.com/galaxyproject/galaxy/compare/bf5d472e2850...c5beedef6b9f