Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c5a51967173b7e5b0ecf6bbb1340db9ff54a3aed https://github.com/galaxyproject/galaxy/commit/c5a51967173b7e5b0ecf6bbb1340d... Author: Dannon Baker dannon.baker@gmail.com Date: 2016-09-23 (Fri, 23 Sep 2016)

Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-workflow.js M client/galaxy/style/less/base.less M static/maps/mvc/tool/tool-form-workflow.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tool/tool-form-workflow.js M static/style/blue/base.css M templates/webapps/galaxy/workflow/editor.mako

Log Message: ----------- Change wording to be more clear about how workflow output cleanup works. Also adjust styling so that the rows in the workflow editor box are less smashed together.

Commit: 277d3c3e58d28904752674c9210f02b88e481eb7 https://github.com/galaxyproject/galaxy/commit/277d3c3e58d28904752674c9210f0... Author: Dannon Baker dannon.baker@gmail.com Date: 2016-09-23 (Fri, 23 Sep 2016)

Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-workflow.js M static/maps/mvc/tool/tool-form-workflow.js.map M static/scripts/mvc/tool/tool-form-workflow.js

Log Message: ----------- Slight wording tweak.

Commit: 8966b741317431275100c24ab3cc69a221de646c https://github.com/galaxyproject/galaxy/commit/8966b741317431275100c24ab3cc6... Author: Dannon Baker dannon.baker@gmail.com Date: 2016-09-27 (Tue, 27 Sep 2016)

Changed paths: M client/galaxy/style/less/ui.less M static/scripts/bundled/libs.bundled.js.map M static/style/blue/base.css

Log Message: ----------- Swap to section row selector

Commit: 5028e2a25107e8f4cd2f136ab275853b5e31bb7f https://github.com/galaxyproject/galaxy/commit/5028e2a25107e8f4cd2f136ab2758... Author: Dannon Baker dannon.baker@gmail.com Date: 2016-11-16 (Wed, 16 Nov 2016)

Changed paths: M .ci/flake8_blacklist.txt A .ci/flake8_docstrings_include_list.txt M .ci/flake8_lint_include_list.txt M .ci/flake8_wrapper.sh A .ci/flake8_wrapper_docstrings.sh M .ci/py3_sources.txt M .gitignore M .travis.yml M CONTRIBUTORS.md M Makefile M client/galaxy/scripts/apps/history-panel.js M client/galaxy/scripts/layout/masthead.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/history/options-menu.js M client/galaxy/scripts/mvc/library/library-dataset-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/tool/tool-form-base.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/tool/tool-form-workflow.js M client/galaxy/scripts/mvc/tool/tool-form.js M client/galaxy/scripts/mvc/tool/tools.js M client/galaxy/scripts/mvc/ui/ui-buttons.js M client/galaxy/scripts/mvc/ui/ui-modal.js M client/galaxy/scripts/mvc/ui/ui-portlet.js M client/galaxy/scripts/mvc/ui/ui-select-content.js M client/galaxy/scripts/mvc/ui/ui-tabs.js A client/galaxy/scripts/mvc/ui/ui-thumbnails.js A client/galaxy/scripts/mvc/webhooks.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M client/galaxy/scripts/utils/utils.js M client/galaxy/style/less/ui.less M client/galaxy/style/source_material/circle.py M config/datatypes_conf.xml.sample M config/galaxy.ini.sample M config/job_conf.xml.sample_advanced M config/plugins/tours/core.galaxy_ui.yaml R config/plugins/visualizations/charts/Gruntfile.js M config/plugins/visualizations/charts/config/charts.xml M config/plugins/visualizations/charts/package.json R config/plugins/visualizations/charts/sample.txt R config/plugins/visualizations/charts/static/app.css R config/plugins/visualizations/charts/static/app.js R config/plugins/visualizations/charts/static/charts/jqplot/bar/config.js R config/plugins/visualizations/charts/static/charts/jqplot/bar/logo.png R config/plugins/visualizations/charts/static/charts/jqplot/bar/wrapper.js R config/plugins/visualizations/charts/static/charts/jqplot/boxplot/config.js R config/plugins/visualizations/charts/static/charts/jqplot/boxplot/logo.png R config/plugins/visualizations/charts/static/charts/jqplot/boxplot/wrapper.js R config/plugins/visualizations/charts/static/charts/jqplot/common/config.js R config/plugins/visualizations/charts/static/charts/jqplot/common/plot-config.js R config/plugins/visualizations/charts/static/charts/jqplot/common/wrapper.js R config/plugins/visualizations/charts/static/charts/jqplot/histogram_discrete/config.js R config/plugins/visualizations/charts/static/charts/jqplot/histogram_discrete/logo.png R config/plugins/visualizations/charts/static/charts/jqplot/histogram_discrete/wrapper.js R config/plugins/visualizations/charts/static/charts/jqplot/line/config.js R config/plugins/visualizations/charts/static/charts/jqplot/line/logo.png R config/plugins/visualizations/charts/static/charts/jqplot/line/wrapper.js R config/plugins/visualizations/charts/static/charts/jqplot/scatter/config.js R config/plugins/visualizations/charts/static/charts/jqplot/scatter/logo.png R config/plugins/visualizations/charts/static/charts/jqplot/scatter/wrapper.js R config/plugins/visualizations/charts/static/charts/nvd3/bar/config.js R config/plugins/visualizations/charts/static/charts/nvd3/bar/logo.png R config/plugins/visualizations/charts/static/charts/nvd3/bar/wrapper.js R config/plugins/visualizations/charts/static/charts/nvd3/bar_horizontal/config.js R config/plugins/visualizations/charts/static/charts/nvd3/bar_horizontal/logo.png R config/plugins/visualizations/charts/static/charts/nvd3/bar_horizontal/wrapper.js R config/plugins/visualizations/charts/static/charts/nvd3/bar_horizontal_stacked/config.js R config/plugins/visualizations/charts/static/charts/nvd3/bar_horizontal_stacked/logo.png R config/plugins/visualizations/charts/static/charts/nvd3/bar_horizontal_stacked/wrapper.js R config/plugins/visualizations/charts/static/charts/nvd3/bar_stacked/config.js R config/plugins/visualizations/charts/static/charts/nvd3/bar_stacked/logo.png R config/plugins/visualizations/charts/static/charts/nvd3/bar_stacked/wrapper.js R config/plugins/visualizations/charts/static/charts/nvd3/common/config.js R config/plugins/visualizations/charts/static/charts/nvd3/common/wrapper.js R config/plugins/visualizations/charts/static/charts/nvd3/histogram/config.js R config/plugins/visualizations/charts/static/charts/nvd3/histogram/logo.png R config/plugins/visualizations/charts/static/charts/nvd3/histogram/wrapper.js R config/plugins/visualizations/charts/static/charts/nvd3/histogram_discrete/config.js R config/plugins/visualizations/charts/static/charts/nvd3/histogram_discrete/logo.png R config/plugins/visualizations/charts/static/charts/nvd3/histogram_discrete/wrapper.js R config/plugins/visualizations/charts/static/charts/nvd3/line/config.js R config/plugins/visualizations/charts/static/charts/nvd3/line/logo.png R config/plugins/visualizations/charts/static/charts/nvd3/line/wrapper.js R config/plugins/visualizations/charts/static/charts/nvd3/line_focus/config.js R config/plugins/visualizations/charts/static/charts/nvd3/line_focus/logo.png R config/plugins/visualizations/charts/static/charts/nvd3/line_focus/wrapper.js R config/plugins/visualizations/charts/static/charts/nvd3/pie/config.js R config/plugins/visualizations/charts/static/charts/nvd3/pie/logo.png R config/plugins/visualizations/charts/static/charts/nvd3/pie/wrapper.js R config/plugins/visualizations/charts/static/charts/nvd3/scatter/config.js R config/plugins/visualizations/charts/static/charts/nvd3/scatter/logo.png R config/plugins/visualizations/charts/static/charts/nvd3/scatter/wrapper.js R config/plugins/visualizations/charts/static/charts/nvd3/stackedarea/config.js R config/plugins/visualizations/charts/static/charts/nvd3/stackedarea/logo.png R config/plugins/visualizations/charts/static/charts/nvd3/stackedarea/wrapper.js R config/plugins/visualizations/charts/static/charts/nvd3/stackedarea_full/config.js R config/plugins/visualizations/charts/static/charts/nvd3/stackedarea_full/logo.png R config/plugins/visualizations/charts/static/charts/nvd3/stackedarea_full/wrapper.js R config/plugins/visualizations/charts/static/charts/nvd3/stackedarea_stream/config.js R config/plugins/visualizations/charts/static/charts/nvd3/stackedarea_stream/logo.png R config/plugins/visualizations/charts/static/charts/nvd3/stackedarea_stream/wrapper.js R config/plugins/visualizations/charts/static/charts/others/example/config.js R config/plugins/visualizations/charts/static/charts/others/example/logo.png R config/plugins/visualizations/charts/static/charts/others/example/wrapper.js R config/plugins/visualizations/charts/static/charts/others/heatmap/config.js R config/plugins/visualizations/charts/static/charts/others/heatmap/heatmap-parameters.js R config/plugins/visualizations/charts/static/charts/others/heatmap/heatmap-plugin.js R config/plugins/visualizations/charts/static/charts/others/heatmap/logo.png R config/plugins/visualizations/charts/static/charts/others/heatmap/wrapper.js R config/plugins/visualizations/charts/static/charts/others/heatmap_cluster/config.js R config/plugins/visualizations/charts/static/charts/others/heatmap_cluster/logo.png R config/plugins/visualizations/charts/static/charts/others/heatmap_cluster/wrapper.js R config/plugins/visualizations/charts/static/charts/overview.js R config/plugins/visualizations/charts/static/charts/types.js R config/plugins/visualizations/charts/static/charts/utilities/tabular-datasets.js R config/plugins/visualizations/charts/static/charts/utilities/tabular-form.js R config/plugins/visualizations/charts/static/charts/utilities/tabular-inputs.js R config/plugins/visualizations/charts/static/charts/utilities/tabular-utilities.js A config/plugins/visualizations/charts/static/client/app.css A config/plugins/visualizations/charts/static/client/app.js A config/plugins/visualizations/charts/static/client/components/model.js A config/plugins/visualizations/charts/static/client/components/screenshot.js A config/plugins/visualizations/charts/static/client/views/description.js A config/plugins/visualizations/charts/static/client/views/editor.js A config/plugins/visualizations/charts/static/client/views/groups.js A config/plugins/visualizations/charts/static/client/views/settings.js A config/plugins/visualizations/charts/static/client/views/viewer.js A config/plugins/visualizations/charts/static/client/views/viewport.js R config/plugins/visualizations/charts/static/components/jobs.js R config/plugins/visualizations/charts/static/components/model.js R config/plugins/visualizations/charts/static/components/screenshot.js R config/plugins/visualizations/charts/static/components/storage.js R config/plugins/visualizations/charts/static/plugins/canvg/canvg.js R config/plugins/visualizations/charts/static/plugins/canvg/rgbcolor.js R config/plugins/visualizations/charts/static/plugins/crossfilter/crossfilter.js R config/plugins/visualizations/charts/static/plugins/jqplot/jquery.jqplot.css R config/plugins/visualizations/charts/static/plugins/jqplot/jquery.jqplot.js R config/plugins/visualizations/charts/static/plugins/jqplot/jquery.jqplot.plugins.js R config/plugins/visualizations/charts/static/plugins/jqplot/plugins/jqplot.barRenderer.min.js R config/plugins/visualizations/charts/static/plugins/jqplot/plugins/jqplot.blockRenderer.min.js R config/plugins/visualizations/charts/static/plugins/jqplot/plugins/jqplot.boxplotRenderer.min.js R config/plugins/visualizations/charts/static/plugins/jqplot/plugins/jqplot.canvasAxisLabelRenderer.min.js R config/plugins/visualizations/charts/static/plugins/jqplot/plugins/jqplot.canvasAxisTickRenderer.min.js R config/plugins/visualizations/charts/static/plugins/jqplot/plugins/jqplot.canvasOverlay.min.js R config/plugins/visualizations/charts/static/plugins/jqplot/plugins/jqplot.canvasTextRenderer.min.js R config/plugins/visualizations/charts/static/plugins/jqplot/plugins/jqplot.categoryAxisRenderer.min.js R config/plugins/visualizations/charts/static/plugins/jqplot/plugins/jqplot.cursor.min.js R config/plugins/visualizations/charts/static/plugins/jqplot/plugins/jqplot.enhancedLegendRenderer.min.js R config/plugins/visualizations/charts/static/plugins/jqplot/plugins/jqplot.highlighter.min.js R config/plugins/visualizations/charts/static/plugins/jqplot/plugins/jqplot.ohlcRenderer.min.js R config/plugins/visualizations/charts/static/plugins/nvd3/nv.d3.css R config/plugins/visualizations/charts/static/plugins/nvd3/nv.d3.js A config/plugins/visualizations/charts/static/repository/build/benfred_venn.js A config/plugins/visualizations/charts/static/repository/build/benfred_venn.js.map A config/plugins/visualizations/charts/static/repository/build/biojs_drawrnajs.js A config/plugins/visualizations/charts/static/repository/build/biojs_drawrnajs.js.map A config/plugins/visualizations/charts/static/repository/build/biojs_msa.js A config/plugins/visualizations/charts/static/repository/build/biojs_msa.js.map A config/plugins/visualizations/charts/static/repository/build/cytoscape_basic.js A config/plugins/visualizations/charts/static/repository/build/cytoscape_basic.js.map A config/plugins/visualizations/charts/static/repository/build/jqplot_bar.js A config/plugins/visualizations/charts/static/repository/build/jqplot_bar.js.map A config/plugins/visualizations/charts/static/repository/build/jqplot_boxplot.js A config/plugins/visualizations/charts/static/repository/build/jqplot_boxplot.js.map A config/plugins/visualizations/charts/static/repository/build/jqplot_histogram_discrete.js A config/plugins/visualizations/charts/static/repository/build/jqplot_histogram_discrete.js.map A config/plugins/visualizations/charts/static/repository/build/jqplot_line.js A config/plugins/visualizations/charts/static/repository/build/jqplot_line.js.map A config/plugins/visualizations/charts/static/repository/build/jqplot_scatter.js A config/plugins/visualizations/charts/static/repository/build/jqplot_scatter.js.map A config/plugins/visualizations/charts/static/repository/build/nvd3_bar.js A config/plugins/visualizations/charts/static/repository/build/nvd3_bar.js.map A config/plugins/visualizations/charts/static/repository/build/nvd3_bar_horizontal.js A config/plugins/visualizations/charts/static/repository/build/nvd3_bar_horizontal.js.map A config/plugins/visualizations/charts/static/repository/build/nvd3_bar_horizontal_stacked.js A config/plugins/visualizations/charts/static/repository/build/nvd3_bar_horizontal_stacked.js.map A config/plugins/visualizations/charts/static/repository/build/nvd3_bar_stacked.js A config/plugins/visualizations/charts/static/repository/build/nvd3_bar_stacked.js.map A config/plugins/visualizations/charts/static/repository/build/nvd3_histogram.js A config/plugins/visualizations/charts/static/repository/build/nvd3_histogram.js.map A config/plugins/visualizations/charts/static/repository/build/nvd3_histogram_discrete.js A config/plugins/visualizations/charts/static/repository/build/nvd3_histogram_discrete.js.map A config/plugins/visualizations/charts/static/repository/build/nvd3_line.js A config/plugins/visualizations/charts/static/repository/build/nvd3_line.js.map A config/plugins/visualizations/charts/static/repository/build/nvd3_line_focus.js A config/plugins/visualizations/charts/static/repository/build/nvd3_line_focus.js.map A config/plugins/visualizations/charts/static/repository/build/nvd3_pie.js A config/plugins/visualizations/charts/static/repository/build/nvd3_pie.js.map A config/plugins/visualizations/charts/static/repository/build/nvd3_scatter.js A config/plugins/visualizations/charts/static/repository/build/nvd3_scatter.js.map A config/plugins/visualizations/charts/static/repository/build/nvd3_stackedarea.js A config/plugins/visualizations/charts/static/repository/build/nvd3_stackedarea.js.map A config/plugins/visualizations/charts/static/repository/build/nvd3_stackedarea_full.js A config/plugins/visualizations/charts/static/repository/build/nvd3_stackedarea_full.js.map A config/plugins/visualizations/charts/static/repository/build/nvd3_stackedarea_stream.js A config/plugins/visualizations/charts/static/repository/build/nvd3_stackedarea_stream.js.map A config/plugins/visualizations/charts/static/repository/build/others_example.js A config/plugins/visualizations/charts/static/repository/build/others_example.js.map A config/plugins/visualizations/charts/static/repository/build/others_heatmap.js A config/plugins/visualizations/charts/static/repository/build/others_heatmap.js.map A config/plugins/visualizations/charts/static/repository/build/others_heatmap_cluster.js A config/plugins/visualizations/charts/static/repository/build/others_heatmap_cluster.js.map A config/plugins/visualizations/charts/static/repository/build/pv_viewer.js A config/plugins/visualizations/charts/static/repository/build/pv_viewer.js.map A config/plugins/visualizations/charts/static/repository/build/registry.js A config/plugins/visualizations/charts/static/repository/build/registry.js.map A config/plugins/visualizations/charts/static/repository/build/registry.tmp.js A config/plugins/visualizations/charts/static/repository/plugins/benfred/venn.css A config/plugins/visualizations/charts/static/repository/plugins/benfred/venn.js A config/plugins/visualizations/charts/static/repository/plugins/biojs/biojs.msa.js A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/drawrna.js A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/layouts/layout.js A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/layouts/naview/base.js A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/layouts/naview/connection.js A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/layouts/naview/getnaview.js A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/layouts/naview/loop.js A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/layouts/naview/naview.js A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/layouts/naview/radloop.js A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/layouts/naview/region.js A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/layouts/radiate/getradiate.js A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/models/link.js A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/models/linkcol.js A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/models/ncanno.js A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/models/residue.js A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/models/residuecol.js A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/models/structure.js A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/utils/.Rhistory A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/utils/lasso.js A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/utils/parsedbr.js A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/utils/spectrum.js A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/utils/style.js A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/views/annoview.js A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/views/optspanel.js A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/views/seqpanel.js A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/views/vispanel.js A config/plugins/visualizations/charts/static/repository/plugins/cytoscape/cytoscape.js A config/plugins/visualizations/charts/static/repository/plugins/jqplot/jquery.jqplot.css A config/plugins/visualizations/charts/static/repository/plugins/jqplot/jquery.jqplot.js A config/plugins/visualizations/charts/static/repository/plugins/jqplot/jquery.jqplot.plugins.js A config/plugins/visualizations/charts/static/repository/plugins/nvd3/nv.d3.css A config/plugins/visualizations/charts/static/repository/plugins/nvd3/nv.d3.js A config/plugins/visualizations/charts/static/repository/plugins/pv/viewer.js A config/plugins/visualizations/charts/static/repository/registry.json A config/plugins/visualizations/charts/static/repository/utilities/jobs.js A config/plugins/visualizations/charts/static/repository/utilities/utils.js A config/plugins/visualizations/charts/static/repository/visualizations/benfred/venn/config.js A config/plugins/visualizations/charts/static/repository/visualizations/benfred/venn/logo.png A config/plugins/visualizations/charts/static/repository/visualizations/benfred/venn/wrapper.js A config/plugins/visualizations/charts/static/repository/visualizations/biojs/drawrnajs/config.js A config/plugins/visualizations/charts/static/repository/visualizations/biojs/drawrnajs/logo.png A config/plugins/visualizations/charts/static/repository/visualizations/biojs/drawrnajs/wrapper.js A config/plugins/visualizations/charts/static/repository/visualizations/biojs/msa/config.js A config/plugins/visualizations/charts/static/repository/visualizations/biojs/msa/logo.png A config/plugins/visualizations/charts/static/repository/visualizations/biojs/msa/wrapper.js A config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/basic/config.js A config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/basic/logo.png A config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/basic/wrapper.js A config/plugins/visualizations/charts/static/repository/visualizations/jqplot/bar/config.js A config/plugins/visualizations/charts/static/repository/visualizations/jqplot/bar/logo.png A config/plugins/visualizations/charts/static/repository/visualizations/jqplot/bar/wrapper.js A config/plugins/visualizations/charts/static/repository/visualizations/jqplot/boxplot/config.js A config/plugins/visualizations/charts/static/repository/visualizations/jqplot/boxplot/logo.png A config/plugins/visualizations/charts/static/repository/visualizations/jqplot/boxplot/wrapper.js A config/plugins/visualizations/charts/static/repository/visualizations/jqplot/common/config.js A config/plugins/visualizations/charts/static/repository/visualizations/jqplot/common/plot-config.js A config/plugins/visualizations/charts/static/repository/visualizations/jqplot/common/wrapper.js A config/plugins/visualizations/charts/static/repository/visualizations/jqplot/histogram_discrete/config.js A config/plugins/visualizations/charts/static/repository/visualizations/jqplot/histogram_discrete/logo.png A config/plugins/visualizations/charts/static/repository/visualizations/jqplot/histogram_discrete/wrapper.js A config/plugins/visualizations/charts/static/repository/visualizations/jqplot/line/config.js A config/plugins/visualizations/charts/static/repository/visualizations/jqplot/line/logo.png A config/plugins/visualizations/charts/static/repository/visualizations/jqplot/line/wrapper.js A config/plugins/visualizations/charts/static/repository/visualizations/jqplot/scatter/config.js A config/plugins/visualizations/charts/static/repository/visualizations/jqplot/scatter/logo.png A config/plugins/visualizations/charts/static/repository/visualizations/jqplot/scatter/wrapper.js A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar/config.js A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar/logo.png A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar/wrapper.js A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar_horizontal/config.js A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar_horizontal/logo.png A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar_horizontal/wrapper.js A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar_horizontal_stacked/config.js A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar_horizontal_stacked/logo.png A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar_horizontal_stacked/wrapper.js A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar_stacked/config.js A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar_stacked/logo.png A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar_stacked/wrapper.js A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/common/config.js A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/common/wrapper.js A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/histogram/config.js A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/histogram/logo.png A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/histogram/wrapper.js A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/histogram_discrete/config.js A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/histogram_discrete/logo.png A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/histogram_discrete/wrapper.js A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/line/config.js A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/line/logo.png A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/line/wrapper.js A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/line_focus/config.js A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/line_focus/logo.png A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/line_focus/wrapper.js A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/pie/config.js A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/pie/logo.png A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/pie/wrapper.js A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/scatter/config.js A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/scatter/logo.png A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/scatter/wrapper.js A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/stackedarea/config.js A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/stackedarea/logo.png A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/stackedarea/wrapper.js A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/stackedarea_full/config.js A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/stackedarea_full/logo.png A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/stackedarea_full/wrapper.js A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/stackedarea_stream/config.js A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/stackedarea_stream/logo.png A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/stackedarea_stream/wrapper.js A config/plugins/visualizations/charts/static/repository/visualizations/others/example/config.js A config/plugins/visualizations/charts/static/repository/visualizations/others/example/logo.png A config/plugins/visualizations/charts/static/repository/visualizations/others/example/wrapper.js A config/plugins/visualizations/charts/static/repository/visualizations/others/heatmap/config.js A config/plugins/visualizations/charts/static/repository/visualizations/others/heatmap/heatmap-parameters.js A config/plugins/visualizations/charts/static/repository/visualizations/others/heatmap/heatmap-plugin.js A config/plugins/visualizations/charts/static/repository/visualizations/others/heatmap/logo.png A config/plugins/visualizations/charts/static/repository/visualizations/others/heatmap/wrapper.js A config/plugins/visualizations/charts/static/repository/visualizations/others/heatmap_cluster/config.js A config/plugins/visualizations/charts/static/repository/visualizations/others/heatmap_cluster/logo.png A config/plugins/visualizations/charts/static/repository/visualizations/others/heatmap_cluster/wrapper.js A config/plugins/visualizations/charts/static/repository/visualizations/pv/viewer/config.js A config/plugins/visualizations/charts/static/repository/visualizations/pv/viewer/logo.png A config/plugins/visualizations/charts/static/repository/visualizations/pv/viewer/wrapper.js A config/plugins/visualizations/charts/static/repository/visualizations/utilities/tabular-datasets.js A config/plugins/visualizations/charts/static/repository/visualizations/utilities/tabular-form.js A config/plugins/visualizations/charts/static/repository/visualizations/utilities/tabular-utilities.js R config/plugins/visualizations/charts/static/views/description.js R config/plugins/visualizations/charts/static/views/editor.js R config/plugins/visualizations/charts/static/views/groups.js R config/plugins/visualizations/charts/static/views/settings.js R config/plugins/visualizations/charts/static/views/types.js R config/plugins/visualizations/charts/static/views/viewer.js R config/plugins/visualizations/charts/static/views/viewport.js M config/plugins/visualizations/charts/templates/charts.mako A config/plugins/visualizations/charts/webpack.config.js A config/plugins/webhooks/demo/history_test1/config/history_test1.yml A config/plugins/webhooks/demo/history_test2/config/history_test2.yml A config/plugins/webhooks/demo/masthead_test/config/masthead_test.yml A config/plugins/webhooks/demo/phdcomics/config/phdcomics.yaml A config/plugins/webhooks/demo/phdcomics/helper/__init__.py A config/plugins/webhooks/demo/phdcomics/static/script.js A config/plugins/webhooks/demo/phdcomics/static/styles.css A config/plugins/webhooks/demo/trans_object/config/trans_object.yaml A config/plugins/webhooks/demo/trans_object/helper/__init__.py A config/plugins/webhooks/demo/xkcd/config/xkcd.yml A config/plugins/webhooks/demo/xkcd/static/script.js A config/plugins/webhooks/demo/xkcd/static/styles.css M config/tool_conf.xml.sample M config/tool_data_table_conf.xml.sample M contrib/galaxy_config_merger.py M contrib/nagios/check_galaxy.py M cron/add_manual_builds.py M cron/build_chrom_db.py M cron/parse_builds.py M cron/parse_builds_3_sites.py M doc/Makefile M doc/parse_gx_xsd.py M doc/patch.py M doc/schema_template.md M doc/source/admin/conda_faq.rst M doc/source/admin/dependency_resolvers.rst A doc/source/admin/images_webhooks/history-menu.png A doc/source/admin/images_webhooks/masthead.png A doc/source/admin/images_webhooks/masthead_trans_object.png A doc/source/admin/images_webhooks/tool.png A doc/source/admin/images_webhooks/workflow.png M doc/source/admin/index.rst M doc/source/admin/interactive_environments.rst R doc/source/admin/interactive_environments_success.png A doc/source/admin/mulled_containers.rst A doc/source/admin/webhooks.rst M doc/source/api/guidelines.rst M doc/source/conf.py M doc/source/dev/build_a_job_runner.rst M doc/source/dev/index.rst A doc/source/dev/inherit.png A doc/source/dev/interactive_environments_success.png A doc/source/dev/queue.png A doc/source/dev/queue_b.png A doc/source/dev/runner_diag.png M doc/source/index.rst M doc/source/lib/galaxy.datatypes.converters.rst M doc/source/lib/galaxy.jobs.rst M doc/source/lib/galaxy.rst M doc/source/lib/galaxy.tools.linters.rst M doc/source/lib/galaxy.tools.parameters.rst R doc/source/lib/galaxy.util.backports.importlib.rst M doc/source/lib/galaxy.util.backports.rst M doc/source/lib/galaxy.util.rst M doc/source/project/issues.rst M doc/source/releases/16.04.rst M doc/source/releases/16.04_announce.rst M doc/source/releases/16.07.rst M doc/source/releases/index.rst A doc/source/slideshow/architecture/galaxy_architecture.md A doc/source/slideshow/architecture/images/backbone-model-view.svg A doc/source/slideshow/architecture/images/cluster_support.svg A doc/source/slideshow/architecture/images/data_managers.svg A doc/source/slideshow/architecture/images/docker-chart.png A doc/source/slideshow/architecture/images/family/team.png A doc/source/slideshow/architecture/images/galaxy_schema.png A doc/source/slideshow/architecture/images/hda.svg A doc/source/slideshow/architecture/images/hda_dataset.plantuml.svg A doc/source/slideshow/architecture/images/hda_dataset.plantuml.txt A doc/source/slideshow/architecture/images/hda_hdca.plantuml.svg A doc/source/slideshow/architecture/images/hda_hdca.plantuml.txt A doc/source/slideshow/architecture/images/jsload.png A doc/source/slideshow/architecture/images/libraries.svg A doc/source/slideshow/architecture/images/library_permissions.svg A doc/source/slideshow/architecture/images/objectstore.plantuml.svg A doc/source/slideshow/architecture/images/objectstore.plantuml.txt A doc/source/slideshow/architecture/images/objectstore_diagram.svg A doc/source/slideshow/architecture/images/plantuml_options.txt A doc/source/slideshow/architecture/images/sequence.json A doc/source/slideshow/architecture/images/server_client.plantuml.svg A doc/source/slideshow/architecture/images/server_client.plantuml.txt A doc/source/slideshow/architecture/images/server_client_old.plantuml.svg A doc/source/slideshow/architecture/images/server_client_old.plantuml.txt A doc/source/slideshow/architecture/images/sqla_arch_small.png A doc/source/slideshow/architecture/images/usegalaxy_webservers.svg A doc/source/slideshow/architecture/images/usegalaxyorg.svg A doc/source/slideshow/architecture/images/webapp.plantuml.svg A doc/source/slideshow/architecture/images/webapp.plantuml.txt A doc/source/slideshow/architecture/images/what-is-webpack.svg A doc/source/slideshow/architecture/images/workflow_definition.svg A doc/source/slideshow/architecture/images/workflow_run.svg A doc/source/slideshow/architecture/images/wsgi_app.svg A doc/source/slideshow/architecture/images/wsgi_request.svg A doc/source/slideshow/architecture/remark-latest.min.js A doc/source/slideshow/architecture/style.css 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 M lib/galaxy/config.py M lib/galaxy/datatypes/assembly.py M lib/galaxy/datatypes/binary.py A lib/galaxy/datatypes/blast.py M lib/galaxy/datatypes/checkers.py M lib/galaxy/datatypes/constructive_solid_geometry.py M lib/galaxy/datatypes/converters/bam_to_bigwig_converter.xml M lib/galaxy/datatypes/converters/bed_to_fli_converter.xml M lib/galaxy/datatypes/converters/bed_to_gff_converter.py M lib/galaxy/datatypes/converters/bed_to_gff_converter.xml M lib/galaxy/datatypes/converters/bed_to_tabix_converter.xml M lib/galaxy/datatypes/converters/bedgraph_to_array_tree_converter.py M lib/galaxy/datatypes/converters/bedgraph_to_array_tree_converter.xml M lib/galaxy/datatypes/converters/bedgraph_to_bigwig_converter.xml M lib/galaxy/datatypes/converters/bgzip.py M lib/galaxy/datatypes/converters/cml_to_inchi_converter.xml M lib/galaxy/datatypes/converters/cml_to_mol2_converter.xml M lib/galaxy/datatypes/converters/cml_to_sdf_converter.xml M lib/galaxy/datatypes/converters/cml_to_smi_converter.xml M lib/galaxy/datatypes/converters/encodepeak_to_bgzip_converter.xml M lib/galaxy/datatypes/converters/encodepeak_to_tabix_converter.xml M lib/galaxy/datatypes/converters/fasta_to_2bit.xml M lib/galaxy/datatypes/converters/fasta_to_bowtie_base_index_converter.xml M lib/galaxy/datatypes/converters/fasta_to_bowtie_color_index_converter.xml M lib/galaxy/datatypes/converters/fasta_to_len.py M lib/galaxy/datatypes/converters/fasta_to_len.xml M lib/galaxy/datatypes/converters/fasta_to_tabular_converter.xml M lib/galaxy/datatypes/converters/fastq_to_fqtoc.xml M lib/galaxy/datatypes/converters/fastqsolexa_to_fasta_converter.py M lib/galaxy/datatypes/converters/fastqsolexa_to_fasta_converter.xml M lib/galaxy/datatypes/converters/fastqsolexa_to_qual_converter.py M lib/galaxy/datatypes/converters/fastqsolexa_to_qual_converter.xml M lib/galaxy/datatypes/converters/gff_to_bed_converter.py M lib/galaxy/datatypes/converters/gff_to_bed_converter.xml M lib/galaxy/datatypes/converters/gff_to_bgzip_converter.xml M lib/galaxy/datatypes/converters/gff_to_fli_converter.xml M lib/galaxy/datatypes/converters/gff_to_interval_index_converter.py M lib/galaxy/datatypes/converters/gff_to_interval_index_converter.xml M lib/galaxy/datatypes/converters/gff_to_tabix_converter.xml M lib/galaxy/datatypes/converters/inchi_to_cml_converter.xml M lib/galaxy/datatypes/converters/inchi_to_mol2_converter.xml M lib/galaxy/datatypes/converters/inchi_to_mol_converter.xml M lib/galaxy/datatypes/converters/inchi_to_sdf_converter.xml M lib/galaxy/datatypes/converters/inchi_to_smi_converter.xml M lib/galaxy/datatypes/converters/interval_to_bed12_converter.xml M lib/galaxy/datatypes/converters/interval_to_bed6_converter.xml M lib/galaxy/datatypes/converters/interval_to_bed_converter.py M lib/galaxy/datatypes/converters/interval_to_bed_converter.xml M lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.py M lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.xml M lib/galaxy/datatypes/converters/interval_to_bgzip_converter.xml M lib/galaxy/datatypes/converters/interval_to_bigwig_converter.xml M lib/galaxy/datatypes/converters/interval_to_coverage.py M lib/galaxy/datatypes/converters/interval_to_coverage.xml M lib/galaxy/datatypes/converters/interval_to_fli.py M lib/galaxy/datatypes/converters/interval_to_interval_index_converter.py M lib/galaxy/datatypes/converters/interval_to_interval_index_converter.xml M lib/galaxy/datatypes/converters/interval_to_tabix_converter.py M lib/galaxy/datatypes/converters/interval_to_tabix_converter.xml M lib/galaxy/datatypes/converters/len_to_linecount.xml M lib/galaxy/datatypes/converters/maf_to_fasta_converter.xml M lib/galaxy/datatypes/converters/maf_to_interval_converter.xml M lib/galaxy/datatypes/converters/mol2_to_cml_converter.xml M lib/galaxy/datatypes/converters/mol2_to_inchi_converter.xml M lib/galaxy/datatypes/converters/mol2_to_mol_converter.xml M lib/galaxy/datatypes/converters/mol2_to_sdf_converter.xml M lib/galaxy/datatypes/converters/mol2_to_smi_converter.xml M lib/galaxy/datatypes/converters/mol_to_cml_converter.xml M lib/galaxy/datatypes/converters/mol_to_inchi_converter.xml M lib/galaxy/datatypes/converters/mol_to_mol2_converter.xml M lib/galaxy/datatypes/converters/picard_interval_list_to_bed6_converter.py M lib/galaxy/datatypes/converters/picard_interval_list_to_bed6_converter.xml M lib/galaxy/datatypes/converters/pileup_to_interval_index_converter.py M lib/galaxy/datatypes/converters/pileup_to_interval_index_converter.xml M lib/galaxy/datatypes/converters/ref_to_seq_taxonomy_converter.py M lib/galaxy/datatypes/converters/ref_to_seq_taxonomy_converter.xml M lib/galaxy/datatypes/converters/sam_to_bam.py M lib/galaxy/datatypes/converters/sam_to_bam.xml M lib/galaxy/datatypes/converters/sam_to_bigwig_converter.xml M lib/galaxy/datatypes/converters/sdf_to_cml_converter.xml M lib/galaxy/datatypes/converters/sdf_to_inchi_converter.xml M lib/galaxy/datatypes/converters/sdf_to_mol2_converter.xml M lib/galaxy/datatypes/converters/sdf_to_smi_converter.xml M lib/galaxy/datatypes/converters/smi_to_cml_converter.xml M lib/galaxy/datatypes/converters/smi_to_inchi_converter.xml M lib/galaxy/datatypes/converters/smi_to_mol2_converter.xml M lib/galaxy/datatypes/converters/smi_to_mol_converter.xml M lib/galaxy/datatypes/converters/smi_to_sdf_converter.xml M lib/galaxy/datatypes/converters/smi_to_smi_converter.xml M lib/galaxy/datatypes/converters/tabular_to_dbnsfp.py M lib/galaxy/datatypes/converters/tabular_to_dbnsfp.xml M lib/galaxy/datatypes/converters/vcf_to_bgzip_converter.xml M lib/galaxy/datatypes/converters/vcf_to_interval_index_converter.py M lib/galaxy/datatypes/converters/vcf_to_interval_index_converter.xml M lib/galaxy/datatypes/converters/vcf_to_tabix_converter.xml M lib/galaxy/datatypes/converters/vcf_to_vcf_bgzip.py M lib/galaxy/datatypes/converters/wig_to_bigwig_converter.xml M lib/galaxy/datatypes/converters/wiggle_to_array_tree_converter.py M lib/galaxy/datatypes/converters/wiggle_to_array_tree_converter.xml M lib/galaxy/datatypes/converters/wiggle_to_simple_converter.py M lib/galaxy/datatypes/converters/wiggle_to_simple_converter.xml M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/dataproviders/__init__.py M lib/galaxy/datatypes/dataproviders/column.py M lib/galaxy/datatypes/dataproviders/dataset.py M lib/galaxy/datatypes/dataproviders/decorators.py M lib/galaxy/datatypes/dataproviders/line.py M lib/galaxy/datatypes/display_applications/parameters.py M lib/galaxy/datatypes/images.py M lib/galaxy/datatypes/metadata.py M lib/galaxy/datatypes/msa.py M lib/galaxy/datatypes/neo4j.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/tblastn_four_human_vs_rhodopsin.xml A lib/galaxy/datatypes/test/test.CEL M lib/galaxy/datatypes/triples.py R lib/galaxy/datatypes/util/image_util.py M lib/galaxy/dependencies/conda-environment.txt M lib/galaxy/dependencies/pinned-hashed-requirements.txt M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt M lib/galaxy/exceptions/__init__.py M lib/galaxy/exceptions/error_codes.py M lib/galaxy/external_services/actions.py M lib/galaxy/external_services/parameters.py M lib/galaxy/external_services/result_handlers/basic.py M lib/galaxy/external_services/service.py M lib/galaxy/forms/forms.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/command_factory.py M lib/galaxy/jobs/deferred/data_transfer.py M lib/galaxy/jobs/deferred/manual_data_transfer.py M lib/galaxy/jobs/deferred/pacific_biosciences_smrt_portal.py M lib/galaxy/jobs/dynamic_tool_destination.py M lib/galaxy/jobs/metrics/__init__.py M lib/galaxy/jobs/metrics/collectl/__init__.py M lib/galaxy/jobs/metrics/collectl/cli.py M lib/galaxy/jobs/metrics/collectl/processes.py M lib/galaxy/jobs/metrics/collectl/subsystems.py M lib/galaxy/jobs/metrics/formatting.py M lib/galaxy/jobs/metrics/instrumenters/__init__.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 M lib/galaxy/jobs/metrics/instrumenters/meminfo.py M lib/galaxy/jobs/metrics/instrumenters/uname.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/cli.py M lib/galaxy/jobs/runners/condor.py M lib/galaxy/jobs/runners/drmaa.py A lib/galaxy/jobs/runners/godocker.py M lib/galaxy/jobs/runners/kubernetes.py M lib/galaxy/jobs/runners/local.py M lib/galaxy/jobs/runners/pbs.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/jobs/runners/slurm.py M lib/galaxy/jobs/runners/state_handlers/resubmit.py M lib/galaxy/jobs/runners/tasks.py M lib/galaxy/jobs/runners/util/__init__.py M lib/galaxy/jobs/runners/util/drmaa/__init__.py M lib/galaxy/jobs/runners/util/job_script/__init__.py M lib/galaxy/managers/__init__.py M lib/galaxy/managers/base.py M lib/galaxy/managers/collections_util.py M lib/galaxy/managers/datasets.py M lib/galaxy/managers/libraries.py M lib/galaxy/managers/rbac_secured.py M lib/galaxy/managers/roles.py M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/model/item_attrs.py M lib/galaxy/model/mapping.py M lib/galaxy/model/metadata.py M lib/galaxy/model/migrate/check.py M lib/galaxy/model/migrate/versions/0007_sharing_histories.py M lib/galaxy/model/migrate/versions/0008_galaxy_forms.py M lib/galaxy/model/migrate/versions/0010_hda_display_at_authz_table.py M lib/galaxy/model/migrate/versions/0011_v0010_mysql_index_fix.py M lib/galaxy/model/migrate/versions/0012_user_address.py M lib/galaxy/model/migrate/versions/0013_change_lib_item_templates_to_forms.py M lib/galaxy/model/migrate/versions/0016_v0015_mysql_index_fix.py M lib/galaxy/model/migrate/versions/0018_ordered_tags_and_page_tags.py M lib/galaxy/model/migrate/versions/0020_library_upload_job.py M lib/galaxy/model/migrate/versions/0026_cloud_tables.py M lib/galaxy/model/migrate/versions/0050_drop_cloud_tables.py M lib/galaxy/model/migrate/versions/0052_sample_dataset_table.py M lib/galaxy/model/migrate/versions/0091_add_tool_version_tables.py M lib/galaxy/model/orm/now.py M lib/galaxy/objectstore/__init__.py M lib/galaxy/objectstore/rods.py M lib/galaxy/queue_worker.py M lib/galaxy/sample_tracking/data_transfer.py M lib/galaxy/sample_tracking/request_types.py M lib/galaxy/sample_tracking/sample.py M lib/galaxy/security/passwords.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/cwl/__init__.py M lib/galaxy/tools/cwl/cwltool_deps.py M lib/galaxy/tools/cwl/parser.py M lib/galaxy/tools/cwl/runtime_actions.py M lib/galaxy/tools/cwl/schema.py M lib/galaxy/tools/data/__init__.py M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/commands.py A lib/galaxy/tools/deps/conda_compat.py M lib/galaxy/tools/deps/conda_util.py A lib/galaxy/tools/deps/container_resolvers/__init__.py A lib/galaxy/tools/deps/container_resolvers/explicit.py A lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/tools/deps/containers.py M lib/galaxy/tools/deps/docker_util.py A lib/galaxy/tools/deps/installable.py A lib/galaxy/tools/deps/mulled/__init__.py A lib/galaxy/tools/deps/mulled/_cli.py A lib/galaxy/tools/deps/mulled/invfile.lua A lib/galaxy/tools/deps/mulled/mulled_build.py A lib/galaxy/tools/deps/mulled/mulled_build_channel.py A lib/galaxy/tools/deps/mulled/mulled_build_files.py A lib/galaxy/tools/deps/mulled/mulled_build_tool.py A lib/galaxy/tools/deps/mulled/mulled_search.py A lib/galaxy/tools/deps/mulled/util.py M lib/galaxy/tools/deps/requirements.py M lib/galaxy/tools/deps/resolvers/__init__.py M lib/galaxy/tools/deps/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/modules.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/exception_handling.py M lib/galaxy/tools/execute.py M lib/galaxy/tools/filter_failed_collection.xml M lib/galaxy/tools/imp_exp/exp_history_to_archive.xml M lib/galaxy/tools/imp_exp/export_history.py M lib/galaxy/tools/loader.py M lib/galaxy/tools/loader_directory.py A lib/galaxy/tools/merge_collection.xml 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/grouping.py M lib/galaxy/tools/parameters/meta.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/tools/parameters/validation.py M lib/galaxy/tools/parameters/wrapped.py M lib/galaxy/tools/parameters/wrapped_json.py M lib/galaxy/tools/parser/__init__.py M lib/galaxy/tools/parser/factory.py M lib/galaxy/tools/parser/output_actions.py M lib/galaxy/tools/parser/output_collection_def.py M lib/galaxy/tools/toolbox/__init__.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/integrated_panel.py M lib/galaxy/tools/toolbox/lineages/__init__.py M lib/galaxy/tools/toolbox/lineages/factory.py M lib/galaxy/tools/toolbox/lineages/tool_shed.py M lib/galaxy/tools/toolbox/parser.py M lib/galaxy/tools/util/galaxyops/__init__.py M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/util/__init__.py M lib/galaxy/util/checkers.py M lib/galaxy/util/hash_util.py A lib/galaxy/util/image_util.py M lib/galaxy/util/json.py M lib/galaxy/util/object_wrapper.py M lib/galaxy/util/pastescript/loadwsgi.py M lib/galaxy/util/pastescript/serve.py M lib/galaxy/util/properties.py M lib/galaxy/util/simplegraph.py M lib/galaxy/util/topsort.py M lib/galaxy/web/__init__.py M lib/galaxy/web/buildapp.py M lib/galaxy/web/framework/__init__.py M lib/galaxy/web/framework/base.py M lib/galaxy/web/framework/middleware/error.py M lib/galaxy/web/framework/middleware/static.py M lib/galaxy/web/framework/middleware/translogger.py M lib/galaxy/web/framework/openid_manager.py M lib/galaxy/webapps/galaxy/api/genomes.py M lib/galaxy/webapps/galaxy/api/history_contents.py M lib/galaxy/webapps/galaxy/api/tours.py A lib/galaxy/webapps/galaxy/api/webhooks.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/webapps/galaxy/controllers/userskeys.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/webapps/reports/__init__.py M lib/galaxy/webapps/reports/config.py M lib/galaxy/webapps/tool_shed/__init__.py M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/config.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/galaxy/webapps/tool_shed/controllers/user.py M lib/galaxy/webapps/tool_shed/model/__init__.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0013_add_review_tables.py A lib/galaxy/webhooks/__init__.py M lib/galaxy/workflow/extract.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run.py M lib/galaxy/workflow/run_request.py M lib/galaxy/workflow/schedulers/core.py M lib/galaxy_utils/sequence/fastq.py M lib/galaxy_utils/sequence/vcf.py M lib/mimeparse.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M lib/tool_shed/metadata/metadata_generator.py M lib/tool_shed/tools/tool_validator.py M lib/tool_shed/util/metadata_util.py M lib/tool_shed/util/workflow_util.py M run_tool_shed.sh M scripts/api/data_manager_example_execute.py M scripts/api/example_watch_folder.py M scripts/api/filter_failed_datasets_from_collection.py M scripts/api/import_workflows_from_installed_tool_shed_repository.py M scripts/api/install_tool_shed_repositories.py M scripts/api/load_data_with_metadata.py M scripts/api/repair_tool_shed_repository.py M scripts/api/reset_metadata_on_installed_repositories.py M scripts/api/search.py M scripts/api/sequencer_configuration_create.py M scripts/api/workflow_execute.py M scripts/api/workflow_execute_parameters.py M scripts/api/workflow_import.py M scripts/auth/pam_auth_helper.py M scripts/bootstrap_history.py R scripts/bootstrap_history_announce_template.rst M scripts/build_toolbox.py M scripts/build_universe_config.py M scripts/check_galaxy.py M scripts/check_python.py M scripts/cleanup_datasets/cleanup_datasets.py M scripts/cleanup_datasets/pgcleanup.py M scripts/cleanup_datasets/rename_purged_datasets.py M scripts/cleanup_datasets/update_dataset_size.py M scripts/cleanup_datasets/update_metadata.py M scripts/communication/communication_server.py M scripts/create_db.py M scripts/data_libraries/build_lucene_index.py M scripts/data_libraries/build_whoosh_index.py M scripts/db_shell.py M scripts/drmaa_external_killer.py M scripts/drmaa_external_runner.py M scripts/external_chown_script.py M scripts/extract_dataset_part.py M scripts/extract_toolbox_sections.py M scripts/functional_tests.py M scripts/galaxy-main M scripts/grt.py M scripts/loc_files/create_all_fasta_loc.py M scripts/manage_db.py M scripts/microbes/BeautifulSoup.py M scripts/microbes/create_bacteria_loc_file.py M scripts/microbes/create_bacteria_table.py M scripts/microbes/get_builds_lengths.py M scripts/microbes/harvest_bacteria.py M scripts/others/incorrect_gops_jobs.py M scripts/others/incorrect_gops_join_jobs.py M scripts/set_dataset_sizes.py M scripts/set_user_disk_usage.py A scripts/slideshow/__init__.py A scripts/slideshow/build_slideshow.py A scripts/slideshow/example.md A scripts/slideshow/slideshow_template.html A scripts/slideshow/style.sample.css M scripts/summarize_timings.py M scripts/sync_reports_config.py M scripts/tool_shed/api/add_repository_registry_entry.py M scripts/tool_shed/api/create_categories.py M scripts/tool_shed/api/create_users.py M scripts/tool_shed/api/export.py M scripts/tool_shed/api/get_filtered_repository_revisions.py M scripts/tool_shed/api/import_capsule.py M scripts/tool_shed/api/remove_repository_registry_entry.py M scripts/tool_shed/api/reset_metadata_on_repositories.py M scripts/tool_shed/bootstrap_tool_shed/bootstrap_util.py M scripts/tool_shed/bootstrap_tool_shed/create_user_with_api_key.py M scripts/tool_shed/build_ts_whoosh_index.py M scripts/tool_shed/check_download_urls.py M scripts/tool_shed/check_filesystem_for_empty_tool_dependency_installation_paths.py M scripts/tool_shed/check_s3_for_empty_tool_dependency_installation_paths.py M scripts/tool_shed/clean_up_tool_dependency_directory.py M scripts/tool_shed/deprecate_repositories_without_metadata.py M scripts/tool_shed/migrate_tools_to_repositories.py M scripts/tool_shed/show_tool_dependency_installation_dir_contents.py M scripts/tools/maf/check_loc_file.py M scripts/tools/re_escape_output.py M scripts/transfer.py M scripts/update_shed_config_path.py M setup.cfg M static/maps/layout/menu.js.map M static/maps/mvc/dataset/dataset-li-edit.js.map M static/maps/mvc/dataset/dataset-li.js.map M static/maps/mvc/history/options-menu.js.map M static/maps/mvc/library/library-dataset-view.js.map M static/maps/mvc/library/library-folderrow-view.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/maps/mvc/tool/tool-form-base.js.map M static/maps/mvc/tool/tool-form-composite.js.map M static/maps/mvc/tool/tool-form-workflow.js.map M static/maps/mvc/tool/tool-form.js.map A static/maps/mvc/tool/tool-webhooks.js.map M static/maps/mvc/tool/tools.js.map M static/maps/mvc/ui/ui-buttons.js.map M static/maps/mvc/ui/ui-modal.js.map M static/maps/mvc/ui/ui-portlet.js.map M static/maps/mvc/ui/ui-tabs.js.map A static/maps/mvc/ui/ui-thumbnails.js.map A static/maps/mvc/webhooks.js.map M static/maps/mvc/workflow/workflow-view.js.map M static/maps/utils/utils.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/layout/menu.js M static/scripts/mvc/dataset/dataset-li-edit.js M static/scripts/mvc/history/options-menu.js M static/scripts/mvc/library/library-dataset-view.js M static/scripts/mvc/library/library-folderrow-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/tool/tool-form-base.js M static/scripts/mvc/tool/tool-form-composite.js M static/scripts/mvc/tool/tool-form-workflow.js M static/scripts/mvc/tool/tool-form.js A static/scripts/mvc/tool/tool-webhooks.js M static/scripts/mvc/tool/tools.js M static/scripts/mvc/ui/ui-buttons.js M static/scripts/mvc/ui/ui-modal.js M static/scripts/mvc/ui/ui-portlet.js M static/scripts/mvc/ui/ui-select-content.js M static/scripts/mvc/ui/ui-tabs.js A static/scripts/mvc/ui/ui-thumbnails.js A static/scripts/mvc/webhooks.js M static/scripts/mvc/workflow/workflow-view.js M static/scripts/utils/utils.js M static/style/blue/base.css M static/welcome.html.sample M templates/user/index.mako M templates/webapps/galaxy/dataset/copy_view.mako M templates/webapps/galaxy/library/common/common.mako M templates/webapps/galaxy/workflow/editor.mako R templates/webapps/galaxy/workflow/index.mako R templates/webapps/galaxy/workflow/missing_tools.mako R templates/webapps/galaxy/workflow/myexp_export_content.mako R templates/webapps/galaxy/workflow/rename.mako M templates/webapps/galaxy/workflow/run.mako R templates/webapps/galaxy/workflow/run_complete.mako M templates/webapps/tool_shed/repository/tool_form.mako M test/api/helpers.py M test/api/test_api_batch.py M test/api/test_authenticate.py M test/api/test_dataset_collections.py M test/api/test_histories.py M test/api/test_history_contents.py M test/api/test_libraries.py M test/api/test_page_revisions.py M test/api/test_pages.py M test/api/test_tool_data.py M test/api/test_tools.py M test/api/test_users.py A test/api/test_workflow_batch.ga M test/api/test_workflow_extraction.py M test/api/test_workflows.py M test/api/workflows_format_2/__init__.py M test/api/workflows_format_2/converter.py M test/api/workflows_format_2/main.py M test/base/api.py M test/base/api_asserts.py M test/base/driver_util.py M test/base/integration_util.py M test/base/interactor.py M test/base/test_logging.py M test/base/twilltestcase.py M test/functional/test_data_managers.py M test/functional/test_library_templates.py M test/functional/test_toolbox.py A test/functional/tools/color_param.xml A test/functional/tools/metadata_column_names.xml A test/functional/tools/mulled_example_multi_1.xml A test/functional/tools/multi_data_optional.xml M test/functional/tools/samples_tool_conf.xml A test/functional/tools/version_command.py A test/functional/tools/version_command_interpreter.xml A test/functional/tools/version_command_plain.xml A test/functional/tools/version_command_tool_dir.xml M test/functional/workflow.py M test/integration/test_resolvers.py M test/manual/workflows_scaling.py M test/qunit/package.json M test/qunit/tests/form_tests.js M test/qunit/tests/ui_tests.js M test/shed_functional/base/test_db_util.py M test/shed_functional/functional/test_0300_reset_all_metadata.py M test/shed_functional/functional/test_1140_simple_repository_dependency_multiple_owners.py M test/shed_functional/functional/test_1300_reset_all_metadata.py M test/shed_functional/functional/test_1400_review_migration_stages.py M test/shed_functional/functional_tests.py M test/unit/dataset_collections/test_matching.py M test/unit/datatypes/dataproviders/test_base_dataproviders.py M test/unit/datatypes/dataproviders/test_line_dataproviders.py M test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py M test/unit/jobs/test_command_factory.py M test/unit/jobs/test_job_configuration.py M test/unit/jobs/test_job_output_checker.py M test/unit/jobs/test_job_wrapper.py M test/unit/jobs/test_mapper.py M test/unit/jobs/test_rule_helper.py M test/unit/jobs/test_runner_local.py M test/unit/managers/base.py M test/unit/managers/test_CollectionManager.py M test/unit/managers/test_DatasetManager.py M test/unit/managers/test_HDAManager.py M test/unit/managers/test_HDCAManager.py M test/unit/managers/test_HistoryContentsManager.py M test/unit/managers/test_HistoryManager.py M test/unit/managers/test_UserManager.py M test/unit/shed_unit/test_fabric_util.py M test/unit/shed_unit/test_td_common_util.py M test/unit/shed_unit/test_tool_panel_manager.py M test/unit/test_galaxy_mapping.py M test/unit/test_galaxy_transactions.py M test/unit/test_routes.py M test/unit/tools/test_actions.py M test/unit/tools/test_citations.py M test/unit/tools/test_collect_primary_datasets.py M test/unit/tools/test_column_parameters.py M test/unit/tools/test_conda_resolution.py M test/unit/tools/test_data_parameters.py M test/unit/tools/test_dataset_matcher.py M test/unit/tools/test_evaluation.py M test/unit/tools/test_execution.py M test/unit/tools/test_history_imp_exp.py M test/unit/tools/test_parameter_parsing.py M test/unit/tools/test_select_parameters.py M test/unit/tools/test_tool_dependency_description.py M test/unit/tools/test_tool_external_files.py M test/unit/tools/test_toolbox.py M test/unit/tools/test_wrappers.py M test/unit/tools_support.py M test/unit/unittest_utils/galaxy_mock.py M test/unit/unittest_utils/tempfilecache.py M test/unit/unittest_utils/utility.py M test/unit/visualizations/plugins/test_VisualizationPlugin.py M test/unit/visualizations/plugins/test_VisualizationsRegistry.py M test/unit/web/base/test_HookPluginManager.py M test/unit/web/base/test_PageServingPluginManager.py M test/unit/web/base/test_PluginManager.py M test/unit/web/framework/test_webapp.py M test/unit/workflows/test_modules.py M test/unit/workflows/test_run_parameters.py M test/unit/workflows/test_workflow_progress.py M test/unit/workflows/workflow_support.py A tool-data/blastdb.loc.sample A tool-data/blastdb_d.loc.sample A tool-data/blastdb_p.loc.sample M tools/data_source/data_source.py M tools/data_source/genbank.py M tools/data_source/hbvar_filter.py M tools/data_source/microbial_import_code.py M tools/data_source/upload.py M tools/evolution/add_scores.py M tools/evolution/codingSnps_filter.py M tools/extract/extract_genomic_dna.py M tools/extract/liftOver_wrapper.py M tools/filters/axt_to_concat_fasta.py M tools/filters/axt_to_fasta.py M tools/filters/axt_to_lav.py M tools/filters/axt_to_lav_code.py M tools/filters/bed_to_gff_converter.py M tools/filters/catWrapper.py M tools/filters/convert_characters.py M tools/filters/gff/extract_GFF_Features.py M tools/filters/gff/gff_filter_by_attribute.py M tools/filters/gff/gff_filter_by_feature_count.py M tools/filters/gff/gtf_filter_by_attribute_values_list.py M tools/filters/gff_to_bed_converter.py M tools/filters/grep.py M tools/filters/gtf_to_bedgraph_converter.py M tools/filters/join.py M tools/filters/joinWrapper.py M tools/filters/lav_to_bed.py M tools/filters/lav_to_bed_code.py M tools/filters/mergeCols.py M tools/filters/random_lines_two_pass.py M tools/filters/randomlines.py M tools/filters/secure_hash_message_digest.py M tools/filters/sff_extract.py M tools/filters/sorter.py M tools/filters/trimmer.py M tools/filters/ucsc_gene_bed_to_exon_bed.py M tools/filters/ucsc_gene_bed_to_intron_bed.py M tools/filters/ucsc_gene_table_to_intervals.py M tools/filters/uniq.py M tools/filters/wiggle_to_simple.py M tools/genomespace/genomespace_exporter.py M tools/genomespace/genomespace_file_browser.py M tools/genomespace/genomespace_importer.py M tools/maf/interval2maf.py M tools/maf/interval_maf_to_merged_fasta.py M tools/maf/maf_by_block_number.py M tools/maf/maf_filter.py M tools/maf/maf_limit_size.py M tools/maf/maf_limit_to_species.py M tools/maf/maf_reverse_complement.py M tools/maf/maf_split_by_species.py M tools/maf/maf_stats.py M tools/maf/maf_thread_for_species.py M tools/maf/maf_to_bed.py M tools/maf/maf_to_bed_code.py M tools/maf/maf_to_fasta_concat.py M tools/maf/maf_to_fasta_multiple_sets.py M tools/maf/maf_to_interval.py M tools/maf/vcf_to_maf_customtrack.py M tools/meme/fimo_wrapper.py M tools/metag_tools/blat_wrapper.py M tools/metag_tools/shrimp_color_wrapper.py M tools/metag_tools/shrimp_wrapper.py M tools/next_gen_conversion/fastq_conversions.py M tools/next_gen_conversion/fastq_gen_conv.py M tools/next_gen_conversion/solid2fastq.py M tools/next_gen_conversion/solid_to_fastq.py M tools/ngs_simulation/ngs_simulation.py M tools/phenotype_association/pagetag.py M tools/phenotype_association/senatag.py M tools/solid_tools/maq_cs_wrapper.py M tools/solid_tools/solid_qual_stats.py M tools/sr_assembly/velvetg_wrapper.py M tools/sr_assembly/velveth_wrapper.py M tools/sr_mapping/bfast_wrapper.py M tools/sr_mapping/srma_wrapper.py M tools/stats/aggregate_scores_in_intervals.py M tools/stats/filtering.py M tools/stats/grouping.py M tools/stats/gsummary.py M tools/visualization/LAJ_code.py M tox.ini

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

Commit: e5b69a711d14fa8e8876041f92160db19da3e9bf https://github.com/galaxyproject/galaxy/commit/e5b69a711d14fa8e8876041f92160... Author: John Chilton jmchilton@gmail.com Date: 2016-11-16 (Wed, 16 Nov 2016)

Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-workflow.js M client/galaxy/style/less/base.less M client/galaxy/style/less/ui.less M static/maps/mvc/tool/tool-form-workflow.js.map M static/scripts/mvc/tool/tool-form-workflow.js M static/style/blue/base.css M templates/webapps/galaxy/workflow/editor.mako

Log Message: ----------- Merge pull request #2966 from dannon/workflow_intermediates_ux

Change wording to be more clear about how workflow output cleanup wor…

Compare: https://github.com/galaxyproject/galaxy/compare/ac5b7efc5f88...e5b69a711d14