- galaxy-commits - lists.galaxyproject.org

[galaxyproject/usegalaxy-playbook] 50602c: WIP Swarm Scale improvements
by GitHub 09 Jul '18

09 Jul '18

Branch: refs/heads/swarmscale-2.0 Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 50602ce96c3f1b9486486f23217629537a9e7d51 https://github.com/galaxyproject/usegalaxy-playbook/commit/50602ce96c3f1b94… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-07-09 (Mon, 09 Jul 2018) Changed paths: A roles/usegalaxy_swarmscale/files/_inc_fail.yml M roles/usegalaxy_swarmscale/files/ansible.cfg R roles/usegalaxy_swarmscale/files/delete.yml A roles/usegalaxy_swarmscale/files/group_vars/all/spawn.yml M roles/usegalaxy_swarmscale/files/instance R roles/usegalaxy_swarmscale/files/inventory.head R roles/usegalaxy_swarmscale/files/inventory.spawn A roles/usegalaxy_swarmscale/files/inventory/openstack.yml R roles/usegalaxy_swarmscale/files/leave.yml A roles/usegalaxy_swarmscale/files/resume.yml A roles/usegalaxy_swarmscale/files/roles/docker/defaults/main.yml A roles/usegalaxy_swarmscale/files/roles/docker/handlers/main.yml A roles/usegalaxy_swarmscale/files/roles/docker/tasks/install_debian.yml A roles/usegalaxy_swarmscale/files/roles/docker/tasks/install_redhat.yml A roles/usegalaxy_swarmscale/files/roles/docker/tasks/main.yml R roles/usegalaxy_swarmscale/files/spawn.yml A roles/usegalaxy_swarmscale/files/suspend.yml M roles/usegalaxy_swarmscale/tasks/main.yml Log Message: ----------- WIP Swarm Scale improvements **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

1 0

[galaxyproject/galaxy] 97c344: Fix the --log-file option in the job handlers
by GitHub 09 Jul '18

09 Jul '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 97c344a17a0188a687629103feefcdf03af8e768 https://github.com/galaxyproject/galaxy/commit/97c344a17a0188a687629103feef… Author: Devon Ryan <dpryan79(a)gmail.com> Date: 2018-06-18 (Mon, 18 Jun 2018) Changed paths: M lib/galaxy/config.py Log Message: ----------- Fix the --log-file option in the job handlers Commit: b396d3d10788f752bce2ded0598fab2bd21e605b https://github.com/galaxyproject/galaxy/commit/b396d3d10788f752bce2ded0598f… Author: dpryan79 <dpryan79(a)gmail.com> Date: 2018-06-19 (Tue, 19 Jun 2018) Changed paths: M lib/galaxy/config.py Log Message: ----------- PEP8 Commit: 60fc4baa4c3af7b32fd74dccd7aee1850196bc87 https://github.com/galaxyproject/galaxy/commit/60fc4baa4c3af7b32fd74dccd7ae… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-07-09 (Mon, 09 Jul 2018) Changed paths: M lib/galaxy/config.py Log Message: ----------- Merge pull request #6351 from dpryan79/fixHandlerLogging Fix the --log-file option in the job handlers Compare: https://github.com/galaxyproject/galaxy/compare/ce866b9e2396...60fc4baa4c3a **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

1 0

[galaxyproject/infrastructure-playbook] 06694e: Fix paths to clean scratch on Jetstream
by GitHub 09 Jul '18

09 Jul '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 06694e8a4aa8493ea5582db5ca16138444c75152 https://github.com/galaxyproject/infrastructure-playbook/commit/06694e8a4aa… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-07-09 (Mon, 09 Jul 2018) Changed paths: M env/jscommon/group_vars/controllers.yml Log Message: ----------- Fix paths to clean scratch on Jetstream **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

1 0

[galaxyproject/galaxy] a6173c: Fix bug noticed in sentry
by GitHub 09 Jul '18

09 Jul '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a6173c023e4620430ffe3fc127750e0cb04355b1 https://github.com/galaxyproject/galaxy/commit/a6173c023e4620430ffe3fc12775… Author: Helena Rasche <hxr(a)hx42.org> Date: 2018-07-09 (Mon, 09 Jul 2018) Changed paths: M lib/galaxy/util/create_history_template.py Log Message: ----------- Fix bug noticed in sentry Commit: ce866b9e2396da30f660206e10a7a375e244f583 https://github.com/galaxyproject/galaxy/commit/ce866b9e2396da30f660206e10a7… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-07-09 (Mon, 09 Jul 2018) Changed paths: M lib/galaxy/util/create_history_template.py Log Message: ----------- Merge pull request #6474 from erasche/asdfasdf Fix bug noticed in sentry Compare: https://github.com/galaxyproject/galaxy/compare/068005fd6e1c...ce866b9e2396 **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

1 0

[galaxyproject/galaxy] 0198df: Implement overall structure.
by GitHub 06 Jul '18

06 Jul '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 0198df5406b385c80b0536b0905fee3f0719f635 https://github.com/galaxyproject/galaxy/commit/0198df5406b385c80b0536b0905f… Author: vahid <jalili.vahid(a)gmail.com> Date: 2018-02-13 (Tue, 13 Feb 2018) Changed paths: A lib/galaxy/managers/cloud_storages.py A lib/galaxy/webapps/galaxy/api/cloud_storage.py Log Message: ----------- Implement overall structure. Commit: bdc98d5569dabcf6b82b2d447e75821adb080d03 https://github.com/galaxyproject/galaxy/commit/bdc98d5569dabcf6b82b2d447e75… Author: vahid <jalili.vahid(a)gmail.com> Date: 2018-02-27 (Tue, 27 Feb 2018) Changed paths: M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Add cloud storage api mapper. Commit: 645f74b6b6ae9ded06f8f073c08bae0519ed38c3 https://github.com/galaxyproject/galaxy/commit/645f74b6b6ae9ded06f8f073c08b… Author: vahid <jalili.vahid(a)gmail.com> Date: 2018-02-27 (Tue, 27 Feb 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/cloud_storage.py Log Message: ----------- Capture invalid type of cloud storage api payload, & raise exception. Commit: 140a1f7a8ea8455e4a96fa6e2dbb5148ebb3fe0e https://github.com/galaxyproject/galaxy/commit/140a1f7a8ea8455e4a96fa6e2dbb… Author: vahid <jalili.vahid(a)gmail.com> Date: 2018-02-27 (Tue, 27 Feb 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/cloud_storage.py Log Message: ----------- Unbox payload & check if it contains all data required for cloud storage Commit: 15293d652c724635f294376cb5a23bf4e6d3419f https://github.com/galaxyproject/galaxy/commit/15293d652c724635f294376cb5a2… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-03-13 (Tue, 13 Mar 2018) Changed paths: A lib/galaxy/managers/cloud_storage.py R lib/galaxy/managers/cloud_storages.py M lib/galaxy/webapps/galaxy/api/cloud_storage.py Log Message: ----------- Some refactoring: "Storages" -> "Storage" & "object" -> "obj" Commit: ca0bb57add1c66237e3e6ceff3a0afbac91ba26f https://github.com/galaxyproject/galaxy/commit/ca0bb57add1c66237e3e6ceff3a0… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-03-13 (Tue, 13 Mar 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/cloud_storage.py Log Message: ----------- Add provider as a payload requirement to the cloud storage API. Commit: 164f8d8b1f6a3697ed18ba9b01c188ec688e72c9 https://github.com/galaxyproject/galaxy/commit/164f8d8b1f6a3697ed18ba9b01c1… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-03-13 (Tue, 13 Mar 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/cloud_storage.py Log Message: ----------- Renamed bucket to container to use more generic terminology. Commit: 76aa47f69be61c77a7322a91824675999617f345 https://github.com/galaxyproject/galaxy/commit/76aa47f69be61c77a7322a918246… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-03-13 (Tue, 13 Mar 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/cloud_storage.py Log Message: ----------- Cloud storage api now sends download request to cloud storage manager. Commit: 2e1fbedc7f692fd23eea24e646c6b0b1caa851a2 https://github.com/galaxyproject/galaxy/commit/2e1fbedc7f692fd23eea24e646c6… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-03-13 (Tue, 13 Mar 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/cloud_storage.py Log Message: ----------- Fix a conditional assignment bug. Commit: c725b33ec25d67be1ca2b51faeec5a07186dcf36 https://github.com/galaxyproject/galaxy/commit/c725b33ec25d67be1ca2b51faeec… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-03-27 (Tue, 27 Mar 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/cloud_storage.py Log Message: ----------- Pass trans from cloud_storage api to cloud_storage_manager. Commit: f7d90706f922497d19c398d170c50ae1627fa836 https://github.com/galaxyproject/galaxy/commit/f7d90706f922497d19c398d170c5… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-03-27 (Tue, 27 Mar 2018) Changed paths: M Makefile M client/galaxy/scripts/apps/analysis.js A client/galaxy/scripts/apps/chart.js M client/galaxy/scripts/apps/extended.js M client/galaxy/scripts/apps/panels/tool-panel.js A client/galaxy/scripts/components/DisplayStructured.vue M client/galaxy/scripts/components/HistoryImport.vue A client/galaxy/scripts/components/HistoryView.vue A client/galaxy/scripts/components/PluginList.vue M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/layout/scratchbook.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-li-edit.js M client/galaxy/scripts/mvc/dataset/dataset-model.js M client/galaxy/scripts/mvc/form/form-data.js M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/form/form-wrapper.js M client/galaxy/scripts/mvc/grid/grid-shared.js M client/galaxy/scripts/mvc/grid/grid-template.js M client/galaxy/scripts/mvc/grid/grid-view.js M client/galaxy/scripts/mvc/history/hdca-li-edit.js M client/galaxy/scripts/mvc/history/history-contents.js M client/galaxy/scripts/mvc/history/history-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-form-composite.js M client/galaxy/scripts/mvc/tool/tool-genomespace.js M client/galaxy/scripts/mvc/ui/ui-buttons.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/ui/ui-select-genomespace.js M client/galaxy/scripts/mvc/ui/ui-slider.js M client/galaxy/scripts/mvc/ui/ui-thumbnails.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/mvc/user/user-custom-builds.js M client/galaxy/scripts/mvc/user/user-preferences.js A client/galaxy/scripts/mvc/visualization/chart/chart-client.js A client/galaxy/scripts/mvc/visualization/chart/components/model.js A client/galaxy/scripts/mvc/visualization/chart/components/screenshot.js A client/galaxy/scripts/mvc/visualization/chart/utilities/datasets.js A client/galaxy/scripts/mvc/visualization/chart/utilities/jobs.js A client/galaxy/scripts/mvc/visualization/chart/utilities/series.js A client/galaxy/scripts/mvc/visualization/chart/views/description.js A client/galaxy/scripts/mvc/visualization/chart/views/editor.js A client/galaxy/scripts/mvc/visualization/chart/views/groups.js A client/galaxy/scripts/mvc/visualization/chart/views/menu.js A client/galaxy/scripts/mvc/visualization/chart/views/settings.js A client/galaxy/scripts/mvc/visualization/chart/views/viewer.js M client/galaxy/scripts/mvc/visualization/visualization-model.js M client/galaxy/scripts/mvc/workflow/workflow.js M client/galaxy/scripts/onload.js M client/galaxy/scripts/qunit/tests/ui_tests.js M client/galaxy/scripts/ui/loading-indicator.js M client/galaxy/scripts/ui/pagination.js M client/galaxy/scripts/ui/peek-column-selector.js M client/galaxy/scripts/utils/config.js M client/galaxy/scripts/utils/uploadbox.js M client/galaxy/scripts/utils/utils.js M client/galaxy/scripts/viz/circster.js M client/galaxy/scripts/viz/sweepster.js M client/galaxy/scripts/viz/trackster.js M client/galaxy/scripts/viz/trackster/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 client/galaxy/style/less/base.less A client/galaxy/style/less/charts.less M client/galaxy/style/less/galaxy_variables.less M client/galaxy/style/less/ui.less M client/package.json M client/webpack.config.js M config/datatypes_conf.xml.sample M config/galaxy.yml.sample M config/job_conf.xml.sample_advanced M config/job_metrics_conf.xml.sample R config/plugins/visualizations/charts/config/charts.xml R config/plugins/visualizations/charts/package.json R config/plugins/visualizations/charts/static/client/app.css R config/plugins/visualizations/charts/static/client/app.js R config/plugins/visualizations/charts/static/client/components/model.js R config/plugins/visualizations/charts/static/client/components/screenshot.js R config/plugins/visualizations/charts/static/client/views/description.js R config/plugins/visualizations/charts/static/client/views/editor.js R config/plugins/visualizations/charts/static/client/views/groups.js R config/plugins/visualizations/charts/static/client/views/settings.js R config/plugins/visualizations/charts/static/client/views/viewer.js R config/plugins/visualizations/charts/static/client/views/viewport.js R config/plugins/visualizations/charts/static/repository/build/benfred_venn.js R config/plugins/visualizations/charts/static/repository/build/benfred_venn.js.map R config/plugins/visualizations/charts/static/repository/build/biojs_drawrnajs.js R config/plugins/visualizations/charts/static/repository/build/biojs_drawrnajs.js.map R config/plugins/visualizations/charts/static/repository/build/biojs_msa.js R config/plugins/visualizations/charts/static/repository/build/biojs_msa.js.map R config/plugins/visualizations/charts/static/repository/build/biojs_phylocanvas.js R config/plugins/visualizations/charts/static/repository/build/biojs_phylocanvas.js.map R config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js R config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js.map R config/plugins/visualizations/charts/static/repository/build/jqplot_bar.js R config/plugins/visualizations/charts/static/repository/build/jqplot_bar.js.map R config/plugins/visualizations/charts/static/repository/build/jqplot_boxplot.js R config/plugins/visualizations/charts/static/repository/build/jqplot_boxplot.js.map R config/plugins/visualizations/charts/static/repository/build/jqplot_histogram_discrete.js R config/plugins/visualizations/charts/static/repository/build/jqplot_histogram_discrete.js.map R config/plugins/visualizations/charts/static/repository/build/jqplot_line.js R config/plugins/visualizations/charts/static/repository/build/jqplot_line.js.map R config/plugins/visualizations/charts/static/repository/build/jqplot_scatter.js R config/plugins/visualizations/charts/static/repository/build/jqplot_scatter.js.map R config/plugins/visualizations/charts/static/repository/build/ngl_viewer.js R config/plugins/visualizations/charts/static/repository/build/ngl_viewer.js.map R config/plugins/visualizations/charts/static/repository/build/nvd3_bar.js R config/plugins/visualizations/charts/static/repository/build/nvd3_bar.js.map R config/plugins/visualizations/charts/static/repository/build/nvd3_bar_horizontal.js R config/plugins/visualizations/charts/static/repository/build/nvd3_bar_horizontal.js.map R config/plugins/visualizations/charts/static/repository/build/nvd3_bar_horizontal_stacked.js R config/plugins/visualizations/charts/static/repository/build/nvd3_bar_horizontal_stacked.js.map R config/plugins/visualizations/charts/static/repository/build/nvd3_bar_stacked.js R config/plugins/visualizations/charts/static/repository/build/nvd3_bar_stacked.js.map R config/plugins/visualizations/charts/static/repository/build/nvd3_histogram.js R config/plugins/visualizations/charts/static/repository/build/nvd3_histogram.js.map R config/plugins/visualizations/charts/static/repository/build/nvd3_histogram_discrete.js R config/plugins/visualizations/charts/static/repository/build/nvd3_histogram_discrete.js.map R config/plugins/visualizations/charts/static/repository/build/nvd3_line.js R config/plugins/visualizations/charts/static/repository/build/nvd3_line.js.map R config/plugins/visualizations/charts/static/repository/build/nvd3_line_focus.js R config/plugins/visualizations/charts/static/repository/build/nvd3_line_focus.js.map R config/plugins/visualizations/charts/static/repository/build/nvd3_pie.js R config/plugins/visualizations/charts/static/repository/build/nvd3_pie.js.map R config/plugins/visualizations/charts/static/repository/build/nvd3_scatter.js R config/plugins/visualizations/charts/static/repository/build/nvd3_scatter.js.map R config/plugins/visualizations/charts/static/repository/build/nvd3_stackedarea.js R config/plugins/visualizations/charts/static/repository/build/nvd3_stackedarea.js.map R config/plugins/visualizations/charts/static/repository/build/nvd3_stackedarea_full.js R config/plugins/visualizations/charts/static/repository/build/nvd3_stackedarea_full.js.map R config/plugins/visualizations/charts/static/repository/build/nvd3_stackedarea_stream.js R config/plugins/visualizations/charts/static/repository/build/nvd3_stackedarea_stream.js.map R config/plugins/visualizations/charts/static/repository/build/others_example.js R config/plugins/visualizations/charts/static/repository/build/others_example.js.map R config/plugins/visualizations/charts/static/repository/build/others_heatmap.js R config/plugins/visualizations/charts/static/repository/build/others_heatmap.js.map R config/plugins/visualizations/charts/static/repository/build/others_heatmap_cluster.js R config/plugins/visualizations/charts/static/repository/build/others_heatmap_cluster.js.map R config/plugins/visualizations/charts/static/repository/build/pv_viewer.js R config/plugins/visualizations/charts/static/repository/build/pv_viewer.js.map R config/plugins/visualizations/charts/static/repository/build/registry.js R config/plugins/visualizations/charts/static/repository/build/registry.js.map R config/plugins/visualizations/charts/static/repository/build/registry.tmp.js R config/plugins/visualizations/charts/static/repository/plugins/benfred/venn.css R config/plugins/visualizations/charts/static/repository/plugins/benfred/venn.js R config/plugins/visualizations/charts/static/repository/plugins/biojs/biojs.msa.js R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/drawrna.js R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/layouts/layout.js R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/layouts/naview/base.js R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/layouts/naview/connection.js R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/layouts/naview/getnaview.js R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/layouts/naview/loop.js R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/layouts/naview/naview.js R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/layouts/naview/radloop.js R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/layouts/naview/region.js R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/layouts/radiate/getradiate.js R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/models/link.js R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/models/linkcol.js R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/models/ncanno.js R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/models/residue.js R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/models/residuecol.js R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/models/structure.js R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/utils/.Rhistory R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/utils/lasso.js R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/utils/parsedbr.js R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/utils/spectrum.js R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/utils/style.js R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/views/annoview.js R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/views/optspanel.js R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/views/seqpanel.js R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/views/vispanel.js R config/plugins/visualizations/charts/static/repository/plugins/biojs/phylocanvas/phylocanvas.js R config/plugins/visualizations/charts/static/repository/plugins/cytoscape/cytoscape.js R config/plugins/visualizations/charts/static/repository/plugins/jqplot/jquery.jqplot.css R config/plugins/visualizations/charts/static/repository/plugins/jqplot/jquery.jqplot.js R config/plugins/visualizations/charts/static/repository/plugins/jqplot/jquery.jqplot.plugins.js R config/plugins/visualizations/charts/static/repository/plugins/ngl/viewer.js R config/plugins/visualizations/charts/static/repository/plugins/nvd3/nv.d3.css R config/plugins/visualizations/charts/static/repository/plugins/nvd3/nv.d3.js R config/plugins/visualizations/charts/static/repository/plugins/pv/viewer.js R config/plugins/visualizations/charts/static/repository/registry.json R config/plugins/visualizations/charts/static/repository/utilities/jobs.js R config/plugins/visualizations/charts/static/repository/utilities/sifjson.js R config/plugins/visualizations/charts/static/repository/utilities/utils.js R config/plugins/visualizations/charts/static/repository/visualizations/benfred/venn/config.js R config/plugins/visualizations/charts/static/repository/visualizations/benfred/venn/logo.png R config/plugins/visualizations/charts/static/repository/visualizations/benfred/venn/wrapper.js R config/plugins/visualizations/charts/static/repository/visualizations/biojs/drawrnajs/config.js R config/plugins/visualizations/charts/static/repository/visualizations/biojs/drawrnajs/logo.png R config/plugins/visualizations/charts/static/repository/visualizations/biojs/drawrnajs/wrapper.js R config/plugins/visualizations/charts/static/repository/visualizations/biojs/msa/config.js R config/plugins/visualizations/charts/static/repository/visualizations/biojs/msa/logo.png R config/plugins/visualizations/charts/static/repository/visualizations/biojs/msa/wrapper.js R config/plugins/visualizations/charts/static/repository/visualizations/biojs/phylocanvas/config.js R config/plugins/visualizations/charts/static/repository/visualizations/biojs/phylocanvas/logo.png R config/plugins/visualizations/charts/static/repository/visualizations/biojs/phylocanvas/wrapper.js R config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/config.js R config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/logo.png R config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/wrapper.js R config/plugins/visualizations/charts/static/repository/visualizations/jqplot/bar/config.js R config/plugins/visualizations/charts/static/repository/visualizations/jqplot/bar/logo.png R config/plugins/visualizations/charts/static/repository/visualizations/jqplot/bar/wrapper.js R config/plugins/visualizations/charts/static/repository/visualizations/jqplot/boxplot/config.js R config/plugins/visualizations/charts/static/repository/visualizations/jqplot/boxplot/logo.png R config/plugins/visualizations/charts/static/repository/visualizations/jqplot/boxplot/wrapper.js R config/plugins/visualizations/charts/static/repository/visualizations/jqplot/common/config.js R config/plugins/visualizations/charts/static/repository/visualizations/jqplot/common/plot-config.js R config/plugins/visualizations/charts/static/repository/visualizations/jqplot/common/wrapper.js R config/plugins/visualizations/charts/static/repository/visualizations/jqplot/histogram_discrete/config.js R config/plugins/visualizations/charts/static/repository/visualizations/jqplot/histogram_discrete/logo.png R config/plugins/visualizations/charts/static/repository/visualizations/jqplot/histogram_discrete/wrapper.js R config/plugins/visualizations/charts/static/repository/visualizations/jqplot/line/config.js R config/plugins/visualizations/charts/static/repository/visualizations/jqplot/line/logo.png R config/plugins/visualizations/charts/static/repository/visualizations/jqplot/line/wrapper.js R config/plugins/visualizations/charts/static/repository/visualizations/jqplot/scatter/config.js R config/plugins/visualizations/charts/static/repository/visualizations/jqplot/scatter/logo.png R config/plugins/visualizations/charts/static/repository/visualizations/jqplot/scatter/wrapper.js R config/plugins/visualizations/charts/static/repository/visualizations/ngl/viewer/config.js R config/plugins/visualizations/charts/static/repository/visualizations/ngl/viewer/logo.png R config/plugins/visualizations/charts/static/repository/visualizations/ngl/viewer/wrapper.js R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar/config.js R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar/logo.png R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar/wrapper.js R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar_horizontal/config.js R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar_horizontal/logo.png R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar_horizontal/wrapper.js R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar_horizontal_stacked/config.js R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar_horizontal_stacked/logo.png R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar_horizontal_stacked/wrapper.js R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar_stacked/config.js R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar_stacked/logo.png R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar_stacked/wrapper.js R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/common/config.js R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/common/wrapper.js R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/histogram/config.js R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/histogram/logo.png R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/histogram/wrapper.js R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/histogram_discrete/config.js R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/histogram_discrete/logo.png R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/histogram_discrete/wrapper.js R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/line/config.js R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/line/logo.png R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/line/wrapper.js R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/line_focus/config.js R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/line_focus/logo.png R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/line_focus/wrapper.js R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/pie/config.js R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/pie/logo.png R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/pie/wrapper.js R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/scatter/config.js R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/scatter/logo.png R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/scatter/wrapper.js R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/stackedarea/config.js R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/stackedarea/logo.png R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/stackedarea/wrapper.js R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/stackedarea_full/config.js R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/stackedarea_full/logo.png R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/stackedarea_full/wrapper.js R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/stackedarea_stream/config.js R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/stackedarea_stream/logo.png R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/stackedarea_stream/wrapper.js R config/plugins/visualizations/charts/static/repository/visualizations/others/example/config.js R config/plugins/visualizations/charts/static/repository/visualizations/others/example/logo.png R config/plugins/visualizations/charts/static/repository/visualizations/others/example/wrapper.js R config/plugins/visualizations/charts/static/repository/visualizations/others/heatmap/config.js R config/plugins/visualizations/charts/static/repository/visualizations/others/heatmap/heatmap-parameters.js R config/plugins/visualizations/charts/static/repository/visualizations/others/heatmap/heatmap-plugin.js R config/plugins/visualizations/charts/static/repository/visualizations/others/heatmap/logo.png R config/plugins/visualizations/charts/static/repository/visualizations/others/heatmap/wrapper.js R config/plugins/visualizations/charts/static/repository/visualizations/others/heatmap_cluster/config.js R config/plugins/visualizations/charts/static/repository/visualizations/others/heatmap_cluster/logo.png R config/plugins/visualizations/charts/static/repository/visualizations/others/heatmap_cluster/wrapper.js R config/plugins/visualizations/charts/static/repository/visualizations/pv/viewer/config.js R config/plugins/visualizations/charts/static/repository/visualizations/pv/viewer/logo.png R config/plugins/visualizations/charts/static/repository/visualizations/pv/viewer/wrapper.js R config/plugins/visualizations/charts/static/repository/visualizations/utilities/tabular-datasets.js R config/plugins/visualizations/charts/static/repository/visualizations/utilities/tabular-form.js R config/plugins/visualizations/charts/static/repository/visualizations/utilities/tabular-utilities.js R config/plugins/visualizations/charts/templates/charts.mako R config/plugins/visualizations/charts/webpack.config.js A config/plugins/visualizations/common/templates/chart_entry_point.mako M config/plugins/visualizations/common/templates/script_entry_point.mako M config/plugins/visualizations/csg/config/csg.xml A config/plugins/visualizations/csg/static/logo.png A config/plugins/visualizations/cytoscape/config/cytoscape.xml A config/plugins/visualizations/cytoscape/package.json A config/plugins/visualizations/cytoscape/src/script.js A config/plugins/visualizations/cytoscape/static/logo.png A config/plugins/visualizations/cytoscape/static/script.js A config/plugins/visualizations/drawrna/config/drawrna.xml A config/plugins/visualizations/drawrna/package.json A config/plugins/visualizations/drawrna/src/drawrnajs/drawrna.js A config/plugins/visualizations/drawrna/src/drawrnajs/layouts/layout.js A config/plugins/visualizations/drawrna/src/drawrnajs/layouts/naview/base.js A config/plugins/visualizations/drawrna/src/drawrnajs/layouts/naview/connection.js A config/plugins/visualizations/drawrna/src/drawrnajs/layouts/naview/getnaview.js A config/plugins/visualizations/drawrna/src/drawrnajs/layouts/naview/loop.js A config/plugins/visualizations/drawrna/src/drawrnajs/layouts/naview/naview.js A config/plugins/visualizations/drawrna/src/drawrnajs/layouts/naview/radloop.js A config/plugins/visualizations/drawrna/src/drawrnajs/layouts/naview/region.js A config/plugins/visualizations/drawrna/src/drawrnajs/layouts/radiate/getradiate.js A config/plugins/visualizations/drawrna/src/drawrnajs/models/link.js A config/plugins/visualizations/drawrna/src/drawrnajs/models/linkcol.js A config/plugins/visualizations/drawrna/src/drawrnajs/models/ncanno.js A config/plugins/visualizations/drawrna/src/drawrnajs/models/residue.js A config/plugins/visualizations/drawrna/src/drawrnajs/models/residuecol.js A config/plugins/visualizations/drawrna/src/drawrnajs/models/structure.js A config/plugins/visualizations/drawrna/src/drawrnajs/utils/.Rhistory A config/plugins/visualizations/drawrna/src/drawrnajs/utils/lasso.js A config/plugins/visualizations/drawrna/src/drawrnajs/utils/parsedbr.js A config/plugins/visualizations/drawrna/src/drawrnajs/utils/spectrum.js A config/plugins/visualizations/drawrna/src/drawrnajs/utils/style.js A config/plugins/visualizations/drawrna/src/drawrnajs/views/annoview.js A config/plugins/visualizations/drawrna/src/drawrnajs/views/optspanel.js A config/plugins/visualizations/drawrna/src/drawrnajs/views/seqpanel.js A config/plugins/visualizations/drawrna/src/drawrnajs/views/vispanel.js A config/plugins/visualizations/drawrna/src/script.js A config/plugins/visualizations/drawrna/static/logo.png A config/plugins/visualizations/drawrna/static/script.js A config/plugins/visualizations/example/config/example.xml A config/plugins/visualizations/example/package.json A config/plugins/visualizations/example/src/script.js A config/plugins/visualizations/example/static/logo.png A config/plugins/visualizations/example/static/script.js M config/plugins/visualizations/graphviz/config/graphviz.xml R config/plugins/visualizations/graphviz/static/js/jquery.qtip.js R config/plugins/visualizations/graphviz/static/js/tip_centerwindow.js R config/plugins/visualizations/graphviz/static/js/tip_followscroll.js M config/plugins/visualizations/graphviz/templates/graphviz.mako A config/plugins/visualizations/heatmap/heatmap_cluster/config/heatmap_cluster.xml A config/plugins/visualizations/heatmap/heatmap_cluster/static/logo.png A config/plugins/visualizations/heatmap/heatmap_default/config/heatmap_default.xml A config/plugins/visualizations/heatmap/heatmap_default/config/heatmap_shared.xml A config/plugins/visualizations/heatmap/heatmap_default/package.json A config/plugins/visualizations/heatmap/heatmap_default/src/colorsets.js A config/plugins/visualizations/heatmap/heatmap_default/src/script.js A config/plugins/visualizations/heatmap/heatmap_default/static/logo.png A config/plugins/visualizations/heatmap/heatmap_default/static/script.js A config/plugins/visualizations/jqplot/jqplot_bar/config/jqplot_bar.xml A config/plugins/visualizations/jqplot/jqplot_bar/config/jqplot_shared.xml A config/plugins/visualizations/jqplot/jqplot_bar/package.json A config/plugins/visualizations/jqplot/jqplot_bar/src/script.js A config/plugins/visualizations/jqplot/jqplot_bar/static/logo.png A config/plugins/visualizations/jqplot/jqplot_bar/static/script.css A config/plugins/visualizations/jqplot/jqplot_bar/static/script.js A config/plugins/visualizations/jqplot/jqplot_box/config/jqplot_box.xml A config/plugins/visualizations/jqplot/jqplot_box/static/logo.png A config/plugins/visualizations/jqplot/jqplot_histogram/config/jqplot_histogram.xml A config/plugins/visualizations/jqplot/jqplot_histogram/static/logo.png A config/plugins/visualizations/jqplot/jqplot_line/config/jqplot_line.xml A config/plugins/visualizations/jqplot/jqplot_line/static/logo.png A config/plugins/visualizations/jqplot/jqplot_scatter/config/jqplot_scatter.xml A config/plugins/visualizations/jqplot/jqplot_scatter/static/logo.png A config/plugins/visualizations/msa/config/msa.xml A config/plugins/visualizations/msa/package.json A config/plugins/visualizations/msa/src/msa.js A config/plugins/visualizations/msa/static/logo.png A config/plugins/visualizations/msa/static/script.js A config/plugins/visualizations/ngl/config/ngl.xml A config/plugins/visualizations/ngl/package.json A config/plugins/visualizations/ngl/src/ngl.js A config/plugins/visualizations/ngl/src/viewer.js A config/plugins/visualizations/ngl/static/logo.png A config/plugins/visualizations/ngl/static/ngl.js A config/plugins/visualizations/nvd3/nvd3_bar/.babelrc A config/plugins/visualizations/nvd3/nvd3_bar/config/nvd3_bar.xml A config/plugins/visualizations/nvd3/nvd3_bar/config/nvd3_shared.xml A config/plugins/visualizations/nvd3/nvd3_bar/package.json A config/plugins/visualizations/nvd3/nvd3_bar/src/nvd3.js A config/plugins/visualizations/nvd3/nvd3_bar/static/logo.png A config/plugins/visualizations/nvd3/nvd3_bar/static/nvd3.css A config/plugins/visualizations/nvd3/nvd3_bar/static/nvd3.js A config/plugins/visualizations/nvd3/nvd3_bar_stacked/config/nvd3_bar_stacked.xml A config/plugins/visualizations/nvd3/nvd3_bar_stacked/static/logo.png A config/plugins/visualizations/nvd3/nvd3_histogram/config/nvd3_histogram.xml A config/plugins/visualizations/nvd3/nvd3_histogram/static/logo.png A config/plugins/visualizations/nvd3/nvd3_histogram_discrete/config/nvd3_histogram_discrete.xml A config/plugins/visualizations/nvd3/nvd3_histogram_discrete/static/logo.png A config/plugins/visualizations/nvd3/nvd3_horizontal/config/nvd3_horizontal.xml A config/plugins/visualizations/nvd3/nvd3_horizontal/static/logo.png A config/plugins/visualizations/nvd3/nvd3_horizontal_stacked/config/nvd3_horizontal_stacked.xml A config/plugins/visualizations/nvd3/nvd3_horizontal_stacked/static/logo.png A config/plugins/visualizations/nvd3/nvd3_line/config/nvd3_line.xml A config/plugins/visualizations/nvd3/nvd3_line/static/logo.png A config/plugins/visualizations/nvd3/nvd3_line_focus/config/nvd3_line_focus.xml A config/plugins/visualizations/nvd3/nvd3_line_focus/static/logo.png A config/plugins/visualizations/nvd3/nvd3_pie/config/nvd3_pie.xml A config/plugins/visualizations/nvd3/nvd3_pie/static/logo.png A config/plugins/visualizations/nvd3/nvd3_scatter/config/nvd3_scatter.xml A config/plugins/visualizations/nvd3/nvd3_scatter/static/logo.png A config/plugins/visualizations/nvd3/nvd3_stackedarea/config/nvd3_stackedarea.xml A config/plugins/visualizations/nvd3/nvd3_stackedarea/static/logo.png A config/plugins/visualizations/nvd3/nvd3_stackedarea_full/config/nvd3_stackedarea_full.xml A config/plugins/visualizations/nvd3/nvd3_stackedarea_full/static/logo.png A config/plugins/visualizations/nvd3/nvd3_stackedarea_stream/config/nvd3_stackedarea_stream.xml A config/plugins/visualizations/nvd3/nvd3_stackedarea_stream/static/logo.png A config/plugins/visualizations/phylocanvas/config/phylocanvas.xml A config/plugins/visualizations/phylocanvas/package.json A config/plugins/visualizations/phylocanvas/src/script.js A config/plugins/visualizations/phylocanvas/static/logo.png A config/plugins/visualizations/phylocanvas/static/script.js M config/plugins/visualizations/phyloviz/config/phyloviz.xml A config/plugins/visualizations/phyloviz/static/logo.png A config/plugins/visualizations/pv/config/pv.xml A config/plugins/visualizations/pv/package.json A config/plugins/visualizations/pv/src/pv.js A config/plugins/visualizations/pv/static/logo.png A config/plugins/visualizations/pv/static/pv.js A config/plugins/visualizations/scatterplot/.babelrc M config/plugins/visualizations/scatterplot/config/scatterplot.xml M config/plugins/visualizations/scatterplot/package.json A config/plugins/visualizations/scatterplot/src/jqglobals.js A config/plugins/visualizations/scatterplot/src/numeric-column-stats.js M config/plugins/visualizations/scatterplot/src/scatterplot.js A config/plugins/visualizations/scatterplot/src/worker-stats.js A config/plugins/visualizations/scatterplot/static/8850628034555be072a0e4f882d4d8e5.js A config/plugins/visualizations/scatterplot/static/logo.png R config/plugins/visualizations/scatterplot/static/numeric-column-stats.js R config/plugins/visualizations/scatterplot/static/scatterplot.bundle.js A config/plugins/visualizations/scatterplot/static/scatterplot.js R config/plugins/visualizations/scatterplot/static/worker-stats.js M config/plugins/visualizations/scatterplot/templates/scatterplot.mako R config/plugins/visualizations/scatterplot/webpack.config.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 A config/plugins/visualizations/venn/config/venn.xml A config/plugins/visualizations/venn/package.json A config/plugins/visualizations/venn/src/script.js A config/plugins/visualizations/venn/src/venn.js A config/plugins/visualizations/venn/static/logo.png A config/plugins/visualizations/venn/static/script.css A config/plugins/visualizations/venn/static/script.js M config/plugins/webhooks/demo/search/script.js M config/plugins/webhooks/demo/tour_generator/__init__.py 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/galaxy_options.rst M doc/source/admin/nginx.md M doc/source/admin/scaling.md M doc/source/conf.py A doc/source/conf.versioning.py 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/actions/library.py M lib/galaxy/app.py M lib/galaxy/auth/__init__.py M lib/galaxy/auth/providers/ldap_ad.py M lib/galaxy/config.py M lib/galaxy/containers/docker_model.py M lib/galaxy/dataset_collections/structure.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/bam_to_bigwig_converter.xml M lib/galaxy/datatypes/converters/bed_gff_or_vcf_to_bigwig_converter.xml M lib/galaxy/datatypes/converters/bed_to_gff_converter.py M lib/galaxy/datatypes/converters/fasta_to_len.py A lib/galaxy/datatypes/converters/fastagz_to_fasta.xml 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 R lib/galaxy/datatypes/converters/sam_to_bam_native.xml A lib/galaxy/datatypes/converters/sam_to_unsorted_bam.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/genetics.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/ngsindex.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 A lib/galaxy/datatypes/upload_util.py M lib/galaxy/datatypes/util/gff_util.py M lib/galaxy/datatypes/xml.py R lib/galaxy/dependencies/pinned-hashed-requirements.txt A lib/galaxy/dependencies/pinned-requirements.txt R lib/galaxy/dependencies/pinned-requirements.txt A lib/galaxy/dependencies/pipfiles/default/Pipfile A lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt M lib/galaxy/dependencies/pipfiles/develop/Pipfile.lock R lib/galaxy/dependencies/pipfiles/develop/pinned-hashed-requirements.txt M lib/galaxy/dependencies/pipfiles/develop/pinned-requirements.txt M lib/galaxy/dependencies/pipfiles/flake8/Pipfile.lock R lib/galaxy/dependencies/pipfiles/flake8/pinned-hashed-requirements.txt M lib/galaxy/dependencies/pipfiles/flake8/pinned-requirements.txt M lib/galaxy/dependencies/pipfiles/update.sh R lib/galaxy/dependencies/requirements.txt M lib/galaxy/exceptions/__init__.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/dynamic_tool_destination.py M lib/galaxy/jobs/handler.py M lib/galaxy/jobs/mapper.py A lib/galaxy/jobs/metrics/instrumenters/cgroup.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/kubernetes.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/jobs/runners/util/job_script/MEMORY_STATEMENT.sh M lib/galaxy/managers/collections.py M lib/galaxy/managers/configuration.py M lib/galaxy/managers/containers.py M lib/galaxy/managers/libraries.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/migrate/versions/0005_cleanup_datasets_fix.py M lib/galaxy/model/migrate/versions/0137_add_copied_from_job_id_column.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/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/actions/model_operations.py M lib/galaxy/tools/actions/upload.py M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/tools/cwl/__init__.py M lib/galaxy/tools/cwl/parser.py M lib/galaxy/tools/cwl/representation.py M lib/galaxy/tools/cwl/runtime_actions.py M lib/galaxy/tools/cwl/schema.py A lib/galaxy/tools/cwl/util.py M lib/galaxy/tools/data/__init__.py A lib/galaxy/tools/data_fetch.py A lib/galaxy/tools/data_fetch.xml M lib/galaxy/tools/deps/commands.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/container_resolvers/__init__.py M lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/tools/deps/containers.py M lib/galaxy/tools/deps/docker_util.py M lib/galaxy/tools/deps/mulled/invfile.lua M lib/galaxy/tools/deps/mulled/mulled_build.py M lib/galaxy/tools/deps/mulled/mulled_build_files.py M lib/galaxy/tools/deps/mulled/util.py M lib/galaxy/tools/deps/requirements.py M lib/galaxy/tools/deps/resolvers/__init__.py M lib/galaxy/tools/deps/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/error_reports/plugins/sentry.py M lib/galaxy/tools/execute.py M lib/galaxy/tools/linters/command.py M lib/galaxy/tools/loader_directory.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/tools/parser/interface.py M lib/galaxy/tools/parser/output_objects.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/parser/yaml.py M lib/galaxy/tools/repositories.py M lib/galaxy/tools/special_tools.py M lib/galaxy/tools/test.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/filters/__init__.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/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/tools/wrappers.py M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/util/__init__.py M lib/galaxy/util/checkers.py M lib/galaxy/util/compression_utils.py 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/util/sanitize_html.py M lib/galaxy/util/validation.py M lib/galaxy/util/xml_macros.py M lib/galaxy/visualization/data_providers/genome.py M lib/galaxy/visualization/plugins/config_parser.py M lib/galaxy/visualization/plugins/interactive_environments.py M lib/galaxy/visualization/plugins/plugin.py M lib/galaxy/visualization/plugins/registry.py M lib/galaxy/visualization/plugins/resource_parser.py M lib/galaxy/web/base/controller.py M lib/galaxy/web/framework/decorators.py M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/web/framework/middleware/sentry.py A lib/galaxy/web/framework/middleware/sqldebug.py M lib/galaxy/web/framework/middleware/statsd.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/web/proxy/js/package.json M lib/galaxy/web/stack/__init__.py M lib/galaxy/webapps/config_manage.py A lib/galaxy/webapps/galaxy/api/_fetch_util.py M lib/galaxy/webapps/galaxy/api/annotations.py M lib/galaxy/webapps/galaxy/api/configuration.py M lib/galaxy/webapps/galaxy/api/folder_contents.py M lib/galaxy/webapps/galaxy/api/libraries.py M lib/galaxy/webapps/galaxy/api/library_contents.py M lib/galaxy/webapps/galaxy/api/page_revisions.py M lib/galaxy/webapps/galaxy/api/pages.py A lib/galaxy/webapps/galaxy/api/plugins.py M lib/galaxy/webapps/galaxy/api/remote_files.py M lib/galaxy/webapps/galaxy/api/tools.py A lib/galaxy/webapps/galaxy/api/uploads.py M lib/galaxy/webapps/galaxy/api/users.py M lib/galaxy/webapps/galaxy/api/visualizations.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/config_schema.yml M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/page.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/galaxy/webapps/galaxy/controllers/tag.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/webapps/reports/controllers/query.py M lib/galaxy/webapps/tool_shed/security/__init__.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/workflow/scheduling_manager.py M lib/galaxy_ext/metadata/set_metadata.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M lib/tool_shed/tools/tool_validator.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 lib/tool_shed/util/workflow_util.py M run_tests.sh A scripts/api/fetch_to_library.py A scripts/api/fetch_to_library_example.yml 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 scripts/common_startup.sh M scripts/galaxy-main R scripts/microbes/BeautifulSoup.py M scripts/microbes/harvest_bacteria.py M scripts/migrate_tools/migrate_tools.py R static/scripts/packed M static/style/blue/base.css M templates/js-app.mako R templates/webapps/galaxy/history/display_structured.mako R templates/webapps/galaxy/history/view.mako M templates/webapps/galaxy/workflow/sharing.mako A test-data/1.csv A test-data/example-bag.zip A test-data/qname_sorted.bam A test-data/testdir1.zip M test/api/test_dataset_collections.py M test/api/test_libraries.py M test/api/test_tools.py M test/api/test_tools_upload.py M test/api/test_visualizations.py M test/api/test_workflows.py M test/base/api.py M test/base/driver_util.py M test/base/integration_util.py M test/base/interactor.py M test/base/populators.py M test/base/testcase.py R test/base/tool_shed_util.py R test/casperjs/README.txt R test/casperjs/api-anon-history-permission-tests.js R test/casperjs/api-anon-history-tests.js R test/casperjs/api-hda-tests.js R test/casperjs/api-history-permission-tests.js R test/casperjs/casperjs_runner.py R test/casperjs/modules/api.js R test/casperjs/modules/historyoptions.js R test/casperjs/modules/historypanel.js R test/casperjs/modules/tools.js R test/casperjs/modules/user.js R test/casperjs/page-data/selectors.json R test/casperjs/server_env.py R test/casperjs/spaceghost.js R test/casperjs/test-data/simple_test.ga R test/casperjs/utils/simple-galaxy.js M test/docker/base/Dockerfile M test/functional/test_data_managers.py M test/functional/test_toolbox.py A test/functional/tools/fail_writing_work_dir_file.xml M test/functional/tools/multi_output_recurse.xml 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 M test/functional/twilltestcase.py M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/navigation.yml M test/integration/test_data_manager_table_reload.py A test/integration/test_shed_tool_tests.py M test/integration/test_upload_configuration_options.py A test/integration/uses_shed.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_saved_histories.py M test/selenium_tests/test_tool_form.py M test/shed_functional/base/twilltestcase.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 test/unit/tools/test_parsing.py M test/unit/tools/test_tool_validation.py M test/unit/tools/test_toolbox.py M test/unit/unittest_utils/galaxy_mock.py M test/unit/visualizations/plugins/test_VisualizationsRegistry.py M tools/data_source/upload.py M tools/data_source/upload.xml M tools/genomespace/genomespace_exporter.xml M tools/genomespace/genomespace_importer.xml M tools/genomespace/genomespace_push.xml M tox.ini Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into cloud-storage-api Commit: 6856b81db0f2f6913c7b1f98c4d54ccaaf022480 https://github.com/galaxyproject/galaxy/commit/6856b81db0f2f6913c7b1f98c4d5… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-03-28 (Wed, 28 Mar 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/cloud_storage.py Log Message: ----------- In cloud_storage, receive credentials and pass them to the manager. Commit: dc17e0285a6460c1ded477a976aaa316897caa13 https://github.com/galaxyproject/galaxy/commit/dc17e0285a6460c1ded477a976aa… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-03-28 (Wed, 28 Mar 2018) Changed paths: M lib/galaxy/managers/cloud_storage.py Log Message: ----------- Download data from AWS S3 in cloud_storage manager. Commit: f56e4abb800d09956294323025827ee149e08ae2 https://github.com/galaxyproject/galaxy/commit/f56e4abb800d0995629432302582… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-03-29 (Thu, 29 Mar 2018) Changed paths: M lib/galaxy/managers/cloud_storage.py Log Message: ----------- Call upload tool to persist the dataset copied from cloud-based storage. Commit: 8ceaae7a89457c6688375ddb324c0ecc2893c31c https://github.com/galaxyproject/galaxy/commit/8ceaae7a89457c6688375ddb324c… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-30 (Fri, 30 Mar 2018) Changed paths: M lib/galaxy/managers/cloud_storage.py M lib/galaxy/webapps/galaxy/api/cloud_storage.py Log Message: ----------- Linting fixes while reviewing cloud_storage Commit: a43de58c91e91a3e43aa1e80b7de78457c839491 https://github.com/galaxyproject/galaxy/commit/a43de58c91e91a3e43aa1e80b7de… Author: Vahid <VJalili(a)users.noreply.github.com> Date: 2018-03-30 (Fri, 30 Mar 2018) Changed paths: M lib/galaxy/managers/cloud_storage.py M lib/galaxy/webapps/galaxy/api/cloud_storage.py Log Message: ----------- Merge pull request #5 from dannon/cloud-storage-api Linting fixes while reviewing cloud_storage Commit: 5e4b63bf7635eacf53a808e0c487a476ad1bee1b https://github.com/galaxyproject/galaxy/commit/5e4b63bf7635eacf53a808e0c487… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-03-30 (Fri, 30 Mar 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/cloud_storage.py Log Message: ----------- Add history_id to list of required fields of cloud storage API payload. Commit: ae527da165774d9ca2d7a1ac5b1649fef1ce6d49 https://github.com/galaxyproject/galaxy/commit/ae527da165774d9ca2d7a1ac5b16… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-03-30 (Fri, 30 Mar 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/cloud_storage.py Log Message: ----------- Decode history ID and validate it in cloud storage API. Commit: ab8ca7055bf6d2599c2f3888d8619da9d6bb57dd https://github.com/galaxyproject/galaxy/commit/ab8ca7055bf6d2599c2f3888d861… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-03-30 (Fri, 30 Mar 2018) Changed paths: M lib/galaxy/managers/cloud_storage.py Log Message: ----------- Specify a history to the upload tool in cloud storage manager. Commit: a9d6cab52a5668b815942f1cf18891ee1ef7e7a6 https://github.com/galaxyproject/galaxy/commit/a9d6cab52a5668b815942f1cf188… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-03-30 (Fri, 30 Mar 2018) Changed paths: M lib/galaxy/managers/cloud_storage.py M lib/galaxy/webapps/galaxy/api/cloud_storage.py Log Message: ----------- Merge remote-tracking branch 'origin/cloud-storage-api' into cloud-storage-api Commit: 651d4c7f2ae5861d896ba4ab44518fcd6b33a582 https://github.com/galaxyproject/galaxy/commit/651d4c7f2ae5861d896ba4ab4451… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-04-02 (Mon, 02 Apr 2018) Changed paths: M lib/galaxy/managers/cloud_storage.py M lib/galaxy/webapps/galaxy/api/cloud_storage.py Log Message: ----------- Transaction response is returned in standard http response codes. Commit: 6e0fea91b3e05f0203b25f46a87b375ad93897a8 https://github.com/galaxyproject/galaxy/commit/6e0fea91b3e05f0203b25f46a87b… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-04-02 (Mon, 02 Apr 2018) Changed paths: M lib/galaxy/managers/cloud_storage.py Log Message: ----------- Name dataset with the same name as of the object being downloaded. Commit: 10644a86a95910d9106cd00fddd9632fd1a0d1ee https://github.com/galaxyproject/galaxy/commit/10644a86a95910d9106cd00fddd9… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-04-02 (Mon, 02 Apr 2018) Changed paths: A lib/galaxy/managers/cloud.py R lib/galaxy/managers/cloud_storage.py A lib/galaxy/webapps/galaxy/api/cloud.py R lib/galaxy/webapps/galaxy/api/cloud_storage.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Refactor "CloudStorage" & "cloud_storage" to "Cloud" & "cloud" resp. Commit: fb9656a1a0e7b00c1d9087988ed2efbcf1255595 https://github.com/galaxyproject/galaxy/commit/fb9656a1a0e7b00c1d9087988ed2… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-04-02 (Mon, 02 Apr 2018) Changed paths: M lib/galaxy/managers/cloud.py Log Message: ----------- Delete from-cloud-downloaded staged file after upload job is created. Commit: 547443d396f2c04c05396f3f37c8bc13bd7ed8fd https://github.com/galaxyproject/galaxy/commit/547443d396f2c04c05396f3f37c8… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-04-02 (Mon, 02 Apr 2018) Changed paths: M lib/galaxy/managers/cloud.py Log Message: ----------- Verify credentials when initializing a cloud provider. Commit: d9e5806070662e07dc66af4816b02ed77e1d56bf https://github.com/galaxyproject/galaxy/commit/d9e5806070662e07dc66af4816b0… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-04-02 (Mon, 02 Apr 2018) Changed paths: M lib/galaxy/managers/cloud.py Log Message: ----------- Add support for Azure to cloud storage manager. Commit: eb0df62df78f1b5625961137c20ffde0e11437c3 https://github.com/galaxyproject/galaxy/commit/eb0df62df78f1b5625961137c20f… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-04-02 (Mon, 02 Apr 2018) Changed paths: M lib/galaxy/managers/cloud.py Log Message: ----------- Check for provider-specific missing (None) required credentials. Commit: 23e1209851b16e01b8c9e1acbc36e8070310ab38 https://github.com/galaxyproject/galaxy/commit/23e1209851b16e01b8c9e1acbc36… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-04-02 (Mon, 02 Apr 2018) Changed paths: M lib/galaxy/managers/cloud.py Log Message: ----------- Store supported provides name in a constant. Commit: 177fe583c5c8274850ab69138fb5e664f0bcef2f https://github.com/galaxyproject/galaxy/commit/177fe583c5c8274850ab69138fb5… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-04-02 (Mon, 02 Apr 2018) Changed paths: M lib/galaxy/managers/cloud.py M lib/galaxy/webapps/galaxy/api/cloud.py Log Message: ----------- Throw NotImplementedError for cloud api & manager upload functionality. Commit: 532c5867a19679bfa1d2d8e999be324c76dbdcd5 https://github.com/galaxyproject/galaxy/commit/532c5867a19679bfa1d2d8e999be… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-04-03 (Tue, 03 Apr 2018) Changed paths: M .ci/flake8_blacklist.txt M CONTRIBUTING.md M Makefile M README.rst M client/.babelrc M client/README.md A client/galaxy/scripts/components/RuleCollectionBuilder.vue M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.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/job-states-model.js A client/galaxy/scripts/mvc/upload/collection/rules-input-view.js M client/galaxy/scripts/mvc/upload/upload-ftp.js A client/galaxy/scripts/mvc/upload/upload-utils.js M client/galaxy/scripts/mvc/upload/upload-view.js M client/galaxy/style/less/upload.less M client/package.json M client/webpack.config.js M client/yarn.lock M config/datatypes_conf.xml.sample M config/galaxy.yml.sample M config/reports.yml.sample M config/tool_shed.yml.sample M lib/galaxy/config.py M lib/galaxy/datatypes/binary.py A lib/galaxy/datatypes/converters/genbankgz_to_genbank.xml M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/sequence.py A lib/galaxy/datatypes/test/1.genbank A lib/galaxy/datatypes/test/1.genbank.gz M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/conditional-requirements.txt M lib/galaxy/dependencies/pipfiles/default/Pipfile M lib/galaxy/model/orm/scripts.py M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/repositories.py M lib/galaxy/util/hash_util.py M lib/galaxy/util/script.py M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/web/stack/__init__.py M lib/galaxy/webapps/config_manage.py M lib/galaxy/webapps/galaxy/api/jobs.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/controllers/history.py M scripts/cleanup_datasets/admin_cleanup_datasets.py M scripts/cleanup_datasets/cleanup_datasets.py M scripts/cleanup_datasets/pgcleanup.py M scripts/cleanup_datasets/populate_uuid.py R scripts/cleanup_datasets/remove_renamed_datasets_from_disk.py R scripts/cleanup_datasets/rename_purged_datasets.py M scripts/cleanup_datasets/update_dataset_size.py M scripts/cleanup_datasets/update_metadata.py M scripts/common_startup.sh M scripts/communication/communication_server.py R scripts/data_libraries/build_lucene_index.py R scripts/data_libraries/build_lucene_index.sh R scripts/data_libraries/build_whoosh_index.py R scripts/data_libraries/build_whoosh_index.sh M scripts/db_shell.py M scripts/galaxy-main M scripts/get_uwsgi_args.py M scripts/grt/export.py M scripts/grt/grt.yml.sample M scripts/grt/upload.py M scripts/helper.py M scripts/manage_db.py R scripts/others/incorrect_gops_jobs.py R scripts/others/incorrect_gops_jobs.sh R scripts/others/incorrect_gops_join_jobs.py R scripts/others/incorrect_gops_join_jobs.sh M scripts/runtime_stats.py M scripts/secret_decoder_ring.py M scripts/set_dataset_sizes.py M scripts/set_user_disk_usage.py M scripts/sync_reports_config.py M scripts/transfer.py A test-data/rules/PRJDA60709.tsv A test-data/rules/PRJDB3920.tsv A test-data/rules/PRJNA355367.tsv A test-data/rules/uniprot.json A test-data/rules/uniprot.tsv M test/functional/tools/sample_datatypes_conf.xml M test/galaxy_selenium/has_driver.py M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/navigation.yml M test/galaxy_selenium/smart_components.py A test/integration/test_scripts.py M test/selenium_tests/framework.py M test/selenium_tests/test_collection_builders.py M test/selenium_tests/test_uploads.py M tox.ini Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into cloud-api Commit: 9daa216b830c620ed6d5f8231ed0852a337882b2 https://github.com/galaxyproject/galaxy/commit/9daa216b830c620ed6d5f8231ed0… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-04-03 (Tue, 03 Apr 2018) Changed paths: M lib/galaxy/managers/cloud.py Log Message: ----------- Remove some blank lines and fixed an import. Commit: 70b669992b10682d45c519ef885667ddf52f381c https://github.com/galaxyproject/galaxy/commit/70b669992b10682d45c519ef8856… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-04-03 (Tue, 03 Apr 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/cloud.py Log Message: ----------- Update cloud Download API documentation. Commit: 9960e3bde1eb13506b4f01349fc95d12880ad705 https://github.com/galaxyproject/galaxy/commit/9960e3bde1eb13506b4f01349fc9… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-04-20 (Fri, 20 Apr 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/cloud.py Log Message: ----------- Leverage _future_expose_api for the expose_api decorator in cloud api. Commit: c83194d9bddae4989296f6424f76d59abf3eab54 https://github.com/galaxyproject/galaxy/commit/c83194d9bddae4989296f6424f76… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-04-23 (Mon, 23 Apr 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/cloud.py Log Message: ----------- Replace explicit dict errors in cloud API with Galaxy.exceptions. Commit: 61a1e7eb4c80fdb95c338695a38efa4e0fba0f5e https://github.com/galaxyproject/galaxy/commit/61a1e7eb4c80fdb95c338695a38e… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-04-23 (Mon, 23 Apr 2018) Changed paths: M lib/galaxy/managers/cloud.py M lib/galaxy/webapps/galaxy/api/cloud.py Log Message: ----------- Return summary view of datasets created for data downloaded from cloud. Commit: 907ef7b3ea67530bc41b601f975eda3d2dad0b02 https://github.com/galaxyproject/galaxy/commit/907ef7b3ea67530bc41b601f975e… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-04-23 (Mon, 23 Apr 2018) Changed paths: M lib/galaxy/managers/cloud.py Log Message: ----------- Replace returning http err code in cloud manager with Galaxy Exceptions. Commit: 55646658165aefd6cc48dcb216b8de4d3ac29963 https://github.com/galaxyproject/galaxy/commit/55646658165aefd6cc48dcb216b8… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-04-24 (Tue, 24 Apr 2018) Changed paths: M lib/galaxy/managers/cloud.py Log Message: ----------- close staging file used in cloud api. Commit: 24a1a6bc906cdcbfdab74808c5ef7e116005cb2b https://github.com/galaxyproject/galaxy/commit/24a1a6bc906cdcbfdab74808c5ef… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-04-24 (Tue, 24 Apr 2018) Changed paths: M lib/galaxy/managers/cloud.py Log Message: ----------- Describe functions in cloud manager. Commit: a3de1c5a66e034637cb0cdfb9c99617823ab2eec https://github.com/galaxyproject/galaxy/commit/a3de1c5a66e034637cb0cdfb9c99… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-04-24 (Tue, 24 Apr 2018) Changed paths: M lib/galaxy/managers/cloud.py M lib/galaxy/webapps/galaxy/api/cloud.py Log Message: ----------- Support OpenStack in the cloud download manager. Commit: c656f36ffd7df4d1586bf822cc03a387764ff020 https://github.com/galaxyproject/galaxy/commit/c656f36ffd7df4d1586bf822cc03… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-04-24 (Tue, 24 Apr 2018) Changed paths: M lib/galaxy/managers/cloud.py Log Message: ----------- Change OpenStack required credentials field names. Commit: 8302e574446a8719da430f1174762bf98f8200fe https://github.com/galaxyproject/galaxy/commit/8302e574446a8719da430f117476… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-04-24 (Tue, 24 Apr 2018) Changed paths: M lib/galaxy/managers/cloud.py M lib/galaxy/webapps/galaxy/api/cloud.py Log Message: ----------- Refactor `container` to `bucket` in cloud API and manager. Commit: 6e11334fa7122858012c644038eb0bf58de7e6f2 https://github.com/galaxyproject/galaxy/commit/6e11334fa7122858012c644038eb… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-07-04 (Wed, 04 Jul 2018) Changed paths: M lib/galaxy/managers/cloud.py Log Message: ----------- Refactor cloud download api and use only one handle to the staging file. Commit: 3e551cd9994e76820151bbd002ed782e36c23a69 https://github.com/galaxyproject/galaxy/commit/3e551cd9994e76820151bbd002ed… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M lib/galaxy/managers/cloud.py M lib/galaxy/webapps/galaxy/api/cloud.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Rename the cloud storage APIs from Download and Upload to Copy-from and Copy-To, respectively. Commit: cfe6a9a67757150d7fce0d42f992cd1065cac9ee https://github.com/galaxyproject/galaxy/commit/cfe6a9a67757150d7fce0d42f992… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-07-06 (Fri, 06 Jul 2018) Changed paths: M lib/galaxy/managers/cloud.py M lib/galaxy/webapps/galaxy/api/cloud.py Log Message: ----------- Update documentation of the cloud copy from/to APIs reflecting previous refactoring. Commit: b61bb88daa3566c8b929d81e74f7cc9710875026 https://github.com/galaxyproject/galaxy/commit/b61bb88daa3566c8b929d81e74f7… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-07-06 (Fri, 06 Jul 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/cloud.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Refactor api access to the cloud storage index. Commit: 068005fd6e1c6da73dd08a8c1f8e7c1fdbefe871 https://github.com/galaxyproject/galaxy/commit/068005fd6e1c6da73dd08a8c1f8e… Author: Enis Afgan <afgane(a)gmail.com> Date: 2018-07-06 (Fri, 06 Jul 2018) Changed paths: A lib/galaxy/managers/cloud.py A lib/galaxy/webapps/galaxy/api/cloud.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Merge pull request #5835 from VJalili/cloud-api Copy data from a cloud-based storage to a Galaxy history Compare: https://github.com/galaxyproject/galaxy/compare/3b3c18e0de83...068005fd6e1c **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

1 0

[galaxyproject/galaxy] 6c2bee: Update cliff and other related dependencies
by GitHub 06 Jul '18

06 Jul '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 6c2bee5ea464a6740c7f8c93b3699c6f824a70a4 https://github.com/galaxyproject/galaxy/commit/6c2bee5ea464a6740c7f8c93b369… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-07-06 (Fri, 06 Jul 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt M lib/galaxy/dependencies/pipfiles/develop/Pipfile R lib/galaxy/dependencies/pipfiles/develop/Pipfile.lock M lib/galaxy/dependencies/pipfiles/develop/pinned-requirements.txt R lib/galaxy/dependencies/pipfiles/flake8/Pipfile.lock M lib/galaxy/dependencies/pipfiles/update.sh Log Message: ----------- Update cliff and other related dependencies cliff now has a universal wheel. Remove unused Pipfile.lock files. Skip broken lxml 4.2.2, see https://github.com/lxml/lxml/pull/265 . Fix more oscillating environment markers. Commit: 3b3c18e0de83b535c2cd0235307eaeb821300196 https://github.com/galaxyproject/galaxy/commit/3b3c18e0de83b535c2cd0235307e… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-07-06 (Fri, 06 Jul 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt M lib/galaxy/dependencies/pipfiles/develop/Pipfile R lib/galaxy/dependencies/pipfiles/develop/Pipfile.lock M lib/galaxy/dependencies/pipfiles/develop/pinned-requirements.txt R lib/galaxy/dependencies/pipfiles/flake8/Pipfile.lock M lib/galaxy/dependencies/pipfiles/update.sh Log Message: ----------- Merge pull request #6469 from nsoranzo/update_dependencies Update cliff and other related dependencies Compare: https://github.com/galaxyproject/galaxy/compare/d65789880024...3b3c18e0de83 **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

1 0

[galaxyproject/galaxy] fddc78: Let data managers also use conda python.
by GitHub 06 Jul '18

06 Jul '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: fddc7899c1f09bf20f36369883f091199db0edd0 https://github.com/galaxyproject/galaxy/commit/fddc7899c1f09bf20f36369883f0… Author: rhpvorderman <r.h.p.vorderman(a)lumc.nl> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Let data managers also use conda python. Since data managers only return a json object, there is no need for them to use the galaxy python. Commit: 3f2b2f81fa2dfafee4c2a861b9d1f451b843bd23 https://github.com/galaxyproject/galaxy/commit/3f2b2f81fa2dfafee4c2a861b9d1… Author: rhpvorderman <r.h.p.vorderman(a)lumc.nl> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Style fix Commit: 8e1813b53d00946f298baf1eea86599fb45f7973 https://github.com/galaxyproject/galaxy/commit/8e1813b53d00946f298baf1eea86… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Use profile version to determine if data managers should preserve python env Commit: d6578988002416f95e10ed3751e22b9ed287f565 https://github.com/galaxyproject/galaxy/commit/d6578988002416f95e10ed3751e2… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-07-06 (Fri, 06 Jul 2018) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Merge pull request #6466 from rhpvorderman/patch-2 Let data managers also use conda python. Compare: https://github.com/galaxyproject/galaxy/compare/8df7cafe3ac6...d65789880024 **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

1 0

[galaxyproject/galaxy] 08547f: Intermine from Hack
by GitHub 06 Jul '18

06 Jul '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 08547faddd42858c072c7eca6f45b7422cd4b710 https://github.com/galaxyproject/galaxy/commit/08547faddd42858c072c7eca6f45… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2018-06-30 (Sat, 30 Jun 2018) Changed paths: M config/datatypes_conf.xml.sample M config/tool_conf.xml.main M config/tool_conf.xml.sample M config/tool_data_table_conf.xml.sample A display_applications/intermine/intermine_simple.xml A tools/data_source/intermine.xml Log Message: ----------- Intermine from Hack Commit: 433d4648706be8902f609a4cba1a0d941acb7a0d https://github.com/galaxyproject/galaxy/commit/433d4648706be8902f609a4cba1a… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2018-07-01 (Sun, 01 Jul 2018) Changed paths: M config/tool_conf.xml.sample M tools/data_source/intermine.xml Log Message: ----------- Update InterMine Commit: 5b0088ae43c748edaaccbaa363e0d0c86756a66a https://github.com/galaxyproject/galaxy/commit/5b0088ae43c748edaaccbaa363e0… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2018-07-01 (Sun, 01 Jul 2018) Changed paths: M config/tool_conf.xml.sample Log Message: ----------- Update InterMine Commit: 58c68d408f2eec0c787ad176dabb3330a322d582 https://github.com/galaxyproject/galaxy/commit/58c68d408f2eec0c787ad176dabb… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2018-07-06 (Fri, 06 Jul 2018) Changed paths: A tool-data/intermine_simple_display.loc.sample Log Message: ----------- add missing intermine_simple_display.loc.sample Commit: 8df7cafe3ac6d700f2637f0c41d0dfba8a360076 https://github.com/galaxyproject/galaxy/commit/8df7cafe3ac6d700f2637f0c41d0… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-07-06 (Fri, 06 Jul 2018) Changed paths: M config/datatypes_conf.xml.sample M config/tool_conf.xml.main M config/tool_conf.xml.sample M config/tool_data_table_conf.xml.sample A display_applications/intermine/intermine_simple.xml A tool-data/intermine_simple_display.loc.sample A tools/data_source/intermine.xml Log Message: ----------- Merge pull request #6444 from blankenberg/intermine Intermine Enhancements Compare: https://github.com/galaxyproject/galaxy/compare/0b98e3ed13fe...8df7cafe3ac6 **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

1 0

[galaxyproject/galaxy] d145d9: Allows DatasetMatcher to use multiple filters
by GitHub 05 Jul '18

05 Jul '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d145d9ac92051ecb765d00330a6eb370c6319ac3 https://github.com/galaxyproject/galaxy/commit/d145d9ac92051ecb765d00330a6e… Author: Evan Bolyen <ebolyen(a)gmail.com> Date: 2018-07-01 (Sun, 01 Jul 2018) Changed paths: M lib/galaxy/tools/parameters/dataset_matcher.py M test/unit/tools/test_dataset_matcher.py Log Message: ----------- Allows DatasetMatcher to use multiple filters In particular this enables multiple add_value filters to be used with <options>'s option_filter_attribute. Commit: 0b98e3ed13fe24264b8a5037c1c345dd679c26af https://github.com/galaxyproject/galaxy/commit/0b98e3ed13fe24264b8a5037c1c3… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M lib/galaxy/tools/parameters/dataset_matcher.py M test/unit/tools/test_dataset_matcher.py Log Message: ----------- Merge pull request #6443 from ebolyen/multiple_filter_datasetmatcher Allows DatasetMatcher to use multiple filters Compare: https://github.com/galaxyproject/galaxy/compare/e33427a3b790...0b98e3ed13fe **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

1 0

[galaxyproject/galaxy] 57f5b4: py3: fix workflow extract summary
by GitHub 05 Jul '18

05 Jul '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 57f5b42974929d4090429df87aca9973faae869f https://github.com/galaxyproject/galaxy/commit/57f5b42974929d4090429df87aca… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M test/unit/workflows/test_extract_summary.py Log Message: ----------- py3: fix workflow extract summary Commit: af6b572eac2e2571e5f6f0b46945f7f76fce685b https://github.com/galaxyproject/galaxy/commit/af6b572eac2e2571e5f6f0b46945… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M test/unit/tools/test_history_imp_exp.py Log Message: ----------- py3: Fix history/import export Commit: 048f7737dda50c8dc64fc211a5e59c971aa92041 https://github.com/galaxyproject/galaxy/commit/048f7737dda50c8dc64fc211a5e5… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M lib/galaxy/tools/parameters/output_collect.py Log Message: ----------- Fix job disocvery Commit: c52d1476122adf82b62e6e1045cd7155f34bb9f7 https://github.com/galaxyproject/galaxy/commit/c52d1476122adf82b62e6e1045cd… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M test/unit/tools/test_evaluation.py Log Message: ----------- No need to explicitly compare to bytestring Commit: 492ee207e0ac9884178249251f1047181148c458 https://github.com/galaxyproject/galaxy/commit/492ee207e0ac9884178249251f10… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Cast odict.items() and odict.values() to list Commit: b773aedfa7670ee7fe13d43618f956a4bea3d5da https://github.com/galaxyproject/galaxy/commit/b773aedfa7670ee7fe13d43618f9… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M lib/galaxy/jobs/runners/local.py Log Message: ----------- py3: open job script in text mode Commit: c03a86caea4f7cb945a5a8ae539cb7d8ea3ccce8 https://github.com/galaxyproject/galaxy/commit/c03a86caea4f7cb945a5a8ae539c… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M test/unit/tools/test_collect_primary_datasets.py Log Message: ----------- py3: fix test_job_param unit test Commit: 3af3591e626ddb7204cb958ef414e1fba203e843 https://github.com/galaxyproject/galaxy/commit/3af3591e626ddb7204cb958ef414… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M lib/galaxy/jobs/rule_helper.py Log Message: ----------- py3: fix rule-helper Commit: 25b93c78b6d2a68917bd0aad1e27f155f9d5600c https://github.com/galaxyproject/galaxy/commit/25b93c78b6d2a68917bd0aad1e27… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M lib/galaxy/config.py M test/unit/web/framework/test_webapp.py Log Message: ----------- Fix CORS unit test Commit: 05f8f2063a69e682bc5349933e44d751b2c9e477 https://github.com/galaxyproject/galaxy/commit/05f8f2063a69e682bc5349933e44… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M lib/galaxy/tools/parser/output_collection_def.py Log Message: ----------- Fix output collection unit test Commit: e649f7876fc7753ec76d356e04992169476d619d https://github.com/galaxyproject/galaxy/commit/e649f7876fc7753ec76d356e0499… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M lib/galaxy/jobs/runners/__init__.py Log Message: ----------- Fix recheck_missing_job_retries by casting retries to integer Commit: 0e9adcca823dc0b0a273486ef3137cc030d54db3 https://github.com/galaxyproject/galaxy/commit/0e9adcca823dc0b0a273486ef313… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M lib/galaxy/util/rules_dsl.py Log Message: ----------- Fix rules_dsl comparison by converting to key-style sort function Commit: 37e112323ec8b7e17d11921a781b6b49f2bf05a2 https://github.com/galaxyproject/galaxy/commit/37e112323ec8b7e17d11921a781b… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M lib/galaxy/web/security/__init__.py Log Message: ----------- Fix MAXIMUM_ID_SECRET_LENGTH constant Commit: 192633b0b200130b9f718f25c9070deea34981ad https://github.com/galaxyproject/galaxy/commit/192633b0b200130b9f718f25c907… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M .travis.yml Log Message: ----------- Remove py34-unit from allowed failures Commit: 71b9024769d2ba008740e9e071eac46139258987 https://github.com/galaxyproject/galaxy/commit/71b9024769d2ba008740e9e071ea… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M lib/galaxy/tools/parser/output_collection_def.py Log Message: ----------- Flake8 fix Commit: db10b5b679217c36414dcf2a80189e46ef9cc680 https://github.com/galaxyproject/galaxy/commit/db10b5b679217c36414dcf2a8018… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- py3: Fix has_limit Commit: cde7784606947eb452d1b3c98ca3eaca99b25ea8 https://github.com/galaxyproject/galaxy/commit/cde7784606947eb452d1b3c98ca3… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M lib/galaxy/model/metadata.py M lib/galaxy_ext/metadata/set_metadata.py Log Message: ----------- py3: Fix metadata setting Commit: 84dc5cd02ff0ceab8529cd9e11f825eaed2e3633 https://github.com/galaxyproject/galaxy/commit/84dc5cd02ff0ceab8529cd9e11f8… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- py3: Get unicode strings from ElementTree on py3 Commit: c8f720d71c3d14c2e90d5ebcf0fa41d7bb2726b5 https://github.com/galaxyproject/galaxy/commit/c8f720d71c3d14c2e90d5ebcf0fa… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M lib/galaxy/web/framework/decorators.py Log Message: ----------- py3: don't case payload to bytestring. Doesn't seem to affect py2 either Commit: f29ebb7389a8e695020e11ec4c4c759e89c0a062 https://github.com/galaxyproject/galaxy/commit/f29ebb7389a8e695020e11ec4c4c… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M lib/galaxy/tools/deps/conda_util.py Log Message: ----------- py3: fix generting conda env hash Commit: c16d8531b9948f71d9861692b40a005e7d8c2a21 https://github.com/galaxyproject/galaxy/commit/c16d8531b9948f71d9861692b40a… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M lib/galaxy/tools/parser/output_actions.py Log Message: ----------- py3: fix StringFunctionFilter Commit: 7e29d5d83b55846e0bbe5ec43ced2870b7bb1913 https://github.com/galaxyproject/galaxy/commit/7e29d5d83b55846e0bbe5ec43ced… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M lib/galaxy/jobs/runners/util/cli/shell/rsh.py M test/unit/test_remote_shell.py Log Message: ----------- py3: fix paramiko shell runner by casting to unicode Commit: 962b1fe176e1120d5a093726d74271fda860884f https://github.com/galaxyproject/galaxy/commit/962b1fe176e1120d5a093726d742… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- py3: fix check_limits Commit: 6bad1027a7b22c833ca241214c93090badc66d37 https://github.com/galaxyproject/galaxy/commit/6bad1027a7b22c833ca241214c93… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M lib/galaxy/tools/execute.py Log Message: ----------- py3: fix collection mapping over Commit: 9d547dd5e439ea67193e94242b8354b5e6ec1b92 https://github.com/galaxyproject/galaxy/commit/9d547dd5e439ea67193e94242b83… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M lib/galaxy/web/framework/helpers/grids.py M templates/tagging_common.mako Log Message: ----------- py3: fix 'saved histories' menu Commit: e08c2b347e8e2c625c97f719bc6048e5e956ca9d https://github.com/galaxyproject/galaxy/commit/e08c2b347e8e2c625c97f719bc60… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/text.py M lib/galaxy/datatypes/triples.py Log Message: ----------- Fix some datatype sniffers and `guess_ext()` doctests Commit: 09e39e90794234ae2cbcc2ea6b747888a5075dcd https://github.com/galaxyproject/galaxy/commit/09e39e90794234ae2cbcc2ea6b74… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M lib/galaxy/web/framework/webapp.py Log Message: ----------- py3: Fix mako template rendering in multiple history view and workflow editor Commit: ea440345facd8c9e1cb6c6636970cacfa0544a6f https://github.com/galaxyproject/galaxy/commit/ea440345facd8c9e1cb6c6636970… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M lib/galaxy/web/framework/helpers/grids.py M templates/tagging_common.mako Log Message: ----------- py3: fix published workflows grid Commit: 252913b84a4de19d61294790d10ffca93944e520 https://github.com/galaxyproject/galaxy/commit/252913b84a4de19d61294790d10f… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M lib/galaxy/model/orm/scripts.py Log Message: ----------- Fix SafeConfigParser import for Python 3 Commit: e9f3afa0f3d6451116283a592c680c47a986bbef https://github.com/galaxyproject/galaxy/commit/e9f3afa0f3d6451116283a592c68… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M lib/tool_shed/util/web_util.py Log Message: ----------- py3: fix tool_shed.util.web_util.escape doctest Commit: 7cf76bc66aa9c8b95a74f699a934c4dd81debd57 https://github.com/galaxyproject/galaxy/commit/7cf76bc66aa9c8b95a74f699a934… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M lib/galaxy/jobs/dynamic_tool_destination.py Log Message: ----------- Fix documentation Commit: d5d245ff65841a33c8cb8a32a146a63b14663a7a https://github.com/galaxyproject/galaxy/commit/d5d245ff65841a33c8cb8a32a146… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M lib/galaxy/jobs/runners/util/job_script/__init__.py Log Message: ----------- py3: Fix job_script writing Commit: 0c3a447f25d74132f5b449cac4c744f57af48198 https://github.com/galaxyproject/galaxy/commit/0c3a447f25d74132f5b449cac4c7… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M lib/galaxy/containers/docker_swarm.py Log Message: ----------- Import docker.types Might fix the last failing unit test? Commit: 84af674f9c84182094803a81091ff932873d80a5 https://github.com/galaxyproject/galaxy/commit/84af674f9c84182094803a81091f… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/web/framework/decorators.py Log Message: ----------- Fix loading workflow in the editor under Python 3 Commit: a177fc6240c90985183807fc141b18e06e436cda https://github.com/galaxyproject/galaxy/commit/a177fc6240c90985183807fc141b… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M lib/galaxy/web/framework/webapp.py Log Message: ----------- Fix login under Python 3 Commit: b49c4be21c6c090448d899857e53c1fed8be5d5a https://github.com/galaxyproject/galaxy/commit/b49c4be21c6c090448d899857e53… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M lib/galaxy/model/migrate/versions/0136_collection_and_workflow_state.py M lib/tool_shed/util/readme_util.py Log Message: ----------- Misc Python 3 fixes Commit: d15b6cc7360d3e00780dc1b9ee39353707ba786f https://github.com/galaxyproject/galaxy/commit/d15b6cc7360d3e00780dc1b9ee39… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Code clarifications Commit: e33427a3b79073b1f78a91e848a154f27798ec6c https://github.com/galaxyproject/galaxy/commit/e33427a3b79073b1f78a91e848a1… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M .travis.yml M lib/galaxy/config.py M lib/galaxy/containers/docker_swarm.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/text.py M lib/galaxy/datatypes/triples.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/dynamic_tool_destination.py M lib/galaxy/jobs/rule_helper.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/local.py M lib/galaxy/jobs/runners/util/cli/shell/rsh.py M lib/galaxy/jobs/runners/util/job_script/__init__.py M lib/galaxy/model/metadata.py M lib/galaxy/model/migrate/versions/0136_collection_and_workflow_state.py M lib/galaxy/model/orm/scripts.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/execute.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/tools/parser/output_actions.py M lib/galaxy/tools/parser/output_collection_def.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/util/__init__.py M lib/galaxy/util/rules_dsl.py M lib/galaxy/web/framework/decorators.py M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/web/security/__init__.py M lib/galaxy_ext/metadata/set_metadata.py M lib/tool_shed/util/readme_util.py M lib/tool_shed/util/web_util.py M templates/tagging_common.mako M test/unit/test_remote_shell.py M test/unit/tools/test_collect_primary_datasets.py M test/unit/tools/test_evaluation.py M test/unit/tools/test_history_imp_exp.py M test/unit/web/framework/test_webapp.py M test/unit/workflows/test_extract_summary.py Log Message: ----------- Merge pull request #6450 from mvdbeek/py3_workflow_and_tool_unit_fixes Fix all remaining unit tests under Python 3 Compare: https://github.com/galaxyproject/galaxy/compare/9a06474a30cb...e33427a3b790 **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

1 0

[galaxyproject/galaxy] 0c97d4: GIE static url; https://github.com/galaxyproject/g...
by GitHub 05 Jul '18

05 Jul '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: 0c97d4ff5c83318551319524582619656ae848b8 https://github.com/galaxyproject/galaxy/commit/0c97d4ff5c833185513195245826… Author: thobalose <lose.thoba(a)gmail.com> Date: 2018-07-04 (Wed, 04 Jul 2018) Changed paths: M lib/galaxy/visualization/plugins/interactive_environments.py Log Message: ----------- GIE static url; https://github.com/galaxyproject/galaxy/issues/6459 Commit: 3fe88a9bfe1b010ca30ffac32e5c4e200398c48e https://github.com/galaxyproject/galaxy/commit/3fe88a9bfe1b010ca30ffac32e5c… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M lib/galaxy/visualization/plugins/interactive_environments.py Log Message: ----------- Merge pull request #6465 from dannon/backport-gie-static-again [18.05] Backport of IE static url fix (to actual 18.05) Compare: https://github.com/galaxyproject/galaxy/compare/39d7cf2eb731...3fe88a9bfe1b **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

1 0

[galaxyproject/galaxy] 1a2cd7: added daa (diamond alignment) datatype
by GitHub 04 Jul '18

04 Jul '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 1a2cd725bb303e8db6fa07118f4714b7c0516e60 https://github.com/galaxyproject/galaxy/commit/1a2cd725bb303e8db6fa07118f47… Author: M Bernt <m.bernt(a)ufz.de> Date: 2018-06-20 (Wed, 20 Jun 2018) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py Log Message: ----------- added daa (diamond alignment) datatype Commit: 68dc4c26508087829150b8e5c6d3530a47202304 https://github.com/galaxyproject/galaxy/commit/68dc4c26508087829150b8e5c6d3… Author: M Bernt <m.bernt(a)ufz.de> Date: 2018-06-20 (Wed, 20 Jun 2018) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- removed try-except and used with Commit: 3b6ab3ecd087786113daa81e8cb0beda9a8eff82 https://github.com/galaxyproject/galaxy/commit/3b6ab3ecd087786113daa81e8cb0… Author: M Bernt <m.bernt(a)ufz.de> Date: 2018-06-20 (Wed, 20 Jun 2018) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- shortened code Commit: e636bf00c64354bea8236cbfec81074f19b6a295 https://github.com/galaxyproject/galaxy/commit/e636bf00c64354bea8236cbfec81… Author: M Bernt <m.bernt(a)ufz.de> Date: 2018-06-20 (Wed, 20 Jun 2018) Changed paths: A lib/galaxy/datatypes/test/diamond.daa Log Message: ----------- added missing test file Commit: a651b6af1ea04041aa4fa4230786e255b5fb954a https://github.com/galaxyproject/galaxy/commit/a651b6af1ea04041aa4fa4230786… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-06-20 (Wed, 20 Jun 2018) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- Minor cosmetics on diamond datatypes Commit: 46788b99b2386c165a9edc899d9a0a7fdafaba05 https://github.com/galaxyproject/galaxy/commit/46788b99b2386c165a9edc899d9a… Author: M Bernt <m.bernt(a)ufz.de> Date: 2018-06-20 (Wed, 20 Jun 2018) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- added sniffer entry in data_types.conf.sample Commit: 891b8923bfbdd9c51e41f334185589b4ca87280d https://github.com/galaxyproject/galaxy/commit/891b8923bfbdd9c51e41f3341855… Author: M Bernt <m.bernt(a)ufz.de> Date: 2018-06-21 (Thu, 21 Jun 2018) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- fixed typo in test this commit introduces also debug output for DAA and DMND snifferes which needs to be removed before merging Commit: 116c7051c9f4cc8e4b36577a3477a1bfcdc4b7d9 https://github.com/galaxyproject/galaxy/commit/116c7051c9f4cc8e4b36577a3477… Author: M Bernt <m.bernt(a)ufz.de> Date: 2018-06-22 (Fri, 22 Jun 2018) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- daa detection: fixed typo and removed debug output Commit: 14ef3b8643eb96a98b1f39391c1f385596d1cb42 https://github.com/galaxyproject/galaxy/commit/14ef3b8643eb96a98b1f39391c1f… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M .ci/flake8_blacklist.txt M .travis.yml A client/galaxy/docs/galaxy-buttons.md A client/galaxy/docs/galaxy-forms.md A client/galaxy/docs/galaxy-masthead.md A client/galaxy/docs/galaxy-menus.md A client/galaxy/docs/galaxy-messages.md A client/galaxy/docs/galaxy-panels.md R client/galaxy/docs/galaxy-styles.md A client/galaxy/docs/galaxy-tables.md A client/galaxy/docs/galaxy-tabs.md M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/panels/admin-panel.js M client/galaxy/scripts/apps/panels/tool-panel.js M client/galaxy/scripts/components/Citations.vue A client/galaxy/scripts/components/DataDialog.vue A client/galaxy/scripts/components/admin/DataTypes.vue M client/galaxy/scripts/galaxy.pages.js A client/galaxy/scripts/layout/data.js M client/galaxy/scripts/layout/masthead.js M client/galaxy/scripts/layout/modal.js M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/layout/panel.js M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M client/galaxy/scripts/mvc/history/history-view-edit.js M client/galaxy/scripts/mvc/history/job-dag.js M client/galaxy/scripts/mvc/library/library-folderlist-view.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/tool/tool-form.js M client/galaxy/scripts/mvc/tool/tools.js M client/galaxy/scripts/mvc/ui/ui-misc.js M client/galaxy/scripts/mvc/ui/ui-options.js M client/galaxy/scripts/mvc/visualization/chart/components/model.js M client/galaxy/scripts/mvc/workflow/workflow-canvas.js M client/galaxy/scripts/mvc/workflow/workflow-connector.js M client/galaxy/scripts/mvc/workflow/workflow-manager.js M client/galaxy/scripts/mvc/workflow/workflow-view-data.js M client/galaxy/scripts/mvc/workflow/workflow-view-terminals.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M client/galaxy/scripts/reports/run_stats.js M client/galaxy/scripts/utils/config.js M client/galaxy/scripts/utils/uploadbox.js M client/galaxy/scripts/viz/circster.js M client/galaxy/scripts/viz/sweepster.js M client/galaxy/scripts/viz/trackster/painters.js M client/galaxy/scripts/viz/trackster/tracks.js M client/galaxy/scripts/viz/visualization.js M client/galaxy/style/scss/base.scss M client/galaxy/style/scss/galaxy_bootstrap/variables.scss M client/galaxy/style/scss/galaxy_variables.scss M client/galaxy/style/scss/theme/blue.scss M client/galaxy/style/scss/ui.scss M client/galaxy/style/scss/upload.scss M client/package.json M client/styleguide.config.js M client/webpack.config.js M client/yarn.lock M config/datatypes_conf.xml.sample M config/plugins/visualizations/msa/config/msa.xml M lib/galaxy/datatypes/binary.py A lib/galaxy/datatypes/converters/bam_to_bai.xml M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/proteomics.py M lib/galaxy/datatypes/sniff.py A lib/galaxy/datatypes/test/empty.txt M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt M lib/galaxy/dependencies/pipfiles/develop/Pipfile.lock M lib/galaxy/dependencies/pipfiles/develop/pinned-requirements.txt M lib/galaxy/dependencies/pipfiles/flake8/Pipfile.lock M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/dynamic_tool_destination.py R lib/galaxy/jobs/error_level.py M lib/galaxy/jobs/output_checker.py M lib/galaxy/jobs/runners/chronos.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/managers/rbac_secured.py M lib/galaxy/managers/users.py M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/model/custom_types.py M lib/galaxy/model/metadata.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/tools/parser/cwl.py A lib/galaxy/tools/parser/error_level.py M lib/galaxy/tools/parser/interface.py M lib/galaxy/tools/parser/util.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/relabel_from_file.xml M lib/galaxy/tools/util/maf_utilities.py M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/util/__init__.py M lib/galaxy/util/checkers.py M lib/galaxy/util/json.py M lib/galaxy/visualization/plugins/interactive_environments.py M lib/galaxy/visualization/plugins/plugin.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py M scripts/grt/export.py M static/style/blue/base.css R templates/admin/view_datatypes_registry.mako M templates/base/base_panels.mako M templates/webapps/galaxy/galaxy.panels.mako M templates/webapps/galaxy/workflow/editor.mako M templates/webapps/tool_shed/base_panels.mako M test/api/test_tools.py M test/functional/test_data_managers.py M test/functional/test_toolbox.py M test/unit/datatypes/dataproviders/test_base_dataproviders.py M test/unit/datatypes/test_bam.py M test/unit/jobs/test_job_output_checker.py M test/unit/jobs/test_runner_params.py M test/unit/test_galaxy_mapping.py M test/unit/test_security_helper.py M test/unit/tools/test_evaluation.py M test/unit/tools/test_parsing.py M test/unit/tools/test_tool_dependency_description.py M test/unit/tools/test_tool_deps.py M test/unit/unittest_utils/galaxy_mock.py M test/unit/unittest_utils/tempfilecache.py M test/unit/visualizations/plugins/test_VisualizationsRegistry.py M test/unit/workflows/test_extract_summary.py M tools/data_source/upload.py Log Message: ----------- Merge branch 'dev' into topic/daa Commit: 9a06474a30cb82122ee6a78c30eca601af9d6578 https://github.com/galaxyproject/galaxy/commit/9a06474a30cb82122ee6a78c30ec… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py A lib/galaxy/datatypes/test/diamond.daa Log Message: ----------- Merge pull request #6313 from bernt-matthias/topic/daa added daa (diamond alignment) datatype Compare: https://github.com/galaxyproject/galaxy/compare/1f57706abffb...9a06474a30cb **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

1 0

[galaxyproject/galaxy] 0c97d4: GIE static url; https://github.com/galaxyproject/g...
by GitHub 04 Jul '18

04 Jul '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 0c97d4ff5c83318551319524582619656ae848b8 https://github.com/galaxyproject/galaxy/commit/0c97d4ff5c833185513195245826… Author: thobalose <lose.thoba(a)gmail.com> Date: 2018-07-04 (Wed, 04 Jul 2018) Changed paths: M lib/galaxy/visualization/plugins/interactive_environments.py Log Message: ----------- GIE static url; https://github.com/galaxyproject/galaxy/issues/6459 Commit: 1f57706abffb933a1e5300f585ed19c1493b39d2 https://github.com/galaxyproject/galaxy/commit/1f57706abffb933a1e5300f585ed… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2018-07-04 (Wed, 04 Jul 2018) Log Message: ----------- Merge pull request #6464 from dannon/backport-gie-static [18.05] Backport of IE static url fix Compare: https://github.com/galaxyproject/galaxy/compare/6206f706794c...1f57706abffb **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

1 0

[galaxyproject/galaxy] 7f0684: Fix test_toolbox for python 3
by GitHub 04 Jul '18

04 Jul '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 7f0684e3d57f248b74ff5d6fd6f9a2537b07d726 https://github.com/galaxyproject/galaxy/commit/7f0684e3d57f248b74ff5d6fd6f9… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-07-04 (Wed, 04 Jul 2018) Changed paths: M test/functional/test_toolbox.py Log Message: ----------- Fix test_toolbox for python 3 Commit: ae9b6057da7a0056191f27511e2a71fd1bd6dac2 https://github.com/galaxyproject/galaxy/commit/ae9b6057da7a0056191f27511e2a… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-07-04 (Wed, 04 Jul 2018) Changed paths: M test/functional/test_data_managers.py Log Message: ----------- Fix test_data_managers for python 3 Commit: 6206f706794c997ae137381eabba7d0d88852c49 https://github.com/galaxyproject/galaxy/commit/6206f706794c997ae137381eabba… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2018-07-04 (Wed, 04 Jul 2018) Changed paths: M test/functional/test_data_managers.py M test/functional/test_toolbox.py Log Message: ----------- Merge pull request #6463 from mvdbeek/prepare_py3_api_tests Fix test_toolbox for python 3 Compare: https://github.com/galaxyproject/galaxy/compare/d85b65a2e501...6206f706794c **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

1 0

[galaxyproject/galaxy] 54b6a8: py3: Fix the dynamic tool destination unit test
by GitHub 04 Jul '18

04 Jul '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 54b6a8883d9549c0a84204f530332d695676afdb https://github.com/galaxyproject/galaxy/commit/54b6a8883d9549c0a84204f53033… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-07-02 (Mon, 02 Jul 2018) Changed paths: M lib/galaxy/jobs/dynamic_tool_destination.py Log Message: ----------- py3: Fix the dynamic tool destination unit test Commit: d85b65a2e5011e7187817c7f86db0c1e09a788d5 https://github.com/galaxyproject/galaxy/commit/d85b65a2e5011e7187817c7f86db… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2018-07-04 (Wed, 04 Jul 2018) Changed paths: M lib/galaxy/jobs/dynamic_tool_destination.py Log Message: ----------- Merge pull request #6453 from mvdbeek/fix_py3_dtd py3: Fix the dynamic tool destination unit test Compare: https://github.com/galaxyproject/galaxy/compare/37782cf5131e...d85b65a2e501 **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

1 0

[galaxyproject/galaxy] 5745df: GIE static url; https://github.com/galaxyproject/g...
by GitHub 04 Jul '18

04 Jul '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 5745df2318d4907fb0fa40bc9032b44db853bca0 https://github.com/galaxyproject/galaxy/commit/5745df2318d4907fb0fa40bc9032… Author: thobalose <lose.thoba(a)gmail.com> Date: 2018-07-03 (Tue, 03 Jul 2018) Changed paths: M lib/galaxy/visualization/plugins/interactive_environments.py Log Message: ----------- GIE static url; https://github.com/galaxyproject/galaxy/issues/6459 Commit: 37782cf5131eab2be8c08320bedf8365a475abbc https://github.com/galaxyproject/galaxy/commit/37782cf5131eab2be8c08320bedf… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-07-04 (Wed, 04 Jul 2018) Changed paths: M lib/galaxy/visualization/plugins/interactive_environments.py Log Message: ----------- Merge pull request #6460 from thobalose/ie_static_url GIE static url Compare: https://github.com/galaxyproject/galaxy/compare/fb229c251f74...37782cf5131e **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

1 0

[galaxyproject/galaxy] 21f42f: fixes test/unit/jobs/test_job_output_checker.py
by GitHub 04 Jul '18

04 Jul '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 21f42f5bb6f076b3b318f5f98657929d7f66102b https://github.com/galaxyproject/galaxy/commit/21f42f5bb6f076b3b318f5f98657… Author: caleb <caleb.easterly(a)gmail.com> Date: 2018-07-04 (Wed, 04 Jul 2018) Changed paths: M lib/galaxy/tools/parser/interface.py Log Message: ----------- fixes test/unit/jobs/test_job_output_checker.py Commit: fb0cc8bb1f8a786699f861256d5d25632b50af3f https://github.com/galaxyproject/galaxy/commit/fb0cc8bb1f8a786699f861256d5d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-07-04 (Wed, 04 Jul 2018) Changed paths: M lib/galaxy/tools/parser/interface.py Log Message: ----------- Use stdioerrorlevel constants to indicate FATAL Commit: 0d59c9cd54d49fad31767f52c07c995ff963ce18 https://github.com/galaxyproject/galaxy/commit/0d59c9cd54d49fad31767f52c07c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-07-04 (Wed, 04 Jul 2018) Changed paths: R lib/galaxy/jobs/error_level.py M lib/galaxy/jobs/output_checker.py M lib/galaxy/tools/parser/cwl.py A lib/galaxy/tools/parser/error_level.py M lib/galaxy/tools/parser/interface.py M lib/galaxy/tools/parser/util.py M lib/galaxy/tools/parser/xml.py M test/unit/jobs/test_job_output_checker.py Log Message: ----------- Refactor galaxy.jobs.error_level -> galaxy.tools.parser.error_level. Needed after 46170e9bcdcc2eb104ebab72a7afc9b7238bc314 to keep galaxy-lib from importing things outside of galaxy-lib but clearly a good refactoring on its own since it eliminates mid-file imports that were there to prevent circular dependencies from loading Galaxy. Commit: fb229c251f7487215a285967be8b7b331c1d21f2 https://github.com/galaxyproject/galaxy/commit/fb229c251f7487215a285967be8b… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2018-07-04 (Wed, 04 Jul 2018) Changed paths: R lib/galaxy/jobs/error_level.py M lib/galaxy/jobs/output_checker.py M lib/galaxy/tools/parser/cwl.py A lib/galaxy/tools/parser/error_level.py M lib/galaxy/tools/parser/interface.py M lib/galaxy/tools/parser/util.py M lib/galaxy/tools/parser/xml.py M test/unit/jobs/test_job_output_checker.py Log Message: ----------- Merge pull request #6438 from caleb-easterly/test_job_output_checker_py3 fixes test/unit/jobs/test_job_output_checker.py; strange default? Compare: https://github.com/galaxyproject/galaxy/compare/cc0022d5d1cc...fb229c251f74 **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

1 0

[galaxyproject/galaxy] f8281c: py3 compat
by GitHub 03 Jul '18

03 Jul '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f8281cf67f40eab30dc00099b757416f48d7fa78 https://github.com/galaxyproject/galaxy/commit/f8281cf67f40eab30dc00099b757… Author: caleb <caleb.easterly(a)gmail.com> Date: 2018-07-01 (Sun, 01 Jul 2018) Changed paths: M lib/galaxy/tools/deps/__init__.py M test/unit/tools/test_tool_deps.py Log Message: ----------- py3 compat Commit: fe003da510d71ad001bb63ed40e6ce45f4ca23c2 https://github.com/galaxyproject/galaxy/commit/fe003da510d71ad001bb63ed40e6… Author: Caleb Easterly <easte080(a)umn.edu> Date: 2018-07-01 (Sun, 01 Jul 2018) Changed paths: M lib/galaxy/tools/deps/__init__.py Log Message: ----------- fix linting errors Commit: 561330fea9eb1a79a52aa48d986218e1b89d8800 https://github.com/galaxyproject/galaxy/commit/561330fea9eb1a79a52aa48d9862… Author: Caleb Easterly <easte080(a)umn.edu> Date: 2018-07-02 (Mon, 02 Jul 2018) Changed paths: M test/unit/tools/test_tool_deps.py Log Message: ----------- rewind change Commit: cc0022d5d1cc985b23644b6ff6b3e60c29d9caa6 https://github.com/galaxyproject/galaxy/commit/cc0022d5d1cc985b23644b6ff6b3… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2018-07-03 (Tue, 03 Jul 2018) Changed paths: M lib/galaxy/tools/deps/__init__.py Log Message: ----------- Merge pull request #6434 from caleb-easterly/test_tool_deps_py3 py3 compat Compare: https://github.com/galaxyproject/galaxy/compare/f65c77d38530...cc0022d5d1cc **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

1 0

[galaxyproject/galaxy] a1bedf: Lint doctests
by GitHub 03 Jul '18

03 Jul '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a1bedf4be8835f84a14df9cc5e1231dd585302d5 https://github.com/galaxyproject/galaxy/commit/a1bedf4be8835f84a14df9cc5e12… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-07-02 (Mon, 02 Jul 2018) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- Lint doctests Commit: 256d901df20e6703094cf98f693b19ff79384c3e https://github.com/galaxyproject/galaxy/commit/256d901df20e6703094cf98f693b… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-07-02 (Mon, 02 Jul 2018) Changed paths: M lib/galaxy/util/checkers.py Log Message: ----------- Use `with` statement Commit: c03dd53520a4b581af208c1e592ea135a4340016 https://github.com/galaxyproject/galaxy/commit/c03dd53520a4b581af208c1e592e… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-07-02 (Mon, 02 Jul 2018) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- Correctly handle `bytearray`s in `smart_str()` Also: - Use `assert` in doctests - Speed up `unicodify()` on Unicode strings Commit: 7195c224321b0826a9b2297166ea6fa6ce1de007 https://github.com/galaxyproject/galaxy/commit/7195c224321b0826a9b2297166ea… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-07-03 (Tue, 03 Jul 2018) Changed paths: M lib/galaxy/datatypes/sniff.py Log Message: ----------- Encode chunk before comparing with gzip_magic Since commit 8d8299a19315aef2f2daef278a5e8d8c47da63bb , `text_type(util.gzip_magic)` generates the following exception: ``` UnicodeDecodeError: 'ascii' codec can't decode byte 0x8b in position 1: ordinal not in range(128) ``` Commit: 82028d95d0d58532821816d526e2b932ea8ee5ec https://github.com/galaxyproject/galaxy/commit/82028d95d0d58532821816d526e2… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-07-03 (Tue, 03 Jul 2018) Changed paths: M lib/galaxy/datatypes/sniff.py Log Message: ----------- Remove needless check The `filename` file is the destination file and is always empty at this point. Introduced in commit 85ea42b79dcfc30622a55f1b9fc507bc822ae325 . Commit: 64c591a6069c43067ad1871dca06cc3c5a581903 https://github.com/galaxyproject/galaxy/commit/64c591a6069c43067ad1871dca06… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-07-03 (Tue, 03 Jul 2018) Changed paths: M test/unit/tools/test_tool_deps.py Log Message: ----------- More proper fix for some test_tool_deps.py unit tests Follow up to https://github.com/galaxyproject/galaxy/pull/6436/files#r199368686 Commit: f65c77d385303703d1cfcd47140f84d56fadec2b https://github.com/galaxyproject/galaxy/commit/f65c77d385303703d1cfcd47140f… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2018-07-03 (Tue, 03 Jul 2018) Changed paths: M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/sniff.py M lib/galaxy/util/__init__.py M lib/galaxy/util/checkers.py M test/unit/tools/test_tool_deps.py Log Message: ----------- Merge pull request #6455 from nsoranzo/python3 Various Python 3 fixes Compare: https://github.com/galaxyproject/galaxy/compare/59cc94256ca0...f65c77d38530 **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

1 0

[galaxyproject/galaxy] 7b0872: Run workflows from published workflows menu
by GitHub 03 Jul '18

03 Jul '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 7b08728c348c9fa4767683b98632ec763420b39e https://github.com/galaxyproject/galaxy/commit/7b08728c348c9fa4767683b98632… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-06-30 (Sat, 30 Jun 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- Run workflows from published workflows menu Just needed to generate the right URL. Commit: 59cc94256ca011ab68e25d3a9423166c3ad4ec1c https://github.com/galaxyproject/galaxy/commit/59cc94256ca011ab68e25d3a9423… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-07-02 (Mon, 02 Jul 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- Merge pull request #6428 from mvdbeek/run_published_workflows Run workflows from published workflows menu Compare: https://github.com/galaxyproject/galaxy/compare/b46d7c6276d0...59cc94256ca0 **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

1 0

[galaxyproject/galaxy] 9eb1bf: Fix droptarget:drop trigger (wasn't passing the pa...
by GitHub 02 Jul '18

02 Jul '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 9eb1bfe3ff0a17629922156a0465694c3a31b88e https://github.com/galaxyproject/galaxy/commit/9eb1bfe3ff0a17629922156a0465… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-07-02 (Mon, 02 Jul 2018) Changed paths: M client/galaxy/scripts/mvc/history/history-view-edit.js Log Message: ----------- Fix droptarget:drop trigger (wasn't passing the panel) Commit: b46d7c6276d09c160f37f22df8ed64461a96b407 https://github.com/galaxyproject/galaxy/commit/b46d7c6276d09c160f37f22df8ed… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-07-02 (Mon, 02 Jul 2018) Changed paths: M client/galaxy/scripts/mvc/history/history-view-edit.js Log Message: ----------- Merge pull request #6451 from dannon/fixdragdrop Fix droptarget:drop trigger (drag/drop in the multiview) Compare: https://github.com/galaxyproject/galaxy/compare/9957d39b043d...b46d7c6276d0 **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

1 0

[galaxyproject/galaxy] 1eae38: py3: replace e.message with str(e)
by GitHub 02 Jul '18

02 Jul '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 1eae38854b53433a367ec2038e74e30ffa4bfab1 https://github.com/galaxyproject/galaxy/commit/1eae38854b53433a367ec2038e74… Author: caleb <caleb.easterly(a)gmail.com> Date: 2018-07-02 (Mon, 02 Jul 2018) Changed paths: M lib/galaxy/jobs/runners/chronos.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/managers/users.py Log Message: ----------- py3: replace e.message with str(e) Commit: 9957d39b043dd9bc17b7e0c56c5e116ddc45f94f https://github.com/galaxyproject/galaxy/commit/9957d39b043dd9bc17b7e0c56c5e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-07-02 (Mon, 02 Jul 2018) Changed paths: M lib/galaxy/jobs/runners/chronos.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/managers/users.py Log Message: ----------- Merge pull request #6454 from caleb-easterly/exceptions py3: replace e.message with str(e) Compare: https://github.com/galaxyproject/galaxy/compare/19e70b8aeb0c...9957d39b043d **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

1 0

[galaxyproject/galaxy] dc6774: CI - ignore node_modules anywhere, since we use th...
by GitHub 02 Jul '18

02 Jul '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: dc6774b7b2d0bd90705f289fe6cd82ba9e8eed9e https://github.com/galaxyproject/galaxy/commit/dc6774b7b2d0bd90705f289fe6cd… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-07-02 (Mon, 02 Jul 2018) Changed paths: M .ci/flake8_blacklist.txt Log Message: ----------- CI - ignore node_modules anywhere, since we use them in multiple places and not always 'client' Commit: 19e70b8aeb0c8d08b70d050b1dcf2d4d00480b4f https://github.com/galaxyproject/galaxy/commit/19e70b8aeb0c8d08b70d050b1dcf… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-07-02 (Mon, 02 Jul 2018) Changed paths: M .ci/flake8_blacklist.txt Log Message: ----------- Merge pull request #6449 from dannon/node_modules_blacklist CI - ignore node_modules anywhere Compare: https://github.com/galaxyproject/galaxy/compare/5ad321e08540...19e70b8aeb0c **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

1 0

[galaxyproject/galaxy] 72f9e9: py3: fixes test_DatasetManager.py:DatasetManagerTe...
by GitHub 02 Jul '18

02 Jul '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 72f9e9c587e043982a296f4885a88077a720fb1f https://github.com/galaxyproject/galaxy/commit/72f9e9c587e043982a296f4885a8… Author: caleb <caleb.easterly(a)gmail.com> Date: 2018-07-02 (Mon, 02 Jul 2018) Changed paths: M lib/galaxy/managers/rbac_secured.py Log Message: ----------- py3: fixes test_DatasetManager.py:DatasetManagerTestCase Commit: 6d2ff7bad295d9850f2690e4cb81e06f851cc451 https://github.com/galaxyproject/galaxy/commit/6d2ff7bad295d9850f2690e4cb81… Author: Caleb Easterly <easte080(a)umn.edu> Date: 2018-07-02 (Mon, 02 Jul 2018) Changed paths: M lib/galaxy/managers/rbac_secured.py Log Message: ----------- linting fix Commit: 5ad321e08540f6c1a046f397a5c18db16d240c56 https://github.com/galaxyproject/galaxy/commit/5ad321e08540f6c1a046f397a5c1… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-07-02 (Mon, 02 Jul 2018) Changed paths: M lib/galaxy/managers/rbac_secured.py Log Message: ----------- Merge pull request #6452 from caleb-easterly/test_dataset_manager py3: fixes test_DatasetManager.py:DatasetManagerTestCase Compare: https://github.com/galaxyproject/galaxy/compare/f7e43aa22120...5ad321e08540 **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

1 0

[galaxyproject/galaxy] e39881: Drop fix_json, doesn't seem to be necessary and fi...
by GitHub 02 Jul '18

02 Jul '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: e398818ab6329888f8855cde7ffc9ebfd18a9abc https://github.com/galaxyproject/galaxy/commit/e398818ab6329888f8855cde7ffc… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-07-01 (Sun, 01 Jul 2018) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/util/json.py Log Message: ----------- Drop fix_json, doesn't seem to be necessary and fixes workflow unit tests Commit: f7e43aa2212090f08e94ba9ad65ad7afbf4fcfd4 https://github.com/galaxyproject/galaxy/commit/f7e43aa2212090f08e94ba9ad65a… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-07-02 (Mon, 02 Jul 2018) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/util/json.py Log Message: ----------- Merge pull request #6446 from mvdbeek/drop_json_fix Python3: Drop fix_json, doesn't seem to be necessary and fixes workflow unit t… Compare: https://github.com/galaxyproject/galaxy/compare/75511506a882...f7e43aa22120 **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

1 0