April 2018 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/usegalaxy-playbook] 4b2bf1: Updated snpeff_build to 4.3+T.galaxy2
by GitHub 09 Apr '18

09 Apr '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 4b2bf17590afbbbaa78430fe9411d5cf405c1c0a https://github.com/galaxyproject/usegalaxy-playbook/commit/4b2bf17590afbbba… Author: Dave B <dave(a)bx.psu.edu> Date: 2018-04-09 (Mon, 09 Apr 2018) Changed paths: M env/main/files/galaxy/var/integrated_tool_panel.xml M env/main/files/galaxy/var/shed_tool_conf.xml M env/main/files/galaxy/var/shed_tool_data_table_conf.xml Log Message: ----------- Updated snpeff_build to 4.3+T.galaxy2

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[galaxyproject/galaxy] fefd68: Increase yarn's network timeout
by GitHub 09 Apr '18

09 Apr '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: fefd686b298cd573b49b6fc15d4531ffd3d852d2 https://github.com/galaxyproject/galaxy/commit/fefd686b298cd573b49b6fc15d45… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-04-09 (Mon, 09 Apr 2018) Changed paths: M Makefile Log Message: ----------- Increase yarn's network timeout Commit: ed72b94e1e3a11be8ba5c4f8bd63b93877b32cd9 https://github.com/galaxyproject/galaxy/commit/ed72b94e1e3a11be8ba5c4f8bd63… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-04-09 (Mon, 09 Apr 2018) Changed paths: M Makefile Log Message: ----------- Merge pull request #5870 from dannon/yarn-network-timeout Increase yarn's network timeout Compare: https://github.com/galaxyproject/galaxy/compare/d9efb4ff4c2c...ed72b94e1e3a

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[galaxyproject/usegalaxy-playbook] 0d77bf: Align images better on welcome
by GitHub 09 Apr '18

09 Apr '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 0d77bf1811d55988caefb841a67bdf463c5110e9 https://github.com/galaxyproject/usegalaxy-playbook/commit/0d77bf1811d55988… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-04-09 (Mon, 09 Apr 2018) Changed paths: M env/common/templates/galaxy/static/welcome.html.j2 Log Message: ----------- Align images better on welcome

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[galaxyproject/usegalaxy-playbook] a0735a: Warn about downtime for Main next week
by GitHub 09 Apr '18

09 Apr '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: a0735ab8c51411dfdec57e765afdbdafd683c9a9 https://github.com/galaxyproject/usegalaxy-playbook/commit/a0735ab8c51411df… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-09 (Mon, 09 Apr 2018) Changed paths: M env/main/group_vars/galaxyservers/vars.yml Log Message: ----------- Warn about downtime for Main next week

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[galaxyproject/galaxy] 02e92e: Fix conditional parameter handling for textselect ...
by GitHub 09 Apr '18

09 Apr '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 02e92e21155ce19383041477d20c33ea44779f48 https://github.com/galaxyproject/galaxy/commit/02e92e21155ce19383041477d20c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-04-05 (Thu, 05 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/ui/ui-misc.js M lib/galaxy/tools/parameters/basic.py M static/style/blue/base.css Log Message: ----------- Fix conditional parameter handling for textselect field Commit: 54122c15ed351808cde805362d0e47605f88e545 https://github.com/galaxyproject/galaxy/commit/54122c15ed351808cde805362d0e… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-04-05 (Thu, 05 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-misc.js Log Message: ----------- Add wait unwait features to select field handler Commit: b184f197475e72038d3b80e4828d1298723f1f68 https://github.com/galaxyproject/galaxy/commit/b184f197475e72038d3b80e4828d… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-04-06 (Fri, 06 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/ui/ui-misc.js Log Message: ----------- Explicitly specify options parsed to text select wrapper Commit: 4f84b9cacc31c0946d421a01f9729792850c4ae2 https://github.com/galaxyproject/galaxy/commit/4f84b9cacc31c0946d421a01f972… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-04-06 (Fri, 06 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/ui/ui-misc.js Log Message: ----------- Assign change handler from select model Commit: d9efb4ff4c2c15f6ebd2d133760ff08fb80a623f https://github.com/galaxyproject/galaxy/commit/d9efb4ff4c2c15f6ebd2d133760f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-04-09 (Mon, 09 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/ui/ui-misc.js M lib/galaxy/tools/parameters/basic.py M static/style/blue/base.css Log Message: ----------- Merge pull request #5864 from guerler/fix_expansion Fix conditional parameter handling Compare: https://github.com/galaxyproject/galaxy/compare/075abee76665...d9efb4ff4c2c

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[galaxyproject/galaxy] 9ad1ba: Gulpfile standardization anticipating merges.
by GitHub 06 Apr '18

06 Apr '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 9ad1ba07f8d41ac9be62726a10e9a549c39a58fb https://github.com/galaxyproject/galaxy/commit/9ad1ba07f8d41ac9be62726a10e9… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-21 (Wed, 21 Mar 2018) Changed paths: M client/gulpfile.js Log Message: ----------- Gulpfile standardization anticipating merges. Commit: 2e2ad26addfae8c91395821f75e44749c1aa04b2 https://github.com/galaxyproject/galaxy/commit/2e2ad26addfae8c91395821f75e4… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-22 (Thu, 22 Mar 2018) Changed paths: A client/deploy.js M client/gulpfile.js M client/package.json M client/yarn.lock Log Message: ----------- Incremental work testing staging of libs. May dump this, it's awfully slow via gulp and I can do it faster with regular js. Commit: 7fe49481d7cc37541cc9ec010a871694b5987cfb https://github.com/galaxyproject/galaxy/commit/7fe49481d7cc37541cc9ec010a87… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-22 (Thu, 22 Mar 2018) Changed paths: M client/gulpfile.js Log Message: ----------- Try mapping with glob syntax Commit: 913cd1e6d2e784272ad1b4ebcaab6cb64d464d32 https://github.com/galaxyproject/galaxy/commit/913cd1e6d2e784272ad1b4ebcaab… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-22 (Thu, 22 Mar 2018) Changed paths: M .gitignore M client/gulpfile.js Log Message: ----------- Fix up regex, .gitignore static/plugins Commit: 8223c36b34dd221bf95ea591b75bb75ecef6d286 https://github.com/galaxyproject/galaxy/commit/8223c36b34dd221bf95ea591b75b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-23 (Fri, 23 Mar 2018) Changed paths: M client/gulpfile.js Log Message: ----------- Stage plugin static as a part of the client build Commit: b147abe9e58d21ee29722cedbdd12c354a6b095b https://github.com/galaxyproject/galaxy/commit/b147abe9e58d21ee29722cedbdd1… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-23 (Fri, 23 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/visualization/visualization-view.js Log Message: ----------- Minor es6'ing in vizview Commit: 3fbc41af2abb744352c8ebbcf7150ed3ac49b027 https://github.com/galaxyproject/galaxy/commit/3fbc41af2abb744352c8ebbcf715… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-23 (Fri, 23 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/visualization/visualization-view.js Log Message: ----------- Source viz logos out of /static Commit: 38080f721b7c6948f80544752644bcc9a5fad362 https://github.com/galaxyproject/galaxy/commit/38080f721b7c6948f80544752644… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-23 (Fri, 23 Mar 2018) Changed paths: M lib/galaxy/visualization/plugins/plugin.py Log Message: ----------- Fix docstring 'visualization' typo. Commit: 4764b46bba4f126a6bf72f3a0aee9e210426cb7c https://github.com/galaxyproject/galaxy/commit/4764b46bba4f126a6bf72f3a0aee… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-26 (Mon, 26 Mar 2018) Changed paths: R client/deploy.js Log Message: ----------- Not going to pursue this deploy method, yet -- probably will want to do this later with prod/dev scripts to have more control over the build (over a big chain of package scripts) Commit: e206af4f6de57a9d668808538892e54554611b5c https://github.com/galaxyproject/galaxy/commit/e206af4f6de57a9d668808538892… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-26 (Mon, 26 Mar 2018) Changed paths: M client/package.json M client/yarn.lock Log Message: ----------- Remove gulp-ignore, unnecessary Commit: 6875307b2ac84cdb98ebb54a14a3c1ab3a3e6adb https://github.com/galaxyproject/galaxy/commit/6875307b2ac84cdb98ebb54a14a3… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-26 (Mon, 26 Mar 2018) Changed paths: M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Drop static framework mapping for plugins; we're going to stage into the existing static paths instead since this method doesn't work in uwsgi Commit: 4969394a3cce550ea82d7ca7fa69e95c172f56d8 https://github.com/galaxyproject/galaxy/commit/4969394a3cce550ea82d7ca7fa69… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-26 (Mon, 26 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/visualization/visualization-view.js M lib/galaxy/visualization/plugins/plugin.py Log Message: ----------- Static serving of staged logos Commit: cf2e6dc6d2951f316e9641a05d69a3f919feb05e https://github.com/galaxyproject/galaxy/commit/cf2e6dc6d2951f316e9641a05d69… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-26 (Mon, 26 Mar 2018) Changed paths: M config/plugins/visualizations/scatterplot/templates/scatterplot.mako Log Message: ----------- Fix scatterplot as example of mako entrypoint -- this needs to be generalized Commit: c12feecb76f96fd5fe058d9cf90331e7eb956c5b https://github.com/galaxyproject/galaxy/commit/c12feecb76f96fd5fe058d9cf903… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-26 (Mon, 26 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-thumbnails.js Log Message: ----------- Minor linting in ui-thumbnails Commit: 70915dfc9f2b54bd88ebce92812f4edf578e18d4 https://github.com/galaxyproject/galaxy/commit/70915dfc9f2b54bd88ebce92812f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-27 (Tue, 27 Mar 2018) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/components/HistoryImport.vue A client/galaxy/scripts/components/PluginList.vue M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/form/form-wrapper.js M client/galaxy/scripts/mvc/grid/grid-shared.js M client/galaxy/scripts/mvc/history/history-list.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/ui/ui-buttons.js M client/galaxy/scripts/mvc/ui/ui-misc.js M client/galaxy/scripts/mvc/ui/ui-slider.js M client/galaxy/scripts/mvc/visualization/chart/components/model.js M client/galaxy/scripts/mvc/visualization/chart/utilities/datasets.js M client/galaxy/scripts/mvc/visualization/chart/utilities/jobs.js M client/galaxy/scripts/mvc/visualization/chart/views/groups.js M client/galaxy/scripts/mvc/visualization/chart/views/menu.js M client/galaxy/scripts/mvc/visualization/chart/views/viewer.js M client/galaxy/scripts/mvc/visualization/visualization-model.js R client/galaxy/scripts/mvc/visualization/visualization-view.js M client/galaxy/scripts/ui/pagination.js M client/galaxy/scripts/ui/peek-column-selector.js M client/galaxy/scripts/viz/circster.js M client/galaxy/scripts/viz/sweepster.js M client/galaxy/scripts/viz/trackster.js M client/galaxy/scripts/viz/trackster/tracks.js M client/galaxy/style/less/charts.less M config/galaxy.yml.sample M config/plugins/visualizations/csg/config/csg.xml A config/plugins/visualizations/csg/static/logo.png M config/plugins/visualizations/graphviz/config/graphviz.xml M config/plugins/visualizations/heatmap/heatmap_cluster/config/heatmap_cluster.xml M config/plugins/visualizations/heatmap/heatmap_default/config/heatmap_default.xml M config/plugins/visualizations/heatmap/heatmap_default/config/heatmap_shared.xml M config/plugins/visualizations/jqplot/jqplot_box/config/jqplot_box.xml M config/plugins/visualizations/jqplot/jqplot_histogram/config/jqplot_histogram.xml M config/plugins/visualizations/msa/static/script.js M config/plugins/visualizations/nvd3/nvd3_bar/src/nvd3.js M config/plugins/visualizations/nvd3/nvd3_bar/static/nvd3.js M config/plugins/visualizations/nvd3/nvd3_histogram/config/nvd3_histogram.xml M config/plugins/visualizations/nvd3/nvd3_histogram_discrete/config/nvd3_histogram_discrete.xml M config/plugins/visualizations/phyloviz/config/phyloviz.xml A config/plugins/visualizations/phyloviz/static/logo.png A config/plugins/visualizations/scatterplot/.babelrc M config/plugins/visualizations/scatterplot/package.json A config/plugins/visualizations/scatterplot/src/jqglobals.js M config/plugins/visualizations/scatterplot/src/scatterplot.js A config/plugins/visualizations/scatterplot/static/logo.png M config/plugins/visualizations/scatterplot/static/scatterplot.js M config/plugins/visualizations/scatterplot/templates/scatterplot.mako M config/plugins/visualizations/trackster/config/trackster.xml A config/plugins/visualizations/trackster/static/logo.png M config/plugins/visualizations/unipept/config/unipept.xml M config/plugins/visualizations/venn/src/script.js M config/plugins/visualizations/venn/static/script.js M doc/source/admin/galaxy_options.rst M doc/source/releases/18.01_announce.rst M lib/galaxy/auth/providers/ldap_ad.py M lib/galaxy/config.py M lib/galaxy/datatypes/converters/bed_gff_or_vcf_to_bigwig_converter.xml M lib/galaxy/datatypes/converters/interval_to_fli.py M lib/galaxy/datatypes/util/gff_util.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/jobs/__init__.py M lib/galaxy/jobs/runners/kubernetes.py M lib/galaxy/model/__init__.py M lib/galaxy/objectstore/__init__.py M lib/galaxy/tools/actions/model_operations.py M lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/tools/deps/docker_util.py M lib/galaxy/tools/error_reports/plugins/sentry.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/visualization/plugins/config_parser.py M lib/galaxy/visualization/plugins/plugin.py M lib/galaxy/visualization/plugins/registry.py M lib/galaxy/web/framework/middleware/statsd.py M lib/galaxy/web/stack/__init__.py M lib/galaxy/webapps/config_manage.py M lib/galaxy/webapps/galaxy/api/configuration.py A lib/galaxy/webapps/galaxy/api/plugins.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 scripts/galaxy-main M static/style/blue/base.css M test/api/test_tools.py M test/base/populators.py M test/docker/base/Dockerfile M test/selenium_tests/framework.py M test/selenium_tests/test_library_to_collections.py M test/unit/unittest_utils/galaxy_mock.py M test/unit/visualizations/plugins/test_VisualizationsRegistry.py M tools/data_source/upload.py M tox.ini Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into viz-staging Commit: f21965472ca94a71466c4ca39e93bff30add229e https://github.com/galaxyproject/galaxy/commit/f21965472ca94a71466c4ca39e93… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-29 (Thu, 29 Mar 2018) Changed paths: 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 config/datatypes_conf.xml.sample M config/galaxy.yml.sample M config/reports.yml.sample M config/tool_shed.yml.sample A lib/galaxy/datatypes/converters/genbankgz_to_genbank.xml 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/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/workflows.py M lib/galaxy/webapps/galaxy/controllers/history.py M scripts/common_startup.sh M scripts/get_uwsgi_args.py M tox.ini Log Message: ----------- Merge branch 'dev' into viz-staging-finalize Commit: f0dde506d043b3d4070ddc0fa2b48dac23e4d645 https://github.com/galaxyproject/galaxy/commit/f0dde506d043b3d4070ddc0fa2b4… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-30 (Fri, 30 Mar 2018) Changed paths: M config/plugins/visualizations/common/templates/chart_entry_point.mako M config/plugins/visualizations/csg/templates/csg.mako M config/plugins/visualizations/cytoscape/config/cytoscape.xml M config/plugins/visualizations/drawrna/config/drawrna.xml M config/plugins/visualizations/example/config/example.xml M config/plugins/visualizations/graphviz/templates/graphviz.mako M config/plugins/visualizations/heatmap/heatmap_cluster/config/heatmap_cluster.xml M config/plugins/visualizations/heatmap/heatmap_default/config/heatmap_default.xml M config/plugins/visualizations/jqplot/jqplot_bar/config/jqplot_bar.xml M config/plugins/visualizations/jqplot/jqplot_box/config/jqplot_box.xml M config/plugins/visualizations/jqplot/jqplot_histogram/config/jqplot_histogram.xml M config/plugins/visualizations/jqplot/jqplot_line/config/jqplot_line.xml M config/plugins/visualizations/jqplot/jqplot_scatter/config/jqplot_scatter.xml M config/plugins/visualizations/msa/config/msa.xml M config/plugins/visualizations/ngl/config/ngl.xml M config/plugins/visualizations/nvd3/nvd3_bar/config/nvd3_bar.xml M config/plugins/visualizations/nvd3/nvd3_bar_stacked/config/nvd3_bar_stacked.xml M config/plugins/visualizations/nvd3/nvd3_histogram/config/nvd3_histogram.xml M config/plugins/visualizations/nvd3/nvd3_histogram_discrete/config/nvd3_histogram_discrete.xml M config/plugins/visualizations/nvd3/nvd3_horizontal/config/nvd3_horizontal.xml M config/plugins/visualizations/nvd3/nvd3_horizontal_stacked/config/nvd3_horizontal_stacked.xml M config/plugins/visualizations/nvd3/nvd3_line/config/nvd3_line.xml M config/plugins/visualizations/nvd3/nvd3_line_focus/config/nvd3_line_focus.xml M config/plugins/visualizations/nvd3/nvd3_pie/config/nvd3_pie.xml M config/plugins/visualizations/nvd3/nvd3_scatter/config/nvd3_scatter.xml M config/plugins/visualizations/nvd3/nvd3_stackedarea/config/nvd3_stackedarea.xml M config/plugins/visualizations/nvd3/nvd3_stackedarea_full/config/nvd3_stackedarea_full.xml M config/plugins/visualizations/nvd3/nvd3_stackedarea_stream/config/nvd3_stackedarea_stream.xml M config/plugins/visualizations/phylocanvas/config/phylocanvas.xml M config/plugins/visualizations/pv/config/pv.xml M lib/galaxy/visualization/plugins/plugin.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Remove unused static url, fix routes in plugins Commit: e99c8ec65c652f51253155abe73a9b0ce77c2496 https://github.com/galaxyproject/galaxy/commit/e99c8ec65c652f51253155abe73a… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-30 (Fri, 30 Mar 2018) Changed paths: M lib/galaxy/visualization/plugins/plugin.py Log Message: ----------- Remove static path mixin Commit: d288b3baa83018cb9a6a96677ca8fd287d746816 https://github.com/galaxyproject/galaxy/commit/d288b3baa83018cb9a6a96677ca8… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-30 (Fri, 30 Mar 2018) Changed paths: M test/unit/visualizations/plugins/test_VisualizationPlugin.py M test/unit/visualizations/plugins/test_VisualizationsRegistry.py Log Message: ----------- Adjust test cases Commit: f2e5a69629df4dca65e35cf7a431a33874ef51c5 https://github.com/galaxyproject/galaxy/commit/f2e5a69629df4dca65e35cf7a431… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-30 (Fri, 30 Mar 2018) Changed paths: M config/plugins/visualizations/unipept/templates/unipept.mako M config/plugins/visualizations/venn/config/venn.xml Log Message: ----------- Fix unipept and venn viewers Commit: 075abee7666599a9b8dcf74d38ee5d337c7a85eb https://github.com/galaxyproject/galaxy/commit/075abee7666599a9b8dcf74d38ee… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-04-06 (Fri, 06 Apr 2018) Changed paths: M .gitignore M client/galaxy/scripts/mvc/ui/ui-thumbnails.js M client/gulpfile.js M config/plugins/visualizations/common/templates/chart_entry_point.mako M config/plugins/visualizations/csg/templates/csg.mako M config/plugins/visualizations/cytoscape/config/cytoscape.xml M config/plugins/visualizations/drawrna/config/drawrna.xml M config/plugins/visualizations/example/config/example.xml M config/plugins/visualizations/graphviz/templates/graphviz.mako M config/plugins/visualizations/heatmap/heatmap_cluster/config/heatmap_cluster.xml M config/plugins/visualizations/heatmap/heatmap_default/config/heatmap_default.xml M config/plugins/visualizations/jqplot/jqplot_bar/config/jqplot_bar.xml M config/plugins/visualizations/jqplot/jqplot_box/config/jqplot_box.xml M config/plugins/visualizations/jqplot/jqplot_histogram/config/jqplot_histogram.xml M config/plugins/visualizations/jqplot/jqplot_line/config/jqplot_line.xml M config/plugins/visualizations/jqplot/jqplot_scatter/config/jqplot_scatter.xml M config/plugins/visualizations/msa/config/msa.xml M config/plugins/visualizations/ngl/config/ngl.xml M config/plugins/visualizations/nvd3/nvd3_bar/config/nvd3_bar.xml M config/plugins/visualizations/nvd3/nvd3_bar_stacked/config/nvd3_bar_stacked.xml M config/plugins/visualizations/nvd3/nvd3_histogram/config/nvd3_histogram.xml M config/plugins/visualizations/nvd3/nvd3_histogram_discrete/config/nvd3_histogram_discrete.xml M config/plugins/visualizations/nvd3/nvd3_horizontal/config/nvd3_horizontal.xml M config/plugins/visualizations/nvd3/nvd3_horizontal_stacked/config/nvd3_horizontal_stacked.xml M config/plugins/visualizations/nvd3/nvd3_line/config/nvd3_line.xml M config/plugins/visualizations/nvd3/nvd3_line_focus/config/nvd3_line_focus.xml M config/plugins/visualizations/nvd3/nvd3_pie/config/nvd3_pie.xml M config/plugins/visualizations/nvd3/nvd3_scatter/config/nvd3_scatter.xml M config/plugins/visualizations/nvd3/nvd3_stackedarea/config/nvd3_stackedarea.xml M config/plugins/visualizations/nvd3/nvd3_stackedarea_full/config/nvd3_stackedarea_full.xml M config/plugins/visualizations/nvd3/nvd3_stackedarea_stream/config/nvd3_stackedarea_stream.xml M config/plugins/visualizations/phylocanvas/config/phylocanvas.xml M config/plugins/visualizations/pv/config/pv.xml M config/plugins/visualizations/scatterplot/templates/scatterplot.mako M config/plugins/visualizations/unipept/templates/unipept.mako M config/plugins/visualizations/venn/config/venn.xml M lib/galaxy/visualization/plugins/plugin.py M lib/galaxy/webapps/galaxy/buildapp.py M test/unit/visualizations/plugins/test_VisualizationPlugin.py M test/unit/visualizations/plugins/test_VisualizationsRegistry.py Log Message: ----------- Merge pull request #5810 from guerler/viz-staging-finalize Plugin directory staging Compare: https://github.com/galaxyproject/galaxy/compare/a23f0d505761...075abee76665

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[galaxyproject/galaxy] 10ea15: Fix missing `from Import Directory` button
by GitHub 06 Apr '18

06 Apr '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 10ea15079262a41a9e3c895850b111837549c97e https://github.com/galaxyproject/galaxy/commit/10ea15079262a41a9e3c895850b1… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-03-28 (Wed, 28 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- Fix missing `from Import Directory` button when `library_import_dir` is set in `config/galaxy.yml`, but `allow_path_paste` is `false`. Reported by @pvanheus. Commit: 1d0c734fcfcfaf54e676c395acdeeab72b16d517 https://github.com/galaxyproject/galaxy/commit/1d0c734fcfcfaf54e676c395acde… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-03-28 (Wed, 28 Mar 2018) Changed paths: M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/scripts/bundled/extended.bundled.js M static/scripts/bundled/extended.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- Make client-production-maps Commit: 68b87a07635f2ca073286fd0efc7d7ad2e6bcda9 https://github.com/galaxyproject/galaxy/commit/68b87a07635f2ca073286fd0efc7… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-04-06 (Fri, 06 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/scripts/bundled/extended.bundled.js M static/scripts/bundled/extended.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- Merge pull request #5797 from nsoranzo/release_18.01_fix_import_directory [18.01] Fix missing `from Import Directory` button Commit: a23f0d505761ba713da9484af18e7c10fc6dbed2 https://github.com/galaxyproject/galaxy/commit/a23f0d505761ba713da9484af18e… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-04-06 (Fri, 06 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- Merge branch 'release_18.01' into dev Compare: https://github.com/galaxyproject/galaxy/compare/58028e1f6dbf...a23f0d505761

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[galaxyproject/galaxy] 10ea15: Fix missing `from Import Directory` button
by GitHub 06 Apr '18

06 Apr '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: 10ea15079262a41a9e3c895850b111837549c97e https://github.com/galaxyproject/galaxy/commit/10ea15079262a41a9e3c895850b1… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-03-28 (Wed, 28 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- Fix missing `from Import Directory` button when `library_import_dir` is set in `config/galaxy.yml`, but `allow_path_paste` is `false`. Reported by @pvanheus. Commit: 1d0c734fcfcfaf54e676c395acdeeab72b16d517 https://github.com/galaxyproject/galaxy/commit/1d0c734fcfcfaf54e676c395acde… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-03-28 (Wed, 28 Mar 2018) Changed paths: M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/scripts/bundled/extended.bundled.js M static/scripts/bundled/extended.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- Make client-production-maps Commit: 68b87a07635f2ca073286fd0efc7d7ad2e6bcda9 https://github.com/galaxyproject/galaxy/commit/68b87a07635f2ca073286fd0efc7… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-04-06 (Fri, 06 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/scripts/bundled/extended.bundled.js M static/scripts/bundled/extended.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- Merge pull request #5797 from nsoranzo/release_18.01_fix_import_directory [18.01] Fix missing `from Import Directory` button Compare: https://github.com/galaxyproject/galaxy/compare/009921387dc3...68b87a07635f

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[galaxyproject/usegalaxy-playbook] 7c10aa: Installed snpEff wrapper versions 4.3+T.galaxy1
by GitHub 05 Apr '18

05 Apr '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 7c10aa4f55692b71b0cc1130ad34da1bd2b0492f https://github.com/galaxyproject/usegalaxy-playbook/commit/7c10aa4f55692b71… Author: Dave B <dave(a)bx.psu.edu> Date: 2018-04-05 (Thu, 05 Apr 2018) Changed paths: M env/main/files/galaxy/var/integrated_tool_panel.xml M env/main/files/galaxy/var/shed_tool_conf.xml M env/main/files/galaxy/var/shed_tool_data_table_conf.xml Log Message: ----------- Installed snpEff wrapper versions 4.3+T.galaxy1

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[galaxyproject/galaxy] deda75: Do not append '/' to 'js' in GIE static path, this...
by GitHub 05 Apr '18

05 Apr '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: deda753de9f6943251cf06bd02b37dae78bac59e https://github.com/galaxyproject/galaxy/commit/deda753de9f6943251cf06bd02b3… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-05 (Thu, 05 Apr 2018) Changed paths: M config/plugins/interactive_environments/common/templates/ie.mako Log Message: ----------- Do not append '/' to 'js' in GIE static path, this breaks uWSGI static routing. Commit: 58028e1f6dbf0275f08846dc653e94d607079c86 https://github.com/galaxyproject/galaxy/commit/58028e1f6dbf0275f08846dc653e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-04-05 (Thu, 05 Apr 2018) Changed paths: M config/plugins/interactive_environments/common/templates/ie.mako Log Message: ----------- Merge pull request #5859 from natefoo/gie-slashfix Do not append '/' to 'js' in GIE static path, this breaks uWSGI static routing Compare: https://github.com/galaxyproject/galaxy/compare/1da06ba2b34a...58028e1f6dbf

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