[galaxy-commits] [galaxyproject/galaxy] de763b: Initial commit to get working BBI reader into Trac...

GitHub noreply at github.com
Thu Sep 15 13:03:10 EDT 2016


  Branch: refs/heads/dev
  Home:   https://github.com/galaxyproject/galaxy
  Commit: de763bedee23494035752c11abc5a62e26364e47
      https://github.com/galaxyproject/galaxy/commit/de763bedee23494035752c11abc5a62e26364e47
  Author: jgoecks <jgoecks at gwu.edu>
  Date:   2016-08-12 (Fri, 12 Aug 2016)

  Changed paths:
    A client/galaxy/scripts/libs/bbi/bigwig.js
    A client/galaxy/scripts/libs/bbi/jquery-ajax-native.js
    A client/galaxy/scripts/libs/bbi/jszlib.js
    A client/galaxy/scripts/libs/bbi/spans.js
    A client/galaxy/scripts/viz/bbi-data-manager.js
    M client/galaxy/scripts/viz/trackster/tracks.js
    A static/maps/libs/bbi/bigwig.js.map
    A static/maps/libs/bbi/jquery-ajax-native.js.map
    A static/maps/libs/bbi/jszlib.js.map
    A static/maps/libs/bbi/spans.js.map
    A static/maps/viz/bbi-data-manager.js.map
    M static/maps/viz/trackster/tracks.js.map
    A static/scripts/libs/bbi/bigwig.js
    A static/scripts/libs/bbi/jquery-ajax-native.js
    A static/scripts/libs/bbi/jszlib.js
    A static/scripts/libs/bbi/spans.js
    A static/scripts/viz/bbi-data-manager.js
    M static/scripts/viz/trackster/tracks.js

  Log Message:
  -----------
  Initial commit to get working BBI reader into Trackster.


  Commit: cdc82ef2f8d3f7c6c1f5e274fc5896f8e6e7aa48
      https://github.com/galaxyproject/galaxy/commit/cdc82ef2f8d3f7c6c1f5e274fc5896f8e6e7aa48
  Author: jgoecks <jgoecks at gwu.edu>
  Date:   2016-08-19 (Fri, 19 Aug 2016)

  Changed paths:
    M .ci/flake8_lint_include_list.txt
    M client/galaxy/style/less/library.less
    M config/datatypes_conf.xml.sample
    M config/galaxy.ini.sample
    M lib/galaxy/app.py
    M lib/galaxy/config.py
    M lib/galaxy/datatypes/data.py
    M lib/galaxy/datatypes/interval.py
    M lib/galaxy/datatypes/triples.py
    M lib/galaxy/jobs/__init__.py
    M lib/galaxy/jobs/actions/post.py
    M lib/galaxy/jobs/runners/slurm.py
    M lib/galaxy/model/__init__.py
    M lib/galaxy/model/migrate/check.py
    M lib/galaxy/queues.py
    M lib/galaxy/tools/actions/__init__.py
    M lib/galaxy/tools/deps/conda_util.py
    M lib/galaxy/tools/deps/containers.py
    M lib/galaxy/tools/deps/resolvers/conda.py
    M lib/galaxy/tools/parameters/output_collect.py
    M lib/galaxy/tools/parser/xml.py
    M lib/galaxy/tools/toolbox/base.py
    M lib/galaxy/tools/toolbox/watcher.py
    A lib/galaxy/util/postfork.py
    M lib/galaxy/util/template.py
    M lib/galaxy/web/framework/middleware/sentry.py
    M lib/galaxy/web/proxy/__init__.py
    M lib/galaxy/web/proxy/js/lib/main.js
    M lib/galaxy/web/proxy/js/lib/proxy.js
    M lib/galaxy/web/proxy/js/package.json
    M lib/galaxy/webapps/galaxy/api/history_contents.py
    M lib/galaxy/webapps/galaxy/buildapp.py
    M lib/galaxy/webapps/reports/buildapp.py
    M lib/galaxy/webapps/tool_shed/api/repositories.py
    M lib/galaxy/webapps/tool_shed/app.py
    M lib/galaxy/webapps/tool_shed/buildapp.py
    M lib/galaxy/webapps/tool_shed/controllers/hg.py
    M lib/galaxy/webapps/tool_shed/controllers/repository.py
    M lib/galaxy/workflow/modules.py
    M lib/galaxy_ext/metadata/set_metadata.py
    M lib/tool_shed/galaxy_install/update_repository_manager.py
    M static/scripts/bundled/analysis.bundled.js
    M static/scripts/bundled/analysis.bundled.js.map
    M static/scripts/bundled/libs.bundled.js
    M static/scripts/bundled/libs.bundled.js.map
    M static/style/blue/base.css
    M static/style/blue/library.css
    M templates/webapps/galaxy/workflow/run.mako
    M test/base/interactor.py
    A test/functional/tools/dbkey_output_action.xml
    M test/functional/tools/samples_tool_conf.xml
    A test/functional/tools/tool_provided_metadata_1.xml
    A test/functional/tools/tool_provided_metadata_2.xml
    A test/functional/tools/tool_provided_metadata_3.xml

  Log Message:
  -----------
  Merge branch 'dev' into bbi-js3


  Commit: d99cbd79b61005b90ec5871fd90cec113d0ed21e
      https://github.com/galaxyproject/galaxy/commit/d99cbd79b61005b90ec5871fd90cec113d0ed21e
  Author: jgoecks <jgoecks at gwu.edu>
  Date:   2016-08-23 (Tue, 23 Aug 2016)

  Changed paths:
    M config/galaxy.ini.sample
    M config/reports.ini.sample
    M config/tool_shed.ini.sample
    M lib/galaxy/auth/providers/ldap_ad.py
    M lib/galaxy/security/validate_user_input.py
    M lib/galaxy/tools/deps/__init__.py
    M lib/galaxy/util/postfork.py
    M lib/galaxy/webapps/tool_shed/config.py

  Log Message:
  -----------
  Merge branch 'dev' into bbi-js3


  Commit: 41d0ee4f4392d188ec9ededa35391ef592213608
      https://github.com/galaxyproject/galaxy/commit/41d0ee4f4392d188ec9ededa35391ef592213608
  Author: jgoecks <jgoecks at gwu.edu>
  Date:   2016-08-23 (Tue, 23 Aug 2016)

  Changed paths:
    M client/galaxy/scripts/libs/bbi/bigwig.js
    M client/galaxy/scripts/viz/bbi-data-manager.js
    M client/galaxy/scripts/viz/trackster/painters.js
    M client/galaxy/scripts/viz/trackster/tracks.js
    M static/maps/libs/bbi/bigwig.js.map
    M static/maps/viz/bbi-data-manager.js.map
    M static/maps/viz/trackster/painters.js.map
    M static/maps/viz/trackster/tracks.js.map
    M static/scripts/libs/bbi/bigwig.js
    M static/scripts/viz/bbi-data-manager.js
    M static/scripts/viz/trackster/painters.js
    M static/scripts/viz/trackster/tracks.js

  Log Message:
  -----------
  Bring data provided by data manager in line with Trackster's bigwig datatype. Also allow LinePainter to draw regions of variable length.


  Commit: 74be6955b3c73feb5db6fc2ee0c66179672f8a6f
      https://github.com/galaxyproject/galaxy/commit/74be6955b3c73feb5db6fc2ee0c66179672f8a6f
  Author: jgoecks <jgoecks at gwu.edu>
  Date:   2016-08-24 (Wed, 24 Aug 2016)

  Changed paths:
    M client/galaxy/scripts/viz/trackster/tracks.js
    M static/maps/viz/trackster/tracks.js.map
    M static/scripts/viz/trackster/tracks.js

  Log Message:
  -----------
  Detect whether server has byte-range support and set LineTrack data manager appropriately.


  Commit: 7b44cc5470728b59a2b47c64aedd27774706dd8b
      https://github.com/galaxyproject/galaxy/commit/7b44cc5470728b59a2b47c64aedd27774706dd8b
  Author: jgoecks <jgoecks at gwu.edu>
  Date:   2016-08-31 (Wed, 31 Aug 2016)

  Changed paths:
    M .ci/flake8_lint_include_list.txt
    M Makefile
    M client/galaxy/scripts/mvc/dataset/data.js
    M client/galaxy/scripts/mvc/form/form-data.js
    M client/galaxy/scripts/mvc/form/form-view.js
    M client/galaxy/scripts/mvc/ui/ui-color-picker.js
    M client/galaxy/scripts/mvc/ui/ui-tabs.js
    M client/galaxy/scripts/utils/utils.js
    M config/galaxy.ini.sample
    M config/plugins/visualizations/charts/static/app.css
    M config/plugins/visualizations/charts/static/app.js
    R config/plugins/visualizations/charts/static/charts/forms/default.js
    M config/plugins/visualizations/charts/static/charts/jqplot/bar/config.js
    M config/plugins/visualizations/charts/static/charts/jqplot/bar/wrapper.js
    M config/plugins/visualizations/charts/static/charts/jqplot/boxplot/config.js
    M config/plugins/visualizations/charts/static/charts/jqplot/boxplot/wrapper.js
    M config/plugins/visualizations/charts/static/charts/jqplot/common/config.js
    M config/plugins/visualizations/charts/static/charts/jqplot/common/plot-config.js
    M config/plugins/visualizations/charts/static/charts/jqplot/common/wrapper.js
    M config/plugins/visualizations/charts/static/charts/jqplot/histogram_discrete/config.js
    M config/plugins/visualizations/charts/static/charts/jqplot/histogram_discrete/wrapper.js
    M config/plugins/visualizations/charts/static/charts/jqplot/line/config.js
    M config/plugins/visualizations/charts/static/charts/jqplot/line/wrapper.js
    M config/plugins/visualizations/charts/static/charts/jqplot/scatter/config.js
    M config/plugins/visualizations/charts/static/charts/jqplot/scatter/wrapper.js
    M config/plugins/visualizations/charts/static/charts/nvd3/bar/config.js
    M config/plugins/visualizations/charts/static/charts/nvd3/bar/wrapper.js
    M config/plugins/visualizations/charts/static/charts/nvd3/bar_horizontal/config.js
    M config/plugins/visualizations/charts/static/charts/nvd3/bar_horizontal/wrapper.js
    M config/plugins/visualizations/charts/static/charts/nvd3/bar_horizontal_stacked/config.js
    M config/plugins/visualizations/charts/static/charts/nvd3/bar_horizontal_stacked/wrapper.js
    M config/plugins/visualizations/charts/static/charts/nvd3/bar_stacked/config.js
    M config/plugins/visualizations/charts/static/charts/nvd3/bar_stacked/wrapper.js
    M config/plugins/visualizations/charts/static/charts/nvd3/common/config.js
    M config/plugins/visualizations/charts/static/charts/nvd3/common/wrapper.js
    M config/plugins/visualizations/charts/static/charts/nvd3/histogram/config.js
    M config/plugins/visualizations/charts/static/charts/nvd3/histogram/wrapper.js
    M config/plugins/visualizations/charts/static/charts/nvd3/histogram_discrete/config.js
    M config/plugins/visualizations/charts/static/charts/nvd3/histogram_discrete/wrapper.js
    M config/plugins/visualizations/charts/static/charts/nvd3/line/config.js
    M config/plugins/visualizations/charts/static/charts/nvd3/line/wrapper.js
    M config/plugins/visualizations/charts/static/charts/nvd3/line_focus/config.js
    M config/plugins/visualizations/charts/static/charts/nvd3/line_focus/wrapper.js
    M config/plugins/visualizations/charts/static/charts/nvd3/pie/config.js
    M config/plugins/visualizations/charts/static/charts/nvd3/pie/wrapper.js
    M config/plugins/visualizations/charts/static/charts/nvd3/scatter/config.js
    M config/plugins/visualizations/charts/static/charts/nvd3/scatter/wrapper.js
    M config/plugins/visualizations/charts/static/charts/nvd3/stackedarea/config.js
    M config/plugins/visualizations/charts/static/charts/nvd3/stackedarea/wrapper.js
    M config/plugins/visualizations/charts/static/charts/nvd3/stackedarea_full/config.js
    M config/plugins/visualizations/charts/static/charts/nvd3/stackedarea_full/wrapper.js
    M config/plugins/visualizations/charts/static/charts/nvd3/stackedarea_stream/config.js
    M config/plugins/visualizations/charts/static/charts/nvd3/stackedarea_stream/wrapper.js
    A config/plugins/visualizations/charts/static/charts/others/example/config.js
    A config/plugins/visualizations/charts/static/charts/others/example/logo.png
    A config/plugins/visualizations/charts/static/charts/others/example/wrapper.js
    M config/plugins/visualizations/charts/static/charts/others/heatmap/config.js
    M config/plugins/visualizations/charts/static/charts/others/heatmap/heatmap-parameters.js
    M config/plugins/visualizations/charts/static/charts/others/heatmap/heatmap-plugin.js
    M config/plugins/visualizations/charts/static/charts/others/heatmap/wrapper.js
    M config/plugins/visualizations/charts/static/charts/others/heatmap_cluster/config.js
    M config/plugins/visualizations/charts/static/charts/others/heatmap_cluster/wrapper.js
    A config/plugins/visualizations/charts/static/charts/overview.js
    R config/plugins/visualizations/charts/static/charts/tools.js
    M config/plugins/visualizations/charts/static/charts/types.js
    A config/plugins/visualizations/charts/static/charts/utilities/tabular-datasets.js
    A config/plugins/visualizations/charts/static/charts/utilities/tabular-form.js
    A config/plugins/visualizations/charts/static/charts/utilities/tabular-inputs.js
    A config/plugins/visualizations/charts/static/charts/utilities/tabular-utilities.js
    A config/plugins/visualizations/charts/static/components/jobs.js
    A config/plugins/visualizations/charts/static/components/model.js
    A config/plugins/visualizations/charts/static/components/screenshot.js
    A config/plugins/visualizations/charts/static/components/storage.js
    R config/plugins/visualizations/charts/static/library/datasets.js
    R config/plugins/visualizations/charts/static/library/jobs.js
    R config/plugins/visualizations/charts/static/library/screenshot.js
    R config/plugins/visualizations/charts/static/library/storage.js
    R config/plugins/visualizations/charts/static/models/chart.js
    R config/plugins/visualizations/charts/static/models/config.js
    A config/plugins/visualizations/charts/static/views/description.js
    M config/plugins/visualizations/charts/static/views/editor.js
    M config/plugins/visualizations/charts/static/views/groups.js
    M config/plugins/visualizations/charts/static/views/settings.js
    M config/plugins/visualizations/charts/static/views/types.js
    M config/plugins/visualizations/charts/static/views/viewer.js
    M config/plugins/visualizations/charts/static/views/viewport.js
    M config/plugins/visualizations/charts/templates/charts.mako
    A doc/source/admin/chat-0.png
    A doc/source/admin/chat-1.png
    A doc/source/admin/chat-2.png
    A doc/source/admin/chat-3.png
    A doc/source/admin/chat-4.png
    A doc/source/admin/chat.rst
    A doc/source/admin/communication_server.png
    A doc/source/admin/communication_server_rooms.png
    A doc/source/admin/conda_faq.rst
    M doc/source/admin/index.rst
    A doc/source/releases/16.07.rst
    M doc/source/releases/16.07_announce.rst
    A doc/source/releases/16.10_announce.rst
    M lib/galaxy/config.py
    M lib/galaxy/jobs/__init__.py
    M lib/galaxy/tools/deps/conda_util.py
    M lib/galaxy/tools/deps/resolvers/conda.py
    M lib/galaxy/tools/toolbox/base.py
    M lib/galaxy/tools/toolbox/watcher.py
    M lib/galaxy/web/framework/base.py
    A lib/galaxy/web/framework/middleware/batch.py
    M lib/galaxy/web/framework/webapp.py
    M lib/galaxy/webapps/galaxy/api/jobs.py
    M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py
    M lib/galaxy/webapps/galaxy/buildapp.py
    M lib/galaxy/webapps/galaxy/controllers/admin.py
    M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
    M lib/galaxy/webapps/galaxy/controllers/history.py
    M lib/galaxy/webapps/galaxy/controllers/visualization.py
    M scripts/bootstrap_history.py
    M static/maps/mvc/dataset/data.js.map
    M static/maps/mvc/form/form-data.js.map
    M static/maps/mvc/form/form-view.js.map
    M static/maps/mvc/ui/ui-color-picker.js.map
    M static/maps/mvc/ui/ui-tabs.js.map
    M static/maps/utils/utils.js.map
    M static/scripts/bundled/analysis.bundled.js
    M static/scripts/bundled/analysis.bundled.js.map
    M static/scripts/bundled/libs.bundled.js
    M static/scripts/bundled/libs.bundled.js.map
    M static/scripts/mvc/dataset/data.js
    M static/scripts/mvc/form/form-data.js
    M static/scripts/mvc/form/form-view.js
    M static/scripts/mvc/ui/ui-tabs.js
    M static/scripts/utils/utils.js
    R templates/admin/tool_shed_repository/browse_categories.mako
    A templates/admin/tool_shed_repository/browse_toolsheds.mako
    R templates/admin/tool_shed_repository/preview_repository.mako
    M templates/webapps/galaxy/workflow/display.mako
    M templates/webapps/tool_shed/index.mako
    A test/api/test_api_batch.py
    A test/casperjs/api-batch-tests.js

  Log Message:
  -----------
  Merge branch 'dev' into bbi-js3


  Commit: 5518c20a20e6fc38ac1edfbbdaa2a8a4f1737c95
      https://github.com/galaxyproject/galaxy/commit/5518c20a20e6fc38ac1edfbbdaa2a8a4f1737c95
  Author: jgoecks <jgoecks at gwu.edu>
  Date:   2016-08-31 (Wed, 31 Aug 2016)

  Changed paths:
    M client/galaxy/scripts/viz/bbi-data-manager.js
    M client/galaxy/scripts/viz/trackster/painters.js
    M client/galaxy/scripts/viz/trackster/tracks.js
    M static/maps/viz/bbi-data-manager.js.map
    M static/maps/viz/trackster/painters.js.map
    M static/maps/viz/trackster/tracks.js.map
    M static/scripts/viz/bbi-data-manager.js
    M static/scripts/viz/trackster/painters.js
    M static/scripts/viz/trackster/tracks.js

  Log Message:
  -----------
  Cleanup: (a) remove debugging statements; (b) use Galaxy app; and (c) fix offset issue for LinePainter using floor instead of ceil.


  Commit: f553d387a47d0ef1a58a1522c0f437e3b1783a59
      https://github.com/galaxyproject/galaxy/commit/f553d387a47d0ef1a58a1522c0f437e3b1783a59
  Author: John Chilton <jmchilton at gmail.com>
  Date:   2016-09-15 (Thu, 15 Sep 2016)

  Changed paths:
    A client/galaxy/scripts/libs/bbi/bigwig.js
    A client/galaxy/scripts/libs/bbi/jquery-ajax-native.js
    A client/galaxy/scripts/libs/bbi/jszlib.js
    A client/galaxy/scripts/libs/bbi/spans.js
    A client/galaxy/scripts/viz/bbi-data-manager.js
    M client/galaxy/scripts/viz/trackster/painters.js
    M client/galaxy/scripts/viz/trackster/tracks.js
    A static/maps/libs/bbi/bigwig.js.map
    A static/maps/libs/bbi/jquery-ajax-native.js.map
    A static/maps/libs/bbi/jszlib.js.map
    A static/maps/libs/bbi/spans.js.map
    A static/maps/viz/bbi-data-manager.js.map
    M static/maps/viz/trackster/painters.js.map
    M static/maps/viz/trackster/tracks.js.map
    A static/scripts/libs/bbi/bigwig.js
    A static/scripts/libs/bbi/jquery-ajax-native.js
    A static/scripts/libs/bbi/jszlib.js
    A static/scripts/libs/bbi/spans.js
    A static/scripts/viz/bbi-data-manager.js
    M static/scripts/viz/trackster/painters.js
    M static/scripts/viz/trackster/tracks.js

  Log Message:
  -----------
  Merge pull request #2880 from jgoecks/bbi-js3

Trackster: Read numerical data directly from bigwig files


Compare: https://github.com/galaxyproject/galaxy/compare/921933ea9cb1...f553d387a47d


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