Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 8261a2398a7981e77be056bae0e3c15f3a097a85
https://github.com/galaxyproject/galaxy/commit/8261a2398a7981e77be056bae0e3…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2018-04-04 (Wed, 04 Apr 2018)
Changed paths:
M create_db.sh
M doc/source/admin/framework_dependencies.rst
M extract_dataset_parts.sh
M manage_db.sh
M run_tests.sh
M scripts/common_startup.sh
M scripts/common_startup_functions.sh
Log Message:
-----------
Make the startup scripts play just as nicely with Conda as they do with
virtualenv.
Commit: a88e19064a38415d867f4c118dd6938d8e368632
https://github.com/galaxyproject/galaxy/commit/a88e19064a38415d867f4c118dd6…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2018-04-04 (Wed, 04 Apr 2018)
Changed paths:
M config/galaxy.yml.sample
M scripts/get_uwsgi_args.py
Log Message:
-----------
Don't set uWSGI's virtualenv option when running from Conda
Commit: b3eff87a1ba0ec0f07c69045f2b279cab8476a7b
https://github.com/galaxyproject/galaxy/commit/b3eff87a1ba0ec0f07c69045f2b2…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2018-04-04 (Wed, 04 Apr 2018)
Changed paths:
M lib/galaxy/dependencies/conda-file.sh
M scripts/common_startup.sh
M scripts/common_startup_functions.sh
Log Message:
-----------
Clean up and useability enhancements
Commit: c5262e8971679bd431cb0238391f0ec7d5ba087e
https://github.com/galaxyproject/galaxy/commit/c5262e8971679bd431cb0238391f…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2018-04-04 (Wed, 04 Apr 2018)
Changed paths:
M scripts/common_startup.sh
Log Message:
-----------
Look for both `base` and `root` conda envs
Commit: 2829a1f1646b2ba85faf986b56799daccafb1060
https://github.com/galaxyproject/galaxy/commit/2829a1f1646b2ba85faf986b5679…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-04-18 (Wed, 18 Apr 2018)
Changed paths:
M config/galaxy.yml.sample
M create_db.sh
M doc/source/admin/framework_dependencies.rst
M extract_dataset_parts.sh
M lib/galaxy/dependencies/conda-file.sh
M manage_db.sh
M run_tests.sh
M scripts/common_startup.sh
M scripts/common_startup_functions.sh
M scripts/get_uwsgi_args.py
Log Message:
-----------
Merge pull request #5854 from natefoo/run-scripts-conda
Improve startup interoperability with Conda
Compare: https://github.com/galaxyproject/galaxy/compare/65d4aff437d0...2829a1f1646b
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 8833d1a8a49d7b6d4a9c849b0335d3260564b351
https://github.com/galaxyproject/galaxy/commit/8833d1a8a49d7b6d4a9c849b0335…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2018-03-13 (Tue, 13 Mar 2018)
Changed paths:
M doc/source/releases/18.01_announce.rst
Log Message:
-----------
add security announcement to the rn
Commit: e89290c33031d89365aa3ef3b6e4720d68390119
https://github.com/galaxyproject/galaxy/commit/e89290c33031d89365aa3ef3b6e4…
Author: Mehmet Tekman <m.tekman(a)ucl.ac.uk>
Date: 2018-03-18 (Sun, 18 Mar 2018)
Changed paths:
M config/datatypes_conf.xml.sample
M lib/galaxy/datatypes/binary.py
A lib/galaxy/datatypes/test/test.rds
A lib/galaxy/datatypes/test/test.sce
A lib/galaxy/datatypes/test/test_error.rds
Log Message:
-----------
sniffers, test cases
Commit: b0effc107af2bba7c0dfefbd7c5861a1597c9099
https://github.com/galaxyproject/galaxy/commit/b0effc107af2bba7c0dfefbd7c58…
Author: Mehmet Tekman <m.tekman(a)ucl.ac.uk>
Date: 2018-03-19 (Mon, 19 Mar 2018)
Changed paths:
M lib/galaxy/datatypes/binary.py
Log Message:
-----------
fix to class test
Commit: ea993a8912b870de7780c68c003c5433badb469d
https://github.com/galaxyproject/galaxy/commit/ea993a8912b870de7780c68c003c…
Author: Mehmet Tekman <m.tekman(a)ucl.ac.uk>
Date: 2018-03-19 (Mon, 19 Mar 2018)
Changed paths:
M lib/galaxy/dependencies/pipfiles/develop/pinned-requirements.txt
Log Message:
-----------
rpy2 library for loading/testing R objects
Commit: 1d2a0117199bc902896ca97cf5e5aa5b9b20b132
https://github.com/galaxyproject/galaxy/commit/1d2a0117199bc902896ca97cf5e5…
Author: Mehmet Tekman <m.tekman(a)ucl.ac.uk>
Date: 2018-03-19 (Mon, 19 Mar 2018)
Changed paths:
M lib/galaxy/datatypes/binary.py
Log Message:
-----------
linting fix
Commit: a280211ca65ca88b3a7cd92d0d3c1d15b874d462
https://github.com/galaxyproject/galaxy/commit/a280211ca65ca88b3a7cd92d0d3c…
Author: Mehmet Tekman <m.tekman(a)ucl.ac.uk>
Date: 2018-04-13 (Fri, 13 Apr 2018)
Log Message:
-----------
Merge branch 'master' of github.com:galaxyproject/galaxy into singlecellobject
Commit: d31c05a67d40daa12fc3a2dbcdea35d1971d0e3d
https://github.com/galaxyproject/galaxy/commit/d31c05a67d40daa12fc3a2dbcdea…
Author: Mehmet Tekman <m.tekman(a)ucl.ac.uk>
Date: 2018-04-13 (Fri, 13 Apr 2018)
Changed paths:
M config/datatypes_conf.xml.sample
M lib/galaxy/datatypes/binary.py
M lib/galaxy/dependencies/pipfiles/develop/pinned-requirements.txt
Log Message:
-----------
removed sniffers, removed pinned, removed classes
Commit: 695ed3ac68d9f690f649b7e57c1bdf4625cc20fe
https://github.com/galaxyproject/galaxy/commit/695ed3ac68d9f690f649b7e57c1b…
Author: Mehmet Tekman <m.tekman(a)ucl.ac.uk>
Date: 2018-04-13 (Fri, 13 Apr 2018)
Changed paths:
R lib/galaxy/datatypes/test/test.rds
R lib/galaxy/datatypes/test/test.sce
R lib/galaxy/datatypes/test/test_error.rds
Log Message:
-----------
removed test data
Commit: d5cb6f636b19128ce64934fbae91a82e21d4c668
https://github.com/galaxyproject/galaxy/commit/d5cb6f636b19128ce64934fbae91…
Author: Mehmet Tekman <m.tekman(a)ucl.ac.uk>
Date: 2018-04-14 (Sat, 14 Apr 2018)
Changed paths:
M config/datatypes_conf.xml.sample
Log Message:
-----------
renamed type
Commit: 8baea1f7c7551920bc2318b34247a29462a4e035
https://github.com/galaxyproject/galaxy/commit/8baea1f7c7551920bc2318b34247…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-04-18 (Wed, 18 Apr 2018)
Changed paths:
M .ci/flake8_blacklist.txt
M .gitignore
M CONTRIBUTING.md
M Makefile
M README.rst
M client/.babelrc
M client/GruntFile.js
M client/README.md
M client/bower.json
A client/galaxy/docs/bootstrap.md
A client/galaxy/docs/galaxy-styles.md
M client/galaxy/scripts/apps/analysis.js
M client/galaxy/scripts/apps/panels/admin-panel.js
M client/galaxy/scripts/components/Citations.vue
M client/galaxy/scripts/components/HistoryImport.vue
M client/galaxy/scripts/components/HistoryView.vue
A client/galaxy/scripts/components/PluginList.vue
A client/galaxy/scripts/components/RuleCollectionBuilder.vue
M client/galaxy/scripts/components/admin/DataTablesGrid.vue
A client/galaxy/scripts/layout/communication-server-view.js
R client/galaxy/scripts/layout/generic-nav-view.js
M client/galaxy/scripts/layout/masthead.js
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/legacy/grid/grid-view.js
R client/galaxy/scripts/libs/bootstrap-tour.js
R client/galaxy/scripts/libs/bootstrap.js
A client/galaxy/scripts/mocha/test.js
A client/galaxy/scripts/mocha/tests/rules_dsl_spec.yml
A client/galaxy/scripts/mocha/tests/rules_tests.js
M client/galaxy/scripts/mvc/collection/collection-model.js
M client/galaxy/scripts/mvc/collection/collection-view.js
M client/galaxy/scripts/mvc/collection/list-collection-creator.js
M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js
M client/galaxy/scripts/mvc/collection/pair-collection-creator.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-li.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-model.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-item-li.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/job-states-model.js
M client/galaxy/scripts/mvc/history/multi-panel.js
M client/galaxy/scripts/mvc/library/library-dataset-view.js
M client/galaxy/scripts/mvc/library/library-folder-view.js
M client/galaxy/scripts/mvc/library/library-folderlist-view.js
M client/galaxy/scripts/mvc/library/library-folderrow-view.js
M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js
M client/galaxy/scripts/mvc/library/library-library-view.js
M client/galaxy/scripts/mvc/library/library-librarylist-view.js
M client/galaxy/scripts/mvc/library/library-libraryrow-view.js
M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js
M client/galaxy/scripts/mvc/list/list-view.js
A client/galaxy/scripts/mvc/rules/rule-definitions.js
M client/galaxy/scripts/mvc/tag.js
M client/galaxy/scripts/mvc/tool/tool-form-composite.js
M client/galaxy/scripts/mvc/tool/tools.js
M client/galaxy/scripts/mvc/tours.js
M client/galaxy/scripts/mvc/ui/error-modal.js
M client/galaxy/scripts/mvc/ui/ui-buttons.js
M client/galaxy/scripts/mvc/ui/ui-frames.js
M client/galaxy/scripts/mvc/ui/ui-misc.js
M client/galaxy/scripts/mvc/ui/ui-options.js
M client/galaxy/scripts/mvc/ui/ui-popover.js
M client/galaxy/scripts/mvc/ui/ui-portlet.js
M client/galaxy/scripts/mvc/ui/ui-select-content.js
M client/galaxy/scripts/mvc/ui/ui-select-default.js
M client/galaxy/scripts/mvc/ui/ui-slider.js
M client/galaxy/scripts/mvc/ui/ui-tabs.js
M client/galaxy/scripts/mvc/ui/ui-thumbnails.js
A client/galaxy/scripts/mvc/upload/collection/rules-input-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-ftp.js
A client/galaxy/scripts/mvc/upload/upload-utils.js
M client/galaxy/scripts/mvc/upload/upload-view.js
M client/galaxy/scripts/mvc/user/user-custom-builds.js
M client/galaxy/scripts/mvc/user/user-preferences.js
M client/galaxy/scripts/mvc/visualization/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/mvc/workflow/workflow-connector.js
M client/galaxy/scripts/mvc/workflow/workflow-manager.js
M client/galaxy/scripts/mvc/workflow/workflow-view-node.js
M client/galaxy/scripts/mvc/workflow/workflow-view-terminals.js
M client/galaxy/scripts/mvc/workflow/workflow-view.js
M client/galaxy/scripts/mvc/workflow/workflow.js
M client/galaxy/scripts/qunit/test-app.js
M client/galaxy/scripts/qunit/tests/form_tests.js
M client/galaxy/scripts/qunit/tests/masthead_tests.js
M client/galaxy/scripts/qunit/tests/ui_tests.js
M client/galaxy/scripts/toolshed/groups/group-detail-view.js
M client/galaxy/scripts/toolshed/groups/group-list-view.js
M client/galaxy/scripts/ui/filter-control.js
M client/galaxy/scripts/ui/pagination.js
M client/galaxy/scripts/ui/peek-column-selector.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/tracks.js
R client/galaxy/style/less/autocomplete_tagging.less
R client/galaxy/style/less/base.less
R client/galaxy/style/less/bootstrap.less
R client/galaxy/style/less/bootstrap/alerts.less
R client/galaxy/style/less/bootstrap/badges.less
R client/galaxy/style/less/bootstrap/bootstrap.less
R client/galaxy/style/less/bootstrap/breadcrumbs.less
R client/galaxy/style/less/bootstrap/button-groups.less
R client/galaxy/style/less/bootstrap/buttons.less
R client/galaxy/style/less/bootstrap/carousel.less
R client/galaxy/style/less/bootstrap/close.less
R client/galaxy/style/less/bootstrap/code.less
R client/galaxy/style/less/bootstrap/component-animations.less
R client/galaxy/style/less/bootstrap/dropdowns.less
R client/galaxy/style/less/bootstrap/forms.less
R client/galaxy/style/less/bootstrap/glyphicons.less
R client/galaxy/style/less/bootstrap/grid.less
R client/galaxy/style/less/bootstrap/input-groups.less
R client/galaxy/style/less/bootstrap/jumbotron.less
R client/galaxy/style/less/bootstrap/labels.less
R client/galaxy/style/less/bootstrap/list-group.less
R client/galaxy/style/less/bootstrap/media.less
R client/galaxy/style/less/bootstrap/mixins.less
R client/galaxy/style/less/bootstrap/modals.less
R client/galaxy/style/less/bootstrap/navbar.less
R client/galaxy/style/less/bootstrap/navs.less
R client/galaxy/style/less/bootstrap/normalize.less
R client/galaxy/style/less/bootstrap/pager.less
R client/galaxy/style/less/bootstrap/pagination.less
R client/galaxy/style/less/bootstrap/panels.less
R client/galaxy/style/less/bootstrap/popovers.less
R client/galaxy/style/less/bootstrap/print.less
R client/galaxy/style/less/bootstrap/progress-bars.less
R client/galaxy/style/less/bootstrap/responsive-utilities.less
R client/galaxy/style/less/bootstrap/scaffolding.less
R client/galaxy/style/less/bootstrap/tables.less
R client/galaxy/style/less/bootstrap/theme.less
R client/galaxy/style/less/bootstrap/thumbnails.less
R client/galaxy/style/less/bootstrap/tooltip.less
R client/galaxy/style/less/bootstrap/type.less
R client/galaxy/style/less/bootstrap/utilities.less
R client/galaxy/style/less/bootstrap/variables.less
R client/galaxy/style/less/bootstrap/wells.less
R client/galaxy/style/less/charts.less
R client/galaxy/style/less/circster.less
R client/galaxy/style/less/collection.less
R client/galaxy/style/less/dataset.less
R client/galaxy/style/less/embed_item.less
R client/galaxy/style/less/flex.less
R client/galaxy/style/less/fontawesome/bordered-pulled.less
R client/galaxy/style/less/fontawesome/core.less
R client/galaxy/style/less/fontawesome/fixed-width.less
R client/galaxy/style/less/fontawesome/font-awesome.less
R client/galaxy/style/less/fontawesome/icons.less
R client/galaxy/style/less/fontawesome/larger.less
R client/galaxy/style/less/fontawesome/list.less
R client/galaxy/style/less/fontawesome/mixins.less
R client/galaxy/style/less/fontawesome/path.less
R client/galaxy/style/less/fontawesome/rotated-flipped.less
R client/galaxy/style/less/fontawesome/spinning.less
R client/galaxy/style/less/fontawesome/stacked.less
R client/galaxy/style/less/fontawesome/variables.less
R client/galaxy/style/less/frame.less
R client/galaxy/style/less/galaxy_bootstrap.less
R client/galaxy/style/less/galaxy_bootstrap/overrides.less
R client/galaxy/style/less/galaxy_bootstrap/variables.less
R client/galaxy/style/less/galaxy_variables.less
R client/galaxy/style/less/history.less
R client/galaxy/style/less/iconic_stroke.less
R client/galaxy/style/less/job.less
R client/galaxy/style/less/jstree.less
R client/galaxy/style/less/library.less
R client/galaxy/style/less/list-item.less
R client/galaxy/style/less/reports.less
R client/galaxy/style/less/select2.less
R client/galaxy/style/less/theme/blue.less
R client/galaxy/style/less/theme/plain.less
R client/galaxy/style/less/toastr.less
R client/galaxy/style/less/tour.less
R client/galaxy/style/less/trackster.less
R client/galaxy/style/less/ui.less
R client/galaxy/style/less/ui/dataset-choice.less
R client/galaxy/style/less/ui/error-modal.less
R client/galaxy/style/less/ui/icon-btn.less
R client/galaxy/style/less/ui/pagination.less
R client/galaxy/style/less/ui/paired-collection-creator.less
R client/galaxy/style/less/ui/peek-column-selector.less
R client/galaxy/style/less/ui/search-input.less
R client/galaxy/style/less/upload.less
A client/galaxy/style/scss/autocomplete_tagging.scss
A client/galaxy/style/scss/base.scss
A client/galaxy/style/scss/charts.scss
A client/galaxy/style/scss/circster.scss
A client/galaxy/style/scss/collection.scss
A client/galaxy/style/scss/dataset.scss
A client/galaxy/style/scss/embed_item.scss
A client/galaxy/style/scss/flex.scss
A client/galaxy/style/scss/frame.scss
A client/galaxy/style/scss/galaxy_bootstrap/overrides.scss
A client/galaxy/style/scss/galaxy_bootstrap/variables.scss
A client/galaxy/style/scss/galaxy_variables.scss
A client/galaxy/style/scss/history.scss
A client/galaxy/style/scss/iconic_stroke.scss
A client/galaxy/style/scss/job.scss
A client/galaxy/style/scss/jstree.scss
A client/galaxy/style/scss/library.scss
A client/galaxy/style/scss/list-item.scss
A client/galaxy/style/scss/reports.scss
A client/galaxy/style/scss/select2.scss
A client/galaxy/style/scss/theme/blue.scss
A client/galaxy/style/scss/theme/plain.scss
A client/galaxy/style/scss/toastr.scss
A client/galaxy/style/scss/tour.scss
A client/galaxy/style/scss/trackster.scss
A client/galaxy/style/scss/ui.scss
A client/galaxy/style/scss/ui/dataset-choice.scss
A client/galaxy/style/scss/ui/error-modal.scss
A client/galaxy/style/scss/ui/icon-btn.scss
A client/galaxy/style/scss/ui/pagination.scss
A client/galaxy/style/scss/ui/paired-collection-creator.scss
A client/galaxy/style/scss/ui/peek-column-selector.scss
A client/galaxy/style/scss/ui/search-input.scss
A client/galaxy/style/scss/upload.scss
R client/grunt-tasks/style.js
M client/gulpfile.js
M client/karma.config.js
M client/package.json
A client/styleguide.config.js
M client/webpack.config.js
M client/yarn.lock
M config/containers_conf.yml.sample
M config/datatypes_conf.xml.sample
M config/galaxy.yml.sample
M config/job_conf.xml.sample_advanced
A config/oidc_backends_config.xml.sample
A config/oidc_config.xml.sample
M config/plugins/interactive_environments/common/templates/ie.mako
M config/plugins/tours/core.scratchbook.yaml
M config/plugins/visualizations/common/templates/chart_entry_point.mako
M config/plugins/visualizations/csg/config/csg.xml
A config/plugins/visualizations/csg/static/logo.png
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/config/graphviz.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/heatmap/heatmap_default/config/heatmap_shared.xml
A config/plugins/visualizations/hivtrace/config/hivtrace.xml
A config/plugins/visualizations/hivtrace/static/448c34a56d699c29117adc64c43affeb.woff2
A config/plugins/visualizations/hivtrace/static/674f50d287a8c48dc19ba404d20fe713.eot
A config/plugins/visualizations/hivtrace/static/89889688147bd7575d6327160d64e760.svg
A config/plugins/visualizations/hivtrace/static/912ec66d7572ff821749319396470bde.svg
A config/plugins/visualizations/hivtrace/static/af7ae505a9eed503f8b8e6982036873e.woff2
A config/plugins/visualizations/hivtrace/static/b06871f281fee6b241d60582ae9369b9.ttf
A config/plugins/visualizations/hivtrace/static/e18bbf611f2a2e43afc071aa2f4e1512.ttf
A config/plugins/visualizations/hivtrace/static/f4769f9bdb7466be65088239c12046d1.eot
A config/plugins/visualizations/hivtrace/static/fa2772327f55d8198301fdb8bcfc8158.woff
A config/plugins/visualizations/hivtrace/static/fee66e712a8a08eef5805a46892932ad.woff
A config/plugins/visualizations/hivtrace/static/hivtrace.css
A config/plugins/visualizations/hivtrace/static/hivtrace.css.map
A config/plugins/visualizations/hivtrace/static/hivtrace.js
A config/plugins/visualizations/hivtrace/static/hivtrace.js.map
A config/plugins/visualizations/hivtrace/static/logo.png
A config/plugins/visualizations/hivtrace/static/vendor.js
A config/plugins/visualizations/hivtrace/static/vendor.js.map
A config/plugins/visualizations/hivtrace/templates/index.mako
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/msa/static/script.js
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/src/nvd3.js
M config/plugins/visualizations/nvd3/nvd3_bar/static/nvd3.js
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/phyloviz/config/phyloviz.xml
A config/plugins/visualizations/phyloviz/static/logo.png
M config/plugins/visualizations/pv/config/pv.xml
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/unipept/templates/unipept.mako
M config/plugins/visualizations/venn/config/venn.xml
M config/plugins/visualizations/venn/src/script.js
M config/plugins/visualizations/venn/static/script.js
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/authentication.md
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/releases/18.01_announce.rst
M lib/galaxy/app.py
M lib/galaxy/auth/providers/ldap_ad.py
A lib/galaxy/authnz/__init__.py
A lib/galaxy/authnz/managers.py
A lib/galaxy/authnz/psa_authnz.py
M lib/galaxy/config.py
M lib/galaxy/containers/__init__.py
M lib/galaxy/containers/docker.py
M lib/galaxy/containers/docker_model.py
M lib/galaxy/containers/docker_swarm.py
R lib/galaxy/containers/docker_swarm_manager.py
M lib/galaxy/datatypes/annotation.py
M lib/galaxy/datatypes/assembly.py
M lib/galaxy/datatypes/binary.py
M lib/galaxy/datatypes/blast.py
M lib/galaxy/datatypes/constructive_solid_geometry.py
M lib/galaxy/datatypes/converters/bed_gff_or_vcf_to_bigwig_converter.xml
A lib/galaxy/datatypes/converters/genbankgz_to_genbank.xml
M lib/galaxy/datatypes/converters/interval_to_fli.py
M lib/galaxy/datatypes/data.py
M lib/galaxy/datatypes/genetics.py
M lib/galaxy/datatypes/interval.py
M lib/galaxy/datatypes/molecules.py
M lib/galaxy/datatypes/mothur.py
M lib/galaxy/datatypes/msa.py
M lib/galaxy/datatypes/ngsindex.py
M lib/galaxy/datatypes/phylip.py
M lib/galaxy/datatypes/plant_tribes.py
M lib/galaxy/datatypes/proteomics.py
M lib/galaxy/datatypes/qualityscore.py
M lib/galaxy/datatypes/registry.py
M lib/galaxy/datatypes/sequence.py
M lib/galaxy/datatypes/sniff.py
M lib/galaxy/datatypes/tabular.py
A lib/galaxy/datatypes/test/1.afg
A lib/galaxy/datatypes/test/1.arff
A lib/galaxy/datatypes/test/1.genbank
A lib/galaxy/datatypes/test/1.genbank.gz
A lib/galaxy/datatypes/test/1.hdt
A lib/galaxy/datatypes/test/1.obo
A lib/galaxy/datatypes/test/1.owl
A lib/galaxy/datatypes/test/1.phyloxml
A lib/galaxy/datatypes/test/1.stockholm
A lib/galaxy/datatypes/test/1.ttl
A lib/galaxy/datatypes/test/1.xmfa
A lib/galaxy/datatypes/test/2.tabular
A lib/galaxy/datatypes/test/2.txt
A lib/galaxy/datatypes/test/3.txt
A lib/galaxy/datatypes/test/Acanium.hmm
M lib/galaxy/datatypes/text.py
M lib/galaxy/datatypes/triples.py
M lib/galaxy/datatypes/util/gff_util.py
M lib/galaxy/datatypes/xml.py
M lib/galaxy/dependencies/__init__.py
M lib/galaxy/dependencies/conditional-requirements.txt
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
M lib/galaxy/dependencies/requirements.txt
M lib/galaxy/jobs/__init__.py
M lib/galaxy/jobs/dynamic_tool_destination.py
M lib/galaxy/jobs/mapper.py
M lib/galaxy/jobs/runners/kubernetes.py
M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh
M lib/galaxy/jobs/runners/util/job_script/MEMORY_STATEMENT.sh
M lib/galaxy/managers/configuration.py
M lib/galaxy/managers/workflows.py
M lib/galaxy/model/__init__.py
M lib/galaxy/model/mapping.py
A lib/galaxy/model/migrate/versions/0141_add_oidc_tables.py
M lib/galaxy/model/orm/engine_factory.py
M lib/galaxy/model/orm/scripts.py
M lib/galaxy/objectstore/__init__.py
M lib/galaxy/security/__init__.py
M lib/galaxy/security/passwords.py
M lib/galaxy/security/validate_user_input.py
M lib/galaxy/tools/actions/model_operations.py
M lib/galaxy/tools/actions/upload_common.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/error_reports/plugins/sentry.py
M lib/galaxy/tools/execute.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/repositories.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
M lib/galaxy/util/hash_util.py
M lib/galaxy/util/json.py
M lib/galaxy/util/script.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/web/base/controller.py
M lib/galaxy/web/framework/helpers/grids.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
M lib/galaxy/webapps/galaxy/api/jobs.py
A lib/galaxy/webapps/galaxy/api/plugins.py
M lib/galaxy/webapps/galaxy/api/remote_files.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/admin.py
A lib/galaxy/webapps/galaxy/controllers/authnz.py
M lib/galaxy/webapps/galaxy/controllers/history.py
M lib/galaxy/webapps/galaxy/controllers/interactive_environments.py
M lib/galaxy/webapps/galaxy/controllers/user.py
M lib/galaxy/workflow/modules.py
A lib/galaxy/workflow/resources/__init__.py
A lib/galaxy/workflow/resources/example.py.sample
M lib/galaxy/workflow/run_request.py
M lib/galaxy_ext/metadata/set_metadata.py
M lib/tool_shed/util/hg_util.py
M lib/tool_shed/util/shed_util_common.py
M lib/tool_shed/util/tool_util.py
A scripts/apply_tags.py
M scripts/bootstrap_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
A scripts/docker_swarm_manager.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 static/images/fonts/FontAwesome.otf
M static/images/fonts/fontawesome-webfont.eot
A static/images/fonts/fontawesome-webfont.svg
M static/images/fonts/fontawesome-webfont.ttf
M static/images/fonts/fontawesome-webfont.woff
A static/images/fonts/fontawesome-webfont.woff2
M static/style/blue/autocomplete_tagging.css
M static/style/blue/base.css
M static/style/blue/circster.css
M static/style/blue/embed_item.css
M static/style/blue/library.css
M static/style/blue/reports.css
M static/style/blue/trackster.css
M static/welcome.html.sample
R templates/admin/view_data_tables_registry.mako
M templates/admin/view_datatypes_registry.mako
M templates/base/base_panels.mako
M templates/sharing_base.mako
M templates/user/login.mako
M templates/webapps/galaxy/admin/view_display_applications.mako
M templates/webapps/galaxy/data_manager/index.mako
M templates/webapps/galaxy/dataset/copy_view.mako
M templates/webapps/galaxy/galaxy.panels.mako
M templates/webapps/galaxy/workflow/editor.mako
M templates/webapps/reports/index.mako
M templates/webapps/tool_shed/repository/manage_repository.mako
M templates/webapps/tool_shed/repository/view_repository.mako
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/api/test_libraries.py
M test/api/test_tools.py
M test/api/test_workflows.py
A test/base/data/rules_dsl_spec.yml
M test/base/populators.py
A test/base/workflow_fixtures.py
M test/base/workflows_format_2/main.py
M test/docker/base/Dockerfile
M test/functional/tools/sample_datatypes_conf.xml
M test/galaxy_selenium/components.py
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/integration/test_upload_configuration_options.py
R test/selenium_tests/_workflow_fixtures.py
M test/selenium_tests/framework.py
A test/selenium_tests/test_admin_app.py
M test/selenium_tests/test_collection_builders.py
M test/selenium_tests/test_library_landing.py
M test/selenium_tests/test_library_to_collections.py
M test/selenium_tests/test_registration.py
M test/selenium_tests/test_saved_histories.py
M test/selenium_tests/test_uploads.py
M test/selenium_tests/test_workflow_editor.py
M test/selenium_tests/test_workflow_management.py
M test/selenium_tests/test_workflow_run.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/unittest_utils/galaxy_mock.py
M test/unit/visualizations/plugins/test_VisualizationPlugin.py
M test/unit/visualizations/plugins/test_VisualizationsRegistry.py
M test/unit/workflows/test_modules.py
M tools/data_source/upload.py
M tools/data_source/upload.xml
M tox.ini
Log Message:
-----------
Merge remote-tracking branch 'jmchilton/dev' into singlecellobject
Commit: 1c433d7d041d50d6e4c5bd886a606ff3af588d9f
https://github.com/galaxyproject/galaxy/commit/1c433d7d041d50d6e4c5bd886a60…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-04-18 (Wed, 18 Apr 2018)
Changed paths:
M config/datatypes_conf.xml.sample
Log Message:
-----------
Merge pull request #5716 from mtekman/singlecellobject
Add datatype(s): RDS object and SingleCellExperiment class
Compare: https://github.com/galaxyproject/galaxy/compare/fe4bff1fb9d8...1c433d7d041d