Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 050a3f26bbd4c1372f55bdaf2d774f48bdb1b490
https://github.com/galaxyproject/galaxy/commit/050a3f26bbd4c1372f55bdaf2d77…
Author: Scott Szakonyi <sszakony(a)nd.edu>
Date: 2016-08-17 (Wed, 17 Aug 2016)
Changed paths:
M client/galaxy/scripts/layout/menu.js
M client/galaxy/scripts/layout/scratchbook.js
M static/maps/layout/menu.js.map
M static/maps/layout/scratchbook.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/layout/menu.js
M static/scripts/layout/scratchbook.js
Log Message:
-----------
Addressing issue 2747
Commit: 7eacecab0e40fb592393b57fdebed4c789ba088b
https://github.com/galaxyproject/galaxy/commit/7eacecab0e40fb592393b57fdebe…
Author: Scott Szakonyi <sszakony(a)nd.edu>
Date: 2016-08-19 (Fri, 19 Aug 2016)
Changed paths:
M config/galaxy.ini.sample
M lib/galaxy/config.py
M lib/galaxy/datatypes/data.py
M lib/galaxy/jobs/runners/slurm.py
M lib/galaxy/model/__init__.py
M lib/galaxy/model/migrate/check.py
M lib/galaxy/tools/actions/__init__.py
M lib/galaxy/util/template.py
M lib/galaxy/webapps/galaxy/api/history_contents.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/repository.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
A test/functional/tools/dbkey_output_action.xml
M test/functional/tools/samples_tool_conf.xml
Log Message:
-----------
Merge remote branch 'upstream/dev' into dev
Commit: b83b93451c88e87e489a672996bdea9ab4aa2369
https://github.com/galaxyproject/galaxy/commit/b83b93451c88e87e489a672996bd…
Author: Scott Szakonyi <sszakony(a)nd.edu>
Date: 2016-08-22 (Mon, 22 Aug 2016)
Changed paths:
M config/galaxy.ini.sample
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
Log Message:
-----------
Merge remote branch 'upstream/dev' into dev
Commit: 7a496d404afd38a7f85ae55eda799d655ff90241
https://github.com/galaxyproject/galaxy/commit/7a496d404afd38a7f85ae55eda79…
Author: Scott Szakonyi <sszakony(a)nd.edu>
Date: 2016-08-22 (Mon, 22 Aug 2016)
Changed paths:
R database/info.txt
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
Log Message:
-----------
Updating to lastest upstream commit
Commit: c09bd5688a8adb309df33049fd3c8cee0e6b80ac
https://github.com/galaxyproject/galaxy/commit/c09bd5688a8adb309df33049fd3c…
Author: Scott Szakonyi <sszakony(a)nd.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
M config/reports.ini.sample
M config/tool_shed.ini.sample
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/auth/providers/ldap_ad.py
M lib/galaxy/config.py
M lib/galaxy/jobs/__init__.py
M lib/galaxy/security/validate_user_input.py
M lib/galaxy/tools/deps/__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/util/postfork.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 lib/galaxy/webapps/tool_shed/config.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 remote branch 'upstream/dev' into dev
Commit: 0d160900ace430f370330a3343e3c3ed79c78450
https://github.com/galaxyproject/galaxy/commit/0d160900ace430f370330a3343e3…
Author: Aysam Guerler <aysam.guerler(a)gmail.com>
Date: 2016-08-31 (Wed, 31 Aug 2016)
Changed paths:
M client/galaxy/scripts/layout/menu.js
M client/galaxy/scripts/layout/scratchbook.js
R database/info.txt
M static/maps/layout/menu.js.map
M static/maps/layout/scratchbook.js.map
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/layout/menu.js
M static/scripts/layout/scratchbook.js
Log Message:
-----------
Merge pull request #2808 from sszakony/dev
Addressing issue 2747, login appearing in scratchbook window
Compare: https://github.com/galaxyproject/galaxy/compare/5ebdefe40f1d...0d160900ace4
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 633f958e1b6f2179264cdad06d9cda8cc13d0e93
https://github.com/galaxyproject/galaxy/commit/633f958e1b6f2179264cdad06d9c…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-08-25 (Thu, 25 Aug 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/admin.py
Log Message:
-----------
Open tool executions in a different tab from admin/tool_lineage, instead of loading galaxy(whole) within the tab
Commit: ed76484af2ba5d86a9cfee82118f74dde70f21ae
https://github.com/galaxyproject/galaxy/commit/ed76484af2ba5d86a9cfee82118f…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-08-26 (Fri, 26 Aug 2016)
Changed paths:
M lib/galaxy/tools/toolbox/base.py
M lib/galaxy/webapps/galaxy/controllers/admin.py
Log Message:
-----------
Fix toolbox's get_tool 'exact' matching. Previously it'd return a tool
even when exact was specified, though no exact match was made (so,
exact=False behavior, always)
Commit: d14b43abf2694ce3ef6933a9bede181ff1d7f79d
https://github.com/galaxyproject/galaxy/commit/d14b43abf2694ce3ef6933a9bede…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-08-26 (Fri, 26 Aug 2016)
Changed paths:
M lib/galaxy/tools/toolbox/base.py
Log Message:
-----------
Probably still want to match identical tool guids against multiple sheds?
Commit: 5ebdefe40f1d816339c21f553cbe67365a9d7285
https://github.com/galaxyproject/galaxy/commit/5ebdefe40f1d816339c21f553cbe…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-08-30 (Tue, 30 Aug 2016)
Changed paths:
M lib/galaxy/tools/toolbox/base.py
M lib/galaxy/webapps/galaxy/controllers/admin.py
Log Message:
-----------
Merge pull request #2862 from dannon/fix_lineage_onclick
Open tool executions in a different tab from admin/tool_lineage, inst…
Compare: https://github.com/galaxyproject/galaxy/compare/54e589ebad00...5ebdefe40f1d
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: e4e30fda24316033c28cad01b0f639d826afbd97
https://github.com/galaxyproject/galaxy/commit/e4e30fda24316033c28cad01b0f6…
Author: Dave Bouvier <dave(a)bx.psu.edu>
Date: 2016-08-02 (Tue, 02 Aug 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
A templates/admin/tool_shed_repository/browse_toolsheds.mako
M templates/admin/tool_shed_repository/preview_repository.mako
Log Message:
-----------
Add tabs, unify installation UI.
Commit: 10af8ce2b299d8f732cd1eeff538b3a24f55355d
https://github.com/galaxyproject/galaxy/commit/10af8ce2b299d8f732cd1eeff538…
Author: Dave Bouvier <dave(a)bx.psu.edu>
Date: 2016-08-04 (Thu, 04 Aug 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py
M lib/galaxy/webapps/galaxy/buildapp.py
M templates/admin/tool_shed_repository/browse_toolsheds.mako
Log Message:
-----------
Finished repository details.
Commit: 1c093a9771b196b3e6faaa76f1ca803d7f5b3089
https://github.com/galaxyproject/galaxy/commit/1c093a9771b196b3e6faaa76f1ca…
Author: Dave Bouvier <dave(a)bx.psu.edu>
Date: 2016-08-04 (Thu, 04 Aug 2016)
Changed paths:
M .ci/flake8_blacklist.txt
A .ci/flake8_lint_include_list.txt
A .ci/flake8_wrapper_imports.sh
M .ci/py3_sources.txt
M .gitignore
M .travis.yml
M Makefile
M client/bower.json
M client/galaxy/scripts/apps/analysis.js
M client/galaxy/scripts/apps/history-panel.js
A client/galaxy/scripts/layout/generic-nav-view.js
M client/galaxy/scripts/layout/menu.js
M client/galaxy/scripts/layout/page.js
M client/galaxy/scripts/layout/panel.js
A client/galaxy/scripts/libs/jquery.complexify.js
M client/galaxy/scripts/libs/jquery/jquery.js
M client/galaxy/scripts/libs/raven.js
M client/galaxy/scripts/mvc/annotation.js
M client/galaxy/scripts/mvc/base-mvc.js
A client/galaxy/scripts/mvc/base/controlled-fetch-collection.js
M client/galaxy/scripts/mvc/collection/collection-li-edit.js
M client/galaxy/scripts/mvc/collection/collection-li.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-li-edit.js
M client/galaxy/scripts/mvc/dataset/dataset-li.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-repeat.js
M client/galaxy/scripts/mvc/form/form-section.js
M client/galaxy/scripts/mvc/form/form-view.js
M client/galaxy/scripts/mvc/history/copy-dialog.js
M client/galaxy/scripts/mvc/history/hda-li-edit.js
M client/galaxy/scripts/mvc/history/hda-li.js
M client/galaxy/scripts/mvc/history/hda-model.js
M client/galaxy/scripts/mvc/history/hdca-li.js
M client/galaxy/scripts/mvc/history/hdca-model.js
M client/galaxy/scripts/mvc/history/history-content-model.js
M client/galaxy/scripts/mvc/history/history-contents.js
M client/galaxy/scripts/mvc/history/history-model.js
A client/galaxy/scripts/mvc/history/history-preferences.js
M client/galaxy/scripts/mvc/history/history-structure-view.js
M client/galaxy/scripts/mvc/history/history-view-annotated.js
M client/galaxy/scripts/mvc/history/history-view-edit-current.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-item.js
M client/galaxy/scripts/mvc/list/list-view.js
M client/galaxy/scripts/mvc/tool/tool-form-base.js
M client/galaxy/scripts/mvc/tool/tool-form-composite.js
M client/galaxy/scripts/mvc/tool/tool-form.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-misc.js
M client/galaxy/scripts/mvc/ui/ui-modal.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-tabs.js
M client/galaxy/scripts/mvc/upload/composite/composite-row.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-button.js
M client/galaxy/scripts/mvc/upload/upload-ftp.js
M client/galaxy/scripts/mvc/upload/upload-model.js
M client/galaxy/scripts/mvc/upload/upload-settings.js
M client/galaxy/scripts/mvc/upload/upload-view.js
M client/galaxy/scripts/ui/search-input.js
M client/galaxy/scripts/utils/ajax-queue.js
M client/galaxy/style/less/base.less
A client/galaxy/style/less/collection.less
R client/galaxy/style/less/collections.less
A client/galaxy/style/less/dataset.less
A client/galaxy/style/less/flex.less
M client/galaxy/style/less/history.less
M client/galaxy/style/less/list-item.less
M client/galaxy/style/less/ui.less
A client/galaxy/style/less/ui/error-modal.less
M client/galaxy/style/less/ui/search-input.less
M client/galaxy/style/less/upload.less
M client/grunt-tasks/install-libs.js
M client/webpack.config.js
M config/datatypes_conf.xml.sample
M config/galaxy.ini.sample
M config/job_conf.xml.sample_advanced
M config/object_store_conf.xml.sample
A config/plugins/interactive_environments/neo/config/allowed_images.yml.sample
A config/plugins/interactive_environments/neo/config/neo.ini.sample
A config/plugins/interactive_environments/neo/config/neo.xml
A config/plugins/interactive_environments/neo/static/js/neo.js
A config/plugins/interactive_environments/neo/templates/neo.mako
M config/plugins/tours/core.galaxy_ui.yaml
M config/plugins/tours/core.history.yaml
M config/plugins/tours/core.scratchbook.yaml
M config/plugins/visualizations/charts/static/app.css
M config/plugins/visualizations/charts/static/app.js
M config/plugins/visualizations/charts/static/charts/forms/default.js
M config/plugins/visualizations/charts/static/charts/jqplot/common/config.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/pie/config.js
M config/plugins/visualizations/charts/static/library/datasets.js
M config/plugins/visualizations/charts/static/library/jobs.js
M config/plugins/visualizations/charts/static/library/storage.js
R config/plugins/visualizations/charts/static/library/ui-table-form.js
M config/plugins/visualizations/charts/static/models/chart.js
M config/plugins/visualizations/charts/static/models/config.js
R config/plugins/visualizations/charts/static/models/group.js
R config/plugins/visualizations/charts/static/models/groups.js
M config/plugins/visualizations/charts/static/plugins/nvd3/nv.d3.css
M config/plugins/visualizations/charts/static/views/editor.js
R config/plugins/visualizations/charts/static/views/group.js
A 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/tool_data_table_conf.xml.sample
A config/tool_destinations.yml.sample
A display_applications/ucsc/trackhub.xml
A doc/source/admin/grt.rst
M doc/source/admin/index.rst
M doc/source/admin/interactive_environments.rst
M doc/source/dev/index.rst
A doc/source/dev/interactive_environments.rst
M doc/source/lib/galaxy.objectstore.rst
M lib/galaxy/config.py
M lib/galaxy/dataset_collections/subcollections.py
M lib/galaxy/datatypes/assembly.py
M lib/galaxy/datatypes/binary.py
M lib/galaxy/datatypes/constructive_solid_geometry.py
M lib/galaxy/datatypes/data.py
M lib/galaxy/datatypes/dataproviders/base.py
M lib/galaxy/datatypes/images.py
M lib/galaxy/datatypes/msa.py
A lib/galaxy/datatypes/neo4j.py
M lib/galaxy/datatypes/ngsindex.py
M lib/galaxy/datatypes/proteomics.py
M lib/galaxy/datatypes/set_metadata_tool.xml
M lib/galaxy/datatypes/tabular.py
M lib/galaxy/datatypes/tracks.py
M lib/galaxy/dependencies/__init__.py
M lib/galaxy/dependencies/conditional-requirements.txt
M lib/galaxy/dependencies/pinned-requirements.txt
A lib/galaxy/jobs/dynamic_tool_destination.py
M lib/galaxy/jobs/mapper.py
M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh
M lib/galaxy/managers/annotatable.py
M lib/galaxy/managers/base.py
M lib/galaxy/managers/configuration.py
M lib/galaxy/managers/datasets.py
M lib/galaxy/managers/hdas.py
M lib/galaxy/managers/hdcas.py
M lib/galaxy/managers/histories.py
M lib/galaxy/managers/history_contents.py
M lib/galaxy/managers/users.py
M lib/galaxy/model/__init__.py
M lib/galaxy/model/mapping.py
M lib/galaxy/objectstore/__init__.py
A lib/galaxy/objectstore/azure_blob.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/deps/__init__.py
M lib/galaxy/tools/deps/conda_util.py
M lib/galaxy/tools/deps/resolvers/__init__.py
M lib/galaxy/tools/deps/resolvers/brewed_tool_shed_packages.py
M lib/galaxy/tools/deps/resolvers/conda.py
M lib/galaxy/tools/deps/resolvers/galaxy_packages.py
M lib/galaxy/tools/deps/resolvers/homebrew.py
M lib/galaxy/tools/deps/resolvers/modules.py
M lib/galaxy/tools/deps/resolvers/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/deps/views.py
M lib/galaxy/tools/execute.py
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/tools/parameters/dynamic_options.py
A lib/galaxy/tools/toolbox/requirements.py
M lib/galaxy/tools/wrappers.py
M lib/galaxy/util/__init__.py
M lib/galaxy/version.py
M lib/galaxy/web/__init__.py
M lib/galaxy/web/base/controller.py
M lib/galaxy/web/buildapp.py
M lib/galaxy/web/framework/base.py
M lib/galaxy/web/framework/helpers/__init__.py
M lib/galaxy/web/framework/middleware/remoteuser.py
M lib/galaxy/web/framework/webapp.py
M lib/galaxy/webapps/galaxy/api/history_contents.py
M lib/galaxy/webapps/galaxy/api/tool_dependencies.py
M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py
M lib/galaxy/webapps/galaxy/api/tools.py
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
M lib/galaxy/webapps/galaxy/controllers/dataset.py
M lib/galaxy/webapps/galaxy/controllers/forms.py
M lib/galaxy/webapps/galaxy/controllers/history.py
M lib/galaxy/webapps/galaxy/controllers/library_common.py
M lib/galaxy/webapps/galaxy/controllers/root.py
M lib/galaxy/webapps/galaxy/controllers/user.py
M lib/galaxy/webapps/galaxy/controllers/workflow.py
A lib/galaxy/webapps/reports/controllers/history.py
A lib/galaxy/webapps/reports/controllers/tools.py
M lib/galaxy/webapps/reports/controllers/users.py
M lib/galaxy/webapps/tool_shed/config.py
M lib/galaxy/workflow/extract.py
M lib/galaxy/workflow/modules.py
M lib/galaxy/workflow/render.py
M lib/tool_shed/galaxy_install/install_manager.py
M lib/tool_shed/galaxy_install/repair_repository_manager.py
M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py
M lib/tool_shed/util/shed_util_common.py
M run_tests.sh
M scripts/bootstrap_history.py
A scripts/communication/communication_server.py
A scripts/communication/template/communication.css
A scripts/communication/template/communication.html
A scripts/communication/template/communication.js
A scripts/grt.py
A scripts/grt.yml.sample
M scripts/nosetests.py
M setup.cfg
A static/maps/layout/generic-nav-view.js.map
M static/maps/layout/menu.js.map
M static/maps/layout/page.js.map
M static/maps/layout/panel.js.map
A static/maps/libs/jquery.complexify.js.map
M static/maps/libs/jquery/jquery.js.map
M static/maps/libs/raven.js.map
M static/maps/mvc/annotation.js.map
M static/maps/mvc/base-mvc.js.map
A static/maps/mvc/base/controlled-fetch-collection.js.map
M static/maps/mvc/collection/collection-li-edit.js.map
M static/maps/mvc/collection/collection-li.js.map
M static/maps/mvc/collection/collection-model.js.map
M static/maps/mvc/collection/collection-view.js.map
M static/maps/mvc/dataset/dataset-li-edit.js.map
M static/maps/mvc/dataset/dataset-li.js.map
M static/maps/mvc/dataset/dataset-model.js.map
M static/maps/mvc/form/form-data.js.map
M static/maps/mvc/form/form-parameters.js.map
M static/maps/mvc/form/form-repeat.js.map
M static/maps/mvc/form/form-section.js.map
M static/maps/mvc/form/form-view.js.map
M static/maps/mvc/history/copy-dialog.js.map
M static/maps/mvc/history/hda-li-edit.js.map
M static/maps/mvc/history/hda-li.js.map
M static/maps/mvc/history/hda-model.js.map
M static/maps/mvc/history/hdca-li.js.map
M static/maps/mvc/history/hdca-model.js.map
M static/maps/mvc/history/history-content-model.js.map
M static/maps/mvc/history/history-contents.js.map
M static/maps/mvc/history/history-model.js.map
A static/maps/mvc/history/history-preferences.js.map
M static/maps/mvc/history/history-structure-view.js.map
M static/maps/mvc/history/history-view-annotated.js.map
M static/maps/mvc/history/history-view-edit-current.js.map
M static/maps/mvc/history/history-view-edit.js.map
M static/maps/mvc/history/history-view.js.map
M static/maps/mvc/history/multi-panel.js.map
M static/maps/mvc/history/options-menu.js.map
M static/maps/mvc/list/list-item.js.map
M static/maps/mvc/list/list-view.js.map
M static/maps/mvc/tool/tool-form-base.js.map
M static/maps/mvc/tool/tool-form-composite.js.map
M static/maps/mvc/tool/tool-form.js.map
M static/maps/mvc/ui/error-modal.js.map
M static/maps/mvc/ui/ui-buttons.js.map
M static/maps/mvc/ui/ui-misc.js.map
M static/maps/mvc/ui/ui-modal.js.map
M static/maps/mvc/ui/ui-select-content.js.map
M static/maps/mvc/ui/ui-select-default.js.map
M static/maps/mvc/ui/ui-tabs.js.map
M static/maps/mvc/upload/composite/composite-row.js.map
M static/maps/mvc/upload/composite/composite-view.js.map
M static/maps/mvc/upload/default/default-row.js.map
M static/maps/mvc/upload/default/default-view.js.map
M static/maps/mvc/upload/upload-button.js.map
M static/maps/mvc/upload/upload-ftp.js.map
M static/maps/mvc/upload/upload-model.js.map
M static/maps/mvc/upload/upload-settings.js.map
M static/maps/mvc/upload/upload-view.js.map
M static/maps/ui/search-input.js.map
M static/maps/utils/ajax-queue.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/bundled/login.bundled.js
M static/scripts/bundled/login.bundled.js.map
A static/scripts/layout/generic-nav-view.js
M static/scripts/layout/menu.js
M static/scripts/layout/page.js
M static/scripts/layout/panel.js
A static/scripts/libs/jquery.complexify.js
M static/scripts/libs/jquery/jquery.js
M static/scripts/libs/raven.js
M static/scripts/mvc/annotation.js
M static/scripts/mvc/base-mvc.js
A static/scripts/mvc/base/controlled-fetch-collection.js
M static/scripts/mvc/collection/collection-model.js
M static/scripts/mvc/collection/collection-view.js
M static/scripts/mvc/dataset/dataset-li-edit.js
M static/scripts/mvc/dataset/dataset-li.js
M static/scripts/mvc/dataset/dataset-model.js
M static/scripts/mvc/form/form-data.js
M static/scripts/mvc/form/form-parameters.js
M static/scripts/mvc/form/form-repeat.js
M static/scripts/mvc/form/form-section.js
M static/scripts/mvc/form/form-view.js
M static/scripts/mvc/history/copy-dialog.js
M static/scripts/mvc/history/hda-model.js
M static/scripts/mvc/history/hdca-model.js
M static/scripts/mvc/history/history-content-model.js
M static/scripts/mvc/history/history-contents.js
M static/scripts/mvc/history/history-model.js
A static/scripts/mvc/history/history-preferences.js
M static/scripts/mvc/history/history-structure-view.js
M static/scripts/mvc/history/history-view-annotated.js
M static/scripts/mvc/history/history-view-edit-current.js
M static/scripts/mvc/history/history-view-edit.js
M static/scripts/mvc/history/history-view.js
M static/scripts/mvc/history/multi-panel.js
M static/scripts/mvc/history/options-menu.js
M static/scripts/mvc/list/list-item.js
M static/scripts/mvc/list/list-view.js
M static/scripts/mvc/tool/tool-form-base.js
M static/scripts/mvc/tool/tool-form-composite.js
M static/scripts/mvc/tool/tool-form.js
M static/scripts/mvc/ui/error-modal.js
M static/scripts/mvc/ui/ui-buttons.js
M static/scripts/mvc/ui/ui-misc.js
M static/scripts/mvc/ui/ui-modal.js
M static/scripts/mvc/ui/ui-select-content.js
M static/scripts/mvc/ui/ui-select-default.js
M static/scripts/mvc/ui/ui-tabs.js
M static/scripts/mvc/upload/composite/composite-row.js
M static/scripts/mvc/upload/composite/composite-view.js
M static/scripts/mvc/upload/default/default-row.js
M static/scripts/mvc/upload/default/default-view.js
M static/scripts/mvc/upload/upload-button.js
M static/scripts/mvc/upload/upload-ftp.js
M static/scripts/mvc/upload/upload-view.js
M static/scripts/ui/search-input.js
M static/scripts/utils/ajax-queue.js
A static/style/base.css
M static/style/blue/base.css
M static/style/blue/bootstrap-tour.css
M static/style/blue/jquery.rating.css
M templates/admin/tool_shed_repository/browse_toolsheds.mako
M templates/admin/tool_shed_repository/common.mako
M templates/admin/tool_shed_repository/manage_repository.mako
M templates/admin/tool_shed_repository/preview_repository.mako
M templates/admin/tool_shed_repository/reselect_tool_panel_section.mako
M templates/admin/tool_shed_repository/select_shed_tool_panel_config.mako
M templates/admin/tool_shed_repository/select_tool_panel_section.mako
M templates/base.mako
M templates/base/base_panels.mako
M templates/js-app.mako
M templates/user/change_password.mako
A templates/user/communication_settings.mako
M templates/user/index.mako
M templates/user/register.mako
M templates/webapps/galaxy/history/display.mako
M templates/webapps/galaxy/history/embed.mako
M templates/webapps/galaxy/history/grid.mako
M templates/webapps/galaxy/history/view.mako
M templates/webapps/galaxy/history/view_multiple.mako
M templates/webapps/galaxy/workflow/run.mako
A templates/webapps/reports/history_and_dataset_per_user.mako
A templates/webapps/reports/history_and_dataset_type.mako
A templates/webapps/reports/history_per_user.mako
M templates/webapps/reports/index.mako
A templates/webapps/reports/tool_error_messages.mako
A templates/webapps/reports/tool_execution_time.mako
A templates/webapps/reports/tool_execution_time_per_month.mako
A templates/webapps/reports/tools_and_job_state.mako
A templates/webapps/reports/tools_and_job_state_per_month.mako
M templates/webapps/tool_shed/repository/common.mako
M templates/webapps/tool_shed/repository/export_repository.mako
A test-data/neostore.zip
M test/api/test_workflows.py
M test/base/driver_util.py
M test/base/twilltestcase.py
A test/functional/tools/output_filter_exception_1.xml
M test/functional/tools/samples_tool_conf.xml
A test/integration/test_resolvers.py
M test/qunit/tests/history_contents_model_tests.js
M test/qunit/tests/ui_tests.js
M test/qunit/tests/upload_dialog_tests.js
M test/shed_functional/base/twilltestcase.py
M test/shed_functional/functional/test_1010_install_repository_with_tool_dependencies.py
M test/shed_functional/functional/test_1210_uninstall_reinstall_repository_with_tool_dependencies.py
A test/unit/jobs/dynamic_tool_destination/__init__.py
A test/unit/jobs/dynamic_tool_destination/data/dest_fail.yml
A test/unit/jobs/dynamic_tool_destination/data/priority_tool_destination.yml
A test/unit/jobs/dynamic_tool_destination/data/test.empty
A test/unit/jobs/dynamic_tool_destination/data/test.fasta
A test/unit/jobs/dynamic_tool_destination/data/test1.full
A test/unit/jobs/dynamic_tool_destination/data/test3.full
A test/unit/jobs/dynamic_tool_destination/data/test_no_verbose.yml
A test/unit/jobs/dynamic_tool_destination/data/test_num_input_datasets.yml
A test/unit/jobs/dynamic_tool_destination/data/test_users.yml
A test/unit/jobs/dynamic_tool_destination/data/tool_destination.yml
A test/unit/jobs/dynamic_tool_destination/mockGalaxy.py
A test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py
A test/unit/jobs/dynamic_tool_destination/ymltests.py
M test/unit/managers/test_HistoryManager.py
M test/unit/tools/test_conda_resolution.py
M test/unit/tools/test_data_parameters.py
M test/unit/tools/test_tool_deps.py
M tool-data/shared/ucsc/ucsc_build_sites.txt.sample
M tools/stats/gsummary.xml
M tox.ini
Log Message:
-----------
Merge remote-tracking branch 'upstream/dev' into Merge remote-tracking branch 'upstream/dev' into api_install_performance.
Commit: 8e83d3178452cc55ca5938dcf1ed0162764142b7
https://github.com/galaxyproject/galaxy/commit/8e83d3178452cc55ca5938dcf1ed…
Author: Dave Bouvier <dave(a)bx.psu.edu>
Date: 2016-08-04 (Thu, 04 Aug 2016)
Changed paths:
M templates/admin/tool_shed_repository/browse_toolsheds.mako
Log Message:
-----------
Additional minor cleanup.
Commit: c52b046764a95bf237f9af6212565ea6e3c64e15
https://github.com/galaxyproject/galaxy/commit/c52b046764a95bf237f9af621256…
Author: Dave Bouvier <dave(a)bx.psu.edu>
Date: 2016-08-04 (Thu, 04 Aug 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py
M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
R templates/admin/tool_shed_repository/browse_categories.mako
M templates/admin/tool_shed_repository/browse_toolsheds.mako
R templates/admin/tool_shed_repository/preview_repository.mako
Log Message:
-----------
Even more cleanup.
- Removed dangling code.
- Restored Marius' changes.
- Fixed the repository-wide tool panel selection.
Commit: 5425f99ee8471ee59dff84835c5f03744001e1bc
https://github.com/galaxyproject/galaxy/commit/5425f99ee8471ee59dff84835c5f…
Author: Dave Bouvier <dave(a)bx.psu.edu>
Date: 2016-08-05 (Fri, 05 Aug 2016)
Changed paths:
M client/galaxy/style/less/base.less
M config/tool_shed.ini.sample
M lib/galaxy/config.py
M lib/galaxy/datatypes/tracks.py
M lib/galaxy/jobs/runners/__init__.py
M lib/galaxy/jobs/runners/pulsar.py
M lib/galaxy/util/__init__.py
M lib/galaxy/webapps/tool_shed/app.py
M lib/galaxy/webapps/tool_shed/config.py
M static/style/blue/base.css
Log Message:
-----------
Merge branch 'dev' of git://github.com/galaxyproject/galaxy into api_install_performance
Commit: 5ed67c0ab05e82fe1b388711c7291e58d3b7a4a1
https://github.com/galaxyproject/galaxy/commit/5ed67c0ab05e82fe1b388711c729…
Author: Dave Bouvier <dave(a)bx.psu.edu>
Date: 2016-08-08 (Mon, 08 Aug 2016)
Changed paths:
M .ci/flake8_lint_include_list.txt
M .ci/py3_sources.txt
M client/galaxy/scripts/layout/scratchbook.js
M client/galaxy/scripts/mvc/dataset/dataset-li.js
M client/galaxy/scripts/mvc/tool/tool-form.js
M client/galaxy/scripts/mvc/ui/ui-buttons.js
M config/job_conf.xml.sample_advanced
M lib/galaxy/jobs/runners/__init__.py
M lib/galaxy/tools/deps/containers.py
M lib/galaxy/tools/deps/docker_util.py
M lib/tool_shed/capsule/capsule_manager.py
M lib/tool_shed/dependencies/repository/relation_builder.py
M lib/tool_shed/galaxy_install/datatypes/custom_datatype_manager.py
M lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py
M lib/tool_shed/galaxy_install/install_manager.py
M lib/tool_shed/galaxy_install/installed_repository_manager.py
M lib/tool_shed/galaxy_install/migrate/common.py
M lib/tool_shed/galaxy_install/migrate/versions/0001_tools.py
M lib/tool_shed/galaxy_install/migrate/versions/0002_tools.py
M lib/tool_shed/galaxy_install/migrate/versions/0003_tools.py
M lib/tool_shed/galaxy_install/migrate/versions/0004_tools.py
M lib/tool_shed/galaxy_install/migrate/versions/0005_tools.py
M lib/tool_shed/galaxy_install/migrate/versions/0006_tools.py
M lib/tool_shed/galaxy_install/migrate/versions/0007_tools.py
M lib/tool_shed/galaxy_install/migrate/versions/0008_tools.py
M lib/tool_shed/galaxy_install/migrate/versions/0009_tools.py
M lib/tool_shed/galaxy_install/migrate/versions/0010_tools.py
M lib/tool_shed/galaxy_install/migrate/versions/0011_tools.py
M lib/tool_shed/galaxy_install/migrate/versions/0012_tools.py
M lib/tool_shed/galaxy_install/repair_repository_manager.py
M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py
M lib/tool_shed/galaxy_install/tool_dependencies/recipe/install_environment.py
M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py
M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py
M lib/tool_shed/galaxy_install/tool_migration_manager.py
M lib/tool_shed/galaxy_install/tools/data_manager.py
M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py
M lib/tool_shed/galaxy_install/update_repository_manager.py
M lib/tool_shed/grids/admin_grids.py
M lib/tool_shed/grids/repository_grids.py
M lib/tool_shed/grids/repository_review_grids.py
M lib/tool_shed/managers/repositories.py
M lib/tool_shed/metadata/metadata_generator.py
M lib/tool_shed/metadata/repository_metadata_manager.py
M lib/tool_shed/repository_types/registry.py
M lib/tool_shed/tool_shed_registry.py
M lib/tool_shed/tools/data_table_manager.py
M lib/tool_shed/util/hg_util.py
M lib/tool_shed/util/readme_util.py
M lib/tool_shed/util/repository_content_util.py
M lib/tool_shed/util/repository_util.py
M lib/tool_shed/util/shed_util_common.py
M lib/tool_shed/util/tool_util.py
M lib/tool_shed/util/web_util.py
M lib/tool_shed/util/workflow_util.py
M lib/tool_shed/utility_containers/utility_container_manager.py
M scripts/tool_shed/api/common.py
M setup.cfg
M static/maps/layout/scratchbook.js.map
M static/maps/mvc/dataset/dataset-li.js.map
M static/maps/mvc/tool/tool-form.js.map
M static/maps/mvc/ui/ui-buttons.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/layout/scratchbook.js
M static/scripts/mvc/dataset/dataset-li.js
M static/scripts/mvc/tool/tool-form.js
M static/scripts/mvc/ui/ui-buttons.js
R static/style/blue/tool_menu.css
M templates/webapps/galaxy/admin/index.mako
M templates/webapps/galaxy/workflow/editor.mako
M templates/webapps/reports/index.mako
M templates/webapps/tool_shed/admin/index.mako
M templates/webapps/tool_shed/group/index.mako
M templates/webapps/tool_shed/index.mako
Log Message:
-----------
Merge branch 'dev' of git://github.com/galaxyproject/galaxy into api_install_performance
Commit: fe3112fea5d1bfde89317054a818b8a0f244c28e
https://github.com/galaxyproject/galaxy/commit/fe3112fea5d1bfde89317054a818…
Author: Dave Bouvier <dave(a)bx.psu.edu>
Date: 2016-08-08 (Mon, 08 Aug 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py
M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
M templates/admin/tool_shed_repository/browse_toolsheds.mako
Log Message:
-----------
Fix installation, incorporate Marius' conda changes.
Commit: b6bdbdbd6d6193524cab3e058dd6e450dcf5eb52
https://github.com/galaxyproject/galaxy/commit/b6bdbdbd6d6193524cab3e058dd6…
Author: Dave Bouvier <dave(a)bx.psu.edu>
Date: 2016-08-08 (Mon, 08 Aug 2016)
Changed paths:
M templates/admin/tool_shed_repository/browse_toolsheds.mako
Log Message:
-----------
Fix repository details updating when revision is selected.
Commit: 786c50505ed509354ac7a126647eabc3824bd0b9
https://github.com/galaxyproject/galaxy/commit/786c50505ed509354ac7a126647e…
Author: Dave Bouvier <dave(a)bx.psu.edu>
Date: 2016-08-09 (Tue, 09 Aug 2016)
Changed paths:
M Makefile
M client/galaxy/scripts/mvc/history/hdca-model.js
M config/tool_shed.ini.sample
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/deps/resolvers/galaxy_packages.py
M lib/galaxy/tools/deps/resolvers/tool_shed_packages.py
M lib/galaxy/tools/deps/views.py
M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
M lib/galaxy/webapps/tool_shed/buildapp.py
M lib/galaxy/webapps/tool_shed/config.py
M lib/galaxy/webapps/tool_shed/controllers/hg.py
R lib/galaxy/webapps/tool_shed/framework/middleware/hg.py
M scripts/common_startup.sh
M static/maps/mvc/history/hdca-model.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/history/hdca-model.js
M test/shed_functional/functional/test_0310_hg_api_features.py
M test/unit/tools/test_tool_deps.py
Log Message:
-----------
Merge branch 'dev' of git://github.com/galaxyproject/galaxy into api_install_performance
Commit: 21bfcecf477d065c2b2d1ac99b5b2fbf4ef5cace
https://github.com/galaxyproject/galaxy/commit/21bfcecf477d065c2b2d1ac99b5b…
Author: Dave Bouvier <dave(a)bx.psu.edu>
Date: 2016-08-09 (Tue, 09 Aug 2016)
Changed paths:
M templates/admin/tool_shed_repository/browse_toolsheds.mako
Log Message:
-----------
Implement most of the repo installation queue.
- Adding repositories to the queue. Removing repositories from the queue.
- Installation of individual repositories from the queue.
Installing everything in the queue does not yet work.
Commit: 4965c17174778e721b9e9dee5809f6066ca0dd7d
https://github.com/galaxyproject/galaxy/commit/4965c17174778e721b9e9dee5809…
Author: Dave Bouvier <dave(a)bx.psu.edu>
Date: 2016-08-10 (Wed, 10 Aug 2016)
Changed paths:
M templates/admin/tool_shed_repository/browse_toolsheds.mako
Log Message:
-----------
Implement batch installation of the repository queue.
Commit: eada11e9fc36b9dc62a25028370cfe9295489dd9
https://github.com/galaxyproject/galaxy/commit/eada11e9fc36b9dc62a25028370c…
Author: Dave Bouvier <dave(a)bx.psu.edu>
Date: 2016-08-10 (Wed, 10 Aug 2016)
Changed paths:
M client/galaxy/scripts/mvc/form/form-input.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/tool/tool-form-composite.js
M client/galaxy/scripts/mvc/ui/ui-portlet.js
M client/galaxy/scripts/mvc/ui/ui-select-default.js
M client/galaxy/style/less/ui.less
M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py
M static/maps/mvc/form/form-input.js.map
M static/maps/mvc/form/form-parameters.js.map
M static/maps/mvc/form/form-section.js.map
M static/maps/mvc/form/form-view.js.map
M static/maps/mvc/tool/tool-form-composite.js.map
M static/maps/mvc/ui/ui-portlet.js.map
M static/maps/mvc/ui/ui-select-default.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/form/form-input.js
M static/scripts/mvc/form/form-parameters.js
M static/scripts/mvc/form/form-section.js
M static/scripts/mvc/form/form-view.js
M static/scripts/mvc/tool/tool-form-composite.js
M static/scripts/mvc/ui/ui-portlet.js
M static/scripts/mvc/ui/ui-select-default.js
M static/style/blue/base.css
M test/qunit/test-data/fakeserver.js
M test/qunit/tests/form_tests.js
Log Message:
-----------
Merge branch 'dev' of git://github.com/galaxyproject/galaxy into api_install_performance
Commit: fab2c3ecc3b70c824ea5d5d89e4cd4733d98a411
https://github.com/galaxyproject/galaxy/commit/fab2c3ecc3b70c824ea5d5d89e4c…
Author: Dave Bouvier <dave(a)bx.psu.edu>
Date: 2016-08-10 (Wed, 10 Aug 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py
Log Message:
-----------
Improve travis' mood.
Commit: 5081cdc07d9d74bd8d68f2cc32128bfcdae45eee
https://github.com/galaxyproject/galaxy/commit/5081cdc07d9d74bd8d68f2cc3212…
Author: Dave Bouvier <dave(a)bx.psu.edu>
Date: 2016-08-12 (Fri, 12 Aug 2016)
Changed paths:
M templates/admin/tool_shed_repository/browse_toolsheds.mako
Log Message:
-----------
Fix tabs.
Commit: 32da285d5c4d5e479eeeaa7465ddfaf2e5ac1dc1
https://github.com/galaxyproject/galaxy/commit/32da285d5c4d5e479eeeaa7465dd…
Author: Dave Bouvier <dave(a)bx.psu.edu>
Date: 2016-08-12 (Fri, 12 Aug 2016)
Changed paths:
M .ci/first_startup.sh
M client/galaxy/scripts/mvc/form/form-repeat.js
M client/galaxy/scripts/mvc/form/form-section.js
M client/galaxy/scripts/mvc/tool/tool-form-composite.js
M config/galaxy.ini.sample
A doc/source/dev/build_a_job_runner.rst
M lib/galaxy/datatypes/binary.py
M lib/galaxy/datatypes/data.py
M lib/galaxy/datatypes/neo4j.py
M lib/galaxy/dependencies/conditional-requirements.txt
M lib/galaxy/managers/datasets.py
M lib/galaxy/tools/deps/__init__.py
M lib/galaxy/tools/deps/resolvers/conda.py
M lib/galaxy/tools/imp_exp/export_history.py
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/tools/parameters/dataset_matcher.py
M lib/galaxy/util/__init__.py
M lib/galaxy/webapps/galaxy/api/datasets.py
M lib/galaxy/webapps/galaxy/api/lda_datasets.py
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/galaxy/controllers/dataset.py
M lib/galaxy/webapps/galaxy/controllers/library_common.py
M lib/galaxy/webapps/galaxy/controllers/root.py
M lib/galaxy/webapps/galaxy/controllers/workflow.py
M run.sh
M scripts/common_startup.sh
M static/maps/mvc/form/form-repeat.js.map
M static/maps/mvc/form/form-section.js.map
M static/maps/mvc/tool/tool-form-composite.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/form/form-repeat.js
M static/scripts/mvc/form/form-section.js
M static/scripts/mvc/tool/tool-form-composite.js
M test/qunit/test-data/fakeserver.js
M test/qunit/tests/form_tests.js
M tools/genomespace/genomespace_file_browser.py
M tools/genomespace/genomespace_importer.py
Log Message:
-----------
Merge branch 'dev' of git://github.com/galaxyproject/galaxy into api_install_performance
Commit: 571dc2a4dbedad1e0f140ddbf86216b033266015
https://github.com/galaxyproject/galaxy/commit/571dc2a4dbedad1e0f140ddbf862…
Author: Dave Bouvier <dave(a)bx.psu.edu>
Date: 2016-08-15 (Mon, 15 Aug 2016)
Changed paths:
M .ci/flake8_lint_include_list.txt
M client/galaxy/style/less/library.less
M lib/galaxy/app.py
M lib/galaxy/config.py
M lib/galaxy/datatypes/interval.py
M lib/galaxy/queues.py
M lib/galaxy/tools/toolbox/base.py
M lib/galaxy/tools/toolbox/watcher.py
A lib/galaxy/util/postfork.py
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/reports/buildapp.py
M lib/galaxy/webapps/tool_shed/buildapp.py
M lib/galaxy/webapps/tool_shed/controllers/hg.py
M lib/galaxy/workflow/modules.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
Log Message:
-----------
Merge branch 'dev' of git://github.com/galaxyproject/galaxy into api_install_performance
Commit: 46136787e45160e7101b941f8fc1b56a2f3ec6d4
https://github.com/galaxyproject/galaxy/commit/46136787e45160e7101b941f8fc1…
Author: Dave Bouvier <dave(a)bx.psu.edu>
Date: 2016-08-15 (Mon, 15 Aug 2016)
Changed paths:
M templates/admin/tool_shed_repository/browse_toolsheds.mako
Log Message:
-----------
Text fixes, make the queue and its tab always visible.
Commit: 54e589ebad000535c384850df7abe6c195fbe5f5
https://github.com/galaxyproject/galaxy/commit/54e589ebad000535c384850df7ab…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-08-30 (Tue, 30 Aug 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
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
Log Message:
-----------
Merge pull request #2769 from davebx/api_install_performance
Cleanup of and performance enhancements to the API installation of repositories.
Compare: https://github.com/galaxyproject/galaxy/compare/ba6a0a36476c...54e589ebad00
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: f6c1aa0770508c552f074771078a4b7cc4cce400
https://github.com/galaxyproject/galaxy/commit/f6c1aa0770508c552f074771078a…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-08-29 (Mon, 29 Aug 2016)
Changed paths:
M lib/galaxy/web/framework/webapp.py
M lib/galaxy/webapps/galaxy/controllers/history.py
M lib/galaxy/webapps/galaxy/controllers/visualization.py
M templates/webapps/galaxy/workflow/display.mako
Log Message:
-----------
Create a new trans method for getting the most recently touched history.
Swap several uses of get_history (with create=True, only), to use this
new functionality where it makes sense.
Commit: 0bd1ea108e7f6000759583afd3e6d2d7daa3e7be
https://github.com/galaxyproject/galaxy/commit/0bd1ea108e7f6000759583afd3e6…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-08-30 (Tue, 30 Aug 2016)
Changed paths:
M lib/galaxy/web/framework/webapp.py
M lib/galaxy/webapps/galaxy/controllers/history.py
M lib/galaxy/webapps/galaxy/controllers/visualization.py
M templates/webapps/galaxy/workflow/display.mako
Log Message:
-----------
Merge pull request #2870 from dannon/histories.most_recent_v_default
Create a new trans method for getting the most recently touched history.
Compare: https://github.com/galaxyproject/galaxy/compare/e64503697302...0bd1ea108e7f
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: d86ee3706089e59868c16a3352ce61e0257dbb40
https://github.com/galaxyproject/galaxy/commit/d86ee3706089e59868c16a3352ce…
Author: Rémi Marenco <remi.marenco(a)gmail.com>
Date: 2016-08-29 (Mon, 29 Aug 2016)
Changed paths:
M doc/source/admin/conda_faq.rst
Log Message:
-----------
Add the <conda_prefix> in 12. and fix typo
I am adding the ``<conda_prefix>/envs`` to check for the package to have been properly installed (if people have brought their own Conda).
And fixing ``conda_prefix`` to stay consistent in the doc (``<conda_prefix>``).
Commit: 579ea41085501139eebbbeb5b3f72c9c04c03e4c
https://github.com/galaxyproject/galaxy/commit/579ea41085501139eebbbeb5b3f7…
Author: Rémi Marenco <remi.marenco(a)gmail.com>
Date: 2016-08-30 (Tue, 30 Aug 2016)
Changed paths:
M doc/source/admin/conda_faq.rst
Log Message:
-----------
Update Marius advice
Commit: e6450369730230bc844db67d3df05f1cffd3cdad
https://github.com/galaxyproject/galaxy/commit/e6450369730230bc844db67d3df0…
Author: Marius van den Beek <m.vandenbeek(a)gmail.com>
Date: 2016-08-30 (Tue, 30 Aug 2016)
Changed paths:
M doc/source/admin/conda_faq.rst
Log Message:
-----------
Merge pull request #2871 from remimarenco/patch-8
Add the <conda_prefix> in 12. and fix typo
Compare: https://github.com/galaxyproject/galaxy/compare/dbde38c951cd...e64503697302