Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f8e92fe011b17c8a2f3b249453043854a1cff305 https://github.com/galaxyproject/galaxy/commit/f8e92fe011b17c8a2f3b249453043... Author: Dave Bouvier <dave@bx.psu.edu> Date: 2016-08-17 (Wed, 17 Aug 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Add parameter to workflows API to list workflows with missing tools. Commit: ddbbe76c0a8266d4c49694ef43d43ecefb2ac943 https://github.com/galaxyproject/galaxy/commit/ddbbe76c0a8266d4c49694ef43d43... Author: Dave Bouvier <dave@bx.psu.edu> Date: 2016-08-18 (Thu, 18 Aug 2016) Changed paths: 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/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/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/watcher.py M lib/galaxy/util/template.py M lib/galaxy/web/framework/middleware/sentry.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 lib/galaxy_ext/metadata/set_metadata.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 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' of git://github.com/galaxyproject/galaxy into repo_queue_sharing Commit: 24bc782259786c03b0279e5e33b2eb96c1933c89 https://github.com/galaxyproject/galaxy/commit/24bc782259786c03b0279e5e33b2e... Author: Dave Bouvier <dave@bx.psu.edu> Date: 2016-08-18 (Thu, 18 Aug 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/tool_shed/api/repositories.py M templates/admin/tool_shed_repository/browse_toolsheds.mako Log Message: ----------- Implement display of workflows missing tools and the repository that contains those tools. Commit: e8255841573b551c36e444e1559f8665687d3b9d https://github.com/galaxyproject/galaxy/commit/e8255841573b551c36e444e1559f8... Author: Dave Bouvier <dave@bx.psu.edu> Date: 2016-08-19 (Fri, 19 Aug 2016) Changed paths: M config/galaxy.ini.sample M lib/galaxy/model/migrate/check.py Log Message: ----------- Merge branch 'dev' of git://github.com/galaxyproject/galaxy into repo_queue_sharing Commit: ec153e30627ad46a091a1a24a494cc2314ce22b1 https://github.com/galaxyproject/galaxy/commit/ec153e30627ad46a091a1a24a494c... Author: Dave Bouvier <dave@bx.psu.edu> Date: 2016-08-19 (Fri, 19 Aug 2016) Changed paths: M templates/admin/tool_shed_repository/browse_toolsheds.mako Log Message: ----------- Allow adding a repository to the queue from a workflow. Commit: f72f1f106c161d3d4d87dc0670b92a7f42b0207c https://github.com/galaxyproject/galaxy/commit/f72f1f106c161d3d4d87dc0670b92... Author: Dave Bouvier <dave@bx.psu.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 branch 'dev' of git://github.com/galaxyproject/galaxy into repo_queue_sharing Commit: 4a02d0516ff7c661ad9b46dcd428ccdc8cba3717 https://github.com/galaxyproject/galaxy/commit/4a02d0516ff7c661ad9b46dcd428c... Author: Dave Bouvier <dave@bx.psu.edu> Date: 2016-08-22 (Mon, 22 Aug 2016) Changed paths: M lib/galaxy/tools/toolbox/base.py M lib/galaxy/webapps/galaxy/api/workflows.py M templates/admin/tool_shed_repository/browse_toolsheds.mako Log Message: ----------- Move the method that checks for missing tools into the toolbox, where it belongs. Commit: ca987e706fb0a128fc3d68ea6f07f3fd44e83d74 https://github.com/galaxyproject/galaxy/commit/ca987e706fb0a128fc3d68ea6f07f... Author: Dave Bouvier <dave@bx.psu.edu> Date: 2016-08-25 (Thu, 25 Aug 2016) Changed paths: M .ci/flake8_lint_include_list.txt M client/galaxy/scripts/mvc/dataset/data.js M config/galaxy.ini.sample 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/util/postfork.py M lib/galaxy/web/framework/base.py A lib/galaxy/web/framework/middleware/batch.py M lib/galaxy/webapps/galaxy/api/jobs.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/tool_shed/config.py M static/maps/mvc/dataset/data.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 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' of git://github.com/galaxyproject/galaxy into repo_queue_sharing Commit: 73cdfc716bba938921d1fd9262b25a6778cc7f10 https://github.com/galaxyproject/galaxy/commit/73cdfc716bba938921d1fd9262b25... Author: Dave Bouvier <dave@bx.psu.edu> Date: 2016-08-25 (Thu, 25 Aug 2016) Changed paths: M lib/galaxy/tools/toolbox/base.py M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py Log Message: ----------- Rework the return value of /api/workflows?missing_tools=True Commit: 57c01f11af470e62164566af2b4af609d1cbebb9 https://github.com/galaxyproject/galaxy/commit/57c01f11af470e62164566af2b4af... Author: Dave Bouvier <dave@bx.psu.edu> Date: 2016-08-25 (Thu, 25 Aug 2016) Changed paths: M templates/admin/tool_shed_repository/browse_toolsheds.mako Log Message: ----------- Update the display of workflows missing tools. Thus accomodating the API changes made in the previous commit. Commit: 4d85eec0c9b8dda5d971aaf8714e65886f7e2f41 https://github.com/galaxyproject/galaxy/commit/4d85eec0c9b8dda5d971aaf8714e6... Author: Dave Bouvier <dave@bx.psu.edu> Date: 2016-08-29 (Mon, 29 Aug 2016) Changed paths: M Makefile 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/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 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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 doc/source/releases/16.07.rst M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/watcher.py M scripts/bootstrap_history.py 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/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 Log Message: ----------- Merge branch 'dev' of git://github.com/galaxyproject/galaxy into repo_queue_sharing Commit: 5b65f122b3808232656f0b8730cf46a697eb26d2 https://github.com/galaxyproject/galaxy/commit/5b65f122b3808232656f0b8730cf4... Author: Dave Bouvier <dave@bx.psu.edu> Date: 2016-08-29 (Mon, 29 Aug 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/tool_shed/api/repositories.py M templates/admin/tool_shed_repository/browse_toolsheds.mako Log Message: ----------- Finish repository discovery by missing workflow tools. Commit: d9d3f259944b640f2844745c895224f8bb9ea6bd https://github.com/galaxyproject/galaxy/commit/d9d3f259944b640f2844745c89522... Author: Dave Bouvier <dave@bx.psu.edu> Date: 2016-08-30 (Tue, 30 Aug 2016) Changed paths: M doc/source/admin/chat.rst M doc/source/admin/conda_faq.rst M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/webapps/galaxy/controllers/admin.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 branch 'dev' of git://github.com/galaxyproject/galaxy into repo_queue_sharing Commit: de1510f3cc367c036bf6c19bcd15e95f5dc46b30 https://github.com/galaxyproject/galaxy/commit/de1510f3cc367c036bf6c19bcd15e... Author: Dave Bouvier <dave@bx.psu.edu> Date: 2016-08-30 (Tue, 30 Aug 2016) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Fix the imports I broke in an earlier commit. Commit: 6e40fe957a777c6b64218844bc521da946f65279 https://github.com/galaxyproject/galaxy/commit/6e40fe957a777c6b64218844bc521... Author: Dave Bouvier <dave@bx.psu.edu> Date: 2016-09-02 (Fri, 02 Sep 2016) Changed paths: M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/scratchbook.js M doc/source/admin/conda_faq.rst M lib/galaxy/tools/cwl/parser.py M lib/galaxy/tools/deps/resolvers/conda.py R lib/galaxy/tools/toolbox/requirements.py A lib/galaxy/util/filelock.py M lib/galaxy/web/proxy/__init__.py R lib/galaxy/web/proxy/filelock.py M static/maps/layout/menu.js.map M static/maps/layout/scratchbook.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/menu.js M static/scripts/layout/scratchbook.js M templates/admin/tool_shed_repository/common.mako Log Message: ----------- Merge branch 'dev' of git://github.com/galaxyproject/galaxy into repo_queue_sharing Commit: 6998d338cfa22644d1fdc2cec819ee504147e784 https://github.com/galaxyproject/galaxy/commit/6998d338cfa22644d1fdc2cec819e... Author: Dave Bouvier <dave@bx.psu.edu> Date: 2016-09-12 (Mon, 12 Sep 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/tool_shed/api/categories.py M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/tool_shed/util/repository_util.py M templates/admin/tool_shed_repository/browse_toolsheds.mako Log Message: ----------- Integrate whoosh with the API installation's search boxes. Commit: aae40ca9064a67e57b12b30837f96de14bd5a4a9 https://github.com/galaxyproject/galaxy/commit/aae40ca9064a67e57b12b30837f96... Author: Dave Bouvier <dave@bx.psu.edu> Date: 2016-09-12 (Mon, 12 Sep 2016) Changed paths: M .ci/flake8_lint_include_list.txt M .gitignore M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/exceptions/error_codes.py M lib/galaxy/jobs/metrics/__init__.py M lib/galaxy/jobs/metrics/collectl/cli.py M lib/galaxy/jobs/metrics/collectl/processes.py M lib/galaxy/jobs/metrics/instrumenters/__init__.py M lib/galaxy/jobs/metrics/instrumenters/collectl.py M lib/galaxy/jobs/metrics/instrumenters/core.py M lib/galaxy/jobs/metrics/instrumenters/cpuinfo.py M lib/galaxy/jobs/metrics/instrumenters/env.py M lib/galaxy/jobs/metrics/instrumenters/meminfo.py M lib/galaxy/model/tool_shed_install/__init__.py M lib/galaxy/objectstore/__init__.py M lib/galaxy/objectstore/azure_blob.py M lib/galaxy/objectstore/rods.py M lib/galaxy/objectstore/s3.py M lib/galaxy/queue_worker.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/cwl/__init__.py M lib/galaxy/tools/cwl/representation.py M lib/galaxy/tools/cwl/schema.py M lib/galaxy/tools/data/__init__.py M lib/galaxy/tools/data_manager/manager.py M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/brew_exts.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/containers.py M lib/galaxy/tools/deps/dockerfiles.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/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/loader.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parser/__init__.py M lib/galaxy/tools/parser/cwl.py M lib/galaxy/tools/parser/factory.py M lib/galaxy/tools/parser/output_actions.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/parser/yaml.py M lib/galaxy/tools/toolbox/__init__.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/cache.py M lib/galaxy/tools/toolbox/filters/__init__.py M lib/galaxy/tools/toolbox/lineages/__init__.py M lib/galaxy/tools/toolbox/lineages/factory.py M lib/galaxy/tools/toolbox/lineages/tool_shed.py M lib/galaxy/tools/toolbox/panel.py M lib/galaxy/tools/toolbox/parser.py M lib/galaxy/tools/toolbox/tags.py M lib/galaxy/tools/toolbox/watcher.py M lib/galaxy/tools/verify/asserts/xml.py M lib/galaxy/tools/verify/test_data.py M lib/galaxy/tools/wrappers.py M lib/galaxy/util/__init__.py M lib/galaxy/util/biostar.py M lib/galaxy/util/checkers.py M lib/galaxy/util/hash_util.py M lib/galaxy/util/heartbeat.py M lib/galaxy/util/json.py M lib/galaxy/util/lazy_process.py M lib/galaxy/util/none_like.py M lib/galaxy/util/object_wrapper.py M lib/galaxy/util/pastescript/loadwsgi.py M lib/galaxy/util/pastescript/serve.py M lib/galaxy/util/permutations.py M lib/galaxy/util/properties.py M lib/galaxy/util/sanitize_html.py M lib/galaxy/util/sockets.py M lib/galaxy/util/sqlite.py M lib/galaxy/util/streamball.py M lib/galaxy/util/submodules.py M lib/galaxy/util/topsort.py M lib/galaxy/util/validation.py M lib/galaxy/util/xml_macros.py M lib/galaxy/webapps/galaxy/api/configuration.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/tools/tool_version_manager.py M setup.cfg M templates/webapps/galaxy/workflow/run.mako M test/functional/tools/column_multi_param.xml M test/functional/tools/column_param.xml M test/functional/tools/identifier_collection.xml M test/functional/tools/identifier_multiple.xml M test/functional/tools/identifier_single.xml M test/functional/tools/inputs_as_json.xml M test/functional/tools/multi_output.xml M test/functional/tools/multi_output_assign_primary.xml M test/functional/tools/multi_output_configured.xml M test/functional/tools/tool_directory.xml M test/functional/tools/validation_repeat.xml M test/shed_functional/functional/test_1040_install_repository_basic_circular_dependencies.py M test/shed_functional/functional/test_1080_advanced_circular_dependency_installation.py M test/unit/shed_unit/test_tool_panel_manager.py M test/unit/test_objectstore.py M test/unit/tools/test_parsing.py M test/unit/tools/test_tool_deps.py M test/unit/tools/test_tool_loader.py M test/unit/tools/test_toolbox.py M test/unit/tools/test_toolbox_filters.py M test/unit/tools/test_watcher.py M test/unit/tools/test_wrappers.py M test/unit/tools_support.py M tools/data_source/upload.xml Log Message: ----------- Merge branch 'dev' of git://github.com/galaxyproject/galaxy into repo_queue_sharing Commit: 0baf22ca6f891497a265fcefd3141a0796e1fd5d https://github.com/galaxyproject/galaxy/commit/0baf22ca6f891497a265fcefd3141... Author: Dave Bouvier <dave@bx.psu.edu> Date: 2016-09-13 (Tue, 13 Sep 2016) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py A lib/galaxy/model/migrate/versions/0133_add_dependency_column_to_job.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/resolvers/__init__.py M templates/show_params.mako M test/unit/jobs/test_job_wrapper.py Log Message: ----------- Merge branch 'dev' of git://github.com/galaxyproject/galaxy into repo_queue_sharing Commit: 0e1a2291ee77e710e908a7734eee20c43016f12c https://github.com/galaxyproject/galaxy/commit/0e1a2291ee77e710e908a7734eee2... Author: Dave Bouvier <dave@bx.psu.edu> Date: 2016-09-19 (Mon, 19 Sep 2016) Changed paths: A .ci/validate_test_tools.sh M .travis.yml M CONTRIBUTORS.md M LICENSE.txt 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 M lib/galaxy/managers/datasets.py M lib/galaxy/managers/hdcas.py M lib/galaxy/managers/history_contents.py M lib/galaxy/managers/rbac_secured.py M lib/galaxy/tools/parameters/validation.py A lib/galaxy/tools/xsd/LICENSE A lib/galaxy/tools/xsd/README.md A lib/galaxy/tools/xsd/galaxy.jxb A lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/util/__init__.py M lib/galaxy/webapps/galaxy/api/history_contents.py M lib/galaxy/webapps/galaxy/buildapp.py A scripts/validate_tools.sh 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 M templates/webapps/galaxy/workflow/run.mako R test/functional/tools/multi_page.xml M test/functional/tools/samples_tool_conf.xml M test/unit/managers/test_DatasetManager.py M tox.ini Log Message: ----------- Merge branch 'dev' of git://github.com/galaxyproject/galaxy into repo_queue_sharing Commit: 4106d975fa5b8767d72b13671ce183d9a8bd98ad https://github.com/galaxyproject/galaxy/commit/4106d975fa5b8767d72b13671ce18... Author: Dave Bouvier <dave@bx.psu.edu> Date: 2016-09-19 (Mon, 19 Sep 2016) Changed paths: M templates/admin/tool_shed_repository/browse_toolsheds.mako Log Message: ----------- Some cleanup, initial url hash navigation. Commit: cdea4b3cee3024618e99b6b1f498d2f25fa53295 https://github.com/galaxyproject/galaxy/commit/cdea4b3cee3024618e99b6b1f498d... Author: Dave Bouvier <dave@bx.psu.edu> Date: 2016-09-20 (Tue, 20 Sep 2016) Changed paths: A lib/galaxy/datatypes/converters/tabular_to_dbnsfp.py Log Message: ----------- Merge branch 'dev' of git://github.com/galaxyproject/galaxy into repo_queue_sharing Commit: 8d15670a5d4709cf9043ffd0d3b296494fc252fb https://github.com/galaxyproject/galaxy/commit/8d15670a5d4709cf9043ffd0d3b29... Author: Dave Bouvier <dave@bx.psu.edu> Date: 2016-09-20 (Tue, 20 Sep 2016) Changed paths: M templates/admin/tool_shed_repository/browse_toolsheds.mako Log Message: ----------- Remove debugging. Commit: 22240074c30a98c541c36b6dab4fb0947112b6be https://github.com/galaxyproject/galaxy/commit/22240074c30a98c541c36b6dab4fb... Author: Dave Bouvier <dave@bx.psu.edu> Date: 2016-09-20 (Tue, 20 Sep 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/tool_shed/api/tools.py M lib/galaxy/webapps/tool_shed/buildapp.py M templates/admin/tool_shed_repository/browse_toolsheds.mako Log Message: ----------- Initial work to show tool form preview on repository preview page. Commit: ca7fb1db62e6c1f03bfc0836f1bd7aeacb1f0294 https://github.com/galaxyproject/galaxy/commit/ca7fb1db62e6c1f03bfc0836f1bd7... Author: Dave Bouvier <dave@bx.psu.edu> Date: 2016-09-20 (Tue, 20 Sep 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/webapps/tool_shed/api/tools.py Log Message: ----------- Make request_context (trans) the first argument to populate_model. Commit: 18b93014572c04d597b9ea6f0750686e9cba39b4 https://github.com/galaxyproject/galaxy/commit/18b93014572c04d597b9ea6f07506... Author: Dave Bouvier <dave@bx.psu.edu> Date: 2016-09-20 (Tue, 20 Sep 2016) Changed paths: M lib/galaxy/web/framework/decorators.py Log Message: ----------- Merge branch 'dev' of git://github.com/galaxyproject/galaxy into repo_queue_sharing Commit: 07cc3a9462db302478ab4aacd378b6128282e52b https://github.com/galaxyproject/galaxy/commit/07cc3a9462db302478ab4aacd378b... Author: Dave Bouvier <dave@bx.psu.edu> Date: 2016-09-21 (Wed, 21 Sep 2016) Changed paths: M lib/galaxy/security/validate_user_input.py M lib/galaxy/webapps/galaxy/controllers/mobile.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/workflow/extract.py M templates/user/info.mako M templates/user/register.mako M templates/user/username.mako M templates/webapps/galaxy/workflow/build_from_current_history.mako M test/unit/managers/test_UserManager.py Log Message: ----------- Merge branch 'dev' of git://github.com/galaxyproject/galaxy into repo_queue_sharing Commit: 5309c8eeb782140fa7f729d7933a388cf29f6505 https://github.com/galaxyproject/galaxy/commit/5309c8eeb782140fa7f729d7933a3... Author: Dave Bouvier <dave@bx.psu.edu> Date: 2016-09-21 (Wed, 21 Sep 2016) Changed paths: M templates/admin/tool_shed_repository/browse_toolsheds.mako Log Message: ----------- Show a modal with the tool form when clicking on the button. Commit: dd783f418e3fb33a169766235febffa575e0696a https://github.com/galaxyproject/galaxy/commit/dd783f418e3fb33a169766235febf... Author: Dave Bouvier <dave@bx.psu.edu> Date: 2016-09-21 (Wed, 21 Sep 2016) Changed paths: M templates/admin/tool_shed_repository/browse_toolsheds.mako Log Message: ----------- A bit of styling. Commit: 6da7ce304e34db2cb0495cdd88c553514514573b https://github.com/galaxyproject/galaxy/commit/6da7ce304e34db2cb0495cdd88c55... Author: Dave Bouvier <dave@bx.psu.edu> Date: 2016-09-21 (Wed, 21 Sep 2016) Changed paths: M templates/admin/tool_shed_repository/browse_toolsheds.mako Log Message: ----------- Additional styling. Commit: d60bc8a97b5f229bbf9416e4e5a0f92e028aad01 https://github.com/galaxyproject/galaxy/commit/d60bc8a97b5f229bbf9416e4e5a0f... Author: Dave Bouvier <dave@bx.psu.edu> Date: 2016-09-21 (Wed, 21 Sep 2016) Changed paths: M lib/galaxy/webapps/tool_shed/api/tools.py Log Message: ----------- Improve travis' demeanor. Commit: b29d6f55d8546aac4354d4293ee585d08645c790 https://github.com/galaxyproject/galaxy/commit/b29d6f55d8546aac4354d4293ee58... Author: Dave Bouvier <dave@bx.psu.edu> Date: 2016-09-23 (Fri, 23 Sep 2016) Changed paths: M lib/galaxy/webapps/tool_shed/api/tools.py Log Message: ----------- Remove unused import. Commit: adbcc26286909bae7bd0a9c4587ea4815137a8e3 https://github.com/galaxyproject/galaxy/commit/adbcc26286909bae7bd0a9c4587ea... Author: Dave B <dave@bx.psu.edu> Date: 2016-09-26 (Mon, 26 Sep 2016) Changed paths: M templates/admin/tool_shed_repository/browse_toolsheds.mako Log Message: ----------- Fix the per-tool panel selection features. Commit: ea9f22ebf794be55b5c89090acf51b9f0040b582 https://github.com/galaxyproject/galaxy/commit/ea9f22ebf794be55b5c89090acf51... Author: Dave B <dave@bx.psu.edu> Date: 2016-10-04 (Tue, 04 Oct 2016) Changed paths: M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt M .gitignore M Makefile 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-workflow.js M client/galaxy/scripts/mvc/tool/tool-form.js M client/galaxy/scripts/mvc/ui/ui-portlet.js M client/galaxy/scripts/mvc/ui/ui-select-content.js M client/galaxy/scripts/utils/utils.js M client/galaxy/style/less/ui.less A doc/parse_gx_xsd.py A doc/schema_template.md M doc/source/project/issues.rst M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/converters/interval_to_tabix_converter.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/proteomics.py M lib/galaxy/dependencies/conda-environment.txt M lib/galaxy/dependencies/pinned-hashed-requirements.txt M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt M lib/galaxy/exceptions/__init__.py M lib/galaxy/exceptions/error_codes.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/command_factory.py M lib/galaxy/jobs/metrics/__init__.py M lib/galaxy/jobs/metrics/collectl/__init__.py M lib/galaxy/jobs/metrics/collectl/cli.py M lib/galaxy/jobs/metrics/collectl/subsystems.py M lib/galaxy/jobs/metrics/formatting.py M lib/galaxy/jobs/metrics/instrumenters/__init__.py M lib/galaxy/jobs/metrics/instrumenters/collectl.py M lib/galaxy/jobs/metrics/instrumenters/core.py M lib/galaxy/jobs/metrics/instrumenters/cpuinfo.py M lib/galaxy/jobs/metrics/instrumenters/env.py M lib/galaxy/jobs/metrics/instrumenters/meminfo.py M lib/galaxy/jobs/metrics/instrumenters/uname.py M lib/galaxy/jobs/runners/slurm.py M lib/galaxy/managers/workflows.py M lib/galaxy/model/mapping.py M lib/galaxy/queue_worker.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/containers.py M lib/galaxy/tools/deps/requirements.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/util/checkers.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/galaxy/webapps/tool_shed/model/__init__.py M lib/tool_shed/util/metadata_util.py M scripts/bootstrap_history.py M scripts/tool_shed/build_ts_whoosh_index.py 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-workflow.js.map M static/maps/mvc/tool/tool-form.js.map M static/maps/mvc/ui/ui-portlet.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/tool/tool-form-base.js M static/scripts/mvc/tool/tool-form-composite.js M static/scripts/mvc/tool/tool-form-workflow.js M static/scripts/mvc/tool/tool-form.js M static/scripts/mvc/ui/ui-portlet.js M static/scripts/mvc/ui/ui-select-content.js M static/scripts/utils/utils.js M static/style/blue/base.css M templates/webapps/galaxy/dataset/copy_view.mako M templates/webapps/galaxy/library/common/common.mako M templates/webapps/galaxy/workflow/run.mako R templates/webapps/galaxy/workflow/run_complete.mako M templates/webapps/tool_shed/repository/tool_form.mako M test/base/interactor.py A test/functional/tools/metadata_column_names.xml M test/functional/tools/samples_tool_conf.xml M test/qunit/tests/form_tests.js M test/shed_functional/functional/test_1400_review_migration_stages.py M test/unit/test_galaxy_mapping.py M test/unit/tools/test_data_parameters.py M test/unit/tools/test_parameter_parsing.py M test/unit/unittest_utils/galaxy_mock.py M tools/data_source/data_source.py M tools/data_source/hbvar_filter.py M tools/data_source/microbial_import_code.py M tools/evolution/add_scores.py M tools/evolution/codingSnps_filter.py M tools/extract/extract_genomic_dna.py M tools/filters/axt_to_concat_fasta.py M tools/filters/axt_to_fasta.py M tools/filters/axt_to_lav.py M tools/filters/axt_to_lav_code.py M tools/filters/bed_to_gff_converter.py M tools/filters/convert_characters.py M tools/filters/gff/extract_GFF_Features.py M tools/filters/gff/gff_filter_by_attribute.py M tools/filters/gff/gff_filter_by_feature_count.py M tools/filters/gff/gtf_filter_by_attribute_values_list.py M tools/filters/gff_to_bed_converter.py M tools/filters/grep.py M tools/filters/gtf_to_bedgraph_converter.py M tools/filters/join.py M tools/filters/lav_to_bed.py M tools/filters/lav_to_bed_code.py M tools/filters/mergeCols.py M tools/filters/random_lines_two_pass.py M tools/filters/secure_hash_message_digest.py M tools/filters/sff_extract.py M tools/filters/trimmer.py M tools/filters/ucsc_gene_bed_to_exon_bed.py M tools/filters/ucsc_gene_bed_to_intron_bed.py M tools/filters/ucsc_gene_table_to_intervals.py M tools/filters/uniq.py M tools/filters/wiggle_to_simple.py M tools/genomespace/genomespace_exporter.py M tools/genomespace/genomespace_file_browser.py M tools/genomespace/genomespace_importer.py M tools/maf/interval2maf.py M tools/maf/interval_maf_to_merged_fasta.py M tools/maf/maf_by_block_number.py M tools/maf/maf_filter.py M tools/maf/maf_limit_size.py M tools/maf/maf_limit_to_species.py M tools/maf/maf_reverse_complement.py M tools/maf/maf_split_by_species.py M tools/maf/maf_stats.py M tools/maf/maf_thread_for_species.py M tools/maf/maf_to_bed.py M tools/maf/maf_to_bed_code.py M tools/maf/maf_to_fasta_concat.py M tools/maf/maf_to_fasta_multiple_sets.py M tools/maf/vcf_to_maf_customtrack.py M tools/metag_tools/shrimp_color_wrapper.py M tools/metag_tools/shrimp_wrapper.py M tools/next_gen_conversion/solid2fastq.py M tools/next_gen_conversion/solid_to_fastq.py M tools/ngs_simulation/ngs_simulation.py M tools/phenotype_association/pagetag.py M tools/phenotype_association/senatag.py M tools/solid_tools/maq_cs_wrapper.py M tools/solid_tools/solid_qual_stats.py M tools/sr_assembly/velvetg_wrapper.py M tools/sr_mapping/bfast_wrapper.py M tools/stats/filtering.py M tools/stats/grouping.py M tools/stats/gsummary.py M tools/visualization/LAJ_code.py Log Message: ----------- Merge branch 'dev' of git://github.com/galaxyproject/galaxy into repo_queue_sharing Commit: 92724347feedac97f319af6c8ab6f2c703ef9811 https://github.com/galaxyproject/galaxy/commit/92724347feedac97f319af6c8ab6f... Author: Dave B <dave@bx.psu.edu> Date: 2016-10-04 (Tue, 04 Oct 2016) Changed paths: M templates/admin/tool_shed_repository/browse_toolsheds.mako Log Message: ----------- Fix repository installation. Commit: 84545674af6fc81e0f5a2dd87448aaee176106eb https://github.com/galaxyproject/galaxy/commit/84545674af6fc81e0f5a2dd87448a... Author: Dave B <dave@bx.psu.edu> Date: 2016-10-04 (Tue, 04 Oct 2016) Changed paths: M templates/admin/tool_shed_repository/browse_toolsheds.mako Log Message: ----------- Fix the 'Add from workflow' button. Commit: 60b12bf6734b460881e28a257b5d28301129785d https://github.com/galaxyproject/galaxy/commit/60b12bf6734b460881e28a257b5d2... Author: Dave B <dave@bx.psu.edu> Date: 2016-10-07 (Fri, 07 Oct 2016) Changed paths: A .ci/flake8_docstrings_include_list.txt M .ci/flake8_wrapper.sh A .ci/flake8_wrapper_docstrings.sh M .travis.yml 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/ui-modal.js M doc/source/admin/conda_faq.rst M doc/source/api/guidelines.rst M lib/galaxy/managers/workflows.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/meta.py M lib/galaxy/util/__init__.py M lib/galaxy/webapps/galaxy/api/genomes.py M lib/galaxy/webapps/galaxy/api/workflows.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/workflow/modules.py M lib/galaxy/workflow/run.py M lib/galaxy/workflow/run_request.py M setup.cfg M static/maps/mvc/tool/tool-form-composite.js.map M static/maps/mvc/tool/tool-form.js.map M static/maps/mvc/ui/ui-modal.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/tool/tool-form-composite.js M static/scripts/mvc/tool/tool-form.js M static/scripts/mvc/ui/ui-modal.js A test/api/test_workflow_batch.ga M test/api/test_workflows.py M test/unit/workflows/test_run_parameters.py M tox.ini Log Message: ----------- Merge branch 'dev' of git://github.com/galaxyproject/galaxy into repo_queue_sharing Commit: 02719c6547e91cc1357ad6ed49e97096c46f5473 https://github.com/galaxyproject/galaxy/commit/02719c6547e91cc1357ad6ed49e97... Author: Dave B <dave@bx.psu.edu> Date: 2016-10-07 (Fri, 07 Oct 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Remove unused imports. Commit: 815a713226c72f3d063ba7f1bf2e0f721dc2407d https://github.com/galaxyproject/galaxy/commit/815a713226c72f3d063ba7f1bf2e0... Author: Dave B <dave@bx.psu.edu> Date: 2016-11-09 (Wed, 09 Nov 2016) Changed paths: M .ci/flake8_blacklist.txt M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt M .gitignore M .travis.yml M CONTRIBUTORS.md M Makefile M client/galaxy/scripts/apps/history-panel.js M client/galaxy/scripts/layout/masthead.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/history/options-menu.js M client/galaxy/scripts/mvc/library/library-dataset-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/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/tool/tools.js M client/galaxy/scripts/mvc/ui/ui-buttons.js M client/galaxy/scripts/mvc/ui/ui-tabs.js A client/galaxy/scripts/mvc/ui/ui-thumbnails.js A client/galaxy/scripts/mvc/webhooks.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M client/galaxy/scripts/utils/utils.js M client/galaxy/style/less/ui.less M client/galaxy/style/source_material/circle.py M config/datatypes_conf.xml.sample M config/galaxy.ini.sample M config/job_conf.xml.sample_advanced R config/plugins/visualizations/charts/Gruntfile.js M config/plugins/visualizations/charts/config/charts.xml M config/plugins/visualizations/charts/package.json R config/plugins/visualizations/charts/sample.txt R config/plugins/visualizations/charts/static/app.css R config/plugins/visualizations/charts/static/app.js R config/plugins/visualizations/charts/static/charts/jqplot/bar/config.js R config/plugins/visualizations/charts/static/charts/jqplot/bar/logo.png R config/plugins/visualizations/charts/static/charts/jqplot/bar/wrapper.js R config/plugins/visualizations/charts/static/charts/jqplot/boxplot/config.js R config/plugins/visualizations/charts/static/charts/jqplot/boxplot/logo.png R 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test/shed_functional/functional/test_0300_reset_all_metadata.py M test/shed_functional/functional/test_1140_simple_repository_dependency_multiple_owners.py M test/shed_functional/functional/test_1300_reset_all_metadata.py M test/shed_functional/functional_tests.py M test/unit/jobs/test_job_wrapper.py M test/unit/jobs/test_runner_local.py M test/unit/tools/test_tool_dependency_description.py M test/unit/tools/test_toolbox.py M test/unit/tools_support.py M test/unit/unittest_utils/utility.py A tool-data/blastdb.loc.sample A tool-data/blastdb_d.loc.sample A tool-data/blastdb_p.loc.sample M tools/data_source/upload.py M tools/filters/gff/gff_filter_by_attribute.py M tools/stats/filtering.py Log Message: ----------- Merge branch 'dev' of git://github.com/galaxyproject/galaxy into repo_queue_sharing Commit: 9e37adb93251ea72e6592966e6b5e810a756f9d8 https://github.com/galaxyproject/galaxy/commit/9e37adb93251ea72e6592966e6b5e... Author: Dave B <dave@bx.psu.edu> Date: 2016-11-09 (Wed, 09 Nov 2016) Changed paths: A client/galaxy/scripts/admin.toolshed.js A client/galaxy/scripts/mvc/toolshed/categories-view.js A client/galaxy/scripts/mvc/toolshed/repo-queue-view.js A client/galaxy/scripts/mvc/toolshed/repositories-view.js A client/galaxy/scripts/mvc/toolshed/repository-view.js A client/galaxy/scripts/mvc/toolshed/shed-list-view.js A client/galaxy/scripts/mvc/toolshed/toolshed-model.js M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py A static/maps/admin.toolshed.js.map A static/maps/mvc/toolshed/repo-queue-view.js.map A static/maps/mvc/toolshed/shed-category-view.js.map A static/maps/mvc/toolshed/shed-repo-details-view.js.map A static/maps/mvc/toolshed/shed-repo-list-view.js.map A static/maps/mvc/toolshed/sheds-list-view.js.map A static/maps/mvc/toolshed/toolshed-model.js.map A static/scripts/admin.toolshed.js 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 static/scripts/mvc/toolshed/categories-view.js A static/scripts/mvc/toolshed/repo-queue-view.js A static/scripts/mvc/toolshed/repositories-view.js A static/scripts/mvc/toolshed/repository-view.js A static/scripts/mvc/toolshed/shed-category-view.js A static/scripts/mvc/toolshed/shed-list-view.js A static/scripts/mvc/toolshed/shed-repo-details-view.js A static/scripts/mvc/toolshed/shed-repo-list-view.js A static/scripts/mvc/toolshed/sheds-list-view.js A static/scripts/mvc/toolshed/toolshed-model.js M static/scripts/mvc/ui/ui-thumbnails.js M static/scripts/mvc/webhooks.js R templates/admin/tool_shed_repository/browse_toolsheds.mako Log Message: ----------- Initial backbonification of API repo installation. Commit: 1700b1f3a5ebf72fdacafcf067cba23e3a88db1a https://github.com/galaxyproject/galaxy/commit/1700b1f3a5ebf72fdacafcf067cba... Author: Dave B <dave@bx.psu.edu> Date: 2016-11-10 (Thu, 10 Nov 2016) Changed paths: M client/galaxy/scripts/admin.toolshed.js M client/galaxy/scripts/mvc/toolshed/categories-view.js M client/galaxy/scripts/mvc/toolshed/repositories-view.js M client/galaxy/scripts/mvc/toolshed/repository-view.js M lib/galaxy/webapps/galaxy/buildapp.py M static/scripts/admin.toolshed.js M static/scripts/mvc/toolshed/categories-view.js M static/scripts/mvc/toolshed/repositories-view.js M static/scripts/mvc/toolshed/repository-view.js Log Message: ----------- Fix forward navigation. Commit: 1e8965f1e4f68c4bec8c9bc832bb55330e3942a5 https://github.com/galaxyproject/galaxy/commit/1e8965f1e4f68c4bec8c9bc832bb5... Author: Dave B <dave@bx.psu.edu> Date: 2016-11-11 (Fri, 11 Nov 2016) Changed paths: M client/galaxy/scripts/mvc/toolshed/repository-view.js M static/scripts/mvc/toolshed/repository-view.js Log Message: ----------- Fix installation. Commit: 476df39fe2163a00bbcd441e66f49b14325bf3af https://github.com/galaxyproject/galaxy/commit/476df39fe2163a00bbcd441e66f49... Author: Dave B <dave@bx.psu.edu> Date: 2016-11-11 (Fri, 11 Nov 2016) Changed paths: M lib/galaxy/model/mapping.py M lib/galaxy/tools/toolbox/integrated_panel.py M lib/tool_shed/tools/tool_validator.py M scripts/api/filter_failed_datasets_from_collection.py Log Message: ----------- Merge branch 'dev' of git://github.com/galaxyproject/galaxy into ts_api_backbone Commit: 104aee5114880d744f427dcd96515d193d3798f0 https://github.com/galaxyproject/galaxy/commit/104aee5114880d744f427dcd96515... Author: Dave B <dave@bx.psu.edu> Date: 2016-11-14 (Mon, 14 Nov 2016) Changed paths: M client/galaxy/scripts/mvc/toolshed/repository-view.js M static/scripts/mvc/toolshed/repository-view.js Log Message: ----------- Some cleanup, improved the jstree. Commit: 529c7c5b74470f8a1dfb8a913ca0e84d55f8610d https://github.com/galaxyproject/galaxy/commit/529c7c5b74470f8a1dfb8a913ca0e... Author: Dave B <dave@bx.psu.edu> Date: 2016-11-14 (Mon, 14 Nov 2016) Changed paths: M client/galaxy/scripts/mvc/toolshed/repository-view.js M static/scripts/mvc/toolshed/repository-view.js Log Message: ----------- Fix tool form modal. Commit: edd7417102e51bde3ae199365b05c519cd0d6f3b https://github.com/galaxyproject/galaxy/commit/edd7417102e51bde3ae199365b05c... Author: Dave B <dave@bx.psu.edu> Date: 2016-11-14 (Mon, 14 Nov 2016) Changed paths: M .ci/flake8_lint_include_list.txt M Makefile M config/galaxy.ini.sample M doc/source/admin/interactive_environments.rst M lib/galaxy/datatypes/converters/bed_to_fli_converter.xml M lib/galaxy/datatypes/converters/bed_to_gff_converter.xml M lib/galaxy/datatypes/converters/bed_to_tabix_converter.xml M lib/galaxy/datatypes/converters/bedgraph_to_array_tree_converter.xml M lib/galaxy/datatypes/converters/bedgraph_to_bigwig_converter.xml M lib/galaxy/datatypes/converters/cml_to_inchi_converter.xml M lib/galaxy/datatypes/converters/cml_to_mol2_converter.xml M lib/galaxy/datatypes/converters/cml_to_sdf_converter.xml M lib/galaxy/datatypes/converters/cml_to_smi_converter.xml M lib/galaxy/datatypes/converters/encodepeak_to_bgzip_converter.xml M lib/galaxy/datatypes/converters/encodepeak_to_tabix_converter.xml M lib/galaxy/datatypes/converters/fasta_to_2bit.xml M lib/galaxy/datatypes/converters/fasta_to_bowtie_base_index_converter.xml M lib/galaxy/datatypes/converters/fasta_to_bowtie_color_index_converter.xml M lib/galaxy/datatypes/converters/fasta_to_len.xml M lib/galaxy/datatypes/converters/fasta_to_tabular_converter.xml M lib/galaxy/datatypes/converters/fastq_to_fqtoc.xml M lib/galaxy/datatypes/converters/fastqsolexa_to_fasta_converter.xml M lib/galaxy/datatypes/converters/fastqsolexa_to_qual_converter.xml M lib/galaxy/datatypes/converters/gff_to_bed_converter.xml M lib/galaxy/datatypes/converters/gff_to_bgzip_converter.xml M lib/galaxy/datatypes/converters/gff_to_fli_converter.xml M lib/galaxy/datatypes/converters/gff_to_interval_index_converter.xml M lib/galaxy/datatypes/converters/gff_to_tabix_converter.xml M lib/galaxy/datatypes/converters/inchi_to_cml_converter.xml M lib/galaxy/datatypes/converters/inchi_to_mol2_converter.xml M lib/galaxy/datatypes/converters/inchi_to_mol_converter.xml M lib/galaxy/datatypes/converters/inchi_to_sdf_converter.xml M lib/galaxy/datatypes/converters/inchi_to_smi_converter.xml M lib/galaxy/datatypes/converters/interval_to_bed12_converter.xml M lib/galaxy/datatypes/converters/interval_to_bed6_converter.xml M lib/galaxy/datatypes/converters/interval_to_bed_converter.xml M lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.xml M lib/galaxy/datatypes/converters/interval_to_bgzip_converter.xml M lib/galaxy/datatypes/converters/interval_to_bigwig_converter.xml M lib/galaxy/datatypes/converters/interval_to_coverage.xml M lib/galaxy/datatypes/converters/interval_to_interval_index_converter.xml M lib/galaxy/datatypes/converters/interval_to_tabix_converter.xml M lib/galaxy/datatypes/converters/len_to_linecount.xml M lib/galaxy/datatypes/converters/maf_to_fasta_converter.xml M lib/galaxy/datatypes/converters/maf_to_interval_converter.xml M lib/galaxy/datatypes/converters/mol2_to_cml_converter.xml M lib/galaxy/datatypes/converters/mol2_to_inchi_converter.xml M lib/galaxy/datatypes/converters/mol2_to_mol_converter.xml M lib/galaxy/datatypes/converters/mol2_to_sdf_converter.xml M lib/galaxy/datatypes/converters/mol2_to_smi_converter.xml M lib/galaxy/datatypes/converters/mol_to_cml_converter.xml M lib/galaxy/datatypes/converters/mol_to_inchi_converter.xml M lib/galaxy/datatypes/converters/mol_to_mol2_converter.xml M lib/galaxy/datatypes/converters/picard_interval_list_to_bed6_converter.xml M lib/galaxy/datatypes/converters/pileup_to_interval_index_converter.xml M lib/galaxy/datatypes/converters/ref_to_seq_taxonomy_converter.xml M lib/galaxy/datatypes/converters/sam_to_bam.xml M lib/galaxy/datatypes/converters/sam_to_bigwig_converter.xml M lib/galaxy/datatypes/converters/sdf_to_cml_converter.xml M lib/galaxy/datatypes/converters/sdf_to_inchi_converter.xml M lib/galaxy/datatypes/converters/sdf_to_mol2_converter.xml M lib/galaxy/datatypes/converters/sdf_to_smi_converter.xml M lib/galaxy/datatypes/converters/smi_to_cml_converter.xml M lib/galaxy/datatypes/converters/smi_to_inchi_converter.xml M lib/galaxy/datatypes/converters/smi_to_mol2_converter.xml M lib/galaxy/datatypes/converters/smi_to_mol_converter.xml M lib/galaxy/datatypes/converters/smi_to_sdf_converter.xml M lib/galaxy/datatypes/converters/smi_to_smi_converter.xml M lib/galaxy/datatypes/converters/tabular_to_dbnsfp.xml M lib/galaxy/datatypes/converters/vcf_to_bgzip_converter.xml M lib/galaxy/datatypes/converters/vcf_to_interval_index_converter.xml M lib/galaxy/datatypes/converters/vcf_to_tabix_converter.xml M lib/galaxy/datatypes/converters/wig_to_bigwig_converter.xml M lib/galaxy/datatypes/converters/wiggle_to_array_tree_converter.xml M lib/galaxy/datatypes/converters/wiggle_to_simple_converter.xml M lib/galaxy/datatypes/data.py M lib/galaxy/exceptions/error_codes.py M lib/galaxy/jobs/metrics/__init__.py M lib/galaxy/jobs/metrics/collectl/cli.py M lib/galaxy/jobs/metrics/collectl/subsystems.py M lib/galaxy/jobs/metrics/instrumenters/core.py M lib/galaxy/jobs/metrics/instrumenters/cpuinfo.py M lib/galaxy/jobs/metrics/instrumenters/env.py M lib/galaxy/jobs/metrics/instrumenters/meminfo.py M lib/galaxy/jobs/runners/cli.py M lib/galaxy/model/__init__.py M lib/galaxy/objectstore/rods.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/cwl/runtime_actions.py M lib/galaxy/tools/cwl/schema.py M lib/galaxy/tools/deps/commands.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/tools/deps/containers.py M lib/galaxy/tools/deps/mulled/_cli.py M lib/galaxy/tools/deps/mulled/mulled_build.py M lib/galaxy/tools/deps/mulled/mulled_build_channel.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/deps/resolvers/modules.py M lib/galaxy/tools/imp_exp/exp_history_to_archive.xml M lib/galaxy/tools/parser/output_actions.py M lib/galaxy/tools/parser/output_collection_def.py M lib/galaxy/tools/toolbox/lineages/tool_shed.py M lib/galaxy/tools/toolbox/parser.py M lib/galaxy/util/__init__.py M lib/galaxy/util/hash_util.py M lib/galaxy/util/object_wrapper.py Log Message: ----------- Merge branch 'dev' of git://github.com/galaxyproject/galaxy into ts_api_backbone Commit: 419fb3bde91d792bbda6f2a291c99371cad96d29 https://github.com/galaxyproject/galaxy/commit/419fb3bde91d792bbda6f2a291c99... Author: Dave B <dave@bx.psu.edu> Date: 2016-11-14 (Mon, 14 Nov 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py A lib/galaxy/webapps/galaxy/api/toolshed.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Refactor API endpoints. Commit: d00f89707f591b226b1d501959e648a45f62431b https://github.com/galaxyproject/galaxy/commit/d00f89707f591b226b1d501959e64... Author: Dave B <dave@bx.psu.edu> Date: 2016-11-15 (Tue, 15 Nov 2016) Changed paths: M client/galaxy/scripts/admin.toolshed.js M client/galaxy/scripts/mvc/toolshed/categories-view.js M client/galaxy/scripts/mvc/toolshed/repositories-view.js M client/galaxy/scripts/mvc/toolshed/repository-view.js M client/galaxy/scripts/mvc/toolshed/shed-list-view.js M client/galaxy/scripts/mvc/toolshed/toolshed-model.js M lib/galaxy/webapps/galaxy/api/toolshed.py M static/scripts/admin.toolshed.js M static/scripts/mvc/toolshed/categories-view.js M static/scripts/mvc/toolshed/repositories-view.js M static/scripts/mvc/toolshed/repository-view.js M static/scripts/mvc/toolshed/shed-list-view.js M static/scripts/mvc/toolshed/toolshed-model.js Log Message: ----------- Fix navigation, update API calls. Commit: 3e83e5ba811bbac19864b39f632f294956c7587e https://github.com/galaxyproject/galaxy/commit/3e83e5ba811bbac19864b39f632f2... Author: Dave B <dave@bx.psu.edu> Date: 2016-11-16 (Wed, 16 Nov 2016) Changed paths: M client/galaxy/scripts/mvc/toolshed/repository-view.js M static/scripts/mvc/toolshed/repository-view.js Log Message: ----------- Fix disabling button when changeset is installed. Commit: 8ead327a46b0dfcde163e4591895f41575fac21f https://github.com/galaxyproject/galaxy/commit/8ead327a46b0dfcde163e4591895f... Author: Dave B <dave@bx.psu.edu> Date: 2016-11-16 (Wed, 16 Nov 2016) Changed paths: M client/galaxy/scripts/mvc/toolshed/categories-view.js M client/galaxy/scripts/mvc/toolshed/repositories-view.js M client/galaxy/scripts/mvc/toolshed/repository-view.js M client/galaxy/scripts/mvc/toolshed/shed-list-view.js M static/scripts/mvc/toolshed/categories-view.js M static/scripts/mvc/toolshed/repositories-view.js M static/scripts/mvc/toolshed/repository-view.js M static/scripts/mvc/toolshed/shed-list-view.js Log Message: ----------- Tweaked the UI a bit. Commit: 9463d94a2aa4d30140d18094db55bb4e58e9ebc7 https://github.com/galaxyproject/galaxy/commit/9463d94a2aa4d30140d18094db55b... Author: Dave B <dave@bx.psu.edu> Date: 2017-01-06 (Fri, 06 Jan 2017) Changed paths: M .ci/flake8_lint_include_list.txt A .ci/jenkins/api/run_tests.sh A .ci/jenkins/framework/run_tests.sh A .ci/jenkins/integration/run_tests.sh A .ci/jenkins/selenium/Dockerfile A .ci/jenkins/selenium/docker-compose.yml A .ci/jenkins/selenium/galaxy.ini A .ci/jenkins/selenium/run_galaxy.bash A .ci/jenkins/selenium/run_tests.sh A .ci/jenkins/toolshed/run_tests.sh M .ci/py3_sources.txt M Makefile M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/apps/tool-panel.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/page.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/history/options-menu.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/tool/tool-form-workflow.js M client/galaxy/scripts/mvc/tool/tools.js M client/galaxy/scripts/mvc/ui/ui-misc.js M client/galaxy/scripts/mvc/upload/composite/composite-row.js M client/galaxy/scripts/mvc/upload/default/default-row.js A client/galaxy/scripts/mvc/user/user-preferences.js M client/galaxy/style/less/base.less M client/galaxy/style/less/dataset.less M client/galaxy/style/less/ui.less M client/galaxy/style/source_material/circle.py M config/datatypes_conf.xml.sample M config/galaxy.ini.sample M config/job_conf.xml.sample_advanced M config/plugins/interactive_environments/jupyter/config/jupyter.ini.sample M config/plugins/interactive_environments/jupyter/config/jupyter.xml M config/plugins/interactive_environments/rstudio/config/allowed_images.yml.sample M config/plugins/interactive_environments/rstudio/config/rstudio.xml M config/plugins/interactive_environments/rstudio/static/js/rstudio.js M config/plugins/interactive_environments/rstudio/templates/rstudio.mako M config/plugins/tours/core.galaxy_ui.yaml M config/plugins/tours/core.history.yaml M config/plugins/visualizations/charts/static/repository/build/registry.js M config/plugins/visualizations/charts/static/repository/build/registry.js.map M config/plugins/visualizations/charts/static/repository/visualizations/utilities/tabular-form.js M config/plugins/visualizations/charts/webpack.config.js M contrib/galaxy_config_merger.py M contrib/nagios/check_galaxy.py M cron/add_manual_builds.py M cron/build_chrom_db.py M cron/parse_builds.py M cron/parse_builds_3_sites.py A display_applications/igv/genome_fasta.xml M doc/Makefile A doc/fix_schema_rst.sh M doc/parse_gx_xsd.py M doc/patch.py M doc/source/admin/dependency_resolvers.rst M doc/source/admin/index.rst M doc/source/admin/interactive_environments.rst M doc/source/admin/interactive_environments.svg M doc/source/admin/webhooks.rst M doc/source/dev/faq.rst M doc/source/dev/interactive_environments.rst M doc/source/project/organization.rst A doc/source/releases/16.10.rst M doc/source/releases/16.10_announce.rst A doc/source/releases/17.01_announce.rst M lib/galaxy/actions/admin.py M lib/galaxy/auth/__init__.py M lib/galaxy/auth/providers/ldap_ad.py M lib/galaxy/auth/providers/pam_auth.py M lib/galaxy/config.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/converters/bam_to_bai.xml M lib/galaxy/datatypes/converters/bcf_bgzip_to_bcf_converter.xml M lib/galaxy/datatypes/converters/bcf_to_bcf_bgzip_converter.xml M lib/galaxy/datatypes/converters/bed_gff_or_vcf_to_bigwig_converter.xml M lib/galaxy/datatypes/converters/bed_to_bgzip_converter.xml M lib/galaxy/datatypes/converters/bed_to_fli_converter.xml M lib/galaxy/datatypes/converters/bed_to_gff_converter.py M lib/galaxy/datatypes/converters/bed_to_gff_converter.xml M lib/galaxy/datatypes/converters/bed_to_interval_index_converter.xml M lib/galaxy/datatypes/converters/bed_to_tabix_converter.xml M lib/galaxy/datatypes/converters/bedgraph_to_array_tree_converter.py M lib/galaxy/datatypes/converters/bedgraph_to_array_tree_converter.xml M lib/galaxy/datatypes/converters/bedgraph_to_bigwig_converter.xml M lib/galaxy/datatypes/converters/bgzip.py M lib/galaxy/datatypes/converters/encodepeak_to_bgzip_converter.xml M lib/galaxy/datatypes/converters/encodepeak_to_tabix_converter.xml M lib/galaxy/datatypes/converters/fasta_to_2bit.xml M lib/galaxy/datatypes/converters/fasta_to_bowtie_base_index_converter.xml M lib/galaxy/datatypes/converters/fasta_to_bowtie_color_index_converter.xml A lib/galaxy/datatypes/converters/fasta_to_fai.xml M lib/galaxy/datatypes/converters/fasta_to_len.py M lib/galaxy/datatypes/converters/fasta_to_len.xml M lib/galaxy/datatypes/converters/fasta_to_tabular_converter.xml M lib/galaxy/datatypes/converters/fastq_to_fqtoc.xml M 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tools/stats/aggregate_scores_in_intervals.py M tools/stats/filtering.py M tools/stats/grouping.py M tools/stats/gsummary.py Log Message: ----------- Merge in -dev. Commit: 6954c082fded87b9ab71f97675aa7bc94a975770 https://github.com/galaxyproject/galaxy/commit/6954c082fded87b9ab71f97675aa7... Author: Dave B <dave@bx.psu.edu> Date: 2017-01-06 (Fri, 06 Jan 2017) Changed paths: M client/galaxy/scripts/mvc/toolshed/categories-view.js M client/galaxy/scripts/mvc/toolshed/repositories-view.js A client/galaxy/scripts/mvc/toolshed/repository-queue-view.js A client/galaxy/scripts/mvc/toolshed/util.js M lib/galaxy/webapps/galaxy/api/toolshed.py M static/scripts/mvc/toolshed/categories-view.js M static/scripts/mvc/toolshed/repositories-view.js Log Message: ----------- Preliminary commit before fixing the search autocomplete. Commit: c955e6fd979a9a402b57f083930108146b21f24a https://github.com/galaxyproject/galaxy/commit/c955e6fd979a9a402b57f08393010... Author: Dave B <dave@bx.psu.edu> Date: 2017-01-12 (Thu, 12 Jan 2017) Changed paths: M client/galaxy/scripts/mvc/toolshed/categories-view.js M client/galaxy/scripts/mvc/toolshed/repositories-view.js M client/galaxy/scripts/mvc/toolshed/repository-view.js M client/galaxy/scripts/mvc/toolshed/shed-list-view.js M client/galaxy/scripts/mvc/toolshed/util.js M lib/galaxy/webapps/galaxy/buildapp.py M static/scripts/mvc/toolshed/categories-view.js M static/scripts/mvc/toolshed/repositories-view.js M static/scripts/mvc/toolshed/repository-view.js M static/scripts/mvc/toolshed/shed-list-view.js Log Message: ----------- Fix searching. Commit: de8e43fd65d001a2a076ea4044d192199ae3c446 https://github.com/galaxyproject/galaxy/commit/de8e43fd65d001a2a076ea4044d19... Author: Dave B <dave@bx.psu.edu> Date: 2017-01-19 (Thu, 19 Jan 2017) Changed paths: M client/galaxy/scripts/mvc/toolshed/repository-view.js M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/api/toolshed.py M static/scripts/mvc/toolshed/repository-view.js Log Message: ----------- Fix tool form modal. Commit: 8d5b154ef0d25e4b8cbbba7128d14c26e2c4a758 https://github.com/galaxyproject/galaxy/commit/8d5b154ef0d25e4b8cbbba7128d14... Author: Dave B <dave@bx.psu.edu> Date: 2017-02-02 (Thu, 02 Feb 2017) Changed paths: M client/galaxy/scripts/admin.toolshed.js M client/galaxy/scripts/mvc/toolshed/categories-view.js M client/galaxy/scripts/mvc/toolshed/repositories-view.js M client/galaxy/scripts/mvc/toolshed/repository-queue-view.js M client/galaxy/scripts/mvc/toolshed/repository-view.js M client/galaxy/scripts/mvc/toolshed/shed-list-view.js M client/galaxy/scripts/mvc/toolshed/toolshed-model.js M static/maps/admin.toolshed.js.map M static/maps/mvc/toolshed/toolshed-model.js.map M static/scripts/admin.toolshed.js M static/scripts/mvc/toolshed/categories-view.js M static/scripts/mvc/toolshed/repositories-view.js M static/scripts/mvc/toolshed/repository-view.js M static/scripts/mvc/toolshed/shed-list-view.js M static/scripts/mvc/toolshed/toolshed-model.js Log Message: ----------- Finally got the repository queue rendering semi-properly. Commit: e92fcf1457e0396e3173b1b7541c53b26a33a47b https://github.com/galaxyproject/galaxy/commit/e92fcf1457e0396e3173b1b7541c5... 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tools/filters/pasteWrapper.xml M tools/maf/genebed_maf_to_fasta.xml M tools/maf/interval2maf.xml M tools/maf/interval2maf_pairwise.xml M tools/maf/interval_maf_to_merged_fasta.xml M tools/maf/macros.xml M tools/maf/maf_by_block_number.xml M tools/maf/maf_filter.xml M tools/maf/maf_limit_size.xml M tools/maf/maf_limit_to_species.xml M tools/maf/maf_reverse_complement.xml M tools/maf/maf_split_by_species.xml M tools/maf/maf_stats.xml M tools/maf/maf_thread_for_species.xml M tools/maf/maf_to_bed.xml M tools/maf/maf_to_fasta.xml M tools/maf/maf_to_interval.xml M tools/maf/vcf_to_maf_customtrack.xml M tools/metag_tools/shrimp_color_wrapper.xml M tools/metag_tools/shrimp_wrapper.xml M tools/next_gen_conversion/fastq_gen_conv.xml M tools/plotting/bar_chart.xml M tools/stats/aggregate_binned_scores_in_intervals.xml M tox.ini Log Message: ----------- Merge -dev. Commit: 03ae0d5d6f5c278e0d1d501f68aef49e4f63ff7c https://github.com/galaxyproject/galaxy/commit/03ae0d5d6f5c278e0d1d501f68aef... Author: Dave B <dave@bx.psu.edu> Date: 2017-02-09 (Thu, 09 Feb 2017) Changed paths: M client/galaxy/scripts/admin.toolshed.js A client/galaxy/scripts/mvc/toolshed/repo-status-view.js M client/galaxy/scripts/mvc/toolshed/repositories-view.js M client/galaxy/scripts/mvc/toolshed/repository-queue-view.js M client/galaxy/scripts/mvc/toolshed/repository-view.js M client/galaxy/scripts/mvc/toolshed/toolshed-model.js M client/galaxy/scripts/mvc/toolshed/util.js M lib/galaxy/webapps/galaxy/api/toolshed.py M lib/galaxy/webapps/galaxy/buildapp.py A static/maps/mvc/toolshed/categories-view.js.map A static/maps/mvc/toolshed/repositories-view.js.map A static/maps/mvc/toolshed/repository-queue-view.js.map A static/maps/mvc/toolshed/repository-view.js.map A static/maps/mvc/toolshed/shed-list-view.js.map A static/maps/mvc/toolshed/util.js.map M static/scripts/admin.toolshed.js A static/scripts/mvc/toolshed/repo-status-view.js M static/scripts/mvc/toolshed/repositories-view.js A static/scripts/mvc/toolshed/repository-queue-view.js M static/scripts/mvc/toolshed/repository-view.js M static/scripts/mvc/toolshed/toolshed-model.js A static/scripts/mvc/toolshed/util.js Log Message: ----------- Fix installation from queue, add repository installation status view. Commit: 259c3c5f99522d0b4f0e62f24386ce11548fc3cc https://github.com/galaxyproject/galaxy/commit/259c3c5f99522d0b4f0e62f24386c... Author: Dave B <dave@bx.psu.edu> Date: 2017-02-09 (Thu, 09 Feb 2017) Changed paths: M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt M client/galaxy/scripts/libs/jquery/jquery.autocomplete.js M client/galaxy/scripts/mvc/form/form-input.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-base.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/tool/tool-form-workflow.js M client/galaxy/scripts/mvc/tool/tool-form.js M client/galaxy/scripts/mvc/ui/ui-misc.js M client/galaxy/scripts/mvc/ui/ui-portlet.js M client/galaxy/scripts/mvc/workflow/workflow-manager.js M client/galaxy/scripts/mvc/workflow/workflow-node.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M client/galaxy/scripts/ui/autocom_tagging.js M config/datatypes_conf.xml.sample M config/galaxy.ini.sample M config/plugins/interactive_environments/jupyter/config/jupyter.xml M config/plugins/tours/core.history.yaml M contrib/nagios/check_galaxy M contrib/nagios/check_galaxy.py R doc/source/lib/galaxy_utils.rst R doc/source/lib/galaxy_utils.sequence.rst M doc/source/lib/modules.rst A doc/source/releases/17.01.rst M doc/source/releases/17.01_announce.rst A doc/source/releases/17.05_announce.rst M doc/source/releases/_thanks.rst M doc/source/releases/index.rst M lib/galaxy/config.py M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/managers/deletable.py M lib/galaxy/managers/users.py M lib/galaxy/managers/workflows.py M lib/galaxy/model/migrate/check.py M lib/galaxy/model/migrate/versions/0003_security_and_libraries.py M lib/galaxy/model/migrate/versions/0004_indexes_and_defaults.py M lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py M lib/galaxy/model/migrate/versions/0006_change_qual_datatype.py M lib/galaxy/model/migrate/versions/0007_sharing_histories.py M lib/galaxy/model/migrate/versions/0008_galaxy_forms.py M lib/galaxy/model/migrate/versions/0009_request_table.py M lib/galaxy/model/migrate/versions/0010_hda_display_at_authz_table.py M lib/galaxy/model/migrate/versions/0011_v0010_mysql_index_fix.py M lib/galaxy/model/migrate/versions/0012_user_address.py M lib/galaxy/model/migrate/versions/0013_change_lib_item_templates_to_forms.py M lib/galaxy/model/migrate/versions/0014_pages.py M lib/galaxy/model/migrate/versions/0015_tagging.py M lib/galaxy/model/migrate/versions/0016_v0015_mysql_index_fix.py M lib/galaxy/model/migrate/versions/0017_library_item_indexes.py M lib/galaxy/model/migrate/versions/0018_ordered_tags_and_page_tags.py M lib/galaxy/model/migrate/versions/0019_request_library_folder.py M lib/galaxy/model/migrate/versions/0020_library_upload_job.py M lib/galaxy/model/migrate/versions/0021_user_prefs.py M lib/galaxy/model/migrate/versions/0022_visualization_tables.py M lib/galaxy/model/migrate/versions/0024_page_slug_unique_constraint.py M lib/galaxy/model/migrate/versions/0025_user_info.py M lib/galaxy/model/migrate/versions/0026_cloud_tables.py M lib/galaxy/model/migrate/versions/0027_request_events.py M lib/galaxy/model/migrate/versions/0028_external_metadata_file_override.py M lib/galaxy/model/migrate/versions/0029_user_actions.py M lib/galaxy/model/migrate/versions/0031_community_and_workflow_tags.py M lib/galaxy/model/migrate/versions/0033_published_cols_for_histories_and_workflows.py M lib/galaxy/model/migrate/versions/0034_page_user_share_association.py M lib/galaxy/model/migrate/versions/0035_item_annotations_and_workflow_step_tags.py M lib/galaxy/model/migrate/versions/0036_add_deleted_column_to_library_template_assoc_tables.py M lib/galaxy/model/migrate/versions/0037_samples_library.py M lib/galaxy/model/migrate/versions/0038_add_inheritable_column_to_library_template_assoc_tables.py M lib/galaxy/model/migrate/versions/0039_add_synopsis_column_to_library_table.py M lib/galaxy/model/migrate/versions/0040_page_annotations.py M lib/galaxy/model/migrate/versions/0041_workflow_invocation.py M lib/galaxy/model/migrate/versions/0043_visualization_sharing_tagging_annotating.py M lib/galaxy/model/migrate/versions/0044_add_notify_column_to_request_table.py M lib/galaxy/model/migrate/versions/0045_request_type_permissions_table.py M lib/galaxy/model/migrate/versions/0046_post_job_actions.py M lib/galaxy/model/migrate/versions/0047_job_table_user_id_column.py M lib/galaxy/model/migrate/versions/0048_dataset_instance_state_column.py M lib/galaxy/model/migrate/versions/0049_api_keys_table.py M lib/galaxy/model/migrate/versions/0050_drop_cloud_tables.py M lib/galaxy/model/migrate/versions/0051_imported_col_for_jobs_table.py M lib/galaxy/model/migrate/versions/0052_sample_dataset_table.py M lib/galaxy/model/migrate/versions/0053_item_ratings.py M lib/galaxy/model/migrate/versions/0055_add_pja_assoc_for_jobs.py M lib/galaxy/model/migrate/versions/0057_request_notify.py M lib/galaxy/model/migrate/versions/0058_history_import_export.py M lib/galaxy/model/migrate/versions/0059_sample_dataset_file_path.py M lib/galaxy/model/migrate/versions/0060_history_archive_import.py M lib/galaxy/model/migrate/versions/0062_user_openid_table.py M lib/galaxy/model/migrate/versions/0063_sequencer_table.py M lib/galaxy/model/migrate/versions/0064_add_run_and_sample_run_association_tables.py M lib/galaxy/model/migrate/versions/0065_add_name_to_form_fields_and_values.py M lib/galaxy/model/migrate/versions/0066_deferred_job_and_transfer_job_tables.py M lib/galaxy/model/migrate/versions/0067_populate_sequencer_table.py M lib/galaxy/model/migrate/versions/0068_rename_sequencer_to_external_services.py M lib/galaxy/model/migrate/versions/0069_rename_sequencer_form_type.py M lib/galaxy/model/migrate/versions/0070_add_info_column_to_deferred_job_table.py M lib/galaxy/model/migrate/versions/0071_add_history_and_workflow_to_sample.py M lib/galaxy/model/migrate/versions/0072_add_pid_and_socket_columns_to_transfer_job_table.py M lib/galaxy/model/migrate/versions/0073_add_ldda_to_implicit_conversion_table.py M lib/galaxy/model/migrate/versions/0074_add_purged_column_to_library_dataset_table.py M lib/galaxy/model/migrate/versions/0075_add_subindex_column_to_run_table.py M lib/galaxy/model/migrate/versions/0077_create_tool_tag_association_table.py M lib/galaxy/model/migrate/versions/0078_add_columns_for_disk_usage_accounting.py M lib/galaxy/model/migrate/versions/0079_input_library_to_job_table.py M lib/galaxy/model/migrate/versions/0080_quota_tables.py M lib/galaxy/model/migrate/versions/0081_add_tool_version_to_hda_ldda.py M lib/galaxy/model/migrate/versions/0082_add_tool_shed_repository_table.py M lib/galaxy/model/migrate/versions/0083_add_prepare_files_to_task.py M 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lib/galaxy/model/migrate/versions/0098_genome_index_tool_data_table.py M lib/galaxy/model/migrate/versions/0099_add_tool_dependency_table.py M lib/galaxy/model/migrate/versions/0100_alter_tool_dependency_table_version_column.py M lib/galaxy/model/migrate/versions/0101_drop_installed_changeset_revision_column.py M lib/galaxy/model/migrate/versions/0102_add_tool_dependency_status_columns.py M lib/galaxy/model/migrate/versions/0103_add_tool_shed_repository_status_columns.py M lib/galaxy/model/migrate/versions/0104_update_genome_downloader_job_parameters.py M lib/galaxy/model/migrate/versions/0105_add_cleanup_event_table.py M lib/galaxy/model/migrate/versions/0106_add_missing_indexes.py M lib/galaxy/model/migrate/versions/0107_add_exit_code_to_job_and_task.py M lib/galaxy/model/migrate/versions/0108_add_extended_metadata.py M lib/galaxy/model/migrate/versions/0109_add_repository_dependency_tables.py M lib/galaxy/model/migrate/versions/0110_add_dataset_uuid.py M lib/galaxy/model/migrate/versions/0111_add_job_destinations.py M lib/galaxy/model/migrate/versions/0112_add_data_manager_history_association_and_data_manager_job_association_tables.py M lib/galaxy/model/migrate/versions/0113_update_migrate_tools_table.py M lib/galaxy/model/migrate/versions/0114_update_migrate_tools_table_again.py M lib/galaxy/model/migrate/versions/0115_longer_user_password_field.py M lib/galaxy/model/migrate/versions/0116_drop_update_available_col_add_tool_shed_status_col.py M lib/galaxy/model/migrate/versions/0117_add_user_activation.py M lib/galaxy/model/migrate/versions/0118_add_hda_extended_metadata.py M lib/galaxy/model/migrate/versions/0119_job_metrics.py M lib/galaxy/model/migrate/versions/0120_dataset_collections.py M lib/galaxy/model/migrate/versions/0121_workflow_uuids.py M lib/galaxy/model/migrate/versions/0122_grow_mysql_blobs.py M lib/galaxy/model/migrate/versions/0123_add_workflow_request_tables.py M lib/galaxy/model/migrate/versions/0124_job_state_history.py M lib/galaxy/model/migrate/versions/0125_workflow_step_tracking.py M lib/galaxy/model/migrate/versions/0126_password_reset.py M lib/galaxy/model/migrate/versions/0127_output_collection_adjustments.py M lib/galaxy/model/migrate/versions/0128_session_timeout.py M lib/galaxy/model/migrate/versions/0129_job_external_output_metadata_validity.py M lib/galaxy/model/migrate/versions/0130_change_pref_datatype.py M lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_parameter_modules.py M lib/galaxy/model/migrate/versions/0132_add_lastpasswordchange_to_user.py M lib/galaxy/model/migrate/versions/0133_add_dependency_column_to_job.py A lib/galaxy/model/migrate/versions/0134_hda_set_deleted_if_purged.py M lib/galaxy/tools/data/__init__.py M lib/galaxy/tools/data_manager/manager.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/meta.py M lib/galaxy/tools/toolbox/watcher.py M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/webapps/galaxy/api/histories.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/steps.py R lib/galaxy_utils/__init__.py R lib/galaxy_utils/sequence/__init__.py R lib/galaxy_utils/sequence/fasta.py R lib/galaxy_utils/sequence/fastq.py R lib/galaxy_utils/sequence/sequence.py R lib/galaxy_utils/sequence/transform.py R lib/galaxy_utils/sequence/vcf.py M scripts/bootstrap_history.py M static/maps/libs/jquery/jquery.autocomplete.js.map M static/maps/mvc/form/form-input.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-base.js.map M static/maps/mvc/tool/tool-form-composite.js.map M static/maps/mvc/tool/tool-form-workflow.js.map M static/maps/mvc/tool/tool-form.js.map M static/maps/mvc/ui/ui-misc.js.map M static/maps/mvc/ui/ui-portlet.js.map M static/maps/mvc/workflow/workflow-manager.js.map M static/maps/mvc/workflow/workflow-node.js.map M static/maps/mvc/workflow/workflow-view.js.map M static/maps/ui/autocom_tagging.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/libs/jquery/jquery.autocomplete.js M static/scripts/mvc/form/form-input.js M static/scripts/mvc/form/form-section.js M static/scripts/mvc/form/form-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-workflow.js M static/scripts/mvc/tool/tool-form.js M static/scripts/mvc/ui/ui-misc.js M static/scripts/mvc/ui/ui-portlet.js M static/scripts/mvc/workflow/workflow-manager.js M static/scripts/mvc/workflow/workflow-node.js M static/scripts/mvc/workflow/workflow-view.js M static/scripts/ui/autocom_tagging.js M templates/webapps/tool_shed/repository/tool_form.mako M test/api/test_histories.py M test/api/test_history_contents.py M test/qunit/tests/form_tests.js M test/unit/managers/test_HDAManager.py M test/unit/managers/test_HistoryManager.py Log Message: ----------- Merge with -dev. Commit: b15fdf080ad86e157829e312da056829710dae12 https://github.com/galaxyproject/galaxy/commit/b15fdf080ad86e157829e312da056... Author: Dave B <dave@bx.psu.edu> Date: 2017-02-14 (Tue, 14 Feb 2017) Changed paths: M client/galaxy/scripts/admin.toolshed.js M client/galaxy/scripts/mvc/toolshed/repository-queue-view.js M client/galaxy/scripts/mvc/toolshed/toolshed-model.js A client/galaxy/scripts/mvc/toolshed/workflows-view.js M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/tool_shed/api/repositories.py M static/scripts/admin.toolshed.js M static/scripts/mvc/toolshed/repository-queue-view.js M static/scripts/mvc/toolshed/toolshed-model.js A static/scripts/mvc/toolshed/workflows-view.js Log Message: ----------- Enable preview of repository from workflows missing tools. Commit: dbbcdee9abb88e2479574c9d410fa50cd29b2b41 https://github.com/galaxyproject/galaxy/commit/dbbcdee9abb88e2479574c9d410fa... Author: Dave B <dave@bx.psu.edu> Date: 2017-02-14 (Tue, 14 Feb 2017) Changed paths: M .ci/flake8_lint_include_list.txt M .ci/jenkins/selenium/run_tests.sh M .ci/py3_sources.txt M CONTRIBUTING.md M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/user/user-quotameter.js M config/datatypes_conf.xml.sample M config/plugins/tours/core.galaxy_ui.yaml M doc/source/slideshow/architecture/galaxy_architecture.md M doc/source/slideshow/architecture/images/hda_dataset.plantuml.svg M doc/source/slideshow/architecture/images/hda_hdca.plantuml.svg M doc/source/slideshow/architecture/images/objectstore.plantuml.svg M doc/source/slideshow/architecture/images/plantuml_options.txt M doc/source/slideshow/architecture/images/server_client.plantuml.svg M doc/source/slideshow/architecture/images/server_client_old.plantuml.svg M doc/source/slideshow/architecture/images/webapp.plantuml.svg M doc/source/slideshow/architecture/style.css M lib/galaxy/datatypes/genetics.py M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/proteomics.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/web/base/controllers/admin.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/workflow/steps.py M scripts/slideshow/slideshow_template.html M static/maps/mvc/tool/tool-form-base.js.map M static/maps/mvc/user/user-quotameter.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/tool/tool-form-base.js M static/scripts/mvc/user/user-quotameter.js M templates/admin/reload_tool.mako M test/api/test_tools.py M test/api/test_workflow_extraction.py M test/base/populators.py A test/functional/tools/output_format_deprecated_when.xml M test/functional/tools/samples_tool_conf.xml M test/selenium_tests/framework.py M test/selenium_tests/test_stock_tours.py M test/selenium_tests/test_uploads.py Log Message: ----------- Merge branch 'dev' of git://github.com/galaxyproject/galaxy into ts_api_backbone Commit: e3eecfc0ec7994aa0385a7d3a4e38ebde0c9125e https://github.com/galaxyproject/galaxy/commit/e3eecfc0ec7994aa0385a7d3a4e38... Author: Dave B <dave@bx.psu.edu> Date: 2017-02-14 (Tue, 14 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/toolshed/repository-queue-view.js M static/scripts/mvc/toolshed/repository-queue-view.js Log Message: ----------- Fix repository queue view. Commit: 64ad2fcf084218e9dea63dc0ade49314b650a721 https://github.com/galaxyproject/galaxy/commit/64ad2fcf084218e9dea63dc0ade49... Author: Dave B <dave@bx.psu.edu> Date: 2017-02-15 (Wed, 15 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/toolshed/repository-queue-view.js M client/galaxy/scripts/mvc/toolshed/repository-view.js M client/galaxy/scripts/mvc/toolshed/toolshed-model.js M client/galaxy/scripts/mvc/toolshed/util.js M client/galaxy/scripts/mvc/toolshed/workflows-view.js M lib/galaxy/webapps/galaxy/api/toolshed.py M static/scripts/mvc/toolshed/repository-view.js M static/scripts/mvc/toolshed/toolshed-model.js M static/scripts/mvc/toolshed/util.js M static/scripts/mvc/toolshed/workflows-view.js Log Message: ----------- Implement adding a workflow repository to the installation queue. Commit: da9c57d3656a61c8da31322d54702e509bb69232 https://github.com/galaxyproject/galaxy/commit/da9c57d3656a61c8da31322d54702... Author: Dave B <dave@bx.psu.edu> Date: 2017-02-15 (Wed, 15 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/user/user-quotameter.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/model/mapping.py M lib/galaxy/model/orm/engine_factory.py M lib/galaxy/webapps/galaxy/api/history_contents.py M lib/galaxy/webapps/galaxy/controllers/user.py M static/maps/mvc/user/user-quotameter.js.map M static/maps/mvc/workflow/workflow-view.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/user/user-quotameter.js M static/scripts/mvc/workflow/workflow-view.js M templates/webapps/galaxy/workflow/editor.mako Log Message: ----------- Merge branch 'dev' of git://github.com/galaxyproject/galaxy into ts_api_backbone Commit: 9688b7ba4d08b63033ddd407b9944cf96e4f4032 https://github.com/galaxyproject/galaxy/commit/9688b7ba4d08b63033ddd407b9944... Author: Dave B <dave@bx.psu.edu> Date: 2017-02-15 (Wed, 15 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/toolshed/repository-queue-view.js M client/galaxy/scripts/mvc/toolshed/util.js M client/galaxy/scripts/mvc/toolshed/workflows-view.js M static/scripts/mvc/toolshed/repository-queue-view.js M static/scripts/mvc/toolshed/util.js M static/scripts/mvc/toolshed/workflows-view.js Log Message: ----------- Fix discovering a repository for workflows. Commit: afc7b1c2cd0641d2b57821c5c1a8e0e245a2ad54 https://github.com/galaxyproject/galaxy/commit/afc7b1c2cd0641d2b57821c5c1a8e... Author: Dave B <dave@bx.psu.edu> Date: 2017-02-16 (Thu, 16 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/toolshed/repo-status-view.js M static/scripts/mvc/toolshed/repo-status-view.js Log Message: ----------- Fix styling for repository installation status. Commit: 233b90c610b8ed3d8067da7a4b4944ab6d322000 https://github.com/galaxyproject/galaxy/commit/233b90c610b8ed3d8067da7a4b494... Author: Dave B <dave@bx.psu.edu> Date: 2017-02-16 (Thu, 16 Feb 2017) Changed paths: M client/galaxy/scripts/admin.toolshed.js M client/galaxy/scripts/mvc/toolshed/categories-view.js M client/galaxy/scripts/mvc/toolshed/repo-status-view.js M client/galaxy/scripts/mvc/toolshed/repositories-view.js M client/galaxy/scripts/mvc/toolshed/repository-queue-view.js M client/galaxy/scripts/mvc/toolshed/repository-view.js M client/galaxy/scripts/mvc/toolshed/shed-list-view.js M client/galaxy/scripts/mvc/toolshed/util.js M client/galaxy/scripts/mvc/toolshed/workflows-view.js M static/scripts/admin.toolshed.js M static/scripts/mvc/toolshed/categories-view.js M static/scripts/mvc/toolshed/repo-status-view.js M static/scripts/mvc/toolshed/repositories-view.js M static/scripts/mvc/toolshed/repository-queue-view.js M static/scripts/mvc/toolshed/repository-view.js M static/scripts/mvc/toolshed/shed-list-view.js M static/scripts/mvc/toolshed/util.js M static/scripts/mvc/toolshed/workflows-view.js Log Message: ----------- Style the repository queue properly. Commit: 661e93a139ba5189856d8189886dcce8ac06d7d6 https://github.com/galaxyproject/galaxy/commit/661e93a139ba5189856d8189886dc... Author: Dave B <dave@bx.psu.edu> Date: 2017-02-16 (Thu, 16 Feb 2017) Changed paths: A config/plugins/visualizations/charts/static/repository/build/ngl_viewer.js A config/plugins/visualizations/charts/static/repository/build/ngl_viewer.js.map M config/plugins/visualizations/charts/static/repository/build/registry.js M config/plugins/visualizations/charts/static/repository/build/registry.js.map M config/plugins/visualizations/charts/static/repository/build/registry.tmp.js A config/plugins/visualizations/charts/static/repository/plugins/ngl/viewer.js M config/plugins/visualizations/charts/static/repository/registry.json A config/plugins/visualizations/charts/static/repository/visualizations/ngl/viewer/config.js A config/plugins/visualizations/charts/static/repository/visualizations/ngl/viewer/logo.png A config/plugins/visualizations/charts/static/repository/visualizations/ngl/viewer/wrapper.js A scripts/secret_decoder_ring.py Log Message: ----------- Merge branch 'dev' of git://github.com/galaxyproject/galaxy into ts_api_backbone Commit: ba1ccce10af37ebd84b83a77ad7b764ab4d9efe5 https://github.com/galaxyproject/galaxy/commit/ba1ccce10af37ebd84b83a77ad7b7... Author: Dave B <dave@bx.psu.edu> Date: 2017-02-16 (Thu, 16 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/toolshed/categories-view.js M client/galaxy/scripts/mvc/toolshed/repository-queue-view.js M client/galaxy/scripts/mvc/toolshed/workflows-view.js M static/scripts/mvc/toolshed/workflows-view.js Log Message: ----------- Remove superfluous commands. Commit: 6aa167ba50c3f4f31a7b0c637f88b1d7400dc501 https://github.com/galaxyproject/galaxy/commit/6aa167ba50c3f4f31a7b0c637f88b... Author: Dave B <dave@bx.psu.edu> Date: 2017-02-16 (Thu, 16 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/toolshed/categories-view.js M client/galaxy/scripts/mvc/toolshed/repositories-view.js M static/scripts/mvc/toolshed/categories-view.js M static/scripts/mvc/toolshed/repositories-view.js Log Message: ----------- Made search results more readable. Commit: 73773d269ba4bb014f99d5230fd8ecdc811ede52 https://github.com/galaxyproject/galaxy/commit/73773d269ba4bb014f99d5230fd8e... Author: Dave B <dave@bx.psu.edu> Date: 2017-02-16 (Thu, 16 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/toolshed/repo-status-view.js M client/galaxy/scripts/mvc/toolshed/repository-view.js M static/scripts/mvc/toolshed/repo-status-view.js M static/scripts/mvc/toolshed/repository-view.js Log Message: ----------- Remove queue button from installed repos. Commit: e0bb34cdf5e4ffa6927c758ba03823f1160966c3 https://github.com/galaxyproject/galaxy/commit/e0bb34cdf5e4ffa6927c758ba0382... Author: Dave B <dave@bx.psu.edu> Date: 2017-02-17 (Fri, 17 Feb 2017) Changed paths: M doc/source/releases/17.01_announce.rst M lib/galaxy/model/__init__.py M lib/galaxy/tools/parameters/basic.py M test/unit/tools/test_data_parameters.py M test/unit/tools/test_execution.py Log Message: ----------- Merge branch 'dev' of git://github.com/galaxyproject/galaxy into ts_api_backbone Commit: 68a51acc5395d5a2af0c5a68bf756fe41b14c9f2 https://github.com/galaxyproject/galaxy/commit/68a51acc5395d5a2af0c5a68bf756... Author: Dave B <dave@bx.psu.edu> Date: 2017-02-17 (Fri, 17 Feb 2017) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/api/toolshed.py Log Message: ----------- Correct errors revealed by travis. Commit: 5dc9728d29bc4c0c8b587dc30cd492a87193065a https://github.com/galaxyproject/galaxy/commit/5dc9728d29bc4c0c8b587dc30cd49... Author: Dave B <dave@bx.psu.edu> Date: 2017-02-21 (Tue, 21 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/toolshed/repository-queue-view.js M client/galaxy/scripts/mvc/toolshed/repository-view.js M static/scripts/mvc/toolshed/repository-queue-view.js M static/scripts/mvc/toolshed/repository-view.js Log Message: ----------- Mostly fixed repository dependency jstree. Commit: fdf95d3702118cfee16dd904dc461898316b7bf9 https://github.com/galaxyproject/galaxy/commit/fdf95d3702118cfee16dd904dc461... Author: Dave B <dave@bx.psu.edu> Date: 2017-02-21 (Tue, 21 Feb 2017) Changed paths: 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-workflow.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M config/galaxy.ini.sample M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/webapps/galaxy/api/lda_datasets.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run_request.py M lib/tool_shed/util/workflow_util.py 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-workflow.js.map M static/maps/mvc/workflow/workflow-view.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/tool/tool-form-base.js M static/scripts/mvc/tool/tool-form-composite.js M static/scripts/mvc/tool/tool-form-workflow.js M static/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Merge dev. Commit: fbe557f09b86c97700043a5bd4222b62d9d0d49a https://github.com/galaxyproject/galaxy/commit/fbe557f09b86c97700043a5bd4222... Author: Dave B <dave@bx.psu.edu> Date: 2017-03-06 (Mon, 06 Mar 2017) Changed paths: M .ci/flake8_blacklist.txt M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/grid/grid-view.js M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/history-view.js M client/galaxy/scripts/mvc/history/options-menu.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js R client/galaxy/scripts/mvc/tool/tool-form-workflow.js A client/galaxy/scripts/mvc/workflow/workflow-forms.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M config/datatypes_conf.xml.sample M config/galaxy.ini.sample M config/plugins/interactive_environments/bam_iobio/config/bam_iobio.ini.sample M config/plugins/interactive_environments/jupyter/config/allowed_images.yml.sample M config/plugins/interactive_environments/jupyter/config/jupyter.ini.sample M config/plugins/interactive_environments/neo/config/neo.ini.sample M config/plugins/interactive_environments/phinch/config/phinch.ini.sample M config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample A cron/clean_docker_swarm_mode_services.sh M doc/source/admin/interactive_environments.rst M doc/source/releases/17.01_announce.rst M lib/galaxy/auth/providers/ldap_ad.py M lib/galaxy/config.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/mothur.py M lib/galaxy/datatypes/proteomics.py M lib/galaxy/exceptions/error_codes.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/command_factory.py M lib/galaxy/jobs/dynamic_tool_destination.py M lib/galaxy/managers/workflows.py M lib/galaxy/model/orm/engine_factory.py M lib/galaxy/queue_worker.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/mulled/invfile.lua M lib/galaxy/tools/deps/mulled/mulled_build.py M lib/galaxy/tools/linters/general.py M lib/galaxy/tools/linters/outputs.py M lib/galaxy/tools/linters/stdio.py M lib/galaxy/tools/linters/tests.py M lib/galaxy/tools/search/__init__.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/visualization/plugins/plugin.py M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/web/framework/middleware/remoteuser.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/workflow/modules.py M scripts/bootstrap_history.py M static/maps/mvc/form/form-input.js.map M static/maps/mvc/form/form-section.js.map M static/maps/mvc/grid/grid-view.js.map M static/maps/mvc/history/history-model.js.map M static/maps/mvc/history/history-view.js.map M static/maps/mvc/history/options-menu.js.map M static/maps/mvc/tool/tool-form-composite.js.map R static/maps/mvc/tool/tool-form-workflow.js.map A static/maps/mvc/workflow/workflow-forms.js.map M static/maps/mvc/workflow/workflow-view.js.map R static/maps/mvc/workflow/workflow.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-section.js M static/scripts/mvc/grid/grid-view.js M static/scripts/mvc/history/history-model.js M static/scripts/mvc/history/history-view.js M static/scripts/mvc/history/options-menu.js M static/scripts/mvc/tool/tool-form-composite.js R static/scripts/mvc/tool/tool-form-workflow.js A static/scripts/mvc/workflow/workflow-forms.js M static/scripts/mvc/workflow/workflow-view.js M templates/grid_base.mako A templates/webapps/galaxy/user/manage_info.mako M test/api/test_workflows.py A test/functional/tools/mulled_example_multi_incomplete.xml M test/functional/tools/samples_tool_conf.xml M test/unit/workflows/test_modules.py M tools/data_source/upload.py Log Message: ----------- Merge branch 'dev' of git://github.com/galaxyproject/galaxy into ts_api_backbone Commit: fb5005bba40d1d1b53b826ab620686662d42c39e https://github.com/galaxyproject/galaxy/commit/fb5005bba40d1d1b53b826ab62068... Author: Dave B <dave@bx.psu.edu> Date: 2017-03-06 (Mon, 06 Mar 2017) Changed paths: M client/galaxy/scripts/mvc/toolshed/repository-view.js M lib/galaxy/tools/__init__.py M static/scripts/mvc/toolshed/repository-view.js M static/scripts/mvc/webhooks.js Log Message: ----------- Fix incorrect merge. Commit: 9309cecef039e6a00eb944c6b6d445e8e935c1cf https://github.com/galaxyproject/galaxy/commit/9309cecef039e6a00eb944c6b6d44... Author: Martin Cech <marten@bx.psu.edu> Date: 2017-03-21 (Tue, 21 Mar 2017) Changed paths: M client/galaxy/scripts/mvc/toolshed/shed-list-view.js M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py Log Message: ----------- add small stylystic changes Commit: 0ba78254e57b8f0fd2c8c64a36c4385f3a8bda87 https://github.com/galaxyproject/galaxy/commit/0ba78254e57b8f0fd2c8c64a36c43... Author: Martin Cech <marten@bx.psu.edu> Date: 2017-03-21 (Tue, 21 Mar 2017) Changed paths: M static/maps/admin.toolshed.js.map M static/maps/mvc/toolshed/categories-view.js.map A static/maps/mvc/toolshed/repo-status-view.js.map M static/maps/mvc/toolshed/repositories-view.js.map M static/maps/mvc/toolshed/repository-queue-view.js.map M static/maps/mvc/toolshed/repository-view.js.map M static/maps/mvc/toolshed/shed-list-view.js.map M static/maps/mvc/toolshed/toolshed-model.js.map M static/maps/mvc/toolshed/util.js.map A static/maps/mvc/toolshed/workflows-view.js.map M static/scripts/admin.toolshed.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/toolshed/categories-view.js M static/scripts/mvc/toolshed/repo-status-view.js M static/scripts/mvc/toolshed/repositories-view.js M static/scripts/mvc/toolshed/repository-queue-view.js M static/scripts/mvc/toolshed/repository-view.js M static/scripts/mvc/toolshed/shed-list-view.js M static/scripts/mvc/toolshed/toolshed-model.js M static/scripts/mvc/toolshed/util.js M static/scripts/mvc/toolshed/workflows-view.js M static/scripts/mvc/ui/ui-thumbnails.js Log Message: ----------- repack client (seems to not be done in a while) Commit: 6ba72513e492609e81095cd6c7a75c9c4eb908c6 https://github.com/galaxyproject/galaxy/commit/6ba72513e492609e81095cd6c7a75... Author: Dave B <dave@bx.psu.edu> Date: 2017-03-21 (Tue, 21 Mar 2017) Changed paths: M .ci/py3_sources.txt M README.rst M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/galaxy.interactive_environments.js M client/galaxy/scripts/layout/menu.js A client/galaxy/scripts/mvc/collection/base-creator.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/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/grid/grid-template.js M client/galaxy/scripts/mvc/grid/grid-view.js M client/galaxy/scripts/mvc/history/hda-li.js M client/galaxy/scripts/mvc/tool/tools.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/upload/upload-ftp.js M client/galaxy/scripts/mvc/user/user-preferences.js M client/galaxy/style/less/history.less M client/galaxy/style/less/ui.less M 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static/scripts/mvc/ui/ui-select-default.js M static/scripts/mvc/upload/upload-ftp.js M static/scripts/mvc/user/user-preferences.js M static/style/blue/base.css M templates/grid_base.mako M templates/webapps/galaxy/admin/index.mako A templates/webapps/galaxy/admin/manage_dependencies.mako R templates/webapps/galaxy/user/manage_info.mako M templates/webapps/tool_shed/repository/common.mako M test/TESTING.md M test/docker/base/run_test_wrapper.sh M test/galaxy_selenium/has_driver.py M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/navigation-data.yml M test/integration/test_resolvers.py A test/selenium_tests/test_collection_builders.py M test/unit/tools/test_data_parameters.py Log Message: ----------- Merge with -dev. Commit: 0d87bb58805cb1ec1ee45f5c9c6557e56154a2cf https://github.com/galaxyproject/galaxy/commit/0d87bb58805cb1ec1ee45f5c9c655... Author: Dave B <dave@bx.psu.edu> Date: 2017-03-21 (Tue, 21 Mar 2017) Changed paths: M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Remove duplicate import. Commit: a1f110be7eb86ccf2d72a4bb93c2b61999c9aeae https://github.com/galaxyproject/galaxy/commit/a1f110be7eb86ccf2d72a4bb93c2b... 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test/integration/test_workflow_handler_configuration.py A test/integration/workflow_handler_configuration_job_conf.xml M test/qunit/package.json M test/qunit/test-data/paired-collection-creator.data.js M test/selenium_tests/test_collection_builders.py M test/selenium_tests/test_tool_form.py M test/selenium_tests/test_uploads.py M test/shed_functional/functional/test_1090_repository_dependency_handling.py M test/shed_functional/functional/test_1150_datatype_converters.py M test/unit/tools/test_toolbox.py M test/unit/tools/test_watcher.py M tool-data/shared/ucsc/builds.txt.sample M tool-data/shared/ucsc/ucsc_build_sites.txt.sample M tools/filters/trimmer.py M tools/filters/trimmer.xml Log Message: ----------- Merge with dev. Commit: ee755cb47ad6f8401f02e452e940941b71ce1fe8 https://github.com/galaxyproject/galaxy/commit/ee755cb47ad6f8401f02e452e9409... Author: Dave B <dave@bx.psu.edu> Date: 2017-04-24 (Mon, 24 Apr 2017) Changed paths: M .ci/flake8_docstrings_include_list.txt M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt M client/galaxy/scripts/galaxy.interactive_environments.js M client/galaxy/style/less/ui.less A config/containers_conf.yml.sample M config/galaxy.ini.sample M config/plugins/interactive_environments/common/templates/ie.mako M config/plugins/interactive_environments/ethercalc/static/js/ethercalc.js M config/plugins/interactive_environments/ethercalc/templates/ethercalc.mako M config/tool_conf.xml.sample M lib/galaxy/config.py R lib/galaxy/container/__init__.py R lib/galaxy/container/docker_swarm.py A lib/galaxy/containers/__init__.py A lib/galaxy/containers/docker.py A lib/galaxy/containers/docker_decorators.py A lib/galaxy/containers/docker_model.py A lib/galaxy/containers/docker_swarm.py A lib/galaxy/containers/docker_swarm_manager.py M lib/galaxy/datatypes/text.py M lib/galaxy/exceptions/__init__.py M lib/galaxy/jobs/__init__.py M lib/galaxy/queue_worker.py M lib/galaxy/queues.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/evaluation.py A lib/galaxy/tools/filter_from_file.xml M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/wrapped.py A lib/galaxy/tools/relabel_from_file.xml M lib/galaxy/tools/wrappers.py A lib/galaxy/util/handlers.py M lib/galaxy/util/submodules.py M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/web/proxy/__init__.py M lib/galaxy/webapps/galaxy/controllers/interactive_environments.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M lib/galaxy/workflow/scheduling_manager.py M static/maps/galaxy.interactive_environments.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/galaxy.interactive_environments.js M static/style/blue/base.css M templates/show_params.mako M templates/webapps/galaxy/workflow/display.mako A test-data/filter_labels_1.txt A test-data/new_labels_1.txt A test-data/new_labels_2.txt A test-data/new_labels_bad_1.txt A test-data/new_labels_bad_2.txt M test/functional/tools/samples_tool_conf.xml M test/integration/test_workflow_handler_configuration.py A test/integration/workflow_handler_configuration_workflow_scheduler_conf.xml M test/unit/tools/test_wrappers.py Log Message: ----------- Merge in dev. Commit: 88a3ee1073b939bb161980389f5d55abc483439f https://github.com/galaxyproject/galaxy/commit/88a3ee1073b939bb161980389f5d5... Author: Dave B <dave@bx.psu.edu> Date: 2017-04-24 (Mon, 24 Apr 2017) Changed paths: M config/openid_conf.xml.sample M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/text.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/deferred/__init__.py M lib/galaxy/jobs/handler.py M lib/galaxy/jobs/metrics/__init__.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/local.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/jobs/runners/tasks.py M lib/galaxy/managers/citations.py M lib/galaxy/model/migrate/versions/0048_dataset_instance_state_column.py M lib/galaxy/model/migrate/versions/0062_user_openid_table.py M lib/galaxy/model/migrate/versions/0068_rename_sequencer_to_external_services.py M lib/galaxy/model/migrate/versions/0089_add_object_store_id_columns.py M lib/galaxy/model/migrate/versions/0103_add_tool_shed_repository_status_columns.py M lib/galaxy/model/migrate/versions/0106_add_missing_indexes.py M lib/galaxy/model/migrate/versions/0119_job_metrics.py M lib/galaxy/model/migrate/versions/0120_dataset_collections.py M lib/galaxy/model/migrate/versions/0122_grow_mysql_blobs.py M lib/galaxy/model/migrate/versions/0123_add_workflow_request_tables.py M lib/galaxy/model/migrate/versions/0124_job_state_history.py M lib/galaxy/model/migrate/versions/0125_workflow_step_tracking.py M lib/galaxy/model/migrate/versions/0126_password_reset.py M lib/galaxy/model/migrate/versions/0127_output_collection_adjustments.py M lib/galaxy/model/migrate/versions/0128_session_timeout.py M lib/galaxy/model/migrate/versions/0129_job_external_output_metadata_validity.py M lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_parameter_modules.py M lib/galaxy/model/migrate/versions/0134_hda_set_deleted_if_purged.py M lib/galaxy/queue_worker.py M lib/galaxy/sample_tracking/external_service_types.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/verify/asserts/__init__.py M lib/galaxy/tours/__init__.py M lib/galaxy/util/__init__.py M lib/galaxy/visualization/genomes.py M lib/galaxy/web/base/controller.py M lib/galaxy/webapps/galaxy/api/history_contents.py M lib/galaxy/webapps/galaxy/api/lda_datasets.py M lib/galaxy/webapps/galaxy/api/library_contents.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0024_password_reset.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0025_session_timeout.py M lib/tool_shed/capsule/capsule_manager.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/metadata/metadata_generator.py M lib/tool_shed/metadata/repository_metadata_manager.py M lib/tool_shed/repository_registry.py M lib/tool_shed/util/commit_util.py M lib/tool_shed/util/common_util.py M lib/tool_shed/util/readme_util.py M lib/tool_shed/util/repository_util.py M lib/tool_shed/util/workflow_util.py M lib/tool_shed/utility_containers/__init__.py R openid/google.xml Log Message: ----------- Merge branch 'dev' of git://github.com/galaxyproject/galaxy into ts_api_backbone Commit: 1d620ef260297affe8947fa57d5f542ce418e769 https://github.com/galaxyproject/galaxy/commit/1d620ef260297affe8947fa57d5f5... Author: Dave B <dave@bx.psu.edu> Date: 2017-04-24 (Mon, 24 Apr 2017) Changed paths: M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/nls/fr/locale.js M client/galaxy/scripts/nls/locale.js M static/maps/layout/menu.js.map M static/maps/nls/fr/locale.js.map M static/maps/nls/locale.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/nls/fr/locale.js M static/scripts/nls/locale.js Log Message: ----------- Merge branch 'dev' of git://github.com/galaxyproject/galaxy into ts_api_backbone Commit: 272fbd2235aeaa9ea9d9b257958c8a14301d8e7b https://github.com/galaxyproject/galaxy/commit/272fbd2235aeaa9ea9d9b257958c8... Author: Martin Cech <marten@bx.psu.edu> Date: 2017-05-17 (Wed, 17 May 2017) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py Log Message: ----------- enable TS beta isntallation interface by default Commit: b9fb2de42b53fcb1516422cdd3d40177d507529a https://github.com/galaxyproject/galaxy/commit/b9fb2de42b53fcb1516422cdd3d40... Author: Martin Cech <marten@bx.psu.edu> Date: 2017-05-17 (Wed, 17 May 2017) Changed paths: A client/galaxy/scripts/admin.toolshed.js A client/galaxy/scripts/mvc/toolshed/categories-view.js A client/galaxy/scripts/mvc/toolshed/repo-queue-view.js A client/galaxy/scripts/mvc/toolshed/repo-status-view.js A client/galaxy/scripts/mvc/toolshed/repositories-view.js A client/galaxy/scripts/mvc/toolshed/repository-queue-view.js A client/galaxy/scripts/mvc/toolshed/repository-view.js A client/galaxy/scripts/mvc/toolshed/shed-list-view.js A client/galaxy/scripts/mvc/toolshed/toolshed-model.js A client/galaxy/scripts/mvc/toolshed/util.js A client/galaxy/scripts/mvc/toolshed/workflows-view.js M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py A lib/galaxy/webapps/galaxy/api/toolshed.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/tool_shed/api/categories.py M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/api/tools.py M lib/galaxy/webapps/tool_shed/buildapp.py M lib/tool_shed/util/repository_util.py A static/maps/admin.toolshed.js.map A static/maps/mvc/toolshed/categories-view.js.map A static/maps/mvc/toolshed/repo-queue-view.js.map A static/maps/mvc/toolshed/repo-status-view.js.map A static/maps/mvc/toolshed/repositories-view.js.map A static/maps/mvc/toolshed/repository-queue-view.js.map A static/maps/mvc/toolshed/repository-view.js.map A static/maps/mvc/toolshed/shed-category-view.js.map A static/maps/mvc/toolshed/shed-list-view.js.map A static/maps/mvc/toolshed/shed-repo-details-view.js.map A static/maps/mvc/toolshed/shed-repo-list-view.js.map A static/maps/mvc/toolshed/sheds-list-view.js.map A static/maps/mvc/toolshed/toolshed-model.js.map A static/maps/mvc/toolshed/util.js.map A static/maps/mvc/toolshed/workflows-view.js.map A static/scripts/admin.toolshed.js A static/scripts/mvc/toolshed/categories-view.js A static/scripts/mvc/toolshed/repo-queue-view.js A static/scripts/mvc/toolshed/repo-status-view.js A static/scripts/mvc/toolshed/repositories-view.js A static/scripts/mvc/toolshed/repository-queue-view.js A static/scripts/mvc/toolshed/repository-view.js A static/scripts/mvc/toolshed/shed-category-view.js A static/scripts/mvc/toolshed/shed-list-view.js A static/scripts/mvc/toolshed/shed-repo-details-view.js A static/scripts/mvc/toolshed/shed-repo-list-view.js A static/scripts/mvc/toolshed/sheds-list-view.js A static/scripts/mvc/toolshed/toolshed-model.js A static/scripts/mvc/toolshed/util.js A static/scripts/mvc/toolshed/workflows-view.js R templates/admin/tool_shed_repository/browse_toolsheds.mako Log Message: ----------- Merge pull request #3626 from davebx/ts_api_backbone API installation of toolshed repositories. Compare: https://github.com/galaxyproject/galaxy/compare/5eadd4842dcd...b9fb2de42b53