Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 2839153eb4b08f0b9a536059912d39fd3ee902a0 https://github.com/galaxyproject/galaxy/commit/2839153eb4b08f0b9a536059912d3... Author: anuprulez <anup.rulez@gmail.com> Date: 2017-03-28 (Tue, 28 Mar 2017) Changed paths: A config/plugins/visualizations/charts/static/repository/build/biojs_phylocanvas.js A config/plugins/visualizations/charts/static/repository/build/biojs_phylocanvas.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/biojs/phylocanvas/phylocanvas.js M config/plugins/visualizations/charts/static/repository/registry.json A config/plugins/visualizations/charts/static/repository/visualizations/biojs/phylocanvas/config.js A config/plugins/visualizations/charts/static/repository/visualizations/biojs/phylocanvas/logo.png A config/plugins/visualizations/charts/static/repository/visualizations/biojs/phylocanvas/wrapper.js M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Adding Phylocanvas visualization for the Galaxy charts Commit: 876c7a2d3df70b1c4edcf4fe738eb51c6e76bcfa https://github.com/galaxyproject/galaxy/commit/876c7a2d3df70b1c4edcf4fe738eb... Author: anuprulez <anup.rulez@gmail.com> Date: 2017-03-28 (Tue, 28 Mar 2017) Changed paths: M config/plugins/visualizations/charts/static/repository/build/biojs_phylocanvas.js M config/plugins/visualizations/charts/static/repository/build/biojs_phylocanvas.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/visualizations/biojs/phylocanvas/config.js M config/plugins/visualizations/charts/static/repository/visualizations/biojs/phylocanvas/logo.png M config/plugins/visualizations/charts/static/repository/visualizations/biojs/phylocanvas/wrapper.js Log Message: ----------- Adding more features like colors, collapse, prune and resize of the tree Commit: 8e1d761beccfc301129070f2c5c0a79939d290a0 https://github.com/galaxyproject/galaxy/commit/8e1d761beccfc301129070f2c5c0a... Author: anuprulez <anup.rulez@gmail.com> Date: 2017-03-28 (Tue, 28 Mar 2017) Changed paths: A config/plugins/interactive_environments/ethercalc/config/allowed_images.yml.sample M config/plugins/interactive_environments/ethercalc/config/ethercalc.ini.sample M config/plugins/visualizations/charts/static/repository/build/biojs_phylocanvas.js M config/plugins/visualizations/charts/static/repository/build/biojs_phylocanvas.js.map R config/plugins/visualizations/charts/static/repository/build/cytoscape_basic.js R config/plugins/visualizations/charts/static/repository/build/cytoscape_basic.js.map A config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js A config/plugins/visualizations/charts/static/repository/build/cytoscape_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 M config/plugins/visualizations/charts/static/repository/registry.json A config/plugins/visualizations/charts/static/repository/utilities/sifjson.js M config/plugins/visualizations/charts/static/repository/utilities/utils.js R config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/basic/config.js R config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/basic/logo.png R config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/basic/wrapper.js A config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/config.js A config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/logo.png A config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/wrapper.js M display_applications/igv/bigwig.xml M doc/source/admin/framework_dependencies.rst M doc/source/admin/index.rst A doc/source/admin/reports.md M doc/source/admin/useful_scripts.rst A doc/source/api/api.rst A doc/source/api/ts_api.rst M doc/source/api_doc.rst M doc/source/conf.py M doc/source/index.rst R doc/source/lib/galaxy.webapps.galaxy.api.rst R doc/source/lib/galaxy.webapps.tool_shed.api.rst M doc/source/releases/_header.rst M doc/source/ts_api_doc.rst M lib/galaxy/tools/__init__.py Log Message: ----------- Merging with dev Commit: 2f66d4563e02e8b585e5c1529b4e414117846858 https://github.com/galaxyproject/galaxy/commit/2f66d4563e02e8b585e5c1529b4e4... Author: anuprulez <anup.rulez@gmail.com> Date: 2017-03-28 (Tue, 28 Mar 2017) Changed paths: M config/plugins/visualizations/charts/static/repository/build/biojs_phylocanvas.js M config/plugins/visualizations/charts/static/repository/build/biojs_phylocanvas.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/visualizations/biojs/phylocanvas/config.js M config/plugins/visualizations/charts/static/repository/visualizations/biojs/phylocanvas/wrapper.js Log Message: ----------- Adding shapes for leaves of phylogenetic tree Commit: e67dc45c26e77d3f2b85ac7e2ab80ac5fdab0cf9 https://github.com/galaxyproject/galaxy/commit/e67dc45c26e77d3f2b85ac7e2ab80... Author: anuprulez <anup.rulez@gmail.com> Date: 2017-03-30 (Thu, 30 Mar 2017) Changed paths: M 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/collection/pair-collection-creator.js M client/galaxy/scripts/mvc/history/history-view-edit.js A client/galaxy/scripts/mvc/upload/collection/collection-row.js A client/galaxy/scripts/mvc/upload/collection/collection-view.js M client/galaxy/scripts/mvc/upload/upload-view.js M client/galaxy/style/less/upload.less M lib/galaxy/tools/parameters/basic.py M static/maps/mvc/collection/base-creator.js.map M static/maps/mvc/collection/list-collection-creator.js.map M static/maps/mvc/collection/list-of-pairs-collection-creator.js.map M static/maps/mvc/collection/pair-collection-creator.js.map M static/maps/mvc/history/history-view-edit.js.map A static/maps/mvc/upload/collection/collection-row.js.map A static/maps/mvc/upload/collection/collection-view.js.map M static/maps/mvc/upload/upload-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 M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/collection/base-creator.js M static/scripts/mvc/collection/list-collection-creator.js M static/scripts/mvc/collection/list-of-pairs-collection-creator.js M static/scripts/mvc/collection/pair-collection-creator.js M static/scripts/mvc/history/history-view-edit.js A static/scripts/mvc/upload/collection/collection-row.js A static/scripts/mvc/upload/collection/collection-view.js M static/scripts/mvc/upload/upload-view.js M static/style/blue/base.css M test/galaxy_selenium/navigates_galaxy.py M test/selenium_tests/test_collection_builders.py M test/selenium_tests/test_uploads.py M test/shed_functional/functional/test_1090_repository_dependency_handling.py Log Message: ----------- Merge branch 'dev' of https://github.com/bgruening/galaxy into phylocanvas Commit: fa086edf22c725b8a98cff92ac6ca6a4ab210237 https://github.com/galaxyproject/galaxy/commit/fa086edf22c725b8a98cff92ac6ca... Author: anuprulez <anup.rulez@gmail.com> Date: 2017-03-31 (Fri, 31 Mar 2017) Changed paths: M config/plugins/visualizations/charts/static/repository/build/biojs_phylocanvas.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/visualizations/biojs/phylocanvas/config.js Log Message: ----------- Adding support for .nhx files (Newick) and removing txt files support Commit: 0c3f7989bb913842e28a8fbb267d1280420caa92 https://github.com/galaxyproject/galaxy/commit/0c3f7989bb913842e28a8fbb267d1... Author: anuprulez <anup.rulez@gmail.com> Date: 2017-04-03 (Mon, 03 Apr 2017) Changed paths: M .ci/flake8_lint_include_list.txt M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/util/gff_util.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/deps/views.py M lib/galaxy/web/base/controllers/admin.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run.py M templates/webapps/galaxy/admin/manage_dependencies.mako M test/api/test_workflows.py M test/api/test_workflows_from_yaml.py M test/base/data/test_workflow_pause.ga M test/base/populators.py A test/integration/test_maximum_worklfow_invocation_duration.py Log Message: ----------- Merging wtih dev Commit: 339566bc03f1a51c7a4c60c2d6a100f43e1d3c15 https://github.com/galaxyproject/galaxy/commit/339566bc03f1a51c7a4c60c2d6a10... Author: anuprulez <anup.rulez@gmail.com> Date: 2017-04-04 (Tue, 04 Apr 2017) Changed paths: M CONTRIBUTING.md M config/datatypes_conf.xml.sample M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/jobs/__init__.py M lib/galaxy/model/__init__.py M lib/galaxy/workflow/scheduling_manager.py M test/api/test_users.py M test/api/test_workflows.py A test/integration/test_workflow_handler_configuration.py A test/integration/workflow_handler_configuration_job_conf.xml Log Message: ----------- Merging with dev Commit: 6f4e242b16487b6032347dad3f60fef00f60464f https://github.com/galaxyproject/galaxy/commit/6f4e242b16487b6032347dad3f60f... Author: Aysam Guerler <aysam.guerler@gmail.com> Date: 2017-04-04 (Tue, 04 Apr 2017) Changed paths: A config/plugins/visualizations/charts/static/repository/build/biojs_phylocanvas.js A config/plugins/visualizations/charts/static/repository/build/biojs_phylocanvas.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/biojs/phylocanvas/phylocanvas.js M config/plugins/visualizations/charts/static/repository/registry.json A config/plugins/visualizations/charts/static/repository/visualizations/biojs/phylocanvas/config.js A config/plugins/visualizations/charts/static/repository/visualizations/biojs/phylocanvas/logo.png A config/plugins/visualizations/charts/static/repository/visualizations/biojs/phylocanvas/wrapper.js Log Message: ----------- Merge pull request #3850 from bgruening/phylocanvas Phylocanvas as a BioJS component for the Galaxy charts Compare: https://github.com/galaxyproject/galaxy/compare/5169fbe917c9...6f4e242b1648