Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: edb51d876b763d0fd321c85d429575d465b754d1 https://github.com/galaxyproject/galaxy/commit/edb51d876b763d0fd321c85d42957... Author: Dave Bouvier <dave@bx.psu.edu> Date: 2016-03-15 (Tue, 15 Mar 2016) Changed paths: M lib/galaxy/util/__init__.py M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/tool_shed/galaxy_install/dependency_display.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py M lib/tool_shed/galaxy_install/tool_migration_manager.py M lib/tool_shed/galaxy_install/update_repository_manager.py M lib/tool_shed/util/common_util.py M lib/tool_shed/util/readme_util.py M lib/tool_shed/util/shed_util_common.py Log Message: ----------- Rename tool_shed_get to url_get. Commit: 9e8890b25bb126a401b17eee616609ce7963f928 https://github.com/galaxyproject/galaxy/commit/9e8890b25bb126a401b17eee61660... Author: Dave Bouvier <dave@bx.psu.edu> Date: 2016-03-23 (Wed, 23 Mar 2016) Changed paths: M Makefile M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/mvc/library/library-folder-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/tool/tool-form-workflow.js M client/galaxy/scripts/mvc/tool/tool-form.js M client/galaxy/style/less/base.less M client/galaxy/style/less/library.less M client/galaxy/style/less/ui.less M client/galaxy/style/less/upload.less M config/datatypes_conf.xml.sample M config/galaxy.ini.sample M config/tool_data_table_conf.xml.sample M contrib/galaxy.fedora-init A contrib/galaxy_reports.fedora-init A display_applications/iobio/bam.xml A display_applications/iobio/vcf.xml M doc/source/releases/index.rst A lib/galaxy/datatypes/converters/cml_to_inchi_converter.xml A lib/galaxy/datatypes/converters/cml_to_mol2_converter.xml A lib/galaxy/datatypes/converters/cml_to_sdf_converter.xml A lib/galaxy/datatypes/converters/cml_to_smi_converter.xml A lib/galaxy/datatypes/converters/inchi_to_cml_converter.xml A lib/galaxy/datatypes/converters/inchi_to_mol2_converter.xml A lib/galaxy/datatypes/converters/inchi_to_mol_converter.xml A lib/galaxy/datatypes/converters/inchi_to_sdf_converter.xml A lib/galaxy/datatypes/converters/inchi_to_smi_converter.xml A lib/galaxy/datatypes/converters/mol2_to_cml_converter.xml A lib/galaxy/datatypes/converters/mol2_to_inchi_converter.xml A lib/galaxy/datatypes/converters/mol2_to_mol_converter.xml A lib/galaxy/datatypes/converters/mol2_to_sdf_converter.xml A lib/galaxy/datatypes/converters/mol2_to_smi_converter.xml A lib/galaxy/datatypes/converters/mol_to_cml_converter.xml A lib/galaxy/datatypes/converters/mol_to_inchi_converter.xml A lib/galaxy/datatypes/converters/mol_to_mol2_converter.xml A lib/galaxy/datatypes/converters/mol_to_smi_converter.xml A lib/galaxy/datatypes/converters/sdf_to_cml_converter.xml A lib/galaxy/datatypes/converters/sdf_to_inchi_converter.xml A lib/galaxy/datatypes/converters/sdf_to_mol2_converter.xml A lib/galaxy/datatypes/converters/sdf_to_smi_converter.xml A lib/galaxy/datatypes/converters/smi_to_cml_converter.xml A lib/galaxy/datatypes/converters/smi_to_inchi_converter.xml A lib/galaxy/datatypes/converters/smi_to_mol2_converter.xml A lib/galaxy/datatypes/converters/smi_to_mol_converter.xml A lib/galaxy/datatypes/converters/smi_to_sdf_converter.xml A lib/galaxy/datatypes/converters/smi_to_smi_converter.xml M lib/galaxy/datatypes/display_applications/application.py A lib/galaxy/datatypes/molecules.py M lib/galaxy/datatypes/sniff.py A lib/galaxy/datatypes/test/5e5z.pdb A lib/galaxy/datatypes/test/drugbank_drugs.cml A lib/galaxy/datatypes/test/drugbank_drugs.inchi A lib/galaxy/datatypes/test/drugbank_drugs.mol2 A lib/galaxy/datatypes/test/drugbank_drugs.sdf A lib/galaxy/datatypes/test/drugbank_drugs.smi A lib/galaxy/datatypes/test/q.fps M lib/galaxy/jobs/handler.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/model/__init__.py M lib/galaxy/model/custom_types.py A lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_parameter_modules.py R lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_paramter_modules.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/deps/containers.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parser/interface.py M lib/galaxy/util/log/fluent_log.py M lib/galaxy/visualization/data_providers/genome.py M lib/galaxy/webapps/galaxy/api/lda_datasets.py M lib/galaxy/webapps/galaxy/api/metrics.py M lib/galaxy/webapps/galaxy/api/remote_files.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/model/__init__.py M lib/galaxy/workflow/run.py M lib/tool_shed/tool_shed_registry.py M run.sh M run_reports.sh M run_tool_shed.sh M scripts/bootstrap_history.py M static/maps/layout/menu.js.map M static/maps/layout/page.js.map M static/maps/mvc/library/library-folder-view.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/maps/mvc/library/library-librarytoolbar-view.js.map M static/maps/mvc/tool/tool-form-base.js.map M static/maps/mvc/tool/tool-form.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/page.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/library/library-librarytoolbar-view.js M static/scripts/mvc/tool/tool-form-base.js M static/scripts/mvc/tool/tool-form-workflow.js M static/scripts/mvc/tool/tool-form.js M static/style/blue/base.css M static/style/blue/library.css M templates/webapps/galaxy/workflow/display.mako M test/base/twilltestcase.py M test/functional/test_toolbox.py M test/functional/tools/collection_creates_list.xml M test/tool_shed/base/twilltestcase.py M test/tool_shed/functional/test_0490_export_import_repositories.py M test/tool_shed/functional/test_0500_export_repository_simple_dependency.py M test/unit/jobs/test_runner_local.py A tool-data/bam_iobio.loc.sample A tool-data/vcf_iobio.loc.sample Log Message: ----------- Merge branch 'dev' of git://github.com/galaxyproject/galaxy into move_tsg Commit: 06b9737e0934823c807b02cbeaf590735437653d https://github.com/galaxyproject/galaxy/commit/06b9737e0934823c807b02cbeaf59... Author: Dave Bouvier <dave@bx.psu.edu> Date: 2016-03-23 (Wed, 23 Mar 2016) Changed paths: M lib/galaxy/util/__init__.py M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/tool_shed/capsule/capsule_manager.py M lib/tool_shed/galaxy_install/dependency_display.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py M lib/tool_shed/galaxy_install/tool_migration_manager.py M lib/tool_shed/galaxy_install/update_repository_manager.py M lib/tool_shed/scripts/api/common.py M lib/tool_shed/scripts/deprecate_repositories_without_metadata.py M lib/tool_shed/tool_shed_registry.py M lib/tool_shed/util/common_util.py M lib/tool_shed/util/readme_util.py M lib/tool_shed/util/shed_util_common.py Log Message: ----------- Cleanup and fix tests. Commit: 7e14f5db6236a5ab1b9df988fe88cd34eaf8ba78 https://github.com/galaxyproject/galaxy/commit/7e14f5db6236a5ab1b9df988fe88c... Author: Dave Bouvier <dave@bx.psu.edu> Date: 2016-03-23 (Wed, 23 Mar 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/tool_shed/galaxy_install/tool_migration_manager.py M lib/tool_shed/scripts/api/common.py M lib/tool_shed/util/common_util.py Log Message: ----------- Address travis' complaints. Commit: ec3fe67ddd2a5fc2017b3d402bb2869c70bac368 https://github.com/galaxyproject/galaxy/commit/ec3fe67ddd2a5fc2017b3d402bb28... Author: John Chilton <jmchilton@gmail.com> Date: 2016-03-25 (Fri, 25 Mar 2016) Changed paths: M lib/galaxy/util/__init__.py M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/tool_shed/capsule/capsule_manager.py M lib/tool_shed/galaxy_install/dependency_display.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py M lib/tool_shed/galaxy_install/tool_migration_manager.py M lib/tool_shed/galaxy_install/update_repository_manager.py M lib/tool_shed/scripts/api/common.py M lib/tool_shed/scripts/deprecate_repositories_without_metadata.py M lib/tool_shed/tool_shed_registry.py M lib/tool_shed/util/common_util.py M lib/tool_shed/util/readme_util.py M lib/tool_shed/util/shed_util_common.py Log Message: ----------- Merge pull request #1918 from davebx/move_tsg Rename tool_shed_get to url_get. Compare: https://github.com/galaxyproject/galaxy/compare/6e34858e0da7...ec3fe67ddd2a