July 2016 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] bb82ec: Merge pull request #1 from galaxyproject/dev
by GitHub 21 Jul '16

21 Jul '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: bb82ec5bec1fec28402768cfbd40e01a7341e2de https://github.com/galaxyproject/galaxy/commit/bb82ec5bec1fec28402768cfbd40… Author: pvanheus <pvh(a)webbedfeet.co.za> Date: 2016-03-15 (Tue, 15 Mar 2016) Changed paths: A .ci/first_startup.sh M .ci/flake8_blacklist.txt M .ci/py3_sources.txt M .travis.yml M Makefile M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/galaxy.library.js M client/galaxy/scripts/layout/masthead.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/layout/scratchbook.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/history/history-contents.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/multi-panel.js M client/galaxy/scripts/mvc/library/library-dataset-view.js M client/galaxy/scripts/mvc/library/library-folder-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/tool/tool-form-workflow.js M client/galaxy/scripts/mvc/tours.js M client/galaxy/scripts/mvc/ui/popup-menu.js M client/galaxy/scripts/mvc/workflow/workflow-canvas.js M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M client/galaxy/scripts/mvc/workflow/workflow-view-node.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M client/galaxy/scripts/onload.js M client/galaxy/scripts/utils/utils.js M client/galaxy/style/less/base.less M client/galaxy/style/less/fontawesome/core.less M client/galaxy/style/less/library.less M client/galaxy/style/less/ui/icon-btn.less M client/grunt-tasks/style.js M client/package.json M config/datatypes_conf.xml.sample M config/galaxy.ini.sample A config/plugins/interactive_environments/phinch/config/phinch.ini.sample A config/plugins/interactive_environments/phinch/config/phinch.xml A config/plugins/interactive_environments/phinch/static/js/phinch.js A config/plugins/interactive_environments/phinch/templates/phinch.mako M config/tool_conf.xml.main M config/tool_conf.xml.sample M contrib/galaxy.fedora-init A contrib/galaxy_reports.fedora-init M create_db.sh M doc/source/admin/framework_dependencies.rst M doc/source/project/organization.rst M doc/source/releases/16.01.rst M doc/source/releases/16.01_announce.rst M lib/galaxy/app.py M lib/galaxy/config.py M lib/galaxy/datatypes/assembly.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/chrominfo.py M lib/galaxy/datatypes/converters/wiggle_to_simple_converter.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/display_applications/application.py M lib/galaxy/datatypes/genetics.py M lib/galaxy/datatypes/images.py M lib/galaxy/datatypes/metadata.py M lib/galaxy/datatypes/ngsindex.py M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/text.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.json M lib/galaxy/external_services/result_handlers/basic.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/actions/post.py M lib/galaxy/jobs/command_factory.py M lib/galaxy/jobs/deferred/data_transfer.py M lib/galaxy/jobs/deferred/pacific_biosciences_smrt_portal.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/cli.py M lib/galaxy/jobs/runners/condor.py M lib/galaxy/jobs/runners/drmaa.py M lib/galaxy/jobs/runners/pbs.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/jobs/runners/util/job_script/__init__.py M lib/galaxy/jobs/transfer_manager.py M lib/galaxy/managers/base.py M lib/galaxy/managers/configuration.py M lib/galaxy/managers/context.py M lib/galaxy/managers/datasets.py M lib/galaxy/managers/hdas.py A lib/galaxy/managers/hdcas.py M lib/galaxy/managers/histories.py M lib/galaxy/managers/history_contents.py M lib/galaxy/managers/ratable.py M lib/galaxy/managers/sharable.py M lib/galaxy/managers/taggable.py M lib/galaxy/managers/tags.py M lib/galaxy/managers/users.py M lib/galaxy/managers/visualizations.py M lib/galaxy/managers/workflows.py R lib/galaxy/metadata M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py A lib/galaxy/model/metadata.py M lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py M lib/galaxy/model/search.py M lib/galaxy/objectstore/__init__.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/actions/metadata.py M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/tools/cwl/__init__.py M lib/galaxy/tools/cwl/parser.py M lib/galaxy/tools/cwl/representation.py M lib/galaxy/tools/cwl/runtime_actions.py M lib/galaxy/tools/data_manager/manager.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/exception_handling.py M lib/galaxy/tools/execute.py M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/tools/imp_exp/export_history.py M lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/tools/parameters/meta.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/tools/parameters/sanitize.py M lib/galaxy/tools/parameters/validation.py M lib/galaxy/tools/parameters/wrapped.py M lib/galaxy/tools/parser/cwl.py M lib/galaxy/tools/parser/factory.py M lib/galaxy/tools/parser/interface.py M lib/galaxy/tools/parser/output_collection_def.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/parser/yaml.py M lib/galaxy/tools/test.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/wrappers.py M lib/galaxy/util/__init__.py M lib/galaxy/util/dbkeys.py M lib/galaxy/util/json.py M lib/galaxy/util/none_like.py M lib/galaxy/util/sanitize_html.py A lib/galaxy/util/ucsc.py M lib/galaxy/visualization/data_providers/basic.py M lib/galaxy/visualization/data_providers/genome.py M lib/galaxy/visualization/data_providers/registry.py M lib/galaxy/visualization/genomes.py M lib/galaxy/visualization/plugins/config_parser.py M lib/galaxy/visualization/plugins/plugin.py M lib/galaxy/visualization/plugins/registry.py M lib/galaxy/visualization/plugins/resource_parser.py M lib/galaxy/web/base/controller.py M lib/galaxy/web/base/controllers/admin.py M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/web/form_builder.py M lib/galaxy/web/framework/base.py M lib/galaxy/web/framework/decorators.py M lib/galaxy/web/framework/helpers/__init__.py M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/web/framework/middleware/sentry.py M lib/galaxy/web/framework/middleware/translogger.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/webapps/galaxy/api/datasets.py M lib/galaxy/webapps/galaxy/api/folder_contents.py M lib/galaxy/webapps/galaxy/api/folders.py M lib/galaxy/webapps/galaxy/api/histories.py M lib/galaxy/webapps/galaxy/api/history_contents.py M lib/galaxy/webapps/galaxy/api/jobs.py M lib/galaxy/webapps/galaxy/api/lda_datasets.py M lib/galaxy/webapps/galaxy/api/libraries.py M lib/galaxy/webapps/galaxy/api/quotas.py M lib/galaxy/webapps/galaxy/api/tool_dependencies.py M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/api/visualizations.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/galaxy/controllers/data_manager.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/galaxy/webapps/galaxy/controllers/page.py M lib/galaxy/webapps/galaxy/controllers/requests_admin.py M lib/galaxy/webapps/galaxy/controllers/requests_common.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/galaxy/webapps/galaxy/controllers/tag.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M lib/galaxy/webapps/galaxy/controllers/workflow.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/users.py M lib/galaxy/webapps/tool_shed/buildapp.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/galaxy/webapps/tool_shed/framework/middleware/hg.py M lib/galaxy/webapps/tool_shed/model/__init__.py M lib/galaxy/webapps/tool_shed/model/mapping.py M lib/galaxy/workflow/extract.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/render.py M lib/galaxy/workflow/run.py M lib/galaxy/workflow/run_request.py M lib/galaxy_utils/sequence/fasta.py M lib/galaxy_utils/sequence/fastq.py M lib/pulsar/client/interface.py M lib/pulsar/client/manager.py M lib/tool_shed/capsule/capsule_manager.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/galaxy_install/repair_repository_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/env_file_builder.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py M lib/tool_shed/galaxy_install/update_repository_manager.py M lib/tool_shed/grids/repository_grids.py M lib/tool_shed/metadata/metadata_generator.py M lib/tool_shed/metadata/repository_metadata_manager.py M lib/tool_shed/scripts/bootstrap_tool_shed/bootstrap_tool_shed.sh M lib/tool_shed/scripts/bootstrap_tool_shed/bootstrap_util.py M lib/tool_shed/scripts/bootstrap_tool_shed/create_user_with_api_key.py M lib/tool_shed/util/basic_util.py M lib/tool_shed/util/commit_util.py M lib/tool_shed/util/common_util.py M lib/tool_shed/util/encoding_util.py M lib/tool_shed/util/metadata_util.py M lib/tool_shed/util/readme_util.py M lib/tool_shed/util/repository_content_util.py M lib/tool_shed/util/repository_util.py M lib/tool_shed/util/shed_util_common.py M lib/tool_shed/util/tool_util.py M lib/tool_shed/util/workflow_util.py M manage_db.sh M manage_tools.sh M run.sh M run_reports.sh M run_tool_shed.sh M scripts/api/common.py M scripts/api/copy_hda_to_library_folder.py M scripts/api/create.py M scripts/api/data_manager_example_execute.py M scripts/api/delete.py M scripts/api/display.py M scripts/api/example_watch_folder.py M scripts/api/form_create_from_xml.py M scripts/api/history_create_history.py M scripts/api/history_delete_history.py M scripts/api/import_library_dataset_to_history.py M scripts/api/import_workflows_from_installed_tool_shed_repository.py M scripts/api/install_tool_shed_repositories.py M scripts/api/library_create_folder.py M scripts/api/library_create_library.py M scripts/api/library_upload_dir.py M scripts/api/library_upload_from_import_dir.py M scripts/api/load_data_with_metadata.py M scripts/api/repair_tool_shed_repository.py M scripts/api/request_type_create_from_xml.py M scripts/api/requests_update_state.py M scripts/api/reset_metadata_on_installed_repositories.py M scripts/api/sample_dataset_update_status.py M scripts/api/sample_update_state.py M scripts/api/search.py M scripts/api/sequencer_configuration_create.py M scripts/api/update.py M scripts/api/upload_to_history.py M scripts/api/workflow_delete.py M scripts/api/workflow_execute.py M scripts/api/workflow_execute_parameters.py M scripts/api/workflow_import.py M scripts/api/workflow_import_from_file_rpark.py M scripts/binary_compatibility.py M scripts/check_galaxy.py M scripts/check_python.py M scripts/cleanup_datasets/cleanup_datasets.py M scripts/cleanup_datasets/pgcleanup.py M scripts/cleanup_datasets/update_metadata.py M scripts/common_startup.sh M scripts/create_db.py M scripts/data_libraries/build_lucene_index.py M scripts/data_libraries/build_whoosh_index.py M scripts/db_shell.py M scripts/edam_mapping.py M scripts/extract_dataset_part.py M scripts/functional_tests.py M scripts/galaxy-main M scripts/get_platforms.py M scripts/helper.py M scripts/loc_files/create_all_fasta_loc.py M scripts/manage_db.py M scripts/manage_tools.py M scripts/microbes/BeautifulSoup.py M scripts/microbes/create_bacteria_loc_file.py M scripts/microbes/create_bacteria_table.py M scripts/microbes/create_nib_seq_loc_file.py M scripts/microbes/get_builds_lengths.py M scripts/microbes/harvest_bacteria.py M scripts/microbes/ncbi_to_ucsc.py M scripts/microbes/util.py M scripts/migrate_tools/migrate_tools.py M scripts/others/incorrect_gops_jobs.py M scripts/others/incorrect_gops_join_jobs.py M scripts/paster.py A scripts/patch.sh M scripts/set_dataset_sizes.py R scripts/set_metadata.py M scripts/set_user_disk_usage.py M scripts/tool_shed/build_ts_whoosh_index.py M scripts/tool_shed/check_download_urls.py M scripts/tool_shed/migrate_tools_to_repositories.py M scripts/tools/maf/check_loc_file.py M scripts/tools/re_escape_output.py M scripts/transfer.py M scripts/update_shed_config_path.py R set_metadata.sh M static/maps/galaxy.library.js.map M static/maps/layout/masthead.js.map M static/maps/layout/menu.js.map M static/maps/layout/page.js.map M static/maps/mvc/dataset/dataset-li-edit.js.map M static/maps/mvc/form/form-input.js.map M static/maps/mvc/form/form-parameters.js.map M static/maps/mvc/form/form-section.js.map M static/maps/mvc/history/history-contents.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/multi-panel.js.map M static/maps/mvc/library/library-dataset-view.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/tool/tool-form-workflow.js.map M static/maps/mvc/tours.js.map M static/maps/mvc/ui/popup-menu.js.map M static/maps/mvc/workflow/workflow-canvas.js.map M static/maps/mvc/workflow/workflow-terminals.js.map M static/maps/mvc/workflow/workflow-view-node.js.map M static/maps/mvc/workflow/workflow-view.js.map M static/maps/onload.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/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/galaxy.library.js M static/scripts/layout/masthead.js M static/scripts/layout/menu.js M static/scripts/layout/page.js M static/scripts/mvc/dataset/dataset-li-edit.js M static/scripts/mvc/form/form-input.js M static/scripts/mvc/form/form-parameters.js M static/scripts/mvc/form/form-section.js M static/scripts/mvc/history/history-contents.js M static/scripts/mvc/history/history-model.js M static/scripts/mvc/history/history-view.js M static/scripts/mvc/history/multi-panel.js M static/scripts/mvc/library/library-dataset-view.js M static/scripts/mvc/library/library-folder-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/tool/tool-form-workflow.js M static/scripts/mvc/tours.js M static/scripts/mvc/ui/popup-menu.js M static/scripts/mvc/workflow/workflow-canvas.js M static/scripts/mvc/workflow/workflow-terminals.js M static/scripts/mvc/workflow/workflow-view-node.js M static/scripts/mvc/workflow/workflow-view.js M static/scripts/onload.js M static/scripts/utils/utils.js M static/style/blue/base.css M static/style/blue/library.css R templates/admin/requests/select_datasets_to_transfer.mako M templates/admin/tool_shed_repository/common.mako M templates/admin/tool_shed_repository/manage_repository.mako M templates/show_params.mako M templates/webapps/galaxy/galaxy.masthead.mako M templates/webapps/galaxy/history/display.mako M templates/webapps/galaxy/requests/common/common.mako M templates/webapps/galaxy/requests/common/view_request_history.mako M templates/webapps/galaxy/requests/common/view_sample_datasets.mako M templates/webapps/galaxy/workflow/editor.mako M templates/webapps/galaxy/workflow/run.mako M templates/webapps/tool_shed/repository/common.mako M templates/webapps/tool_shed/repository/view_repository.mako M test-data/3.bam M test/api/test_tools.py M test/api/test_workflows.py M test/api/test_workflows_from_yaml.py M test/base/twilltestcase.py M test/docker/base/Dockerfile M test/docker/base/run_test_wrapper.sh M test/functional/test_admin_features.py M test/functional/test_data_security.py M test/functional/test_dataset_features.py M test/functional/test_get_data.py M test/functional/test_library_features.py M test/functional/test_library_security.py M test/functional/test_library_templates.py M test/functional/test_metadata_editing.py M test/functional/test_sample_tracking.py M test/functional/test_tags.py M test/functional/test_ucsc_table_browser.py M test/functional/test_user_info.py A test/functional/tools/empty_output.xml M test/functional/tools/output_format.xml A test/functional/tools/paths_as_file.xml M test/functional/tools/samples_tool_conf.xml A test/functional/tools/strict_shell.xml A test/functional/tools/strict_shell_default_off.xml A test/functional/tools/validation_empty_dataset.xml M test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py M test/qunit/tests/masthead_tests.js M test/qunit/tests/workflow_editor_tests.js M test/tool_shed/base/twilltestcase.py M test/tool_shed/functional/test_0000_basic_repository_features.py M test/tool_shed/functional/test_0010_repository_with_tool_dependencies.py M test/tool_shed/functional/test_0020_basic_repository_dependencies.py M test/tool_shed/functional/test_0030_repository_dependency_revisions.py M test/tool_shed/functional/test_0040_repository_circular_dependencies.py M test/tool_shed/functional/test_0050_circular_dependencies_4_levels.py M test/tool_shed/functional/test_0060_workflows.py M test/tool_shed/functional/test_0070_invalid_tool.py M test/tool_shed/functional/test_0080_advanced_circular_dependencies.py M test/tool_shed/functional/test_0090_tool_search.py M test/tool_shed/functional/test_0100_complex_repository_dependencies.py M test/tool_shed/functional/test_0110_invalid_simple_repository_dependencies.py M test/tool_shed/functional/test_0120_simple_repository_dependency_multiple_owners.py M test/tool_shed/functional/test_0130_datatype_converters.py M test/tool_shed/functional/test_0140_tool_help_images.py M test/tool_shed/functional/test_0150_prior_installation_required.py M test/tool_shed/functional/test_0160_circular_prior_installation_required.py M test/tool_shed/functional/test_0170_complex_prior_installation_required.py M test/tool_shed/functional/test_0300_reset_all_metadata.py M test/tool_shed/functional/test_0310_hg_push_from_api.py M test/tool_shed/functional/test_0400_repository_component_reviews.py M test/tool_shed/functional/test_0410_repository_component_review_access_control.py M test/tool_shed/functional/test_0420_citable_urls_for_repositories.py M test/tool_shed/functional/test_0430_browse_utilities.py M test/tool_shed/functional/test_0440_deleting_dependency_definitions.py M test/tool_shed/functional/test_0450_skip_tool_tests.py M test/tool_shed/functional/test_0460_upload_to_repository.py M test/tool_shed/functional/test_0470_tool_dependency_repository_type.py M test/tool_shed/functional/test_0480_tool_dependency_xml_verification.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/tool_shed/functional/test_0510_export_import_repository_complex_dependencies.py M test/tool_shed/functional/test_0520_import_export_circular_dependencies.py M test/tool_shed/functional/test_0530_repository_admin_feature.py A test/tool_shed/functional/test_0540_get_all_metadata_from_api.py M test/tool_shed/functional/test_1000_install_basic_repository.py M test/tool_shed/functional/test_1010_install_repository_with_tool_dependencies.py M test/tool_shed/functional/test_1020_install_repository_with_repository_dependencies.py M test/tool_shed/functional/test_1030_install_repository_with_dependency_revisions.py M test/tool_shed/functional/test_1040_install_repository_basic_circular_dependencies.py M test/tool_shed/functional/test_1050_circular_dependencies_4_levels.py M test/tool_shed/functional/test_1060_install_repository_with_workflow.py M test/tool_shed/functional/test_1070_invalid_tool.py M test/tool_shed/functional/test_1080_advanced_circular_dependency_installation.py R test/tool_shed/functional/test_1085_repository_dependency_handling.py R test/tool_shed/functional/test_1087_install_updated_repository_dependencies.py R test/tool_shed/functional/test_1090_install_tool_from_tool_search.py A test/tool_shed/functional/test_1090_repository_dependency_handling.py R test/tool_shed/functional/test_1100_install_repository_with_complex_dependencies.py A test/tool_shed/functional/test_1100_install_updated_repository_dependencies.py R test/tool_shed/functional/test_1110_install_repository_with_invalid_repository_dependency.py A test/tool_shed/functional/test_1110_install_tool_from_tool_search.py A test/tool_shed/functional/test_1120_install_repository_with_complex_dependencies.py R test/tool_shed/functional/test_1120_simple_repository_dependency_multiple_owners.py R test/tool_shed/functional/test_1130_datatype_converters.py A test/tool_shed/functional/test_1130_install_repository_with_invalid_repository_dependency.py A test/tool_shed/functional/test_1140_simple_repository_dependency_multiple_owners.py R test/tool_shed/functional/test_1140_tool_help_images.py A test/tool_shed/functional/test_1150_datatype_converters.py R test/tool_shed/functional/test_1150_prior_installation_required.py R test/tool_shed/functional/test_1160_circular_prior_installation_required.py A test/tool_shed/functional/test_1160_tool_help_images.py R test/tool_shed/functional/test_1170_complex_prior_installation_required.py A test/tool_shed/functional/test_1170_prior_installation_required.py A test/tool_shed/functional/test_1180_circular_prior_installation_required.py A test/tool_shed/functional/test_1190_complex_prior_installation_required.py M test/tool_shed/functional/test_1200_uninstall_and_reinstall_basic_repository.py M test/tool_shed/functional/test_1210_uninstall_reinstall_repository_with_tool_dependencies.py M test/tool_shed/functional/test_1220_uninstall_reinstall_repository_with_repository_dependencies.py M test/tool_shed/functional/test_1230_uninstall_reinstall_repository_with_dependency_revisions.py M test/tool_shed/functional/test_1300_reset_all_metadata.py M test/tool_shed/functional/test_1400_review_migration_stages.py M test/tool_shed/functional/test_1410_update_manager.py M test/tool_shed/functional/test_1420_tool_dependency_environment_inheritance.py M test/tool_shed/functional/test_1430_repair_installed_repository.py M test/tool_shed/functional/test_1440_missing_env_sh_files.py M test/tool_shed/functional/test_1450_installing_datatypes_sniffers.py M test/tool_shed/functional/test_1460_data_managers.py M test/tool_shed/functional/test_1470_updating_installed_repositories.py A test/tool_shed/test_data/0540_files/column_maker/column_maker.tar A test/tool_shed/test_data/0540_files/column_maker/repository_dependencies.xml A test/tool_shed/test_data/0540_files/convert_chars/convert_chars.tar A test/tool_shed/test_data/0540_files/convert_chars/tool_dependencies.xml A test/tool_shed/test_data/0540_files/package_bwa/tool_dependencies.xml M test/unit/jobs/test_command_factory.py M test/unit/jobs/test_job_wrapper.py A test/unit/managers/test_HDCAManager.py M test/unit/managers/test_HistoryContentsManager.py M test/unit/managers/test_HistoryManager.py M test/unit/test_objectstore.py M test/unit/tools/test_collect_primary_datasets.py M test/unit/tools/test_column_parameters.py M test/unit/tools/test_data_parameters.py M test/unit/tools/test_evaluation.py M test/unit/tools/test_execution.py A test/unit/tools/test_history_imp_exp.py M test/unit/tools/test_parameter_parsing.py M test/unit/tools/test_parsing.py M test/unit/tools/test_select_parameters.py M test/unit/tools_support.py M test/unit/unittest_utils/galaxy_mock.py M test/unit/workflows/test_modules.py M test/unit/workflows/test_render.py M tools/data_source/data_source.py M tools/data_source/fetch.py M tools/data_source/genbank.py M tools/data_source/hbvar_filter.py M tools/data_source/import.py M tools/data_source/microbial_import.py M tools/data_source/microbial_import_code.py M tools/data_source/upload.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/gtf_filter_by_attribute_values_list.py M tools/filters/grep.py M tools/filters/gtf_to_bedgraph_converter.py M tools/filters/join.py M tools/filters/joinWrapper.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/randomlines.py M tools/filters/sff_extract.py M tools/filters/sorter.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_file_browser.py M tools/genomespace/genomespace_importer.py M tools/meme/fimo_wrapper.py M tools/metag_tools/blat_wrapper.py M tools/metag_tools/shrimp_color_wrapper.py M tools/metag_tools/shrimp_wrapper.py M tools/phenotype_association/linkToDavid.xml M tools/phenotype_association/pagetag.py M tools/phenotype_association/senatag.py M tools/plotting/bar_chart.py R tools/plotting/plot_filter.py R tools/plotting/plotter.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_assembly/velveth_wrapper.py M tools/sr_mapping/bfast_wrapper.py M tools/sr_mapping/srma_wrapper.py M tools/sr_mapping/srma_wrapper.xml M tools/stats/aggregate_scores_in_intervals.py R tools/validation/fix_errors.py R tools/validation/fix_errors.xml R tools/validation/fix_errors_code.py R tools/validation/validate.py M tools/visualization/LAJ.py M tools/visualization/LAJ_code.py M tox.ini Log Message: ----------- Merge pull request #1 from galaxyproject/dev pull updates from HEAD of dev Commit: d123b402303a708c2d20d83a0fbc0289d9bc65db https://github.com/galaxyproject/galaxy/commit/d123b402303a708c2d20d83a0fbc… Author: pvanheus <pvh(a)webbedfeet.co.za> Date: 2016-04-01 (Fri, 01 Apr 2016) Changed paths: M .gitignore M Makefile M client/galaxy/scripts/layout/masthead.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-parameters.js R client/galaxy/scripts/mvc/form/form-select-content.js M client/galaxy/scripts/mvc/library/library-dataset-view.js M client/galaxy/scripts/mvc/library/library-folder-view.js M client/galaxy/scripts/mvc/library/library-folderlist-view.js M client/galaxy/scripts/mvc/library/library-folderrow-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/library/library-library-view.js M client/galaxy/scripts/mvc/library/library-librarylist-view.js M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js M client/galaxy/scripts/mvc/library/library-model.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 A client/galaxy/scripts/mvc/ui/ui-select-content.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/galaxy/scripts/utils/utils.js M client/galaxy/scripts/viz/trackster/tracks.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 config/tool_shed.ini.sample A display_applications/iobio/bam.xml A display_applications/iobio/vcf.xml M doc/source/releases/index.rst M lib/galaxy/config.py 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/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/handler.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/managers/base.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/model/util.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/execute.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/wrapped_json.py M lib/galaxy/tools/parser/interface.py M lib/galaxy/util/__init__.py R lib/galaxy/util/dictobj.py M lib/galaxy/util/jstree.py M lib/galaxy/util/log/fluent_log.py M lib/galaxy/util/object_wrapper.py M lib/galaxy/visualization/data_providers/genome.py M lib/galaxy/web/framework/base.py M lib/galaxy/web/framework/middleware/statsd.py M lib/galaxy/webapps/galaxy/api/datasets.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/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/config.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/galaxy/webapps/tool_shed/framework/middleware/hg.py M lib/galaxy/webapps/tool_shed/model/__init__.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run.py M lib/galaxy/workflow/scheduling_manager.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/tools/tool_panel_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 M run.sh M run_reports.sh M run_tests.sh M run_tool_shed.sh M scripts/bootstrap_history.py M scripts/functional_tests.py M scripts/summarize_timings.py M static/maps/layout/masthead.js.map M static/maps/layout/menu.js.map M static/maps/layout/page.js.map M static/maps/mvc/form/form-input.js.map M static/maps/mvc/form/form-parameters.js.map R static/maps/mvc/form/form-select-content.js.map M static/maps/mvc/library/library-dataset-view.js.map M static/maps/mvc/library/library-folder-view.js.map M static/maps/mvc/library/library-folderlist-view.js.map M static/maps/mvc/library/library-folderrow-view.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/maps/mvc/library/library-library-view.js.map M static/maps/mvc/library/library-librarylist-view.js.map M static/maps/mvc/library/library-librarytoolbar-view.js.map M static/maps/mvc/library/library-model.js.map M static/maps/mvc/tool/tool-form-base.js.map M static/maps/mvc/tool/tool-form.js.map A static/maps/mvc/ui/ui-select-content.js.map M static/maps/mvc/ui/ui-select-default.js.map M static/maps/utils/utils.js.map M static/maps/viz/trackster/tracks.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/layout/masthead.js M static/scripts/layout/menu.js M static/scripts/layout/page.js M static/scripts/mvc/form/form-input.js M static/scripts/mvc/form/form-parameters.js R static/scripts/mvc/form/form-select-content.js M static/scripts/mvc/library/library-dataset-view.js M static/scripts/mvc/library/library-folder-view.js M static/scripts/mvc/library/library-folderlist-view.js M static/scripts/mvc/library/library-folderrow-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/library/library-library-view.js M static/scripts/mvc/library/library-librarylist-view.js M static/scripts/mvc/library/library-librarytoolbar-view.js M static/scripts/mvc/library/library-model.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 A static/scripts/mvc/ui/ui-select-content.js M static/scripts/mvc/ui/ui-select-default.js M static/scripts/utils/utils.js M static/scripts/viz/trackster/tracks.js M static/style/blue/base.css M static/style/blue/library.css A templates/admin/tool_shed_repository/browse_categories.mako A templates/admin/tool_shed_repository/browse_category.mako M templates/admin/tool_shed_repository/initiate_repository_installation.mako A templates/admin/tool_shed_repository/preview_repository.mako M templates/base/base_panels.mako M templates/webapps/galaxy/admin/index.mako A templates/webapps/galaxy/admin/toolsheds.mako M templates/webapps/galaxy/library/common/library_info.mako M templates/webapps/galaxy/workflow/display.mako A test/base/driver_util.py M test/base/twilltestcase.py R test/functional/test_admin_features.py R test/functional/test_data_security.py R test/functional/test_dataset_features.py R test/functional/test_get_data.py R test/functional/test_library_features.py R test/functional/test_library_security.py R test/functional/test_metadata_editing.py R test/functional/test_sample_tracking.py R test/functional/test_tags.py M test/functional/test_toolbox.py R test/functional/test_ucsc_table_browser.py R test/functional/test_user_info.py M test/functional/tools/collection_creates_list.xml A test/functional/tools/for_workflows/create_input_collection.xml A test/functional/tools/for_workflows/split.xml M test/functional/tools/samples_tool_conf.xml A test/functional/tools/upload_tool_conf.xml M test/functional/workflow.py R test/install_and_test_tool_shed_repositories/__init__.py R test/install_and_test_tool_shed_repositories/base/__init__.py R test/install_and_test_tool_shed_repositories/base/test_db_util.py R test/install_and_test_tool_shed_repositories/base/twilltestcase.py R test/install_and_test_tool_shed_repositories/base/util.py R test/install_and_test_tool_shed_repositories/functional/__init__.py R test/install_and_test_tool_shed_repositories/functional/test_install_repositories.py R test/install_and_test_tool_shed_repositories/repositories_with_tools/__init__.py R test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py R test/install_and_test_tool_shed_repositories/tool_dependency_definitions/__init__.py R test/install_and_test_tool_shed_repositories/tool_dependency_definitions/functional_tests.py A test/manual/launch_and_run.sh A test/manual/workflow_job_conf.xml M test/manual/workflows_scaling.py M test/qunit/test-app.js A test/qunit/tests/form_tests.html A test/qunit/tests/form_tests.js A test/qunit/tests/page_tests.html A test/qunit/tests/page_tests.js M test/qunit/tests/ui_tests.js M test/tool_shed/base/twilltestcase.py A test/tool_shed/functional/test_0310_hg_api_features.py R test/tool_shed/functional/test_0310_hg_push_from_api.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/tool_shed/functional_tests.py M test/unit/jobs/test_runner_local.py M test/unit/managers/test_HistoryContentsManager.py M test/unit/test_lazy_process.py A tool-data/bam_iobio.loc.sample A tool-data/vcf_iobio.loc.sample Log Message: ----------- Merge pull request #2 from galaxyproject/dev Merge pull request #2 from galaxyproject/dev Commit: 1fed38b28289bee22a00fbac4b1030224dd77150 https://github.com/galaxyproject/galaxy/commit/1fed38b28289bee22a00fbac4b10… Author: Peter van Heusden <pvh(a)sanbi.ac.za> Date: 2016-06-09 (Thu, 09 Jun 2016) Changed paths: M .ci/flake8_wrapper.sh M .ci/py3_sources.txt M .gitignore M CONTRIBUTORS.md M Makefile M README.rst R buildbot_setup.sh M client/README.md M client/bower.json M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/layout/scratchbook.js M client/galaxy/scripts/libs/backbone.js M client/galaxy/scripts/libs/bootstrap-tour.js M client/galaxy/scripts/libs/d3.js M client/galaxy/scripts/libs/jquery/jquery.js M client/galaxy/scripts/libs/jquery/jquery.migrate.js M client/galaxy/scripts/libs/raven.js M client/galaxy/scripts/libs/require.js R client/galaxy/scripts/libs/tracekit.js M client/galaxy/scripts/libs/underscore.js M client/galaxy/scripts/mvc/citation/citation-model.js M client/galaxy/scripts/mvc/collection/collection-li.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-model.js M client/galaxy/scripts/mvc/form/form-data.js M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/history/history-contents.js M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/history-view-annotated.js M client/galaxy/scripts/mvc/history/history-view-edit-current.js M client/galaxy/scripts/mvc/history/history-view.js M client/galaxy/scripts/mvc/history/multi-panel.js M client/galaxy/scripts/mvc/library/library-dataset-view.js M client/galaxy/scripts/mvc/library/library-folder-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/library/library-library-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 R client/galaxy/scripts/mvc/tool/tool-template.js M client/galaxy/scripts/mvc/ui/popup-menu.js M client/galaxy/scripts/mvc/ui/ui-drilldown.js M client/galaxy/scripts/mvc/ui/ui-frames.js M client/galaxy/scripts/mvc/ui/ui-list.js M client/galaxy/scripts/mvc/ui/ui-misc.js M client/galaxy/scripts/mvc/ui/ui-options.js M client/galaxy/scripts/mvc/ui/ui-portlet.js M client/galaxy/scripts/mvc/ui/ui-select-content.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/galaxy/scripts/mvc/ui/ui-select.js M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M client/galaxy/scripts/ui/hoverhighlight.js M client/galaxy/scripts/ui/loading-indicator.js M client/galaxy/scripts/ui/mode-button.js M client/galaxy/scripts/ui/pagination.js M client/galaxy/scripts/ui/peek-column-selector.js M client/galaxy/scripts/utils/localization.js M client/galaxy/scripts/utils/metrics-logger.js M client/galaxy/scripts/utils/utils.js M client/galaxy/style/less/base.less M client/galaxy/style/less/frame.less M client/galaxy/style/less/library.less M client/galaxy/style/less/ui.less M client/grunt-tasks/install-libs.js M client/grunt-tasks/scripts.js M client/grunt-tasks/style.js M config/datatypes_conf.xml.sample M config/galaxy.ini.sample M config/job_conf.xml.sample_advanced A 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/jupyter/templates/jupyter.mako A config/plugins/interactive_environments/rstudio/config/allowed_images.yml.sample M config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample M config/plugins/interactive_environments/rstudio/templates/rstudio.mako M config/plugins/tours/core.galaxy_ui.yaml M config/plugins/tours/core.scratchbook.yaml M config/plugins/visualizations/charts/static/views/group.js R config/plugins/visualizations/graphview/config/graphview.xml R config/plugins/visualizations/graphview/static/graphview.css R config/plugins/visualizations/graphview/static/graphview.js R config/plugins/visualizations/graphview/static/jquery.rdfquery.core.js R config/plugins/visualizations/graphview/templates/graphview.mako M config/reports.ini.sample M config/tool_data_table_conf.xml.sample M config/tool_shed.ini.sample M contrib/galaxy.debian-init M contrib/galaxy_config_merger.py A contrib/galaxy_supervisor.conf M contrib/nagios/check_galaxy.py M cron/build_chrom_db.py M cron/parse_builds.py M cron/parse_builds_3_sites.py A display_applications/biom/biom_simple.xml M doc/source/dev/faq.rst M doc/source/lib/modules.rst R doc/source/lib/pulsar.client.rst R doc/source/lib/pulsar.client.staging.rst R doc/source/lib/pulsar.client.transport.rst R doc/source/lib/pulsar.rst M doc/source/releases/16.01.rst A doc/source/releases/16.04.rst M doc/source/releases/16.04_announce.rst A doc/source/releases/16.07_announce.rst M doc/source/releases/index.rst R install_and_test_tool_shed_repositories.sh M lib/galaxy/auth/providers/ldap_ad.py M lib/galaxy/config.py M lib/galaxy/datatypes/assembly.py M lib/galaxy/datatypes/binary.py A lib/galaxy/datatypes/checkers.py M lib/galaxy/datatypes/converters/bed_to_gff_converter.py M lib/galaxy/datatypes/converters/fastqsolexa_to_fasta_converter.py M lib/galaxy/datatypes/converters/fastqsolexa_to_qual_converter.py M lib/galaxy/datatypes/converters/gff_to_bed_converter.py M lib/galaxy/datatypes/converters/lped_to_fped_converter.py M lib/galaxy/datatypes/converters/lped_to_pbed_converter.py M lib/galaxy/datatypes/converters/pbed_ldreduced_converter.py M lib/galaxy/datatypes/converters/pbed_to_lped_converter.py A lib/galaxy/datatypes/converters/ref_to_seq_taxonomy_converter.py A lib/galaxy/datatypes/converters/ref_to_seq_taxonomy_converter.xml M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/genetics.py M lib/galaxy/datatypes/images.py M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/molecules.py A lib/galaxy/datatypes/mothur.py M lib/galaxy/datatypes/msa.py M lib/galaxy/datatypes/ngsindex.py M lib/galaxy/datatypes/proteomics.py M lib/galaxy/datatypes/qualityscore.py M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/tabular.py A lib/galaxy/datatypes/test/NuBBE_1_obabel_3D.pdbqt A lib/galaxy/datatypes/test/issue1818.tabular A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.axes A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.filter A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.freq A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.lower.dist A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.map A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.oligos A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.otu A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.pair.dist A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.quan A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.ref.taxonomy A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.sabund A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.shared A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.square.dist A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.axes A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.filter A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.freq A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.lower.dist A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.map A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.oligos A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.otu A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.pair.dist A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.quan A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.ref.taxonomy A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.sabund A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.shared A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.square.dist M lib/galaxy/datatypes/text.py M lib/galaxy/datatypes/tracks.py M lib/galaxy/datatypes/triples.py M lib/galaxy/datatypes/xml.py M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/conda-environment.txt M lib/galaxy/dependencies/conditional-requirements.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/external_services/actions.py M lib/galaxy/external_services/parameters.py M lib/galaxy/external_services/service.py M lib/galaxy/forms/forms.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/actions/post.py M lib/galaxy/jobs/command_factory.py M lib/galaxy/jobs/deferred/__init__.py M lib/galaxy/jobs/deferred/data_transfer.py M lib/galaxy/jobs/handler.py M lib/galaxy/jobs/mapper.py M lib/galaxy/jobs/metrics/collectl/processes.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/cli.py M lib/galaxy/jobs/runners/condor.py M lib/galaxy/jobs/runners/drmaa.py A lib/galaxy/jobs/runners/kubernetes.py M lib/galaxy/jobs/runners/local.py M lib/galaxy/jobs/runners/pbs.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/jobs/runners/slurm.py M lib/galaxy/jobs/runners/util/job_script/CLUSTER_SLOTS_STATEMENT.sh M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh M lib/galaxy/jobs/runners/util/job_script/__init__.py M lib/galaxy/jobs/splitters/multi.py M lib/galaxy/jobs/transfer_manager.py M lib/galaxy/managers/base.py M lib/galaxy/managers/citations.py M lib/galaxy/managers/configuration.py M lib/galaxy/managers/context.py M lib/galaxy/managers/folders.py M lib/galaxy/managers/hdas.py M lib/galaxy/managers/hdcas.py M lib/galaxy/managers/histories.py M lib/galaxy/managers/libraries.py M lib/galaxy/managers/roles.py M lib/galaxy/managers/sharable.py M lib/galaxy/managers/tags.py M lib/galaxy/managers/users.py M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py M lib/galaxy/model/migrate/versions/0001_initial_tables.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/0025_user_info.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/0030_history_slug_column.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/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/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/0056_workflow_outputs.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/0061_tasks.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/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 lib/galaxy/model/migrate/versions/0084_add_ldda_id_to_implicit_conversion_table.py M lib/galaxy/model/migrate/versions/0085_add_task_info.py M lib/galaxy/model/migrate/versions/0086_add_tool_shed_repository_table_columns.py M lib/galaxy/model/migrate/versions/0087_tool_id_guid_map_table.py M lib/galaxy/model/migrate/versions/0088_add_installed_changeset_revison_column.py M lib/galaxy/model/migrate/versions/0089_add_object_store_id_columns.py M lib/galaxy/model/migrate/versions/0090_add_tool_shed_repository_table_columns.py M lib/galaxy/model/migrate/versions/0091_add_tool_version_tables.py M lib/galaxy/model/migrate/versions/0092_add_migrate_tools_table.py M lib/galaxy/model/migrate/versions/0093_add_job_params_col.py M lib/galaxy/model/migrate/versions/0094_add_job_handler_col.py M lib/galaxy/model/migrate/versions/0095_hda_subsets.py M lib/galaxy/model/migrate/versions/0096_openid_provider.py M lib/galaxy/model/migrate/versions/0097_add_ctx_rev_column.py M 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/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/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/0121_workflow_uuids.py M lib/galaxy/model/migrate/versions/0123_add_workflow_request_tables.py M lib/galaxy/model/tool_shed_install/mapping.py M lib/galaxy/openid/providers.py M lib/galaxy/security/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/tools/cwl/cwltool_deps.py M lib/galaxy/tools/cwl/parser.py M lib/galaxy/tools/cwl/runtime_actions.py A 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/commands.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/containers.py M lib/galaxy/tools/deps/docker_util.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/unlinked_tool_shed_packages.py M lib/galaxy/tools/errors.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/execute.py M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/tools/imp_exp/export_history.py M lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py M lib/galaxy/tools/lint.py M lib/galaxy/tools/linters/__init__.py M lib/galaxy/tools/linters/citations.py M lib/galaxy/tools/linters/command.py A lib/galaxy/tools/linters/general.py M lib/galaxy/tools/linters/help.py M lib/galaxy/tools/linters/inputs.py M lib/galaxy/tools/linters/outputs.py M lib/galaxy/tools/linters/stdio.py M lib/galaxy/tools/linters/tests.py R lib/galaxy/tools/linters/top_level.py M lib/galaxy/tools/linters/xml_order.py M lib/galaxy/tools/loader_directory.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/dynamic_options.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/tools/parameters/meta.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/tools/parameters/sanitize.py M lib/galaxy/tools/parser/cwl.py M lib/galaxy/tools/parser/factory.py M lib/galaxy/tools/parser/output_objects.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/parser/yaml.py M lib/galaxy/tools/search/__init__.py M lib/galaxy/tools/test.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/lineages/factory.py M lib/galaxy/tools/toolbox/parser.py M lib/galaxy/tools/toolbox/watcher.py M lib/galaxy/tools/util/maf_utilities.py A lib/galaxy/tools/verify/__init__.py A lib/galaxy/tools/verify/asserts/__init__.py A lib/galaxy/tools/verify/asserts/tabular.py A lib/galaxy/tools/verify/asserts/text.py A lib/galaxy/tools/verify/asserts/xml.py A lib/galaxy/tools/verify/test_data.py M lib/galaxy/tools/wrappers.py M lib/galaxy/util/__init__.py R lib/galaxy/util/backports/importlib/__init__.py M lib/galaxy/util/checkers.py M lib/galaxy/util/directory_hash.py M lib/galaxy/util/inflection.py M lib/galaxy/util/log/fluent_log.py M lib/galaxy/util/sanitize_html.py M lib/galaxy/util/validation.py M lib/galaxy/version.py M lib/galaxy/visualization/data_providers/genome.py M lib/galaxy/visualization/genomes.py M lib/galaxy/visualization/plugins/config_parser.py M lib/galaxy/visualization/plugins/registry.py M lib/galaxy/visualization/plugins/resource_parser.py M lib/galaxy/web/base/controller.py M lib/galaxy/web/base/controllers/admin.py M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/web/base/pluginframework.py M lib/galaxy/web/framework/base.py M lib/galaxy/web/framework/helpers/__init__.py M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/web/framework/middleware/remoteuser.py M lib/galaxy/web/framework/middleware/statsd.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/web/proxy/__init__.py M lib/galaxy/web/proxy/js/package.json M lib/galaxy/web/security/__init__.py M lib/galaxy/webapps/galaxy/api/datatypes.py M lib/galaxy/webapps/galaxy/api/folder_contents.py M lib/galaxy/webapps/galaxy/api/group_roles.py M lib/galaxy/webapps/galaxy/api/group_users.py M lib/galaxy/webapps/galaxy/api/history_contents.py M lib/galaxy/webapps/galaxy/api/library_contents.py M lib/galaxy/webapps/galaxy/api/quotas.py M lib/galaxy/webapps/galaxy/api/remote_files.py M lib/galaxy/webapps/galaxy/api/search.py M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/api/visualizations.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/async.py M lib/galaxy/webapps/galaxy/controllers/biostar.py M lib/galaxy/webapps/galaxy/controllers/data_manager.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/external_services.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/galaxy/webapps/galaxy/controllers/page.py M lib/galaxy/webapps/galaxy/controllers/requests_common.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/galaxy/webapps/galaxy/controllers/tool_runner.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M lib/galaxy/webapps/galaxy/controllers/workflow.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/repository_revisions.py M lib/galaxy/webapps/tool_shed/api/users.py M lib/galaxy/webapps/tool_shed/buildapp.py M lib/galaxy/webapps/tool_shed/config.py M lib/galaxy/webapps/tool_shed/controllers/admin.py M lib/galaxy/webapps/tool_shed/controllers/hg.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/galaxy/webapps/tool_shed/controllers/repository_review.py M lib/galaxy/webapps/tool_shed/controllers/upload.py M lib/galaxy/webapps/tool_shed/framework/middleware/hg.py M lib/galaxy/webapps/tool_shed/model/__init__.py M lib/galaxy/webapps/tool_shed/model/mapping.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0001_initial_tables.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0002_add_tool_suite_column.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0003_review_and_review_association_tables.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0004_repository_tables.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0005_drop_tool_related_tables.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0006_add_email_alerts_column.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0007_add_long_description_times_downloaded_columns.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0008_add_repository_metadata_table.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0009_add_malicious_column.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0010_add_new_repo_alert_column.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0011_add_tool_versions_column.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0012_add_downloadable_column.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0013_add_review_tables.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0014_add_deprecated_column.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0015_add_api_keys_table.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0016_add_do_not_test_tools_functionally_correct_errors_columns.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0017_add_galaxy_utility_columns_to_repository_metadata_table.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0018_add_repository_metadata_flag_columns.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0019_add_skip_tool_test_table_and_test_install_error_column.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0020_add_repository_type_column.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0022_add_repository_admin_roles.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0023_add_repository_url_and_hompeage_url.py M lib/galaxy/webapps/tool_shed/security/__init__.py M lib/galaxy/webapps/tool_shed/util/hgweb_config.py M lib/galaxy/workflow/extract.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run.py M lib/galaxy_ext/metadata/set_metadata.py M lib/galaxy_utils/sequence/fastq.py M lib/galaxy_utils/sequence/vcf.py R lib/pulsar/__init__.py R lib/pulsar/client/__init__.py R lib/pulsar/client/action_mapper.py R lib/pulsar/client/amqp_exchange.py R lib/pulsar/client/amqp_exchange_factory.py R lib/pulsar/client/client.py R lib/pulsar/client/config_util.py R lib/pulsar/client/decorators.py R lib/pulsar/client/destination.py R lib/pulsar/client/interface.py R lib/pulsar/client/job_directory.py R lib/pulsar/client/manager.py R lib/pulsar/client/object_client.py R lib/pulsar/client/path_mapper.py R lib/pulsar/client/setup_handler.py R lib/pulsar/client/staging/__init__.py R lib/pulsar/client/staging/down.py R lib/pulsar/client/staging/up.py R lib/pulsar/client/transport/__init__.py R lib/pulsar/client/transport/curl.py R lib/pulsar/client/transport/poster.py R lib/pulsar/client/transport/requests.py R lib/pulsar/client/transport/ssh.py R lib/pulsar/client/transport/standard.py R lib/pulsar/client/util.py M lib/tool_shed/capsule/capsule_manager.py M lib/tool_shed/dependencies/attribute_handlers.py M lib/tool_shed/dependencies/repository/relation_builder.py M lib/tool_shed/galaxy_install/dependency_display.py M lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/galaxy_install/installed_repository_manager.py M lib/tool_shed/galaxy_install/metadata/installed_repository_metadata_manager.py M lib/tool_shed/galaxy_install/migrate/common.py M lib/tool_shed/galaxy_install/repair_repository_manager.py M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/env_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/env_file_builder.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/install_environment.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py M lib/tool_shed/galaxy_install/tool_migration_manager.py M lib/tool_shed/galaxy_install/tools/data_manager.py M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py M lib/tool_shed/galaxy_install/update_repository_manager.py M lib/tool_shed/galaxy_install/utility_containers/__init__.py M lib/tool_shed/grids/repository_grids.py M lib/tool_shed/grids/util.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/repository_types/metadata.py R lib/tool_shed/scripts/api/add_repository_registry_entry.py R lib/tool_shed/scripts/api/common.py R lib/tool_shed/scripts/api/create_categories.py R lib/tool_shed/scripts/api/create_users.py R lib/tool_shed/scripts/api/export.py R lib/tool_shed/scripts/api/get_filtered_repository_revisions.py R lib/tool_shed/scripts/api/import_capsule.py R lib/tool_shed/scripts/api/remove_repository_registry_entry.py R lib/tool_shed/scripts/api/reset_metadata_on_repositories.py R lib/tool_shed/scripts/api/tool_shed_repository_revision_update.py R lib/tool_shed/scripts/bootstrap_tool_shed/bootstrap_tool_shed.sh R lib/tool_shed/scripts/bootstrap_tool_shed/bootstrap_util.py R lib/tool_shed/scripts/bootstrap_tool_shed/create_user_with_api_key.py R lib/tool_shed/scripts/bootstrap_tool_shed/parse_run_sh_args.sh R lib/tool_shed/scripts/bootstrap_tool_shed/user_info.xml.sample R lib/tool_shed/scripts/check_filesystem_for_empty_tool_dependency_installation_paths.py R lib/tool_shed/scripts/check_repositories_for_functional_tests.py R lib/tool_shed/scripts/check_s3_for_empty_tool_dependency_installation_paths.py R lib/tool_shed/scripts/check_tool_dependency_definition_repositories.py R lib/tool_shed/scripts/clean_up_tool_dependency_directory.py R lib/tool_shed/scripts/deprecate_repositories_without_metadata.py R lib/tool_shed/scripts/show_tool_dependency_installation_dir_contents.py M lib/tool_shed/tool_shed_registry.py M lib/tool_shed/tools/data_table_manager.py M lib/tool_shed/tools/tool_validator.py M lib/tool_shed/tools/tool_version_manager.py M lib/tool_shed/util/basic_util.py M lib/tool_shed/util/commit_util.py M lib/tool_shed/util/common_util.py M lib/tool_shed/util/container_util.py M lib/tool_shed/util/hg_util.py M lib/tool_shed/util/metadata_util.py M lib/tool_shed/util/readme_util.py M lib/tool_shed/util/repository_util.py M lib/tool_shed/util/shed_util_common.py M lib/tool_shed/util/tool_dependency_util.py M lib/tool_shed/util/tool_util.py M lib/tool_shed/util/workflow_util.py M lib/tool_shed/util/xml_util.py M lib/tool_shed/utility_containers/__init__.py M lib/tool_shed/utility_containers/utility_container_manager.py M run_tests.sh M run_tool_shed.sh M scripts/api/data_manager_example_execute.py A scripts/api/filter_failed_datasets_from_collection.py M scripts/api/search.py M scripts/api/upload_to_history.py M scripts/bootstrap_history.py M scripts/check_galaxy.py M scripts/cleanup_datasets/admin_cleanup_datasets.py M scripts/cleanup_datasets/cleanup_datasets.py M scripts/cleanup_datasets/pgcleanup.py M scripts/cleanup_datasets/populate_uuid.py M scripts/cleanup_datasets/remove_renamed_datasets_from_disk.py M scripts/cleanup_datasets/rename_purged_datasets.py M scripts/cleanup_datasets/update_dataset_size.py M scripts/cleanup_datasets/update_metadata.py M scripts/common_startup.sh M scripts/data_libraries/build_lucene_index.py M scripts/data_libraries/build_whoosh_index.py M scripts/drmaa_external_killer.py M scripts/drmaa_external_runner.py M scripts/extract_dataset_part.py M scripts/functional_tests.py M scripts/microbes/BeautifulSoup.py M scripts/microbes/harvest_bacteria.py M scripts/others/incorrect_gops_jobs.py M scripts/others/incorrect_gops_join_jobs.py M scripts/runtime_stats.py A scripts/tool_shed/api/add_repository_registry_entry.py A scripts/tool_shed/api/common.py A scripts/tool_shed/api/create_categories.py A scripts/tool_shed/api/create_users.py A scripts/tool_shed/api/export.py A scripts/tool_shed/api/get_filtered_repository_revisions.py A scripts/tool_shed/api/import_capsule.py A scripts/tool_shed/api/remove_repository_registry_entry.py A scripts/tool_shed/api/reset_metadata_on_repositories.py A scripts/tool_shed/api/tool_shed_repository_revision_update.py A scripts/tool_shed/bootstrap_tool_shed/bootstrap_tool_shed.sh A scripts/tool_shed/bootstrap_tool_shed/bootstrap_util.py A scripts/tool_shed/bootstrap_tool_shed/create_user_with_api_key.py A scripts/tool_shed/bootstrap_tool_shed/parse_run_sh_args.sh A scripts/tool_shed/bootstrap_tool_shed/user_info.xml.sample M scripts/tool_shed/build_ts_whoosh_index.py M scripts/tool_shed/check_download_urls.py A scripts/tool_shed/check_filesystem_for_empty_tool_dependency_installation_paths.py A scripts/tool_shed/check_s3_for_empty_tool_dependency_installation_paths.py A scripts/tool_shed/clean_up_tool_dependency_directory.py A scripts/tool_shed/deprecate_repositories_without_metadata.py A scripts/tool_shed/show_tool_dependency_installation_dir_contents.py M scripts/tools/maf/check_loc_file.py M scripts/transfer.py M static/maps/layout/menu.js.map M static/maps/layout/page.js.map M static/maps/layout/scratchbook.js.map M static/maps/libs/backbone.js.map M static/maps/libs/bootstrap-tour.js.map M static/maps/libs/d3.js.map M static/maps/libs/jquery/jquery.js.map M static/maps/libs/jquery/jquery.migrate.js.map M static/maps/libs/raven.js.map M static/maps/libs/require.js.map R static/maps/libs/tracekit.js.map M static/maps/libs/underscore.js.map M static/maps/mvc/citation/citation-model.js.map M static/maps/mvc/collection/collection-li.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/dataset/dataset-model.js.map M static/maps/mvc/form/form-data.js.map M static/maps/mvc/form/form-input.js.map M static/maps/mvc/form/form-parameters.js.map M static/maps/mvc/form/form-section.js.map M static/maps/mvc/form/form-view.js.map M static/maps/mvc/history/history-contents.js.map M static/maps/mvc/history/history-model.js.map M static/maps/mvc/history/history-view-annotated.js.map M static/maps/mvc/history/history-view-edit-current.js.map M static/maps/mvc/history/history-view.js.map M static/maps/mvc/history/multi-panel.js.map M static/maps/mvc/library/library-dataset-view.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-library-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/popup-menu.js.map M static/maps/mvc/ui/ui-drilldown.js.map M static/maps/mvc/ui/ui-frames.js.map M static/maps/mvc/ui/ui-list.js.map M static/maps/mvc/ui/ui-misc.js.map M static/maps/mvc/ui/ui-options.js.map M static/maps/mvc/ui/ui-portlet.js.map M static/maps/mvc/ui/ui-select-content.js.map M static/maps/mvc/ui/ui-select-default.js.map M static/maps/mvc/ui/ui-select.js.map M static/maps/mvc/workflow/workflow-terminals.js.map M static/maps/ui/hoverhighlight.js.map M static/maps/ui/loading-indicator.js.map M static/maps/ui/mode-button.js.map M static/maps/ui/pagination.js.map M static/maps/ui/peek-column-selector.js.map M static/maps/utils/localization.js.map M static/maps/utils/metrics-logger.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/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/layout/menu.js M static/scripts/layout/page.js M static/scripts/layout/scratchbook.js M static/scripts/libs/backbone.js M static/scripts/libs/bootstrap-tour.js M static/scripts/libs/d3.js M static/scripts/libs/jquery/jquery.js M static/scripts/libs/jquery/jquery.migrate.js M static/scripts/libs/raven.js M static/scripts/libs/require.js R static/scripts/libs/tracekit.js M static/scripts/libs/underscore.js M static/scripts/mvc/citation/citation-model.js M static/scripts/mvc/collection/collection-li.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/dataset/dataset-model.js M static/scripts/mvc/form/form-data.js M static/scripts/mvc/form/form-input.js M static/scripts/mvc/form/form-parameters.js M static/scripts/mvc/form/form-section.js M static/scripts/mvc/form/form-view.js M static/scripts/mvc/history/history-contents.js M static/scripts/mvc/history/history-model.js M static/scripts/mvc/history/history-view-annotated.js M static/scripts/mvc/history/history-view-edit-current.js M static/scripts/mvc/history/history-view.js M static/scripts/mvc/history/multi-panel.js M static/scripts/mvc/library/library-dataset-view.js M static/scripts/mvc/library/library-folder-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/library/library-library-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/popup-menu.js M static/scripts/mvc/ui/ui-drilldown.js M static/scripts/mvc/ui/ui-frames.js M static/scripts/mvc/ui/ui-list.js M static/scripts/mvc/ui/ui-misc.js M static/scripts/mvc/ui/ui-options.js M static/scripts/mvc/ui/ui-portlet.js M static/scripts/mvc/ui/ui-select-content.js M static/scripts/mvc/ui/ui-select-default.js M static/scripts/mvc/ui/ui-select.js M static/scripts/mvc/workflow/workflow-terminals.js M static/scripts/ui/hoverhighlight.js M static/scripts/ui/loading-indicator.js M static/scripts/ui/mode-button.js M static/scripts/ui/pagination.js M static/scripts/ui/peek-column-selector.js M static/scripts/utils/localization.js M static/scripts/utils/metrics-logger.js M static/scripts/utils/utils.js M static/style/blue/base.css M static/style/blue/library.css M templates/admin/tool_shed_repository/preview_repository.mako M templates/admin/tool_shed_repository/repair_repository.mako M templates/base.mako M templates/base/base_panels.mako M templates/display_base.mako M templates/js-app.mako M templates/sharing_base.mako M templates/show_params.mako A templates/slug_editing_js.mako M templates/webapps/galaxy/admin/index.mako M templates/webapps/galaxy/data_manager/view_job.mako M templates/webapps/galaxy/galaxy.masthead.mako M templates/webapps/galaxy/galaxy.panels.mako M templates/webapps/galaxy/history/display.mako M templates/webapps/galaxy/library/common/browse_library.mako M templates/webapps/galaxy/library/common/ldda_info.mako A templates/webapps/galaxy/visualization/gie.mako M templates/webapps/galaxy/workflow/display.mako M templates/webapps/galaxy/workflow/editor_tool_form.mako R templates/webapps/galaxy/workflow/export.mako M templates/webapps/galaxy/workflow/list.mako M templates/webapps/galaxy/workflow/run.mako M templates/webapps/galaxy/workflow/sharing.mako M templates/webapps/tool_shed/index.mako M templates/webapps/tool_shed/repository/common.mako M templates/webapps/tool_shed/repository/manage_repository.mako M templates/webapps/tool_shed/repository/view_changeset.mako A test-data/biom1_metadata_test.txt A test-data/composite_output_expected_log A test-data/input_taxonomy.biom1 M test/api/test_datasets.py M test/api/test_tools.py M test/api/test_workflows.py M test/api/test_workflows_from_yaml.py M test/api/workflows_format_2/converter.py M test/api/workflows_format_2/interface.py M test/api/workflows_format_2/main.py R test/base/asserts/__init__.py R test/base/asserts/tabular.py R test/base/asserts/text.py R test/base/asserts/xml.py M test/base/driver_util.py A test/base/integration_util.py M test/base/interactor.py R test/base/test_data.py M test/base/twilltestcase.py M test/casperjs/casperjs_runner.py M test/casperjs/server_env.py M test/functional/test_data_managers.py M test/functional/test_toolbox.py A test/functional/tools/checksum.xml M test/functional/tools/composite_output.xml A test/functional/tools/composite_output_tests.xml A test/functional/tools/metadata_biom1.xml A test/functional/tools/multi_data_repeat.xml M test/functional/tools/sample_datatypes_conf.xml M test/functional/tools/samples_tool_conf.xml M test/functional/tools/simple_constructs.yml M test/functional/tools/upload_tool_conf.xml A test/integration/__init__.py A test/integration/embedded_pulsar_job_conf.xml A test/integration/test_pulsar_embedded.py M test/qunit/test-app.js M test/qunit/test-common.js M test/qunit/test-data/fakeserver.js R test/qunit/test-libs/qunit-1.14.0.css R test/qunit/test-libs/qunit-1.14.0.js A test/qunit/test-libs/qunit-1.23.1.css A test/qunit/test-libs/qunit-1.23.1.js A test/qunit/test-libs/sinon-1.17.3.js R test/qunit/test-libs/sinon-1.9.1.js M test/qunit/tests/form_tests.js M test/qunit/tests/list-of-pairs-collection-creator.js M test/qunit/tests/metrics-logger.js M test/qunit/tests/modal_tests.js M test/qunit/tests/page_tests.js M test/qunit/tests/ui_tests.js A test/qunit/tests/utils_test.html A test/qunit/tests/utils_test.js M test/qunit/tests/workflow_editor_tests.js A test/shed_functional/__init__.py A test/shed_functional/base/__init__.py A test/shed_functional/base/common.py A test/shed_functional/base/test_db_util.py A test/shed_functional/base/twilltestcase.py A test/shed_functional/functional/__init__.py A test/shed_functional/functional/test_0000_basic_repository_features.py A test/shed_functional/functional/test_0010_repository_with_tool_dependencies.py A test/shed_functional/functional/test_0020_basic_repository_dependencies.py A test/shed_functional/functional/test_0030_repository_dependency_revisions.py A test/shed_functional/functional/test_0040_repository_circular_dependencies.py A test/shed_functional/functional/test_0050_circular_dependencies_4_levels.py A test/shed_functional/functional/test_0060_workflows.py A test/shed_functional/functional/test_0070_invalid_tool.py A test/shed_functional/functional/test_0080_advanced_circular_dependencies.py A test/shed_functional/functional/test_0090_tool_search.py A test/shed_functional/functional/test_0100_complex_repository_dependencies.py A test/shed_functional/functional/test_0110_invalid_simple_repository_dependencies.py A test/shed_functional/functional/test_0120_simple_repository_dependency_multiple_owners.py A test/shed_functional/functional/test_0130_datatype_converters.py A test/shed_functional/functional/test_0140_tool_help_images.py A test/shed_functional/functional/test_0150_prior_installation_required.py A test/shed_functional/functional/test_0160_circular_prior_installation_required.py A test/shed_functional/functional/test_0170_complex_prior_installation_required.py A test/shed_functional/functional/test_0300_reset_all_metadata.py A test/shed_functional/functional/test_0310_hg_api_features.py A test/shed_functional/functional/test_0400_repository_component_reviews.py A test/shed_functional/functional/test_0410_repository_component_review_access_control.py A test/shed_functional/functional/test_0420_citable_urls_for_repositories.py A test/shed_functional/functional/test_0430_browse_utilities.py A test/shed_functional/functional/test_0440_deleting_dependency_definitions.py A test/shed_functional/functional/test_0460_upload_to_repository.py A test/shed_functional/functional/test_0470_tool_dependency_repository_type.py A test/shed_functional/functional/test_0480_tool_dependency_xml_verification.py A test/shed_functional/functional/test_0490_export_import_repositories.py A test/shed_functional/functional/test_0500_export_repository_simple_dependency.py A test/shed_functional/functional/test_0510_export_import_repository_complex_dependencies.py A test/shed_functional/functional/test_0520_import_export_circular_dependencies.py A test/shed_functional/functional/test_0530_repository_admin_feature.py A test/shed_functional/functional/test_0540_get_all_metadata_from_api.py A test/shed_functional/functional/test_0550_metadata_updated_dependencies.py A test/shed_functional/functional/test_1000_install_basic_repository.py A test/shed_functional/functional/test_1010_install_repository_with_tool_dependencies.py A test/shed_functional/functional/test_1020_install_repository_with_repository_dependencies.py A test/shed_functional/functional/test_1030_install_repository_with_dependency_revisions.py A test/shed_functional/functional/test_1040_install_repository_basic_circular_dependencies.py A test/shed_functional/functional/test_1050_circular_dependencies_4_levels.py A test/shed_functional/functional/test_1060_install_repository_with_workflow.py A test/shed_functional/functional/test_1070_invalid_tool.py A test/shed_functional/functional/test_1080_advanced_circular_dependency_installation.py A test/shed_functional/functional/test_1090_repository_dependency_handling.py A test/shed_functional/functional/test_1100_install_updated_repository_dependencies.py A test/shed_functional/functional/test_1110_install_tool_from_tool_search.py A test/shed_functional/functional/test_1120_install_repository_with_complex_dependencies.py A test/shed_functional/functional/test_1130_install_repository_with_invalid_repository_dependency.py A test/shed_functional/functional/test_1140_simple_repository_dependency_multiple_owners.py A test/shed_functional/functional/test_1150_datatype_converters.py A test/shed_functional/functional/test_1160_tool_help_images.py A test/shed_functional/functional/test_1170_prior_installation_required.py A test/shed_functional/functional/test_1180_circular_prior_installation_required.py A test/shed_functional/functional/test_1190_complex_prior_installation_required.py A test/shed_functional/functional/test_1200_uninstall_and_reinstall_basic_repository.py A test/shed_functional/functional/test_1210_uninstall_reinstall_repository_with_tool_dependencies.py A test/shed_functional/functional/test_1220_uninstall_reinstall_repository_with_repository_dependencies.py A test/shed_functional/functional/test_1230_uninstall_reinstall_repository_with_dependency_revisions.py A test/shed_functional/functional/test_1300_reset_all_metadata.py A test/shed_functional/functional/test_1400_review_migration_stages.py A test/shed_functional/functional/test_1410_update_manager.py A test/shed_functional/functional/test_1420_tool_dependency_environment_inheritance.py A test/shed_functional/functional/test_1430_repair_installed_repository.py A test/shed_functional/functional/test_1440_missing_env_sh_files.py A test/shed_functional/functional/test_1450_installing_datatypes_sniffers.py A test/shed_functional/functional/test_1460_data_managers.py A test/shed_functional/functional/test_1470_updating_installed_repositories.py A test/shed_functional/functional_tests.py A test/shed_functional/test_data/0460_files/repository_dependencies.xml A test/shed_functional/test_data/0460_files/repository_dependencies_in_root.tar A test/shed_functional/test_data/0460_files/repository_dependencies_in_subfolder.tar A test/shed_functional/test_data/0460_files/tool_dependencies.xml A test/shed_functional/test_data/0460_files/tool_dependencies_in_root.tar A test/shed_functional/test_data/0460_files/tool_dependencies_in_subfolder.tar A test/shed_functional/test_data/0480_files/tool_dependencies.xml A test/shed_functional/test_data/0540_files/column_maker/column_maker.tar A test/shed_functional/test_data/0540_files/column_maker/repository_dependencies.xml A test/shed_functional/test_data/0540_files/convert_chars/convert_chars.tar A test/shed_functional/test_data/0540_files/convert_chars/tool_dependencies.xml A test/shed_functional/test_data/0540_files/package_bwa/tool_dependencies.xml A test/shed_functional/test_data/0550_files/filtering_1.0.tgz A test/shed_functional/test_data/0550_files/package_freebayes_1_0550.tgz A test/shed_functional/test_data/0550_files/package_freebayes_2_0550.tgz A test/shed_functional/test_data/0550_files/package_samtools_1_0550.tgz A test/shed_functional/test_data/0550_files/package_samtools_2_0550.tgz A test/shed_functional/test_data/0550_files/temp/tool_dependencies.xml A test/shed_functional/test_data/1420_files/binary_tarballs/atlas.tar A test/shed_functional/test_data/1420_files/binary_tarballs/boost.tar A test/shed_functional/test_data/1420_files/binary_tarballs/bzlib.tar A test/shed_functional/test_data/1420_files/binary_tarballs/lapack.tar A test/shed_functional/test_data/1420_files/binary_tarballs/numpy.tar A test/shed_functional/test_data/1420_files/binary_tarballs/rdkit.tar A test/shed_functional/test_data/1420_files/package_atlas_3_10_1420/tool_dependencies.xml A test/shed_functional/test_data/1420_files/package_boost_1_53_1420/tool_dependencies.xml A test/shed_functional/test_data/1420_files/package_bzlib_1_0_1420/tool_dependencies.xml A test/shed_functional/test_data/1420_files/package_lapack_3_4_1420/tool_dependencies.xml A test/shed_functional/test_data/1420_files/package_numpy_1_7_1420/tool_dependencies.xml A test/shed_functional/test_data/1420_files/package_rdkit_2012_12_1420/tool_dependencies.xml A test/shed_functional/test_data/1440_files/complex_dependency/tool_dependencies.xml A test/shed_functional/test_data/1440_files/dependency_definition/tool_dependencies.xml A test/shed_functional/test_data/1460_files/data_manager_files/test_data_manager.tar A test/shed_functional/test_data/bed_to_gff_converter/bed_to_gff_converter.tar A test/shed_functional/test_data/bismark/bismark.tar A test/shed_functional/test_data/bismark/bismark_methylation_extractor.xml A test/shed_functional/test_data/blast/blast_datatypes.tar A test/shed_functional/test_data/blast/blastxml_to_top_descr.tar A test/shed_functional/test_data/bwa/bwa_base.tar A test/shed_functional/test_data/bwa/bwa_color.tar A test/shed_functional/test_data/bwa/complex/bwa_base.tar A test/shed_functional/test_data/bwa/complex/readme/tool_dependencies.xml A test/shed_functional/test_data/bwa/complex/tool_dependencies.xml A test/shed_functional/test_data/column_maker/column_maker.tar A test/shed_functional/test_data/convert_chars/convert_chars.tar A test/shed_functional/test_data/emboss/0470_files/emboss_complex_dependency.tar A test/shed_functional/test_data/emboss/0470_files/tool_dependencies.xml A test/shed_functional/test_data/emboss/datatypes/datatypes_conf.xml A test/shed_functional/test_data/emboss/emboss.tar A test/shed_functional/test_data/emboss/emboss_5_0_0/first_tool_dependency/tool_dependencies.xml A test/shed_functional/test_data/emboss/emboss_5_0_0/second_tool_dependency/tool_dependencies.xml A test/shed_functional/test_data/emboss/libx11_proto/first_tool_dependency/tool_dependencies.xml A test/shed_functional/test_data/emboss/libx11_proto/second_tool_dependency/tool_dependencies.xml A test/shed_functional/test_data/filtering/README A test/shed_functional/test_data/filtering/filtering_0000.txt A test/shed_functional/test_data/filtering/filtering_1.1.0.tar A test/shed_functional/test_data/filtering/filtering_2.2.0.tar A test/shed_functional/test_data/filtering/filtering_test_data.tar A test/shed_functional/test_data/filtering/readme.txt A test/shed_functional/test_data/filtering_workflow/Workflow_for_0060_filter_workflow_repository.ga A test/shed_functional/test_data/freebayes/freebayes.tar A test/shed_functional/test_data/freebayes/freebayes.xml A test/shed_functional/test_data/freebayes/invalid_tool_dependencies/tool_dependencies.xml A test/shed_functional/test_data/freebayes/malformed_tool_dependencies/tool_dependencies.xml A test/shed_functional/test_data/freebayes/sam_fa_indices.loc.sample A test/shed_functional/test_data/freebayes/tool_data_table_conf.xml.sample A test/shed_functional/test_data/freebayes/tool_dependencies.xml A test/shed_functional/test_data/htseq_count/htseq_count.tar A test/shed_functional/test_data/package_matplotlib/package_matplotlib_1_2.tar A test/shed_functional/test_data/package_matplotlib/tool_dependencies.xml A test/shed_functional/test_data/package_numpy/package_numpy_1_7.tar A test/shed_functional/test_data/proteomics_datatypes/proteomics_datatypes.tar A test/shed_functional/test_data/readme.txt A test/shed_functional/test_data/repository_capsules/0490_filtering.tar.gz A test/shed_functional/test_data/repository_capsules/0500_emboss_5.tar.gz A test/shed_functional/test_data/repository_capsules/0510_trans_proteomic_pipeline.tar.gz A test/shed_functional/test_data/repository_capsules/0520_filtering.tar.gz R test/tool_shed/__init__.py R test/tool_shed/base/__init__.py R test/tool_shed/base/common.py R test/tool_shed/base/test_db_util.py R test/tool_shed/base/twilltestcase.py R test/tool_shed/functional/__init__.py R test/tool_shed/functional/test_0000_basic_repository_features.py R test/tool_shed/functional/test_0010_repository_with_tool_dependencies.py R test/tool_shed/functional/test_0020_basic_repository_dependencies.py R test/tool_shed/functional/test_0030_repository_dependency_revisions.py R test/tool_shed/functional/test_0040_repository_circular_dependencies.py R test/tool_shed/functional/test_0050_circular_dependencies_4_levels.py R test/tool_shed/functional/test_0060_workflows.py R test/tool_shed/functional/test_0070_invalid_tool.py R test/tool_shed/functional/test_0080_advanced_circular_dependencies.py R test/tool_shed/functional/test_0090_tool_search.py R test/tool_shed/functional/test_0100_complex_repository_dependencies.py R test/tool_shed/functional/test_0110_invalid_simple_repository_dependencies.py R test/tool_shed/functional/test_0120_simple_repository_dependency_multiple_owners.py R test/tool_shed/functional/test_0130_datatype_converters.py R test/tool_shed/functional/test_0140_tool_help_images.py R test/tool_shed/functional/test_0150_prior_installation_required.py R test/tool_shed/functional/test_0160_circular_prior_installation_required.py R test/tool_shed/functional/test_0170_complex_prior_installation_required.py R test/tool_shed/functional/test_0300_reset_all_metadata.py R test/tool_shed/functional/test_0310_hg_api_features.py R test/tool_shed/functional/test_0400_repository_component_reviews.py R test/tool_shed/functional/test_0410_repository_component_review_access_control.py R test/tool_shed/functional/test_0420_citable_urls_for_repositories.py R test/tool_shed/functional/test_0430_browse_utilities.py R test/tool_shed/functional/test_0440_deleting_dependency_definitions.py R test/tool_shed/functional/test_0450_skip_tool_tests.py R test/tool_shed/functional/test_0460_upload_to_repository.py R test/tool_shed/functional/test_0470_tool_dependency_repository_type.py R test/tool_shed/functional/test_0480_tool_dependency_xml_verification.py R test/tool_shed/functional/test_0490_export_import_repositories.py R test/tool_shed/functional/test_0500_export_repository_simple_dependency.py R test/tool_shed/functional/test_0510_export_import_repository_complex_dependencies.py R test/tool_shed/functional/test_0520_import_export_circular_dependencies.py R test/tool_shed/functional/test_0530_repository_admin_feature.py R test/tool_shed/functional/test_0540_get_all_metadata_from_api.py R test/tool_shed/functional/test_1000_install_basic_repository.py R test/tool_shed/functional/test_1010_install_repository_with_tool_dependencies.py R test/tool_shed/functional/test_1020_install_repository_with_repository_dependencies.py R test/tool_shed/functional/test_1030_install_repository_with_dependency_revisions.py R test/tool_shed/functional/test_1040_install_repository_basic_circular_dependencies.py R test/tool_shed/functional/test_1050_circular_dependencies_4_levels.py R test/tool_shed/functional/test_1060_install_repository_with_workflow.py R test/tool_shed/functional/test_1070_invalid_tool.py R test/tool_shed/functional/test_1080_advanced_circular_dependency_installation.py R test/tool_shed/functional/test_1090_repository_dependency_handling.py R test/tool_shed/functional/test_1100_install_updated_repository_dependencies.py R test/tool_shed/functional/test_1110_install_tool_from_tool_search.py R test/tool_shed/functional/test_1120_install_repository_with_complex_dependencies.py R test/tool_shed/functional/test_1130_install_repository_with_invalid_repository_dependency.py R test/tool_shed/functional/test_1140_simple_repository_dependency_multiple_owners.py R test/tool_shed/functional/test_1150_datatype_converters.py R test/tool_shed/functional/test_1160_tool_help_images.py R test/tool_shed/functional/test_1170_prior_installation_required.py R test/tool_shed/functional/test_1180_circular_prior_installation_required.py R test/tool_shed/functional/test_1190_complex_prior_installation_required.py R test/tool_shed/functional/test_1200_uninstall_and_reinstall_basic_repository.py R test/tool_shed/functional/test_1210_uninstall_reinstall_repository_with_tool_dependencies.py R test/tool_shed/functional/test_1220_uninstall_reinstall_repository_with_repository_dependencies.py R test/tool_shed/functional/test_1230_uninstall_reinstall_repository_with_dependency_revisions.py R test/tool_shed/functional/test_1300_reset_all_metadata.py R test/tool_shed/functional/test_1400_review_migration_stages.py R test/tool_shed/functional/test_1410_update_manager.py R test/tool_shed/functional/test_1420_tool_dependency_environment_inheritance.py R test/tool_shed/functional/test_1430_repair_installed_repository.py R test/tool_shed/functional/test_1440_missing_env_sh_files.py R test/tool_shed/functional/test_1450_installing_datatypes_sniffers.py R test/tool_shed/functional/test_1460_data_managers.py R test/tool_shed/functional/test_1470_updating_installed_repositories.py R test/tool_shed/functional_tests.py R test/tool_shed/test_data/0460_files/repository_dependencies.xml R test/tool_shed/test_data/0460_files/repository_dependencies_in_root.tar R test/tool_shed/test_data/0460_files/repository_dependencies_in_subfolder.tar R test/tool_shed/test_data/0460_files/tool_dependencies.xml R test/tool_shed/test_data/0460_files/tool_dependencies_in_root.tar R test/tool_shed/test_data/0460_files/tool_dependencies_in_subfolder.tar R test/tool_shed/test_data/0480_files/tool_dependencies.xml R test/tool_shed/test_data/0540_files/column_maker/column_maker.tar R test/tool_shed/test_data/0540_files/column_maker/repository_dependencies.xml R test/tool_shed/test_data/0540_files/convert_chars/convert_chars.tar R test/tool_shed/test_data/0540_files/convert_chars/tool_dependencies.xml R test/tool_shed/test_data/0540_files/package_bwa/tool_dependencies.xml R test/tool_shed/test_data/1420_files/binary_tarballs/atlas.tar R test/tool_shed/test_data/1420_files/binary_tarballs/boost.tar R test/tool_shed/test_data/1420_files/binary_tarballs/bzlib.tar R test/tool_shed/test_data/1420_files/binary_tarballs/lapack.tar R test/tool_shed/test_data/1420_files/binary_tarballs/numpy.tar R test/tool_shed/test_data/1420_files/binary_tarballs/rdkit.tar R test/tool_shed/test_data/1420_files/package_atlas_3_10_1420/tool_dependencies.xml R test/tool_shed/test_data/1420_files/package_boost_1_53_1420/tool_dependencies.xml R test/tool_shed/test_data/1420_files/package_bzlib_1_0_1420/tool_dependencies.xml R test/tool_shed/test_data/1420_files/package_lapack_3_4_1420/tool_dependencies.xml R test/tool_shed/test_data/1420_files/package_numpy_1_7_1420/tool_dependencies.xml R test/tool_shed/test_data/1420_files/package_rdkit_2012_12_1420/tool_dependencies.xml R test/tool_shed/test_data/1440_files/complex_dependency/tool_dependencies.xml R test/tool_shed/test_data/1440_files/dependency_definition/tool_dependencies.xml R test/tool_shed/test_data/1460_files/data_manager_files/test_data_manager.tar R test/tool_shed/test_data/bed_to_gff_converter/bed_to_gff_converter.tar R test/tool_shed/test_data/bismark/bismark.tar R test/tool_shed/test_data/bismark/bismark_methylation_extractor.xml R test/tool_shed/test_data/blast/blast_datatypes.tar R test/tool_shed/test_data/blast/blastxml_to_top_descr.tar R test/tool_shed/test_data/bwa/bwa_base.tar R test/tool_shed/test_data/bwa/bwa_color.tar R test/tool_shed/test_data/bwa/complex/bwa_base.tar R test/tool_shed/test_data/bwa/complex/readme/tool_dependencies.xml R test/tool_shed/test_data/bwa/complex/tool_dependencies.xml R test/tool_shed/test_data/column_maker/column_maker.tar R test/tool_shed/test_data/convert_chars/convert_chars.tar R test/tool_shed/test_data/emboss/0470_files/emboss_complex_dependency.tar R test/tool_shed/test_data/emboss/0470_files/tool_dependencies.xml R test/tool_shed/test_data/emboss/datatypes/datatypes_conf.xml R test/tool_shed/test_data/emboss/emboss.tar R test/tool_shed/test_data/emboss/emboss_5_0_0/first_tool_dependency/tool_dependencies.xml R test/tool_shed/test_data/emboss/emboss_5_0_0/second_tool_dependency/tool_dependencies.xml R test/tool_shed/test_data/emboss/libx11_proto/first_tool_dependency/tool_dependencies.xml R test/tool_shed/test_data/emboss/libx11_proto/second_tool_dependency/tool_dependencies.xml R test/tool_shed/test_data/filtering/README R test/tool_shed/test_data/filtering/filtering_0000.txt R test/tool_shed/test_data/filtering/filtering_1.1.0.tar R test/tool_shed/test_data/filtering/filtering_2.2.0.tar R test/tool_shed/test_data/filtering/filtering_test_data.tar R test/tool_shed/test_data/filtering/readme.txt R test/tool_shed/test_data/filtering_workflow/Workflow_for_0060_filter_workflow_repository.ga R test/tool_shed/test_data/freebayes/freebayes.tar R test/tool_shed/test_data/freebayes/freebayes.xml R test/tool_shed/test_data/freebayes/invalid_tool_dependencies/tool_dependencies.xml R test/tool_shed/test_data/freebayes/malformed_tool_dependencies/tool_dependencies.xml R test/tool_shed/test_data/freebayes/sam_fa_indices.loc.sample R test/tool_shed/test_data/freebayes/tool_data_table_conf.xml.sample R test/tool_shed/test_data/freebayes/tool_dependencies.xml R test/tool_shed/test_data/htseq_count/htseq_count.tar R test/tool_shed/test_data/package_matplotlib/package_matplotlib_1_2.tar R test/tool_shed/test_data/package_matplotlib/tool_dependencies.xml R test/tool_shed/test_data/package_numpy/package_numpy_1_7.tar R test/tool_shed/test_data/proteomics_datatypes/proteomics_datatypes.tar R test/tool_shed/test_data/readme.txt R test/tool_shed/test_data/repository_capsules/0490_filtering.tar.gz R test/tool_shed/test_data/repository_capsules/0500_emboss_5.tar.gz R test/tool_shed/test_data/repository_capsules/0510_trans_proteomic_pipeline.tar.gz R test/tool_shed/test_data/repository_capsules/0520_filtering.tar.gz M test/unit/jobs/test_command_factory.py M test/unit/managers/test_CollectionManager.py M test/unit/managers/test_DatasetManager.py M test/unit/managers/test_HDAManager.py M test/unit/managers/test_HistoryContentsManager.py M test/unit/managers/test_HistoryManager.py A test/unit/shed_unit/__init__.py A test/unit/shed_unit/test_fabric_util.py A test/unit/shed_unit/test_td_common_util.py A test/unit/shed_unit/test_tool_panel_manager.py M test/unit/test_objectstore.py R test/unit/tool_shed_unit_tests/__init__.py R test/unit/tool_shed_unit_tests/test_fabric_util.py R test/unit/tool_shed_unit_tests/test_td_common_util.py R test/unit/tool_shed_unit_tests/test_tool_panel_manager.py M test/unit/tools/test_actions.py M test/unit/tools/test_conda_resolution.py M test/unit/tools/test_execution.py M test/unit/tools/test_select_parameters.py M test/unit/unittest_utils/galaxy_mock.py M test/unit/visualizations/plugins/test_VisualizationPlugin.py M test/unit/visualizations/plugins/test_VisualizationsRegistry.py M test/unit/web/base/test_HookPluginManager.py M test/unit/web/base/test_PageServingPluginManager.py M test/unit/web/base/test_PluginManager.py M test/unit/web/framework/test_webapp.py M test/unit/workflows/test_run_parameters.py A tool-data/biom_simple_display.loc.sample M tool_list.py M tools/data_source/biomart.xml M tools/data_source/data_source.py M tools/data_source/fetch.py M tools/data_source/genbank.py M tools/data_source/hbvar_filter.py M tools/data_source/import.py M tools/data_source/microbial_import.py M tools/data_source/microbial_import_code.py M tools/data_source/upload.py M tools/evolution/add_scores.py M tools/extract/extract_genomic_dna.py M tools/extract/liftOver_wrapper.py M tools/filters/axt_to_concat_fasta.xml M tools/filters/axt_to_fasta.xml M tools/filters/axt_to_lav.py M tools/filters/axt_to_lav.xml M tools/filters/bed2gff.xml M tools/filters/bed_to_bigbed.xml M tools/filters/bed_to_gff_converter.py M tools/filters/gff/extract_GFF_Features.py M tools/filters/gff/gff_filter_by_attribute.py M tools/filters/gff2bed.xml M tools/filters/gff_to_bed_converter.py M tools/filters/gtf2bedgraph.xml M tools/filters/gtf_to_bedgraph_converter.py M tools/filters/join.py M tools/filters/joinWrapper.py M tools/filters/lav_to_bed.py M tools/filters/mergeCols.py M tools/filters/sff_extract.py M tools/filters/sorter.py M tools/filters/trimmer.xml M tools/filters/wiggle_to_simple.py M tools/genomespace/genomespace_exporter.py M tools/genomespace/genomespace_file_browser.py M tools/maf/interval_maf_to_merged_fasta.py M tools/maf/maf_split_by_species.py M tools/maf/maf_thread_for_species.py M tools/maf/maf_to_fasta_concat.py M tools/maf/maf_to_fasta_multiple_sets.py M tools/metag_tools/blat_wrapper.py M tools/metag_tools/shrimp_color_wrapper.py M tools/metag_tools/shrimp_wrapper.py M tools/next_gen_conversion/fastq_conversions.py M tools/next_gen_conversion/fastq_gen_conv.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/velveth_wrapper.py M tools/sr_mapping/bfast_wrapper.py M tools/stats/aggregate_scores_in_intervals.py M tools/stats/filtering.py M tools/stats/filtering.xml M tools/stats/grouping.py M tools/stats/grouping.xml M tools/stats/gsummary.py M tools/stats/gsummary.xml Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into dev Commit: 5fda00fb7e4317db309a712dd773f8adb66ce2ad https://github.com/galaxyproject/galaxy/commit/5fda00fb7e4317db309a712dd773… Author: Peter van Heusden <pvh(a)sanbi.ac.za> Date: 2016-06-25 (Sat, 25 Jun 2016) Changed paths: M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Make conda autoinstall of packages safer: * Expand check of installed environments to see if environment really contains package it should * Check to see if install of environment succeeds from return code * Remove failed environment installs Commit: 578914baf558a910b97846bac9d2bbcd851d0907 https://github.com/galaxyproject/galaxy/commit/578914baf558a910b97846bac9d2… Author: Peter van Heusden <pvh(a)sanbi.ac.za> Date: 2016-06-25 (Sat, 25 Jun 2016) Changed paths: M lib/galaxy/tools/deps/conda_util.py Log Message: ----------- Remove duplicate open() Commit: e4d101eeaef38ea86bd87bffe0f334990f5d5f20 https://github.com/galaxyproject/galaxy/commit/e4d101eeaef38ea86bd87bffe0f3… Author: Peter van Heusden <pvh(a)sanbi.ac.za> Date: 2016-06-25 (Sat, 25 Jun 2016) Changed paths: M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Remove trailing whitespace Commit: f53ef165290d0cbc397c6f1fce8c94512e0af2f7 https://github.com/galaxyproject/galaxy/commit/f53ef165290d0cbc397c6f1fce8c… Author: Peter van Heusden <pvh(a)sanbi.ac.za> Date: 2016-06-25 (Sat, 25 Jun 2016) Changed paths: M test/unit/tools/test_conda_resolution.py Log Message: ----------- Add test to trigger conda issue https://github.com/rtfd/readthedocs.org/issues/1902 Commit: de52665d30223134b69e3e7cdc868ea2e81c7ad9 https://github.com/galaxyproject/galaxy/commit/de52665d30223134b69e3e7cdc86… Author: Peter van Heusden <pvh(a)sanbi.ac.za> Date: 2016-06-25 (Sat, 25 Jun 2016) Changed paths: M lib/galaxy/tools/deps/conda_util.py M test/unit/tools/test_conda_resolution.py Log Message: ----------- * Simplify handling of files in is_conda_target_installed * Fix typo in test script docstring Commit: 2e1ecb9b473a0dafdfe074781a24f446c50efe99 https://github.com/galaxyproject/galaxy/commit/2e1ecb9b473a0dafdfe074781a24… Author: Peter van Heusden <pvh(a)sanbi.ac.za> Date: 2016-06-25 (Sat, 25 Jun 2016) Changed paths: M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Add warning message for when conda prefix is > 50 chars Commit: 891b7b5a1898677599e575308d026c0e26ca8fce https://github.com/galaxyproject/galaxy/commit/891b7b5a1898677599e575308d02… Author: Peter van Heusden <pvh(a)sanbi.ac.za> Date: 2016-06-25 (Sat, 25 Jun 2016) Changed paths: M test/unit/tools/test_conda_resolution.py Log Message: ----------- Add whitespace around arithmetic operator Commit: defb594cb9b249593e1c572f6e27b48b399f6abf https://github.com/galaxyproject/galaxy/commit/defb594cb9b249593e1c572f6e27… Author: Peter van Heusden <pvh(a)sanbi.ac.za> Date: 2016-06-25 (Sat, 25 Jun 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tools.js M config/datatypes_conf.xml.sample M config/galaxy.ini.sample M config/job_conf.xml.sample_advanced M config/tool_conf.xml.sample M lib/galaxy/config.py M lib/galaxy/datatypes/mothur.py M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/jobs/actions/post.py M lib/galaxy/jobs/command_factory.py M lib/galaxy/jobs/metrics/instrumenters/collectl.py M lib/galaxy/jobs/runners/drmaa.py M lib/galaxy/jobs/runners/kubernetes.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/model/__init__.py M lib/galaxy/objectstore/__init__.py M lib/galaxy/objectstore/s3.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py A lib/galaxy/tools/actions/model_operations.py M lib/galaxy/tools/cwl/parser.py M lib/galaxy/tools/cwl/schema.py M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/execute.py A lib/galaxy/tools/filter_failed_collection.xml A lib/galaxy/tools/flatten_collection.xml M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/dataset_matcher.py M lib/galaxy/tools/parameters/wrapped.py M lib/galaxy/tools/parser/cwl.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/filters/__init__.py A lib/galaxy/tools/unzip_collection.xml A lib/galaxy/tools/zip_collection.xml M lib/galaxy/util/__init__.py R lib/galaxy/util/directory_hash.py M lib/galaxy/webapps/galaxy/api/visualizations.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/webapps/tool_shed/model/__init__.py M lib/galaxy/workflow/modules.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M lib/tool_shed/util/basic_util.py M lib/tool_shed/util/repository_util.py M static/maps/mvc/tool/tools.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/tools.js M templates/webapps/galaxy/dataset/copy_view.mako M templates/webapps/galaxy/library/common/import_datasets_to_histories.mako M templates/webapps/galaxy/workflow/sharing.mako M test/api/helpers.py M test/api/test_tools.py M test/api/test_workflows.py M test/base/twilltestcase.py A test/functional/tools/exit_code_from_file.xml M test/functional/tools/samples_tool_conf.xml M test/unit/tools/test_conda_resolution.py M test/unit/tools/test_data_parameters.py M test/unit/tools/test_dataset_matcher.py M test/unit/tools/test_parameter_parsing.py M test/unit/tools/test_select_parameters.py M tools/filters/sff_extract.py Log Message: ----------- Merge branch 'dev' of github.com:pvanheus/galaxy into dev Commit: 97c052a1ec65e443b7c0f9e08c2847e8e9d7db81 https://github.com/galaxyproject/galaxy/commit/97c052a1ec65e443b7c0f9e08c28… Author: Peter van Heusden <pvh(a)sanbi.ac.za> Date: 2016-06-25 (Sat, 25 Jun 2016) Changed paths: M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Remove trailing whitespace Commit: 2075af4de80f7ffd7be127889a430f87038601c4 https://github.com/galaxyproject/galaxy/commit/2075af4de80f7ffd7be127889a43… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-07-21 (Thu, 21 Jul 2016) Changed paths: M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/resolvers/conda.py M test/unit/tools/test_conda_resolution.py Log Message: ----------- Merge pull request #2538 from pvanheus/dev Make conda autoinstall of packages safer: Compare: https://github.com/galaxyproject/galaxy/compare/8b324e8f456f...2075af4de80f

1 0

[galaxyproject/galaxy] d02f1f: * Update docs on Interactive Environments
by GitHub 21 Jul '16

21 Jul '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d02f1f1d6a1a236be7619a596c35ac04d0cfebaf https://github.com/galaxyproject/galaxy/commit/d02f1f1d6a1a236be7619a596c35… Author: Peter van Heusden <pvh(a)sanbi.ac.za> Date: 2016-06-25 (Sat, 25 Jun 2016) Changed paths: M doc/source/admin/interactive_environments.rst A doc/source/dev/interactive_environments.rst Log Message: ----------- * Update docs on Interactive Environments * Move docs on writing IEs to developer docs Commit: 19ab4f793bb1394005206cfe3deaad44636e3a60 https://github.com/galaxyproject/galaxy/commit/19ab4f793bb1394005206cfe3dea… Author: Peter van Heusden <pvh(a)sanbi.ac.za> Date: 2016-06-25 (Sat, 25 Jun 2016) Changed paths: M doc/source/dev/index.rst Log Message: ----------- Add link to IE dev docs Commit: e73a8071f5efc0a7e19143a71bbe63eb9d617cc9 https://github.com/galaxyproject/galaxy/commit/e73a8071f5efc0a7e19143a71bbe… Author: Peter van Heusden <pvh(a)sanbi.ac.za> Date: 2016-06-25 (Sat, 25 Jun 2016) Changed paths: M doc/source/admin/interactive_environments.rst Log Message: ----------- Addressed @erasche's comments Commit: 63abe20ab84ff7860400e6a4d726e01f6a80b3b7 https://github.com/galaxyproject/galaxy/commit/63abe20ab84ff7860400e6a4d726… Author: Peter van Heusden <pvh(a)sanbi.ac.za> Date: 2016-06-25 (Sat, 25 Jun 2016) Changed paths: M doc/source/admin/interactive_environments.rst Log Message: ----------- Replace single ` with `` Commit: cd0932600f5701f2d01bc28d9f79c77de0e8ee76 https://github.com/galaxyproject/galaxy/commit/cd0932600f5701f2d01bc28d9f79… Author: Peter van Heusden <pvh(a)sanbi.ac.za> Date: 2016-06-25 (Sat, 25 Jun 2016) Changed paths: M doc/source/admin/interactive_environments.rst Log Message: ----------- Modified Apache/nginx settings suggestions Commit: 4860cc715613bee1ab9527d10f8a654e5a29a6be https://github.com/galaxyproject/galaxy/commit/4860cc715613bee1ab9527d10f8a… Author: Peter van Heusden <pvh(a)sanbi.ac.za> Date: 2016-06-25 (Sat, 25 Jun 2016) Changed paths: M doc/source/dev/index.rst Log Message: ----------- Added correct link to index.rst Commit: 8b324e8f456f17ecbed22f0f19a18cb819601745 https://github.com/galaxyproject/galaxy/commit/8b324e8f456f17ecbed22f0f19a1… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-07-21 (Thu, 21 Jul 2016) Changed paths: M doc/source/admin/interactive_environments.rst M doc/source/dev/index.rst A doc/source/dev/interactive_environments.rst Log Message: ----------- Merge pull request #2543 from pvanheus/interactive_env_docs Updates to Interactive Environment docs Compare: https://github.com/galaxyproject/galaxy/compare/9291c8ae34d2...8b324e8f456f

1 0

[galaxyproject/infrastructure-playbook] c09fc0: Proxy images through duvel since performance from ...
by GitHub 21 Jul '16

21 Jul '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: c09fc029d2e83d251e1b0002e37bbc021d38fa75 https://github.com/galaxyproject/infrastructure-playbook/commit/c09fc029d2e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-07-21 (Thu, 21 Jul 2016) Changed paths: M galaxyenv/host_vars/duvel.galaxyproject.org.yml A galaxyenv/templates/nginx/images-proxy.j2 M galaxyenv/templates/nginx/images.j2 Log Message: ----------- Proxy images through duvel since performance from outside direct to orval is low (why??)

1 0

[galaxyproject/galaxy] a8147e: add tar to datatype_conf.xml
by GitHub 21 Jul '16

21 Jul '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a8147e537cf8e894d6d5032220909d211235d72f https://github.com/galaxyproject/galaxy/commit/a8147e537cf8e894d6d503222090… Author: maria <maria.bernard(a)jouy.inra.fr> Date: 2016-07-20 (Wed, 20 Jul 2016) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- add tar to datatype_conf.xml Commit: 9291c8ae34d225e97f03ed5b012326ccc3c9893d https://github.com/galaxyproject/galaxy/commit/9291c8ae34d225e97f03ed5b0123… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-07-21 (Thu, 21 Jul 2016) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Merge pull request #2636 from mariabernard/tar_datatype_branch add tar to datatypes_conf.xml Compare: https://github.com/galaxyproject/galaxy/compare/423e85fc8111...9291c8ae34d2

1 0

[galaxyproject/galaxy] a8b7c6: Smart string handling on the wsgi response -- this...
by GitHub 21 Jul '16

21 Jul '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a8b7c6a8eca231b251d59ddeb5ccab88845a757e https://github.com/galaxyproject/galaxy/commit/a8b7c6a8eca231b251d59ddeb5cc… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-19 (Tue, 19 Jul 2016) Changed paths: M lib/galaxy/web/framework/base.py Log Message: ----------- Smart string handling on the wsgi response -- this fixes uwsgi blanking out when handling endpoints that return unicode. Commit: 01cdb9387e4c1b885ab474b5c0c88a05a1147ca2 https://github.com/galaxyproject/galaxy/commit/01cdb9387e4c1b885ab474b5c0c8… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-20 (Wed, 20 Jul 2016) Changed paths: M lib/galaxy/web/framework/base.py Log Message: ----------- Simplify flatten method Commit: 5ba7e5adaeda7d33d869ed71542491cb40f3c5d7 https://github.com/galaxyproject/galaxy/commit/5ba7e5adaeda7d33d869ed715424… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-20 (Wed, 20 Jul 2016) Changed paths: M lib/galaxy/web/framework/base.py Log Message: ----------- Make sure yielded items from a flattened iterable are properly stringified. Commit: a5f9e5b9efd287c1bce5d6f3da41f30affd511ad https://github.com/galaxyproject/galaxy/commit/a5f9e5b9efd287c1bce5d6f3da41… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-20 (Wed, 20 Jul 2016) Changed paths: M lib/galaxy/web/framework/base.py Log Message: ----------- Reverted the refactoring of flatten; generator wasn't unpacking (of course), and caused an infinite loop. Commit: 423e85fc81110cb800b398b485d3aacc97914500 https://github.com/galaxyproject/galaxy/commit/423e85fc81110cb800b398b485d3… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2016-07-21 (Thu, 21 Jul 2016) Changed paths: M lib/galaxy/web/framework/base.py Log Message: ----------- Merge pull request #2630 from dannon/base_framework_string_handling Smart string handling on the wsgi response -- this fixes uwsgi blanki… Compare: https://github.com/galaxyproject/galaxy/compare/f67d3cbe93e3...423e85fc8111

1 0

[galaxyproject/galaxy] 92948b: Overload select wrapper`s concat function
by GitHub 21 Jul '16

21 Jul '16

Branch: refs/heads/release_16.04 Home: https://github.com/galaxyproject/galaxy Commit: 92948b5b0fc062ce904c5987c1d48d3831730a9a https://github.com/galaxyproject/galaxy/commit/92948b5b0fc062ce904c5987c1d4… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-07-18 (Mon, 18 Jul 2016) Changed paths: M lib/galaxy/tools/wrappers.py Log Message: ----------- Overload select wrapper`s concat function Commit: 1de7beca98d0bc8b11b9dca46a4984ac1cee9428 https://github.com/galaxyproject/galaxy/commit/1de7beca98d0bc8b11b9dca46a49… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-21 (Thu, 21 Jul 2016) Changed paths: M lib/galaxy/tools/wrappers.py Log Message: ----------- Merge pull request #2623 from guerler/fix_select_value_concat [16.04] Overload select wrapper`s concat function Compare: https://github.com/galaxyproject/galaxy/compare/68a64182c14a...1de7beca98d0

1 0

[galaxyproject/galaxy] e4a35f: Paste handles encoding automatically when thrown u...
by GitHub 21 Jul '16

21 Jul '16

Branch: refs/heads/release_16.04 Home: https://github.com/galaxyproject/galaxy Commit: e4a35f943b42401c92646d8f6b7b1c1fd515a9c1 https://github.com/galaxyproject/galaxy/commit/e4a35f943b42401c92646d8f6b7b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-19 (Tue, 19 Jul 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/workflow/render.py Log Message: ----------- Paste handles encoding automatically when thrown unicode, but uwsgi does not. This was resulting in unencoded (unicode) workflow drawings (svg) not appearing at all when the gen_image was invoked. Also took the opportunity to add a correct header for a standalone svg document. Commit: 68a64182c14af9f4cc10915c466177292d24ebfc https://github.com/galaxyproject/galaxy/commit/68a64182c14af9f4cc10915c4661… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-07-21 (Thu, 21 Jul 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/workflow/render.py Log Message: ----------- Merge pull request #2628 from dannon/workflow_svg_uwsgi_fix [16.04] Workflow SVG generation fix Compare: https://github.com/galaxyproject/galaxy/compare/132bd4dd57e0...68a64182c14a

1 0

[galaxyproject/galaxy] d8711a: Initial DTD to Galaxy work
by GitHub 21 Jul '16

21 Jul '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d8711a121ce127cce82ed7010ed9ba1bb6ff1479 https://github.com/galaxyproject/galaxy/commit/d8711a121ce127cce82ed7010ed9… Author: Eric Enns <eric.enns(a)phac-aspc.gc.ca> Date: 2016-06-29 (Wed, 29 Jun 2016) Changed paths: A config/tool_destinations.yml.sample A lib/galaxy/jobs/rules/dynamic_tool_destination.py Log Message: ----------- Initial DTD to Galaxy work Commit: c053197beed35f2357c17b887ed60d218b0c7a4c https://github.com/galaxyproject/galaxy/commit/c053197beed35f2357c17b887ed6… Author: Eric Enns <eric.enns(a)phac-aspc.gc.ca> Date: 2016-07-04 (Mon, 04 Jul 2016) Changed paths: M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/jobs/rules/dynamic_tool_destination.py A test/unit/jobs/rules/__init__.py A test/unit/jobs/rules/data/dest_fail.yml A test/unit/jobs/rules/data/priority_tool_destination.yml A test/unit/jobs/rules/data/test.empty A test/unit/jobs/rules/data/test.fasta A test/unit/jobs/rules/data/test1.full A test/unit/jobs/rules/data/test3.full A test/unit/jobs/rules/data/test_no_verbose.yml A test/unit/jobs/rules/data/test_num_input_datasets.yml A test/unit/jobs/rules/data/test_users.yml A test/unit/jobs/rules/data/tool_destination.yml A test/unit/jobs/rules/mockGalaxy.py A test/unit/jobs/rules/test_dynamic_tool_destination.py A test/unit/jobs/rules/vfdb/?bact.test A test/unit/jobs/rules/ymltests.py Log Message: ----------- Added in DTD tests Commit: 99161d6074e5cae86eb5788d641511ad6e47c26a https://github.com/galaxyproject/galaxy/commit/99161d6074e5cae86eb5788d6415… Author: Eric Enns <eric.enns(a)phac-aspc.gc.ca> Date: 2016-07-04 (Mon, 04 Jul 2016) Changed paths: M lib/galaxy/jobs/rules/dynamic_tool_destination.py M test/unit/jobs/rules/mockGalaxy.py M test/unit/jobs/rules/test_dynamic_tool_destination.py M test/unit/jobs/rules/ymltests.py Log Message: ----------- Flake8 fixes Commit: ed48c6c28b72ef63499ff39abcce9171fb684154 https://github.com/galaxyproject/galaxy/commit/ed48c6c28b72ef63499ff39abcce… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-07-20 (Wed, 20 Jul 2016) Changed paths: M lib/galaxy/config.py M lib/galaxy/jobs/rules/dynamic_tool_destination.py Log Message: ----------- Use more traditional Galaxy config handling for DTD. Commit: d87957e1a2030752b5617934b911da0855bae3fe https://github.com/galaxyproject/galaxy/commit/d87957e1a2030752b5617934b911… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-07-20 (Wed, 20 Jul 2016) Changed paths: M config/job_conf.xml.sample_advanced A lib/galaxy/jobs/dynamic_tool_destination.py M lib/galaxy/jobs/mapper.py R lib/galaxy/jobs/rules/dynamic_tool_destination.py M test/unit/jobs/rules/test_dynamic_tool_destination.py Log Message: ----------- Ease configuration and add documentation for using DTD syntax for destinations. Moving rules also means it won't conflict with other peoples custom dynamic destinations and should prevent Galaxy from reloading the Python repeatedly. Commit: 43fccc98879d17cc6c5f1833f12e4ed25cc1329e https://github.com/galaxyproject/galaxy/commit/43fccc98879d17cc6c5f1833f12e… Author: Eric Enns <eric.enns(a)phac-aspc.gc.ca> Date: 2016-07-20 (Wed, 20 Jul 2016) Changed paths: A test/unit/jobs/dynamic_tool_destination/__init__.py A test/unit/jobs/dynamic_tool_destination/data/dest_fail.yml A test/unit/jobs/dynamic_tool_destination/data/priority_tool_destination.yml A test/unit/jobs/dynamic_tool_destination/data/test.empty A test/unit/jobs/dynamic_tool_destination/data/test.fasta A test/unit/jobs/dynamic_tool_destination/data/test1.full A test/unit/jobs/dynamic_tool_destination/data/test3.full A test/unit/jobs/dynamic_tool_destination/data/test_no_verbose.yml A test/unit/jobs/dynamic_tool_destination/data/test_num_input_datasets.yml A test/unit/jobs/dynamic_tool_destination/data/test_users.yml A test/unit/jobs/dynamic_tool_destination/data/tool_destination.yml A test/unit/jobs/dynamic_tool_destination/mockGalaxy.py A test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py A test/unit/jobs/dynamic_tool_destination/ymltests.py R test/unit/jobs/rules/__init__.py R test/unit/jobs/rules/data/dest_fail.yml R test/unit/jobs/rules/data/priority_tool_destination.yml R test/unit/jobs/rules/data/test.empty R test/unit/jobs/rules/data/test.fasta R test/unit/jobs/rules/data/test1.full R test/unit/jobs/rules/data/test3.full R test/unit/jobs/rules/data/test_no_verbose.yml R test/unit/jobs/rules/data/test_num_input_datasets.yml R test/unit/jobs/rules/data/test_users.yml R test/unit/jobs/rules/data/tool_destination.yml R test/unit/jobs/rules/mockGalaxy.py R test/unit/jobs/rules/test_dynamic_tool_destination.py R test/unit/jobs/rules/vfdb/?bact.test R test/unit/jobs/rules/ymltests.py Log Message: ----------- Moved dtd tests into a different folder Commit: 5ae1058272c788efcf35f37f0d927b8eaefa3b73 https://github.com/galaxyproject/galaxy/commit/5ae1058272c788efcf35f37f0d92… Author: Eric Enns <eric.enns(a)phac-aspc.gc.ca> Date: 2016-07-20 (Wed, 20 Jul 2016) Changed paths: M config/tool_destinations.yml.sample Log Message: ----------- Updated tool_destinations.yml.sample to include a little more information Commit: a4c713bf64851d1a2bbc99fd0102f5c506f6ecfe https://github.com/galaxyproject/galaxy/commit/a4c713bf64851d1a2bbc99fd0102… Author: Eric Enns <eric.enns(a)phac-aspc.gc.ca> Date: 2016-07-20 (Wed, 20 Jul 2016) Changed paths: M lib/galaxy/jobs/dynamic_tool_destination.py Log Message: ----------- Fix dict iteration in dtd default_destination parsing/validation Commit: f67d3cbe93e36af9809db6bb3cb3e1af64f8174a https://github.com/galaxyproject/galaxy/commit/f67d3cbe93e36af9809db6bb3cb3… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-07-21 (Thu, 21 Jul 2016) Changed paths: M config/job_conf.xml.sample_advanced A config/tool_destinations.yml.sample M lib/galaxy/config.py M lib/galaxy/dependencies/pinned-requirements.txt A lib/galaxy/jobs/dynamic_tool_destination.py M lib/galaxy/jobs/mapper.py A test/unit/jobs/dynamic_tool_destination/__init__.py A test/unit/jobs/dynamic_tool_destination/data/dest_fail.yml A test/unit/jobs/dynamic_tool_destination/data/priority_tool_destination.yml A test/unit/jobs/dynamic_tool_destination/data/test.empty A test/unit/jobs/dynamic_tool_destination/data/test.fasta A test/unit/jobs/dynamic_tool_destination/data/test1.full A test/unit/jobs/dynamic_tool_destination/data/test3.full A test/unit/jobs/dynamic_tool_destination/data/test_no_verbose.yml A test/unit/jobs/dynamic_tool_destination/data/test_num_input_datasets.yml A test/unit/jobs/dynamic_tool_destination/data/test_users.yml A test/unit/jobs/dynamic_tool_destination/data/tool_destination.yml A test/unit/jobs/dynamic_tool_destination/mockGalaxy.py A test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py A test/unit/jobs/dynamic_tool_destination/ymltests.py Log Message: ----------- Merge pull request #2579 from phac-nml/add-dtd-to-galaxy Add DTD to Galaxy Compare: https://github.com/galaxyproject/galaxy/compare/47f25f1dc69b...f67d3cbe93e3

1 0

[galaxyproject/galaxy] 706a76: Add tool test for what happens when output filter ...
by GitHub 21 Jul '16

21 Jul '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 706a76ea80308aa00c0e316deaf10c8c46cd427e https://github.com/galaxyproject/galaxy/commit/706a76ea80308aa00c0e316deaf1… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-07-19 (Tue, 19 Jul 2016) Changed paths: A test/functional/tools/output_filter_exception_1.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Add tool test for what happens when output filter throws exception. Run new test with: ``` ./run_tests.sh -framework -id output_filter_exception_1 ``` xref https://github.com/galaxyproject/tools-iuc/pull/883 xref https://github.com/galaxyproject/planemo/commit/a066afb1c2c30f4ef2c3033ab9a… xref https://github.com/galaxy-iuc/standards/pull/31 Commit: 274ec0f953f61fc169bb90086d96dc4b91d45008 https://github.com/galaxyproject/galaxy/commit/274ec0f953f61fc169bb90086d96… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-07-21 (Thu, 21 Jul 2016) Changed paths: M test/functional/tools/output_filter_exception_1.xml Log Message: ----------- Fix typo spotted by @nsoranzo. Commit: 47f25f1dc69b77b69037b5056877a7f153c9e7e5 https://github.com/galaxyproject/galaxy/commit/47f25f1dc69b77b69037b5056877… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2016-07-21 (Thu, 21 Jul 2016) Changed paths: A test/functional/tools/output_filter_exception_1.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge pull request #2631 from jmchilton/output_filter_exception Add tool test for what happens when output filter throws exception. Compare: https://github.com/galaxyproject/galaxy/compare/8d24fbe0fed3...47f25f1dc69b

1 0

[galaxyproject/galaxy] e26930: Properly initialize reference datasets when workfl...
by GitHub 21 Jul '16

21 Jul '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: e269304a0f5c563bd463aeb4d45f9b0518a17b8e https://github.com/galaxyproject/galaxy/commit/e269304a0f5c563bd463aeb4d45f… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-07-19 (Tue, 19 Jul 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/workflow/modules.py Log Message: ----------- Properly initialize reference datasets when workflow form is loaded Commit: 8d24fbe0fed37fbc5502b15b4191df0eadde4e1c https://github.com/galaxyproject/galaxy/commit/8d24fbe0fed37fbc5502b15b4191… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-07-21 (Thu, 21 Jul 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/workflow/modules.py Log Message: ----------- Merge pull request #2632 from guerler/fix_workflow_data_on_load Properly initialize datasets when workflow is loaded for execution Compare: https://github.com/galaxyproject/galaxy/compare/2b3a0334e0bd...8d24fbe0fed3

1 0