Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: e66a091be0fa0cb1e0b9b646331cc4113dc1dfa9 https://github.com/galaxyproject/galaxy/commit/e66a091be0fa0cb1e0b9b646331cc... Author: Jeffrey Thiessen <jeffthiessen@corefacility.ca> Date: 2017-10-19 (Thu, 19 Oct 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M lib/galaxy/jobs/dynamic_tool_destination.py M lib/galaxy/jobs/mapper.py M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py A lib/galaxy/model/migrate/versions/0136_add_workflow_request_input_parameter_job_options.py M lib/galaxy/tools/execute.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run_request.py M static/maps/mvc/tool/tool-form-composite.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tool/tool-form-composite.js Log Message: ----------- Workflow-to-Job Scheduling Parameters Commit: e46156a073d0987d8a743a8ca92b1ae9f33d337e https://github.com/galaxyproject/galaxy/commit/e46156a073d0987d8a743a8ca92b1... Author: Jeffrey Thiessen <jeffthiessen@corefacility.ca> Date: 2017-10-19 (Thu, 19 Oct 2017) Changed paths: M lib/galaxy/managers/workflows.py M lib/galaxy/model/migrate/versions/0136_add_workflow_request_input_parameter_job_options.py M lib/galaxy/workflow/modules.py Log Message: ----------- PEP8 fixes Commit: ddb423b29ae3ad5803451255bb0be2b6b991c75c https://github.com/galaxyproject/galaxy/commit/ddb423b29ae3ad5803451255bb0be... Author: Jeffrey Thiessen <jeffthiessen@corefacility.ca> Date: 2017-10-19 (Thu, 19 Oct 2017) Changed paths: M lib/galaxy/model/migrate/versions/0136_add_workflow_request_input_parameter_job_options.py M test/unit/jobs/dynamic_tool_destination/mockGalaxy.py Log Message: ----------- Update DTD test object Commit: 0a28b4927cf1e727a22761dc9ad1d59af584c2c1 https://github.com/galaxyproject/galaxy/commit/0a28b4927cf1e727a22761dc9ad1d... Author: Jeffrey Thiessen <jeffthiessen@corefacility.ca> Date: 2017-10-27 (Fri, 27 Oct 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js A config/workflow_resource_params_conf.xml.sample M lib/galaxy/config.py M lib/galaxy/managers/workflows.py Log Message: ----------- xml parsing Commit: 6157ce757743ec09ab905303222f3cb8597a072e https://github.com/galaxyproject/galaxy/commit/6157ce757743ec09ab905303222f3... Author: Jeffrey Thiessen <jeffthiessen@corefacility.ca> Date: 2017-10-27 (Fri, 27 Oct 2017) Changed paths: M .ci/flake8_lint_include_list.txt M .travis.yml M Makefile M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/panels/admin-panel.js M client/galaxy/scripts/galaxy.interactive_environments.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/mvc/grid/grid-view.js M client/galaxy/scripts/mvc/library/library-dataset-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-libraryrow-view.js M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js M client/galaxy/scripts/mvc/tours.js M client/galaxy/scripts/utils/utils.js M client/galaxy/style/less/base.less M client/galaxy/style/less/library.less M client/gulpfile.js M client/package.json M client/yarn.lock M config/datatypes_conf.xml.sample M config/galaxy.ini.sample M config/plugins/interactive_environments/jupyter/static/js/jupyter.js M config/plugins/tours/core.galaxy_ui.yaml M config/plugins/tours/core.history.yaml M config/plugins/tours/core.scratchbook.yaml M config/plugins/webhooks/demo/tour_generator/helper/__init__.py M cron/add_manual_builds.py M cron/build_chrom_db.py M cron/parse_builds.py M cron/parse_builds_3_sites.py M doc/schema_template.md A doc/source/releases/17.09.rst M doc/source/releases/17.09_announce.rst A doc/source/releases/18.01_announce.rst M doc/source/releases/index.rst M lib/galaxy/auth/providers/ldap_ad.py M lib/galaxy/config.py M lib/galaxy/containers/docker_model.py M lib/galaxy/datatypes/annotation.py M lib/galaxy/datatypes/assembly.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/constructive_solid_geometry.py M lib/galaxy/datatypes/converters/bed_to_gff_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/interval_to_bed_converter.py M lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.py M lib/galaxy/datatypes/converters/interval_to_coverage.py M lib/galaxy/datatypes/converters/interval_to_fli.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 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/interval.py M lib/galaxy/datatypes/molecules.py M lib/galaxy/datatypes/msa.py M lib/galaxy/datatypes/ngsindex.py M lib/galaxy/datatypes/plant_tribes.py M lib/galaxy/datatypes/proteomics.py M lib/galaxy/datatypes/qualityscore.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/text.py M lib/galaxy/datatypes/tracks.py M lib/galaxy/datatypes/util/generic_util.py M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/deferred/__init__.py M lib/galaxy/jobs/handler.py M lib/galaxy/jobs/output_checker.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/godocker.py M 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/slurm.py M lib/galaxy/jobs/runners/state_handler_factory.py M lib/galaxy/jobs/runners/tasks.py M lib/galaxy/jobs/runners/util/cli/job/slurm.py M lib/galaxy/jobs/runners/util/cli/job/torque.py M lib/galaxy/jobs/transfer_manager.py M lib/galaxy/managers/context.py M lib/galaxy/managers/folders.py M lib/galaxy/managers/libraries.py M lib/galaxy/managers/library_datasets.py M lib/galaxy/managers/users.py M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/model/custom_types.py M lib/galaxy/model/mapping.py M lib/galaxy/model/metadata.py M lib/galaxy/model/migrate/check.py M lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py M lib/galaxy/model/migrate/versions/0024_page_slug_unique_constraint.py M lib/galaxy/model/migrate/versions/0032_stored_workflow_slug_column.py M lib/galaxy/model/migrate/versions/0033_published_cols_for_histories_and_workflows.py M lib/galaxy/model/migrate/versions/0041_workflow_invocation.py M lib/galaxy/model/migrate/versions/0042_workflow_invocation_fix.py M lib/galaxy/model/migrate/versions/0056_workflow_outputs.py M lib/galaxy/model/migrate/versions/0061_tasks.py M lib/galaxy/model/migrate/versions/0076_fix_form_values_data_corruption.py M lib/galaxy/model/migrate/versions/0115_longer_user_password_field.py M lib/galaxy/model/tool_shed_install/migrate/check.py M lib/galaxy/sample_tracking/external_service_types.py M lib/galaxy/sample_tracking/request_types.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/deps/resolvers/unlinked_tool_shed_packages.py M lib/galaxy/tools/imp_exp/__init__.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/validation.py M lib/galaxy/tools/parser/output_actions.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/util/maf_utilities.py M lib/galaxy/tools/wrappers.py M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/tours/__init__.py M lib/galaxy/util/__init__.py M lib/galaxy/util/checkers.py M lib/galaxy/util/dictifiable.py M lib/galaxy/util/hash_util.py M lib/galaxy/util/heartbeat.py M lib/galaxy/util/image_util.py M lib/galaxy/util/object_wrapper.py A lib/galaxy/util/path/__init__.py A lib/galaxy/util/path/ntpath.py A lib/galaxy/util/path/posixpath.py M lib/galaxy/util/sanitize_html.py M lib/galaxy/visualization/data_providers/basic.py M lib/galaxy/visualization/data_providers/genome.py M lib/galaxy/visualization/genomes.py M lib/galaxy/visualization/plugins/interactive_environments.py M lib/galaxy/visualization/plugins/plugin.py M lib/galaxy/web/base/controller.py M lib/galaxy/web/framework/decorators.py M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/web/framework/middleware/error.py M lib/galaxy/web/framework/middleware/sentry.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/web/stack/__init__.py M lib/galaxy/webapps/galaxy/api/authenticate.py M lib/galaxy/webapps/galaxy/api/folder_contents.py M lib/galaxy/webapps/galaxy/api/forms.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/groups.py M lib/galaxy/webapps/galaxy/api/jobs.py M lib/galaxy/webapps/galaxy/api/library_contents.py M lib/galaxy/webapps/galaxy/api/library_datasets.py M lib/galaxy/webapps/galaxy/api/remote_files.py M lib/galaxy/webapps/galaxy/api/request_types.py M lib/galaxy/webapps/galaxy/api/requests.py M lib/galaxy/webapps/galaxy/api/roles.py M lib/galaxy/webapps/galaxy/api/samples.py M lib/galaxy/webapps/galaxy/api/tool_data.py M lib/galaxy/webapps/galaxy/api/users.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/dataset.py R lib/galaxy/webapps/galaxy/controllers/external_service.py R lib/galaxy/webapps/galaxy/controllers/external_services.py M lib/galaxy/webapps/galaxy/controllers/library.py M lib/galaxy/webapps/galaxy/controllers/library_common.py R lib/galaxy/webapps/galaxy/controllers/request_type.py R lib/galaxy/webapps/galaxy/controllers/requests.py R lib/galaxy/webapps/galaxy/controllers/requests_admin.py R 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/visualization.py M lib/galaxy/webapps/reports/buildapp.py M lib/galaxy/webapps/reports/controllers/system.py M lib/galaxy/webapps/tool_shed/buildapp.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/galaxy/webapps/tool_shed/model/migrate/check.py M lib/galaxy_ext/metadata/set_metadata.py M lib/psyco_full.py M lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py M lib/tool_shed/galaxy_install/metadata/installed_repository_metadata_manager.py M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.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/grids/util.py M lib/tool_shed/managers/groups.py M lib/tool_shed/metadata/metadata_generator.py M lib/tool_shed/metadata/repository_metadata_manager.py M lib/tool_shed/tools/tool_validator.py M lib/tool_shed/util/admin_util.py M lib/tool_shed/util/basic_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 run_tests.sh M scripts/bootstrap_history.py M scripts/build_toolbox.py M scripts/check_galaxy.py M scripts/cleanup_datasets/cleanup_datasets.py M scripts/cleanup_datasets/pgcleanup.py M scripts/drmaa_external_runner.py M scripts/helper.py M scripts/loc_files/create_all_fasta_loc.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/others/incorrect_gops_jobs.py M scripts/others/incorrect_gops_join_jobs.py M scripts/paster.py M scripts/rst2html.py M scripts/runtime_stats.py M scripts/tool_shed/migrate_tools_to_repositories.py M setup.cfg M static/maps/galaxy.interactive_environments.js.map M static/maps/layout/menu.js.map M static/maps/layout/page.js.map M static/maps/libs/backbone.js.map M static/maps/libs/bibtex.js.map M static/maps/libs/d3.js.map A static/maps/libs/jquery/jquery.complexify.js.map M static/maps/libs/jquery/jquery.cookie.js.map M static/maps/libs/jquery/jquery.js.map M static/maps/libs/jquery/jquery.migrate.js.map M static/maps/libs/jquery/jquery.mousewheel.js.map M static/maps/libs/raven.js.map M static/maps/libs/require.js.map M static/maps/libs/underscore.js.map M static/maps/mvc/grid/grid-view.js.map M static/maps/mvc/library/library-dataset-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-libraryrow-view.js.map M static/maps/mvc/library/library-librarytoolbar-view.js.map M static/maps/mvc/tours.js.map M static/maps/utils/utils.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.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/galaxy.interactive_environments.js M static/scripts/layout/menu.js M static/scripts/layout/page.js M static/scripts/mvc/grid/grid-view.js M static/scripts/mvc/library/library-dataset-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-libraryrow-view.js M static/scripts/mvc/library/library-librarytoolbar-view.js M static/scripts/mvc/tours.js M static/scripts/utils/utils.js M static/style/blue/base.css M static/style/blue/library.css R templates/admin/external_service/common.mako R templates/admin/external_service/create_external_service.mako R templates/admin/external_service/edit_external_service.mako R templates/admin/external_service/grid.mako R templates/admin/external_service/reload_external_service_types.mako R templates/admin/external_service/view_external_service.mako R templates/admin/request_type/common.mako R templates/admin/request_type/create_request_type.mako R templates/admin/request_type/edit_request_type.mako R templates/admin/request_type/grid.mako R templates/admin/request_type/request_type_permissions.mako R templates/admin/request_type/view_request_type.mako R templates/admin/requests/grid.mako R templates/admin/requests/reject.mako R templates/admin/requests/rename_datasets.mako R templates/admin/requests/sample_datasets_grid.mako R templates/admin/requests/view_sample_dataset.mako R templates/admin/tool_shed_repository/repair_repository.mako M templates/admin/tool_shed_repository/repository_actions_menu.mako M templates/webapps/galaxy/admin/center.mako R templates/webapps/galaxy/requests/common/add_samples.mako R templates/webapps/galaxy/requests/common/common.mako R templates/webapps/galaxy/requests/common/create_request.mako R templates/webapps/galaxy/requests/common/edit_basic_request_info.mako R templates/webapps/galaxy/requests/common/edit_samples.mako R templates/webapps/galaxy/requests/common/find_samples.mako R templates/webapps/galaxy/requests/common/index.mako R templates/webapps/galaxy/requests/common/sample_dataset_transfer_status.mako R templates/webapps/galaxy/requests/common/sample_datasets.mako R templates/webapps/galaxy/requests/common/sample_state.mako R templates/webapps/galaxy/requests/common/view_request.mako R templates/webapps/galaxy/requests/common/view_request_history.mako R templates/webapps/galaxy/requests/common/view_sample.mako R templates/webapps/galaxy/requests/common/view_sample_datasets.mako R templates/webapps/galaxy/requests/common/view_sample_history.mako R templates/webapps/galaxy/requests/find_samples_index.mako R templates/webapps/galaxy/requests/grid.mako R templates/webapps/galaxy/requests/index.mako M test/api/test_tools.py M test/base/testcase.py M test/docker/base/Dockerfile M test/docker/base/ansible_vars.yml M test/docker/base/run_test_wrapper.sh A test/functional/tools/data_source.py M test/functional/tools/samples_tool_conf.xml A test/functional/tools/test_data_source.xml M test/functional/twilltestcase.py M test/qunit/Gruntfile.js M test/qunit/package.json M test/qunit/test-app.js M test/qunit/test-common.js R test/qunit/test-libs/qunit-1.23.1.css R test/qunit/test-libs/qunit-1.23.1.js R test/qunit/test-libs/sinon-1.17.7.js R test/qunit/test-libs/sinon-qunit-1.0.0.js M test/qunit/tests/form_tests.js M test/qunit/tests/galaxy-app-base.js M test/qunit/tests/graph.js M test/qunit/tests/hda-base.js M test/qunit/tests/history_contents_model_tests.js M test/qunit/tests/job-dag.js M test/qunit/tests/list-of-pairs-collection-creator.js M test/qunit/tests/masthead_tests.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/popover_tests.js M test/qunit/tests/ui_tests.js M test/qunit/tests/upload_dialog_tests.js M test/qunit/tests/utils_test.js M test/qunit/tests/workflow_editor_tests.js M test/shed_functional/base/twilltestcase.py M test/shed_functional/functional/test_1100_install_updated_repository_dependencies.py M test/shed_functional/functional/test_1430_repair_installed_repository.py M test/unit/managers/test_UserManager.py M test/unit/tools/test_tool_deps.py M tools/data_source/data_source.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/codingSnps_filter.py M tools/extract/extract_genomic_dna.py M tools/extract/liftOver_wrapper.py M tools/filters/axt_to_lav.py M tools/filters/bed_to_gff_converter.py M tools/filters/catWrapper.py M tools/filters/convert_characters.py M tools/filters/gff/extract_GFF_Features.py M tools/filters/gff/gff_filter_by_attribute.py M tools/filters/gff/gff_filter_by_feature_count.py M tools/filters/gff_to_bed_converter.py M tools/filters/gtf_to_bedgraph_converter.py M tools/filters/join.py M tools/filters/lav_to_bed_code.py M tools/filters/mergeCols.py M tools/filters/sff_extract.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/genomespace/genomespace_importer.py M tools/maf/maf_by_block_number.py M tools/maf/maf_filter.py M tools/maf/maf_limit_size.py M tools/maf/maf_limit_to_species.py M tools/maf/maf_reverse_complement.py M tools/maf/maf_stats.py M tools/maf/maf_thread_for_species.py M tools/maf/maf_to_bed.py M tools/maf/vcf_to_maf_customtrack.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/solid2fastq.py M tools/plotting/bar_chart.py M tools/solid_tools/maq_cs_wrapper.py M tools/solid_tools/solid_qual_stats.py M tools/sr_mapping/bfast_wrapper.py M tools/stats/aggregate_scores_in_intervals.py M tools/stats/filtering.py M tools/stats/grouping.py M tools/stats/gsummary.py M tox.ini Log Message: ----------- update dev branch Commit: 78f64de4a555e2db7ab720d9df5e973de25e3c00 https://github.com/galaxyproject/galaxy/commit/78f64de4a555e2db7ab720d9df5e9... Author: Jeffrey Thiessen <jeffthiessen@corefacility.ca> Date: 2017-10-27 (Fri, 27 Oct 2017) Changed paths: M .ci/flake8_lint_include_list.txt M .travis.yml M Makefile M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/panels/admin-panel.js M client/galaxy/scripts/galaxy.interactive_environments.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/mvc/grid/grid-view.js M client/galaxy/scripts/mvc/library/library-dataset-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-libraryrow-view.js M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js M client/galaxy/scripts/mvc/tours.js M client/galaxy/scripts/utils/utils.js M client/galaxy/style/less/base.less M client/galaxy/style/less/library.less M client/gulpfile.js M client/package.json M client/yarn.lock M config/datatypes_conf.xml.sample M config/galaxy.ini.sample M config/plugins/interactive_environments/jupyter/static/js/jupyter.js M config/plugins/tours/core.galaxy_ui.yaml M config/plugins/tours/core.history.yaml M config/plugins/tours/core.scratchbook.yaml M config/plugins/webhooks/demo/tour_generator/helper/__init__.py M cron/add_manual_builds.py M cron/build_chrom_db.py M cron/parse_builds.py M cron/parse_builds_3_sites.py M doc/schema_template.md A doc/source/releases/17.09.rst M doc/source/releases/17.09_announce.rst A doc/source/releases/18.01_announce.rst M doc/source/releases/index.rst M lib/galaxy/auth/providers/ldap_ad.py M lib/galaxy/config.py M lib/galaxy/containers/docker_model.py M lib/galaxy/datatypes/annotation.py M lib/galaxy/datatypes/assembly.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/constructive_solid_geometry.py M lib/galaxy/datatypes/converters/bed_to_gff_converter.py M 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lib/galaxy/jobs/transfer_manager.py M lib/galaxy/managers/context.py M lib/galaxy/managers/folders.py M lib/galaxy/managers/libraries.py M lib/galaxy/managers/library_datasets.py M lib/galaxy/managers/users.py M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/model/custom_types.py M lib/galaxy/model/mapping.py M lib/galaxy/model/metadata.py M lib/galaxy/model/migrate/check.py M lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py M lib/galaxy/model/migrate/versions/0024_page_slug_unique_constraint.py M lib/galaxy/model/migrate/versions/0032_stored_workflow_slug_column.py M lib/galaxy/model/migrate/versions/0033_published_cols_for_histories_and_workflows.py M lib/galaxy/model/migrate/versions/0041_workflow_invocation.py M lib/galaxy/model/migrate/versions/0042_workflow_invocation_fix.py M lib/galaxy/model/migrate/versions/0056_workflow_outputs.py M lib/galaxy/model/migrate/versions/0061_tasks.py M 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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/others/incorrect_gops_jobs.py M scripts/others/incorrect_gops_join_jobs.py M scripts/paster.py M scripts/rst2html.py M scripts/runtime_stats.py M scripts/tool_shed/migrate_tools_to_repositories.py M setup.cfg M static/maps/galaxy.interactive_environments.js.map M static/maps/layout/menu.js.map M static/maps/layout/page.js.map M static/maps/libs/backbone.js.map M static/maps/libs/bibtex.js.map M static/maps/libs/d3.js.map A static/maps/libs/jquery/jquery.complexify.js.map M static/maps/libs/jquery/jquery.cookie.js.map M static/maps/libs/jquery/jquery.js.map M static/maps/libs/jquery/jquery.migrate.js.map M static/maps/libs/jquery/jquery.mousewheel.js.map M static/maps/libs/raven.js.map M static/maps/libs/require.js.map M 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tools/filters/ucsc_gene_bed_to_intron_bed.py M tools/filters/ucsc_gene_table_to_intervals.py M tools/genomespace/genomespace_importer.py M tools/maf/maf_by_block_number.py M tools/maf/maf_filter.py M tools/maf/maf_limit_size.py M tools/maf/maf_limit_to_species.py M tools/maf/maf_reverse_complement.py M tools/maf/maf_stats.py M tools/maf/maf_thread_for_species.py M tools/maf/maf_to_bed.py M tools/maf/vcf_to_maf_customtrack.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/solid2fastq.py M tools/plotting/bar_chart.py M tools/solid_tools/maq_cs_wrapper.py M tools/solid_tools/solid_qual_stats.py M tools/sr_mapping/bfast_wrapper.py M tools/stats/aggregate_scores_in_intervals.py M tools/stats/filtering.py M tools/stats/grouping.py M tools/stats/gsummary.py M tox.ini Log Message: ----------- update from upstream Commit: f5df695355f03d793ffd84c8d7106ecd495d488a 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Author: Jeffrey Thiessen <jeffthiessen@corefacility.ca> Date: 2017-10-27 (Fri, 27 Oct 2017) Changed paths: M static/maps/mvc/tool/tool-form-composite.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tool/tool-form-composite.js Log Message: ----------- update static files Commit: aa4a1560a70763883e59c001b459400cd1f34ea9 https://github.com/galaxyproject/galaxy/commit/aa4a1560a70763883e59c001b4594... Author: Jeffrey Thiessen <jeffthiessen@corefacility.ca> Date: 2017-10-27 (Fri, 27 Oct 2017) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- pep8 Commit: f8313a3428545cdc89bcfb8b9338a59d9e4ae0f3 https://github.com/galaxyproject/galaxy/commit/f8313a3428545cdc89bcfb8b9338a... Author: Jeffrey Thiessen <jeffthiessen@corefacility.ca> Date: 2017-10-30 (Mon, 30 Oct 2017) Changed paths: M lib/galaxy/jobs/dynamic_tool_destination.py M lib/galaxy/managers/workflows.py Log Message: ----------- small fix and refactor Commit: 3bc9506c547778574f1a5f2f7cfd8f7119f48522 https://github.com/galaxyproject/galaxy/commit/3bc9506c547778574f1a5f2f7cfd8... Author: Jeffrey Thiessen <jeffthiessen@corefacility.ca> Date: 2017-10-30 (Mon, 30 Oct 2017) Changed paths: M lib/galaxy/jobs/dynamic_tool_destination.py M lib/galaxy/managers/workflows.py M lib/galaxy/util/__init__.py Log Message: ----------- Validate users allowed priorities before running job from DTD, + Refactoring Commit: c67523c27e9550b90e3de77a7f759443990d0022 https://github.com/galaxyproject/galaxy/commit/c67523c27e9550b90e3de77a7f759... Author: Jeffrey Thiessen <jeffthiessen@corefacility.ca> Date: 2017-10-30 (Mon, 30 Oct 2017) Changed paths: M config/workflow_resource_params_conf.xml.sample Log Message: ----------- fix sample file Commit: 6a7522b3a4afe573f2533eae7541a8cc521d6ddd https://github.com/galaxyproject/galaxy/commit/6a7522b3a4afe573f2533eae7541a... Author: Jeffrey Thiessen <jeffthiessen@corefacility.ca> Date: 2017-11-02 (Thu, 02 Nov 2017) Changed paths: M lib/galaxy/jobs/mapper.py M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py R lib/galaxy/model/migrate/versions/0136_add_workflow_request_input_parameter_job_options.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run_request.py Log Message: ----------- Fixed use of WorkflowRequestInputParameter Commit: 2aa077fa51714a57cbcb9114e287588e8f6fb7c6 https://github.com/galaxyproject/galaxy/commit/2aa077fa51714a57cbcb9114e2875... Author: Jeffrey Thiessen <jeffthiessen@corefacility.ca> Date: 2017-11-02 (Thu, 02 Nov 2017) Changed paths: M lib/galaxy/workflow/run_request.py Log Message: ----------- cleanup Commit: df05448ea4e24304ff0c3bd91a9a22da83618b84 https://github.com/galaxyproject/galaxy/commit/df05448ea4e24304ff0c3bd91a9a2... Author: Jeffrey Thiessen <jeffreylthiessen@gmail.com> Date: 2017-11-20 (Mon, 20 Nov 2017) Changed paths: R .ci/flake8_lint_include_list.txt R .ci/flake8_wrapper_imports.sh A .ci/jenkins/selenium-compose/Dockerfile A .ci/jenkins/selenium-compose/docker-compose.yml A .ci/jenkins/selenium-compose/galaxy.ini A .ci/jenkins/selenium-compose/run_galaxy.bash A .ci/jenkins/selenium-compose/run_tests.sh R .ci/jenkins/selenium/Dockerfile R .ci/jenkins/selenium/docker-compose.yml R .ci/jenkins/selenium/galaxy.ini R .ci/jenkins/selenium/run_galaxy.bash M .ci/jenkins/selenium/run_tests.sh M .travis.yml M Makefile M README.rst M client/.babelrc M client/galaxy/scripts/admin.toolshed.js M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/apps/login.js M client/galaxy/scripts/apps/panels/admin-panel.js M client/galaxy/scripts/apps/panels/history-panel.js M client/galaxy/scripts/apps/panels/tool-panel.js M 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test/unit/tools/test_select_parameters.py M test/unit/tools/test_tool_deps.py M test/unit/tools/test_tool_loader.py M test/unit/tools/test_toolbox.py M test/unit/tools/test_watcher.py M test/unit/tools_support.py M test/unit/visualizations/plugins/test_VisualizationPlugin.py M test/unit/visualizations/plugins/test_VisualizationsRegistry.py M test/unit/web/framework/test_webapp.py M test/unit/workflows/test_modules.py M test/unit/workflows/test_run_parameters.py M test/unit/workflows/test_workflow_progress.py M tools/data_source/microbial_import.xml M tools/filters/gff/gff_filter_by_attribute.py M tools/filters/gff/gff_filter_by_feature_count.py M tools/phenotype_association/senatag.py M tox.ini Log Message: ----------- merge conflicts Commit: 784431b9819f1b04664431c53f8b6816055015ca https://github.com/galaxyproject/galaxy/commit/784431b9819f1b04664431c53f8b6... Author: Jeffrey Thiessen <jeffreylthiessen@gmail.com> Date: 2017-11-20 (Mon, 20 Nov 2017) Changed paths: M static/maps/mvc/tool/tool-form-composite.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tool/tool-form-composite.js Log Message: ----------- update static files after merge confict fix Commit: 497df0d4a8728a2741533e4f3bc7e3637b04303b https://github.com/galaxyproject/galaxy/commit/497df0d4a8728a2741533e4f3bc7e... Author: Jeffrey Thiessen <jeffreylthiessen@gmail.com> Date: 2017-11-21 (Tue, 21 Nov 2017) Changed paths: M lib/galaxy/jobs/dynamic_tool_destination.py Log Message: ----------- fix import order Commit: b7b55ad0a4f20087f0196d6828c6ec9daaf25e11 https://github.com/galaxyproject/galaxy/commit/b7b55ad0a4f20087f0196d6828c6e... Author: John Chilton <jmchilton@gmail.com> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M config/galaxy.ini.sample A config/workflow_resource_mapper_conf.yml.sample M config/workflow_resource_params_conf.xml.sample M lib/galaxy/config.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/dynamic_tool_destination.py M lib/galaxy/jobs/mapper.py M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/execute.py M lib/galaxy/util/__init__.py M lib/galaxy/workflow/modules.py A lib/galaxy/workflow/resources/__init__.py A lib/galaxy/workflow/resources/example.py.sample M lib/galaxy/workflow/run_request.py Log Message: ----------- Refactor workflow resource parameters. This refactoring is untested and definitely broken in a couple places - but it illustrates broad directions I'd like the work to move in. - On the input side of things - it serializes the individual parameters to the database each as its own instance of a WorkflowRequestInputParameter. In a couple places I've retried to refactor away from the terminology of "workflow_options" toward resource parameters - there are already other kinds of workflow options. - On the backend - I've moved a lot of the logic into galaxy.workflow.resources and tried to make it more extensible. The goal is to allow the admin to specify any kind of function to define the parameters as they want for a given workflow and user - but to implement the existing "group based" variant desired by phac-nml as just one potential variant of that with a convient YAML description. - This moves the priority validation for workflow priorities out of the plugin and handles it up when the request is being handled. This is kind of a hack - but it results in cleaner separation between the DTD and code for defining workflow priorities so that the DTD would work with any potential workflow parameter mapping XML format or dynamic mapping Python function. - This exposes the workflow parameters to traditional dynamic job destinations (the DTD framework re-computes it from the "job" object and that is fine). Commit: 5c44ed54b66271d412b87b97f29e88241e491c98 https://github.com/galaxyproject/galaxy/commit/5c44ed54b66271d412b87b97f29e8... Author: Jeffrey Thiessen <jeffreylthiessen@gmail.com> Date: 2017-12-12 (Tue, 12 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M config/workflow_resource_mapper_conf.yml.sample M lib/galaxy/jobs/dynamic_tool_destination.py M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/resources/__init__.py M lib/galaxy/workflow/resources/example.py.sample M lib/galaxy/workflow/run_request.py M static/maps/mvc/tool/tool-form-composite.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tool/tool-form-composite.js Log Message: ----------- Added and fixed changes from 'Refactor workflow resource parameters.' by jmchilton Commit: f1879bee2e4e352a68f70ed223149cf5721dcccd https://github.com/galaxyproject/galaxy/commit/f1879bee2e4e352a68f70ed223149... Author: Jeffrey Thiessen <jeffreylthiessen@gmail.com> Date: 2017-12-12 (Tue, 12 Dec 2017) Changed paths: M .gitignore M .travis.yml M Makefile M client/README.md M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/analysis.js A client/galaxy/scripts/apps/extended.js M client/galaxy/scripts/apps/panels/admin-panel.js M client/galaxy/scripts/apps/panels/history-panel.js M client/galaxy/scripts/apps/panels/tool-panel.js A client/galaxy/scripts/components/Citations.vue A client/galaxy/scripts/components/HistoryImport.vue A client/galaxy/scripts/components/UserAPIKeys.vue M client/galaxy/scripts/galaxy.library.js M client/galaxy/scripts/galaxy.pages.js M client/galaxy/scripts/layout/generic-nav-view.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/panel.js M client/galaxy/scripts/layout/scratchbook.js R client/galaxy/scripts/mvc/citation/citation-model.js R client/galaxy/scripts/mvc/citation/citation-view.js M 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test/unit/unittest_utils/galaxy_mock.py M test/unit/workflows/test_workflow_progress.py M tools/data_source/data_source.py M tools/data_source/upload.py M tools/data_source/upload.xml M tools/stats/aggregate_scores_in_intervals.py M tools/stats/gsummary.py M tox.ini Log Message: ----------- merge conflicts from dev Commit: 477525e1063fbec784d035ff6194d8d79cb91733 https://github.com/galaxyproject/galaxy/commit/477525e1063fbec784d035ff6194d... Author: Jeffrey Thiessen <jeffreylthiessen@gmail.com> Date: 2017-12-12 (Tue, 12 Dec 2017) Changed paths: M lib/galaxy/tools/execute.py M lib/galaxy/workflow/modules.py Log Message: ----------- Remove dead code + fix merge confict mistake Commit: 7dbfe67b844e84e9fba36b5e4a7e09c7a4c978de https://github.com/galaxyproject/galaxy/commit/7dbfe67b844e84e9fba36b5e4a7e0... 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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/ui/popupmenu.js M static/scripts/ui/scroll-panel.js M static/scripts/ui/search-input.js M static/scripts/utils/add-logging.js M static/scripts/utils/ajax-queue.js M static/scripts/utils/async-save-text.js M static/scripts/utils/config.js M static/scripts/utils/deferred.js M static/scripts/utils/graph.js M static/scripts/utils/levenshtein.js M static/scripts/utils/localization.js M static/scripts/utils/metrics-logger.js M static/scripts/utils/natural-sort.js M static/scripts/utils/query-string-parsing.js M static/scripts/utils/uploadbox.js M static/scripts/utils/utils.js M static/scripts/viz/bbi-data-manager.js M static/scripts/viz/circster.js M static/scripts/viz/phyloviz.js M static/scripts/viz/sweepster.js M static/scripts/viz/trackster.js M static/scripts/viz/trackster/filters.js M static/scripts/viz/trackster/painters.js M static/scripts/viz/trackster/slotting.js M static/scripts/viz/trackster/tracks.js M static/scripts/viz/trackster/util.js M static/scripts/viz/visualization.js M static/scripts/viz/viz_views.js Log Message: ----------- fix static files Commit: bac40dcb21e37292062a02bcb5b7df54a2c6a66e https://github.com/galaxyproject/galaxy/commit/bac40dcb21e37292062a02bcb5b7d... Author: Jeffrey Thiessen <jeffreylthiessen@gmail.com> Date: 2017-12-13 (Wed, 13 Dec 2017) Changed paths: M lib/galaxy/jobs/dynamic_tool_destination.py M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/workflow/resources/__init__.py M lib/galaxy/workflow/resources/example.py M test/unit/jobs/test_mapper.py Log Message: ----------- pep8 + tests Commit: cb45e57367a9383d192dc49335ea0ee3524342de https://github.com/galaxyproject/galaxy/commit/cb45e57367a9383d192dc49335ea0... Author: Jeffrey Thiessen <jeffreylthiessen@gmail.com> Date: 2017-12-13 (Wed, 13 Dec 2017) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/workflow/resources/__init__.py M test/unit/jobs/test_mapper.py Log Message: ----------- undo test case change Commit: a9912296f768e3fc2acab2cc34c044dc25880df9 https://github.com/galaxyproject/galaxy/commit/a9912296f768e3fc2acab2cc34c04... Author: Jeffrey Thiessen <jeffreylthiessen@gmail.com> Date: 2017-12-13 (Wed, 13 Dec 2017) Changed paths: M lib/galaxy/workflow/resources/__init__.py Log Message: ----------- flake8 Commit: fef1208a1049a453e6c3249f179ded4e3cc7a394 https://github.com/galaxyproject/galaxy/commit/fef1208a1049a453e6c3249f179de... Author: Jeffrey Thiessen <jeffreylthiessen@gmail.com> Date: 2017-12-13 (Wed, 13 Dec 2017) Changed paths: M lib/galaxy/workflow/resources/__init__.py Log Message: ----------- fixed pep8 Commit: 2d35acafd1806f35f25ba76e0c22f07a24f1356c https://github.com/galaxyproject/galaxy/commit/2d35acafd1806f35f25ba76e0c22f... Author: Jeffrey Thiessen <jeffreylthiessen@gmail.com> Date: 2017-12-13 (Wed, 13 Dec 2017) Changed paths: M lib/galaxy/tools/execute.py Log Message: ----------- fix unit test cases Commit: 7c3c984242161378bcbe626369755b58dc8e6131 https://github.com/galaxyproject/galaxy/commit/7c3c984242161378bcbe626369755... Author: Jeffrey Thiessen <jeffreylthiessen@gmail.com> Date: 2017-12-13 (Wed, 13 Dec 2017) Changed paths: M lib/galaxy/workflow/resources/__init__.py Log Message: ----------- Changed 'option' to 'parameter' where appropriate Commit: 3d7b318f66d341ac788eb48a342521125c562e08 https://github.com/galaxyproject/galaxy/commit/3d7b318f66d341ac788eb48a34252... 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templates/webapps/galaxy/visualization/display.mako M templates/webapps/galaxy/visualization/phyloviz.mako M templates/webapps/galaxy/visualization/sweepster.mako R templates/webapps/reports/grid.mako M templates/webapps/reports/run_stats.mako M templates/webapps/tool_shed/category/grid.mako M templates/webapps/tool_shed/category/valid_grid.mako M templates/webapps/tool_shed/common/grid_common.mako M templates/webapps/tool_shed/group/index.mako M templates/webapps/tool_shed/repository_review/grid.mako M test-data/neostore.zip A test-data/new_element_sort_order.txt M test/api/test_configuration.py M test/api/test_history_contents.py M test/api/test_jobs.py M test/api/test_libraries.py M test/api/test_tools.py M test/api/test_tools_upload.py M test/api/test_workflows.py M test/base/api.py M test/base/data/test_workflow_1.ga M test/base/driver_util.py M test/base/interactor.py M test/base/populators.py A test/functional/tools/compressed_neostorezip_neostore_conversion.xml A 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tools/data_source/microbial_import_code.py M tools/data_source/upload.py M tools/genomespace/genomespace_importer.py M tox.ini Log Message: ----------- Merge dev into branch + merge conflict fixes Commit: 33c01aba6fb5dcdf4c2e33c1756eec1cbf2cfb90 https://github.com/galaxyproject/galaxy/commit/33c01aba6fb5dcdf4c2e33c1756ee... Author: Jeffrey Thiessen <jeffreylthiessen@gmail.com> Date: 2018-01-18 (Thu, 18 Jan 2018) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- fixed missing comma Commit: af3a69b1afa6637308ca4f667a745b2e02859ae2 https://github.com/galaxyproject/galaxy/commit/af3a69b1afa6637308ca4f667a745... Author: Jeffrey Thiessen <jeffreylthiessen@gmail.com> Date: 2018-02-06 (Tue, 06 Feb 2018) Changed paths: M lib/galaxy/jobs/dynamic_tool_destination.py M lib/galaxy/model/__init__.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/resources/__init__.py R lib/galaxy/workflow/resources/example.py Log Message: ----------- remove/fix todo's Commit: 8cd6df15828d69739915d7c1bf6d6e0f0116fe10 https://github.com/galaxyproject/galaxy/commit/8cd6df15828d69739915d7c1bf6d6... Author: Jeffrey Thiessen <jeffreylthiessen@gmail.com> Date: 2018-02-06 (Tue, 06 Feb 2018) Changed paths: M .ci/check_py3_compatibility.sh M .ci/flake8_blacklist.txt M .ci/flake8_wrapper.sh M .ci/flake8_wrapper_docstrings.sh M .ci/jenkins/api/run_tests.sh M .ci/jenkins/selenium-compose/run_tests.sh M .ci/jenkins/selenium/run_tests.sh M .gitignore M .travis.yml M Makefile M client/galaxy/scripts/apps/extended.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/mvc/base/controlled-fetch-collection.js M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/history/hdca-li-edit.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/multi-panel.js M client/galaxy/scripts/mvc/history/options-menu.js M 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static/scripts/utils/graph.js R static/scripts/utils/levenshtein.js R static/scripts/utils/localization.js R static/scripts/utils/metrics-logger.js R static/scripts/utils/natural-sort.js R static/scripts/utils/query-string-parsing.js R static/scripts/utils/uploadbox.js R static/scripts/utils/utils.js R static/scripts/viz/bbi-data-manager.js R static/scripts/viz/circster.js R static/scripts/viz/phyloviz.js R static/scripts/viz/sweepster.js R static/scripts/viz/trackster.js R static/scripts/viz/trackster/filters.js R static/scripts/viz/trackster/painters.js R static/scripts/viz/trackster/slotting.js R static/scripts/viz/trackster/tracks.js R static/scripts/viz/trackster/util.js R static/scripts/viz/visualization.js R static/scripts/viz/viz_views.js M templates/admin/tool_shed_repository/deactivate_or_uninstall_repository.mako M templates/admin/tool_shed_repository/manage_repository_tool_dependencies.mako M templates/admin/tool_shed_repository/reset_metadata_on_selected_repositories.mako 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test/functional/webhooks/trans_object/config.yaml R test/functional/webhooks/trans_object/config/trans_object.yaml R test/functional/webhooks/trans_object/helper/__init__.py A test/functional/webhooks/xkcd/config.yml R test/functional/webhooks/xkcd/config/xkcd.yml A test/functional/webhooks/xkcd/script.js R test/functional/webhooks/xkcd/static/script.js R test/functional/webhooks/xkcd/static/styles.css A test/functional/webhooks/xkcd/styles.css A test/integration/dockerized_job_conf.xml A test/integration/sets_tmp_dir_expression_job_conf.xml A test/integration/sets_tmp_dir_to_true_job_conf.xml A test/integration/simple_job_conf.xml A test/integration/test_dockerized_jobs.py A test/integration/test_job_environments.py M test/manual/launch_and_run.sh M test/selenium_tests/test_tool_describing_tours.py M test/shed_functional/base/twilltestcase.py A test/unit/config/1705_allow_path_paste/config/galaxy.ini A test/unit/config/__init__.py M test/unit/config/test_config_manage.py M test/unit/jobs/test_mapper.py M test/unit/jobs/test_runner_local.py M test/unit/managers/test_HistoryManager.py M test/unit/tools/test_evaluation.py M tox.ini Log Message: ----------- merge conflicts Commit: 7d8cddb40087fa1186dc16350f485d1e863fa30e https://github.com/galaxyproject/galaxy/commit/7d8cddb40087fa1186dc16350f485... Author: Jeffrey Thiessen <jeffreylthiessen@gmail.com> Date: 2018-02-08 (Thu, 08 Feb 2018) Changed paths: M config/galaxy.yml.sample M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- move vars from galaxy.ini to galaxy.yml Commit: 3bcb80386300c17db33d51397f71d120693d9306 https://github.com/galaxyproject/galaxy/commit/3bcb80386300c17db33d51397f71d... Author: Jeffrey Thiessen <jeffreylthiessen@gmail.com> Date: 2018-02-08 (Thu, 08 Feb 2018) Changed paths: M client/galaxy/scripts/galaxy.js M client/galaxy/scripts/utils/localization.js M client/package.json M config/datatypes_conf.xml.sample M config/galaxy.yml.sample M config/user_preferences_extra_conf.yml.sample M doc/source/admin/galaxy_options.rst M lib/galaxy/config.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/genetics.py M lib/galaxy/jobs/actions/post.py M lib/galaxy/managers/configuration.py M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/views.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/web/framework/middleware/sentry.py M lib/galaxy/web/security/__init__.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/config_schema.yml M scripts/common_startup.sh M static/style/blue/base.css M templates/webapps/galaxy/galaxy.masthead.mako M test/functional/twilltestcase.py Log Message: ----------- merge in dev Commit: 182bfbe50d9277f7bda6a2deb9fc83060160e14f https://github.com/galaxyproject/galaxy/commit/182bfbe50d9277f7bda6a2deb9fc8... Author: Jeffrey Thiessen <jeffreylthiessen@gmail.com> Date: 2018-02-13 (Tue, 13 Feb 2018) Changed paths: M Makefile M config/datatypes_conf.xml.sample M config/reports.yml.sample M config/tool_conf.xml.sample M doc/source/admin/reports_options.rst M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/interval.py M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt M lib/galaxy/managers/taggable.py M lib/galaxy/managers/tags.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/basic.py A lib/galaxy/tools/tag_collection_from_file.xml M lib/galaxy/web/framework/middleware/sentry.py M lib/tool_shed/tools/tool_validator.py M templates/webapps/galaxy/workflow/sharing.mako A test-data/new_tags_1.txt M test/base/interactor.py M test/functional/tools/samples_tool_conf.xml M test/unit/tools/test_tool_validation.py Log Message: ----------- merge dev into branch Commit: 1a66a8d2e6f33aed07e9e50d34d7d561eb5b3274 https://github.com/galaxyproject/galaxy/commit/1a66a8d2e6f33aed07e9e50d34d7d... Author: Jeffrey Thiessen <jeffreylthiessen@gmail.com> Date: 2018-02-13 (Tue, 13 Feb 2018) Changed paths: M lib/galaxy/workflow/resources/__init__.py Log Message: ----------- fix by group validation Commit: 9c4494490944d64915240a5b45909e09eab401bc https://github.com/galaxyproject/galaxy/commit/9c4494490944d64915240a5b45909... Author: Jeffrey Thiessen <jeffreylthiessen@gmail.com> Date: 2018-02-13 (Tue, 13 Feb 2018) Changed paths: R static/maps/mvc/tool/tool-form-composite.js.map R static/scripts/bundled/analysis.bundled.js.map R static/scripts/bundled/libs.bundled.js.map R static/scripts/libs/bibtex.js Log Message: ----------- remove static files Commit: 2e10bff10ea3cbdf63c8df345cc6fc4f041d10b1 https://github.com/galaxyproject/galaxy/commit/2e10bff10ea3cbdf63c8df345cc6f... 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lib/galaxy/datatypes/converters/bam_native_to_bam_converter.xml M lib/galaxy/datatypes/converters/sam_to_bam_native.xml M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/model/mapping.py M lib/galaxy/util/xml_macros.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/web/framework/helpers/grids.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/history.py M lib/galaxy/webapps/galaxy/controllers/page.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M lib/galaxy/webapps/galaxy/controllers/workflow.py R static/scripts/packed M static/style/blue/base.css M templates/js-app.mako M test/api/test_visualizations.py Log Message: ----------- merge from dev Commit: 451342ed9ea0f60d674b04256c67abdf441d1189 https://github.com/galaxyproject/galaxy/commit/451342ed9ea0f60d674b04256c67a... Author: Jeffrey Thiessen <jeffreylthiessen@gmail.com> Date: 2018-03-20 (Tue, 20 Mar 2018) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/apps/extended.js M client/galaxy/scripts/apps/panels/tool-panel.js A client/galaxy/scripts/components/DisplayStructured.vue A client/galaxy/scripts/components/HistoryView.vue M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/collection/collection-view.js M client/galaxy/scripts/mvc/dataset/dataset-model.js M client/galaxy/scripts/mvc/form/form-data.js M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/grid/grid-shared.js M client/galaxy/scripts/mvc/grid/grid-template.js M client/galaxy/scripts/mvc/grid/grid-view.js M client/galaxy/scripts/mvc/history/hdca-li-edit.js M client/galaxy/scripts/mvc/history/history-contents.js M 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test/integration/test_shed_tool_tests.py M test/integration/test_upload_configuration_options.py A test/integration/uses_shed.py M test/selenium_tests/framework.py M test/selenium_tests/test_collection_builders.py M test/selenium_tests/test_jupyter.py M test/selenium_tests/test_library_to_collections.py M test/selenium_tests/test_saved_histories.py M test/selenium_tests/test_tool_form.py M test/shed_functional/base/twilltestcase.py M test/shed_functional/test_data/emboss/datatypes/datatypes_conf.xml M test/unit/tools/test_parsing.py M test/unit/tools/test_toolbox.py M tools/data_source/upload.py M tools/data_source/upload.xml M tools/genomespace/genomespace_exporter.xml M tools/genomespace/genomespace_importer.xml M tools/genomespace/genomespace_push.xml Log Message: ----------- fix merge conflict Commit: d95b3dbfd5fecb776aa95337c6405d8dd5093e39 https://github.com/galaxyproject/galaxy/commit/d95b3dbfd5fecb776aa95337c6405... Author: John Chilton <jmchilton@gmail.com> Date: 2018-03-20 (Tue, 20 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M config/galaxy.yml.sample A config/workflow_resource_mapper_conf.yml.sample A config/workflow_resource_params_conf.xml.sample M lib/galaxy/config.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/dynamic_tool_destination.py M lib/galaxy/jobs/mapper.py M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/execute.py M lib/galaxy/util/__init__.py M lib/galaxy/webapps/galaxy/config_schema.yml M lib/galaxy/workflow/modules.py A lib/galaxy/workflow/resources/__init__.py A lib/galaxy/workflow/resources/example.py.sample M lib/galaxy/workflow/run_request.py M test/unit/jobs/dynamic_tool_destination/mockGalaxy.py Log Message: ----------- Merge pull request #4830 from phac-nml/dev Workflow-to-Job Scheduling Parameters Compare: https://github.com/galaxyproject/galaxy/compare/2f41ccc13d04...d95b3dbfd5fe