[galaxy-commits] [galaxyproject/galaxy] bb82ec: Merge pull request #1 from galaxyproject/dev

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: bb82ec5bec1fec28402768cfbd40e01a7341e2de https://github.com/galaxyproject/galaxy/commit/bb82ec5bec1fec28402768cfbd40e... Author: pvanheus <pvh@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 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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/d123b402303a708c2d20d83a0fbc0... Author: pvanheus <pvh@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 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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/1fed38b28289bee22a00fbac4b103... Author: Peter van Heusden <pvh@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 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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/5fda00fb7e4317db309a712dd773f... Author: Peter van Heusden <pvh@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/578914baf558a910b97846bac9d2b... Author: Peter van Heusden <pvh@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/e4d101eeaef38ea86bd87bffe0f33... Author: Peter van Heusden <pvh@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/f53ef165290d0cbc397c6f1fce8c9... Author: Peter van Heusden <pvh@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/de52665d30223134b69e3e7cdc868... Author: Peter van Heusden <pvh@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/2e1ecb9b473a0dafdfe074781a24f... Author: Peter van Heusden <pvh@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/891b7b5a1898677599e575308d026... Author: Peter van Heusden <pvh@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/defb594cb9b249593e1c572f6e27b... Author: Peter van Heusden <pvh@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/97c052a1ec65e443b7c0f9e08c284... Author: Peter van Heusden <pvh@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/2075af4de80f7ffd7be127889a430... Author: John Chilton <jmchilton@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