Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 5a83e56168369a3fccde6aae34015ffc21721188 https://github.com/galaxyproject/galaxy/commit/5a83e56168369a3fccde6aae34015... Author: Evgeny Anatskiy <evgeny.anatskiy@gmail.com> Date: 2017-03-05 (Sun, 05 Mar 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/tool/tool-form.js M client/galaxy/scripts/mvc/webhooks.js M client/galaxy/scripts/onload.js M client/galaxy/scripts/utils/uploadbox.js M config/plugins/visualizations/charts/static/repository/utilities/jobs.js M config/plugins/webhooks/demo/phdcomics/helper/__init__.py M config/plugins/webhooks/demo/trans_object/helper/__init__.py A config/plugins/webhooks/tour_generator/config/tour_generator.yml A config/plugins/webhooks/tour_generator/helper/__init__.py A config/plugins/webhooks/tour_generator/static/script.js A config/plugins/webhooks/tour_generator/static/styles.css M lib/galaxy/webapps/galaxy/api/webhooks.py M lib/galaxy/webapps/galaxy/buildapp.py M static/maps/mvc/tool/tool-form-base.js.map M static/maps/mvc/tool/tool-form.js.map M static/maps/mvc/webhooks.js.map M static/maps/onload.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/tool/tool-form-base.js M static/scripts/mvc/tool/tool-form.js M static/scripts/mvc/webhooks.js M static/scripts/onload.js Log Message: ----------- upload tool's test data into the History panel Commit: 4fdb554629e10e4fd20a99806c9b2e8e883cb844 https://github.com/galaxyproject/galaxy/commit/4fdb554629e10e4fd20a99806c9b2... Author: Evgeny Anatskiy <evgeny.anatskiy@gmail.com> Date: 2017-04-05 (Wed, 05 Apr 2017) Changed paths: M .gitignore M config/galaxy.ini.sample A config/plugins/webhooks/demo/tour_generator/config/tour_generator.yml A config/plugins/webhooks/demo/tour_generator/helper/__init__.py A config/plugins/webhooks/demo/tour_generator/static/script.js A config/plugins/webhooks/demo/tour_generator/static/styles.css R config/plugins/webhooks/tour_generator/config/tour_generator.yml R config/plugins/webhooks/tour_generator/helper/__init__.py R config/plugins/webhooks/tour_generator/static/script.js R config/plugins/webhooks/tour_generator/static/styles.css Log Message: ----------- generate tool tours Commit: bef2e2fc00030dbcdf32acc3dcfe30175db80506 https://github.com/galaxyproject/galaxy/commit/bef2e2fc00030dbcdf32acc3dcfe3... Author: Evgeny Anatskiy <evgeny.anatskiy@gmail.com> Date: 2017-04-07 (Fri, 07 Apr 2017) Changed paths: M config/plugins/webhooks/demo/tour_generator/helper/__init__.py M config/plugins/webhooks/demo/tour_generator/static/script.js Log Message: ----------- deal with different input types + bugfixes Commit: c7f3de9713c07ba51f61f7a2761e1a685b68d4eb https://github.com/galaxyproject/galaxy/commit/c7f3de9713c07ba51f61f7a2761e1... Author: Evgeny Anatskiy <evgeny.anatskiy@gmail.com> Date: 2017-04-08 (Sat, 08 Apr 2017) Changed paths: M client/galaxy/scripts/onload.js M config/plugins/webhooks/demo/tour_generator/helper/__init__.py M config/plugins/webhooks/demo/tour_generator/static/script.js M static/maps/onload.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/onload.js Log Message: ----------- improve frontend script + bugfixes Commit: 73e90fc7f53fff6c9fdf901b9b06a66a801f0c6c https://github.com/galaxyproject/galaxy/commit/73e90fc7f53fff6c9fdf901b9b06a... Author: Evgeny Anatskiy <evgeny.anatskiy@gmail.com> Date: 2017-04-08 (Sat, 08 Apr 2017) Changed paths: M .ci/flake8_blacklist.txt M .ci/flake8_lint_include_list.txt M .ci/jenkins/selenium/run_galaxy.bash M .ci/jenkins/selenium/run_tests.sh M .ci/py3_sources.txt M CONTRIBUTING.md M README.rst M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/galaxy.interactive_environments.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/libs/jquery/jquery.autocomplete.js A client/galaxy/scripts/mvc/collection/base-creator.js M client/galaxy/scripts/mvc/collection/collection-view-edit.js M client/galaxy/scripts/mvc/collection/collection-view.js M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M client/galaxy/scripts/mvc/collection/pair-collection-creator.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/dataset/dataset-li.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/grid/grid-template.js M client/galaxy/scripts/mvc/grid/grid-view.js M client/galaxy/scripts/mvc/history/hda-li.js M client/galaxy/scripts/mvc/history/hdca-li.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-edit.js M client/galaxy/scripts/mvc/history/history-view.js M client/galaxy/scripts/mvc/history/options-menu.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/tag.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js R client/galaxy/scripts/mvc/tool/tool-form-workflow.js M client/galaxy/scripts/mvc/tool/tool-form.js M client/galaxy/scripts/mvc/tool/tools.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-table.js A client/galaxy/scripts/mvc/upload/collection/collection-row.js A client/galaxy/scripts/mvc/upload/collection/collection-view.js M client/galaxy/scripts/mvc/upload/upload-ftp.js M client/galaxy/scripts/mvc/upload/upload-view.js A client/galaxy/scripts/mvc/user/user-custom-builds.js M client/galaxy/scripts/mvc/user/user-preferences.js M client/galaxy/scripts/mvc/user/user-quotameter.js M client/galaxy/scripts/mvc/workflow/workflow-canvas.js A client/galaxy/scripts/mvc/workflow/workflow-forms.js A client/galaxy/scripts/mvc/workflow/workflow-icons.js M client/galaxy/scripts/mvc/workflow/workflow-manager.js M client/galaxy/scripts/mvc/workflow/workflow-node.js M client/galaxy/scripts/mvc/workflow/workflow-view-node.js M client/galaxy/scripts/mvc/workflow/workflow-view.js A client/galaxy/scripts/nls/fr/locale.js M client/galaxy/scripts/nls/ja/locale.js M client/galaxy/scripts/nls/locale.js M client/galaxy/scripts/nls/zh/locale.js M client/galaxy/scripts/ui/autocom_tagging.js M client/galaxy/scripts/viz/trackster/tracks.js M client/galaxy/style/less/base.less M client/galaxy/style/less/history.less M client/galaxy/style/less/ui.less M client/galaxy/style/less/ui/paired-collection-creator.less M client/galaxy/style/less/upload.less M client/package.json M client/webpack.config.js A config/build_sites.yml.sample M config/datatypes_conf.xml.sample M config/dependency_resolvers_conf.xml.sample M config/galaxy.ini.sample M config/job_conf.xml.sample_advanced A config/local_conda_mapping.yml.sample M config/plugins/interactive_environments/bam_iobio/config/bam_iobio.ini.sample M config/plugins/interactive_environments/bam_iobio/static/js/bam_iobio.js M config/plugins/interactive_environments/bam_iobio/templates/bam_iobio.mako M config/plugins/interactive_environments/common/templates/ie.mako A config/plugins/interactive_environments/ethercalc/config/allowed_images.yml.sample A config/plugins/interactive_environments/ethercalc/config/ethercalc.ini.sample A config/plugins/interactive_environments/ethercalc/config/ethercalc.xml A config/plugins/interactive_environments/ethercalc/static/js/ethercalc.js A config/plugins/interactive_environments/ethercalc/templates/ethercalc.mako M 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/config/jupyter.xml M config/plugins/interactive_environments/jupyter/static/js/jupyter.js M config/plugins/interactive_environments/jupyter/templates/jupyter.mako M config/plugins/interactive_environments/neo/config/neo.ini.sample M config/plugins/interactive_environments/neo/static/js/neo.js M config/plugins/interactive_environments/neo/templates/neo.mako M config/plugins/interactive_environments/phinch/config/phinch.ini.sample M config/plugins/interactive_environments/phinch/static/js/phinch.js M config/plugins/interactive_environments/phinch/templates/phinch.mako M config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample M config/plugins/interactive_environments/rstudio/config/rstudio.xml M config/plugins/interactive_environments/rstudio/static/js/rstudio.js M config/plugins/interactive_environments/rstudio/templates/rstudio.mako M config/plugins/tours/core.galaxy_ui.yaml M config/plugins/tours/core.history.yaml A config/plugins/visualizations/charts/static/repository/build/biojs_phylocanvas.js A config/plugins/visualizations/charts/static/repository/build/biojs_phylocanvas.js.map R config/plugins/visualizations/charts/static/repository/build/cytoscape_basic.js R config/plugins/visualizations/charts/static/repository/build/cytoscape_basic.js.map A config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js A config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js.map A config/plugins/visualizations/charts/static/repository/build/ngl_viewer.js A config/plugins/visualizations/charts/static/repository/build/ngl_viewer.js.map M config/plugins/visualizations/charts/static/repository/build/registry.js M config/plugins/visualizations/charts/static/repository/build/registry.js.map M config/plugins/visualizations/charts/static/repository/build/registry.tmp.js A config/plugins/visualizations/charts/static/repository/plugins/biojs/phylocanvas/phylocanvas.js A config/plugins/visualizations/charts/static/repository/plugins/ngl/viewer.js M config/plugins/visualizations/charts/static/repository/registry.json A config/plugins/visualizations/charts/static/repository/utilities/sifjson.js M config/plugins/visualizations/charts/static/repository/utilities/utils.js A config/plugins/visualizations/charts/static/repository/visualizations/biojs/phylocanvas/config.js A config/plugins/visualizations/charts/static/repository/visualizations/biojs/phylocanvas/logo.png A config/plugins/visualizations/charts/static/repository/visualizations/biojs/phylocanvas/wrapper.js R config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/basic/config.js R config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/basic/logo.png R config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/basic/wrapper.js A config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/config.js A config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/logo.png A config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/wrapper.js A config/plugins/visualizations/charts/static/repository/visualizations/ngl/viewer/config.js A config/plugins/visualizations/charts/static/repository/visualizations/ngl/viewer/logo.png A config/plugins/visualizations/charts/static/repository/visualizations/ngl/viewer/wrapper.js M config/plugins/visualizations/charts/templates/charts.mako M config/plugins/visualizations/csg/templates/csg.mako M config/plugins/visualizations/graphviz/templates/graphviz.mako M config/plugins/visualizations/scatterplot/templates/scatterplot.mako R config/plugins/webhooks/demo/history_test1/config/history_test1.yml R config/plugins/webhooks/demo/history_test2/config/history_test2.yml R config/plugins/webhooks/demo/masthead_test/config/masthead_test.yml R config/plugins/webhooks/demo/phdcomics/config/phdcomics.yaml R config/plugins/webhooks/demo/phdcomics/helper/__init__.py R config/plugins/webhooks/demo/phdcomics/static/script.js R config/plugins/webhooks/demo/phdcomics/static/styles.css A config/plugins/webhooks/demo/search/config/searchover.yaml A config/plugins/webhooks/demo/search/static/script.js A config/plugins/webhooks/demo/search/static/styles.css A config/plugins/webhooks/demo/tool_list/config/tool_list.yml A config/plugins/webhooks/demo/tool_list/helper/__init__.py R config/plugins/webhooks/demo/trans_object/config/trans_object.yaml R config/plugins/webhooks/demo/trans_object/helper/__init__.py R config/plugins/webhooks/demo/xkcd/config/xkcd.yml R config/plugins/webhooks/demo/xkcd/static/script.js R config/plugins/webhooks/demo/xkcd/static/styles.css A config/swarm_manager_conf.yml.sample M config/tool_destinations.yml.sample M contrib/nagios/check_galaxy M contrib/nagios/check_galaxy.py M display_applications/igv/bigwig.xml A display_applications/igv/genome_fasta.xml M doc/schema_template.md A doc/source/admin/authentication.md R doc/source/admin/chat-0.png R doc/source/admin/chat-1.png R doc/source/admin/chat-2.png R doc/source/admin/chat-3.png R doc/source/admin/chat-4.png R doc/source/admin/chat.rst R doc/source/admin/communication_server.png R doc/source/admin/communication_server_rooms.png M doc/source/admin/conda_faq.rst M doc/source/admin/dependency_resolvers.rst M doc/source/admin/framework_dependencies.rst R doc/source/admin/grt.rst R doc/source/admin/images_webhooks/history-menu.png R doc/source/admin/images_webhooks/masthead.png R doc/source/admin/images_webhooks/masthead_trans_object.png R doc/source/admin/images_webhooks/tool.png R doc/source/admin/images_webhooks/workflow.png M doc/source/admin/index.rst R doc/source/admin/interactive_environments.png R doc/source/admin/interactive_environments.rst R doc/source/admin/interactive_environments.svg R doc/source/admin/mulled_containers.rst A doc/source/admin/reports.md A doc/source/admin/special_topics/chat-0.png A doc/source/admin/special_topics/chat-1.png A doc/source/admin/special_topics/chat-2.png A doc/source/admin/special_topics/chat-3.png A doc/source/admin/special_topics/chat-4.png A doc/source/admin/special_topics/chat.rst A doc/source/admin/special_topics/communication_server.png A doc/source/admin/special_topics/communication_server_rooms.png A doc/source/admin/special_topics/grt.rst A doc/source/admin/special_topics/images_webhooks/history-menu.png A doc/source/admin/special_topics/images_webhooks/masthead.png A doc/source/admin/special_topics/images_webhooks/masthead_trans_object.png A doc/source/admin/special_topics/images_webhooks/tool.png A doc/source/admin/special_topics/images_webhooks/workflow.png A doc/source/admin/special_topics/index.rst A doc/source/admin/special_topics/interactive_environments.png A doc/source/admin/special_topics/interactive_environments.rst A doc/source/admin/special_topics/interactive_environments.svg A doc/source/admin/special_topics/mulled_containers.rst A doc/source/admin/special_topics/webhooks.rst A doc/source/admin/tool_panel.rst M doc/source/admin/useful_scripts.rst R doc/source/admin/webhooks.rst A doc/source/api/api.rst M doc/source/api/guidelines.rst A doc/source/api/ts_api.rst M doc/source/api_doc.rst M doc/source/conf.py M doc/source/dev/faq.rst M doc/source/dev/index.rst M doc/source/dev/interactive_environments.rst M doc/source/index.rst R doc/source/lib/galaxy.webapps.galaxy.api.rst R doc/source/lib/galaxy.webapps.tool_shed.api.rst R doc/source/lib/galaxy_utils.rst R doc/source/lib/galaxy_utils.sequence.rst M doc/source/lib/modules.rst M doc/source/project/issues.rst M doc/source/project/organization.rst A doc/source/releases/17.01.rst M doc/source/releases/17.01_announce.rst A doc/source/releases/17.05_announce.rst M doc/source/releases/_header.rst M doc/source/releases/_thanks.rst M doc/source/releases/index.rst M doc/source/slideshow/architecture/galaxy_architecture.md M doc/source/slideshow/architecture/images/hda_dataset.plantuml.svg M doc/source/slideshow/architecture/images/hda_hdca.plantuml.svg M doc/source/slideshow/architecture/images/objectstore.plantuml.svg M doc/source/slideshow/architecture/images/plantuml_options.txt M doc/source/slideshow/architecture/images/server_client.plantuml.svg M doc/source/slideshow/architecture/images/server_client_old.plantuml.svg M doc/source/slideshow/architecture/images/webapp.plantuml.svg M doc/source/slideshow/architecture/style.css M doc/source/ts_api_doc.rst M lib/galaxy/app.py M lib/galaxy/auth/providers/__init__.py M lib/galaxy/auth/providers/ldap_ad.py M lib/galaxy/config.py A lib/galaxy/container/__init__.py A lib/galaxy/container/docker_swarm.py M lib/galaxy/dataset_collections/types/__init__.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/constructive_solid_geometry.py A lib/galaxy/datatypes/converters/fasta_to_fai.xml A lib/galaxy/datatypes/converters/fastqbz2_to_fastq.xml A lib/galaxy/datatypes/converters/fastqcssangerbz2_to_fastqcssanger.xml A lib/galaxy/datatypes/converters/fastqcssangergz_to_fastqcssanger.xml A lib/galaxy/datatypes/converters/fastqgz_to_fastq.xml A lib/galaxy/datatypes/converters/fastqilluminabz2_to_fastqillumina.xml A lib/galaxy/datatypes/converters/fastqilluminagz_to_fastqillumina.xml A lib/galaxy/datatypes/converters/fastqsangerbz2_to_fastqsanger.xml A lib/galaxy/datatypes/converters/fastqsangergz_to_fastqsanger.xml A lib/galaxy/datatypes/converters/fastqsolexabz2_to_fastqsolexa.xml A lib/galaxy/datatypes/converters/fastqsolexagz_to_fastqsolexa.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/mothur.py M lib/galaxy/datatypes/proteomics.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/1.smat A lib/galaxy/datatypes/test/diamond_db.dmnd M lib/galaxy/datatypes/text.py M lib/galaxy/datatypes/util/gff_util.py 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/exceptions/error_codes.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/datasets.py M lib/galaxy/jobs/dynamic_tool_destination.py M lib/galaxy/jobs/metrics/instrumenters/__init__.py M lib/galaxy/jobs/metrics/instrumenters/env.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/condor.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/jobs/runners/util/cli/__init__.py M lib/galaxy/jobs/runners/util/cli/job/__init__.py M lib/galaxy/jobs/runners/util/cli/job/slurm.py M lib/galaxy/jobs/runners/util/cli/shell/__init__.py M lib/galaxy/jobs/runners/util/cli/shell/local.py M lib/galaxy/jobs/runners/util/cli/shell/rsh.py M lib/galaxy/jobs/runners/util/condor/__init__.py 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/runners/util/kill.py M lib/galaxy/jobs/runners/util/retry.py M lib/galaxy/jobs/runners/util/sudo.py M lib/galaxy/managers/collections.py M lib/galaxy/managers/collections_util.py M lib/galaxy/managers/datasets.py M lib/galaxy/managers/deletable.py M lib/galaxy/managers/hdas.py M lib/galaxy/managers/hdcas.py M lib/galaxy/managers/tags.py M lib/galaxy/managers/users.py M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py M lib/galaxy/model/migrate/check.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/0022_visualization_tables.py M lib/galaxy/model/migrate/versions/0024_page_slug_unique_constraint.py M lib/galaxy/model/migrate/versions/0025_user_info.py M lib/galaxy/model/migrate/versions/0026_cloud_tables.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/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/0039_add_synopsis_column_to_library_table.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/0044_add_notify_column_to_request_table.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/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/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/0069_rename_sequencer_form_type.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/0104_update_genome_downloader_job_parameters.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/0115_longer_user_password_field.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/0119_job_metrics.py M lib/galaxy/model/migrate/versions/0120_dataset_collections.py M lib/galaxy/model/migrate/versions/0121_workflow_uuids.py M lib/galaxy/model/migrate/versions/0122_grow_mysql_blobs.py M lib/galaxy/model/migrate/versions/0123_add_workflow_request_tables.py M lib/galaxy/model/migrate/versions/0124_job_state_history.py M lib/galaxy/model/migrate/versions/0125_workflow_step_tracking.py M lib/galaxy/model/migrate/versions/0126_password_reset.py M lib/galaxy/model/migrate/versions/0127_output_collection_adjustments.py M lib/galaxy/model/migrate/versions/0128_session_timeout.py M lib/galaxy/model/migrate/versions/0129_job_external_output_metadata_validity.py M lib/galaxy/model/migrate/versions/0130_change_pref_datatype.py M lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_parameter_modules.py M lib/galaxy/model/migrate/versions/0132_add_lastpasswordchange_to_user.py M lib/galaxy/model/migrate/versions/0133_add_dependency_column_to_job.py A lib/galaxy/model/migrate/versions/0134_hda_set_deleted_if_purged.py M lib/galaxy/model/orm/engine_factory.py M lib/galaxy/model/orm/scripts.py M lib/galaxy/queue_worker.py M lib/galaxy/queues.py R lib/galaxy/tags/__init__.py R lib/galaxy/tags/tag_handler.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/cwl/cwltool_deps.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/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/conda_util.py M lib/galaxy/tools/deps/container_resolvers/__init__.py M lib/galaxy/tools/deps/container_resolvers/explicit.py M lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/tools/deps/containers.py M lib/galaxy/tools/deps/dependencies.py M lib/galaxy/tools/deps/installable.py M lib/galaxy/tools/deps/mulled/invfile.lua M lib/galaxy/tools/deps/mulled/mulled_build.py M lib/galaxy/tools/deps/requirements.py M lib/galaxy/tools/deps/resolvers/__init__.py M lib/galaxy/tools/deps/resolvers/brewed_tool_shed_packages.py M lib/galaxy/tools/deps/resolvers/conda.py A lib/galaxy/tools/deps/resolvers/default_conda_mapping.yml M lib/galaxy/tools/deps/resolvers/galaxy_packages.py M lib/galaxy/tools/deps/resolvers/homebrew.py M lib/galaxy/tools/deps/resolvers/modules.py M lib/galaxy/tools/deps/resolvers/resolver_mixins.py M lib/galaxy/tools/deps/views.py M lib/galaxy/tools/errors.py M lib/galaxy/tools/evaluation.py A lib/galaxy/tools/fetcher.py M lib/galaxy/tools/filter_failed_collection.xml M lib/galaxy/tools/flatten_collection.xml 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/linters/general.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 M lib/galaxy/tools/loader_directory.py A lib/galaxy/tools/locations/__init__.py A lib/galaxy/tools/locations/dockstore.py A lib/galaxy/tools/locations/file.py A lib/galaxy/tools/locations/http.py M lib/galaxy/tools/merge_collection.xml 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/parser/cwl.py M lib/galaxy/tools/parser/factory.py M lib/galaxy/tools/parser/interface.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/search/__init__.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/cache.py M lib/galaxy/tools/toolbox/filters/examples.py.sample M lib/galaxy/tools/toolbox/lineages/interface.py M lib/galaxy/tools/toolbox/tags.py M lib/galaxy/tools/toolbox/watcher.py M lib/galaxy/tools/unzip_collection.xml M lib/galaxy/tools/util/galaxyops/__init__.py M lib/galaxy/tools/util/maf_utilities.py M lib/galaxy/tools/verify/__init__.py M lib/galaxy/tools/verify/asserts/__init__.py M lib/galaxy/tools/verify/asserts/text.py M lib/galaxy/tools/verify/asserts/xml.py M lib/galaxy/tools/verify/test_data.py M lib/galaxy/tools/wrappers.py M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/tools/zip_collection.xml A lib/galaxy/util/compression_utils.py M lib/galaxy/util/json.py M lib/galaxy/util/object_wrapper.py A lib/galaxy/util/oset.py R lib/galaxy/util/postfork.py M lib/galaxy/util/properties.py M lib/galaxy/version.py M lib/galaxy/visualization/plugins/plugin.py M lib/galaxy/visualization/plugins/registry.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/framework/base.py M lib/galaxy/web/framework/decorators.py M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/web/framework/middleware/batch.py M lib/galaxy/web/framework/middleware/remoteuser.py M lib/galaxy/web/framework/middleware/sentry.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/web/proxy/__init__.py M lib/galaxy/web/proxy/js/Dockerfile M lib/galaxy/web/proxy/js/lib/mapper.js A lib/galaxy/web/stack/__init__.py M lib/galaxy/webapps/galaxy/api/configuration.py M lib/galaxy/webapps/galaxy/api/folder_contents.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/library_contents.py M lib/galaxy/webapps/galaxy/api/tool_dependencies.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/api/users.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/buildapp.py A lib/galaxy/webapps/galaxy/config_watchers.py M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/history.py A lib/galaxy/webapps/galaxy/controllers/interactive_environments.py M lib/galaxy/webapps/galaxy/controllers/library_common.py R lib/galaxy/webapps/galaxy/controllers/search.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/reports/app.py M lib/galaxy/webapps/reports/buildapp.py M lib/galaxy/webapps/tool_shed/app.py M lib/galaxy/webapps/tool_shed/buildapp.py M lib/galaxy/webapps/util.py M lib/galaxy/webhooks/__init__.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run.py M lib/galaxy/workflow/run_request.py M lib/galaxy/workflow/schedulers/__init__.py M lib/galaxy/workflow/scheduling_manager.py M lib/galaxy/workflow/steps.py R lib/galaxy_utils/__init__.py R lib/galaxy_utils/sequence/__init__.py R lib/galaxy_utils/sequence/fasta.py R lib/galaxy_utils/sequence/fastq.py R lib/galaxy_utils/sequence/sequence.py R lib/galaxy_utils/sequence/transform.py R lib/galaxy_utils/sequence/vcf.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/update_repository_manager.py M lib/tool_shed/util/shed_util_common.py M lib/tool_shed/util/workflow_util.py M run.sh M run_tests.sh M scripts/api/README M scripts/bootstrap_history.py M scripts/common_startup.sh M scripts/functional_tests.py A scripts/manage_tool_dependencies.py R scripts/run_selenium_tests.sh A scripts/secret_decoder_ring.py M scripts/slideshow/slideshow_template.html A static/GruntFile.js A static/GruntFile.js.map A static/maps/analysis.js.map A static/maps/app.js.map A static/maps/app/analysis.js.map M static/maps/galaxy.interactive_environments.js.map M static/maps/layout/menu.js.map M static/maps/libs/jquery/jquery.autocomplete.js.map A static/maps/libs/showdown.js.map A static/maps/mvc/collection/base-creator.js.map M static/maps/mvc/collection/collection-view-edit.js.map M static/maps/mvc/collection/collection-view.js.map M static/maps/mvc/collection/list-collection-creator.js.map M static/maps/mvc/collection/list-of-pairs-collection-creator.js.map M static/maps/mvc/collection/pair-collection-creator.js.map M static/maps/mvc/dataset/dataset-li-edit.js.map M static/maps/mvc/dataset/dataset-li.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/grid/grid-template.js.map M static/maps/mvc/grid/grid-view.js.map M static/maps/mvc/history/hda-li.js.map M static/maps/mvc/history/hdca-li.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-edit.js.map M static/maps/mvc/history/history-view.js.map M static/maps/mvc/history/options-menu.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/maps/mvc/tag.js.map M static/maps/mvc/tool/tool-form-base.js.map M static/maps/mvc/tool/tool-form-composite.js.map R static/maps/mvc/tool/tool-form-workflow.js.map M static/maps/mvc/tool/tool-form.js.map M static/maps/mvc/tool/tools.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-table.js.map A static/maps/mvc/upload/collection/collection-row.js.map A static/maps/mvc/upload/collection/collection-view.js.map M static/maps/mvc/upload/upload-ftp.js.map M static/maps/mvc/upload/upload-view.js.map A static/maps/mvc/user/user-custom-builds.js.map M static/maps/mvc/user/user-preferences.js.map M static/maps/mvc/user/user-quotameter.js.map M static/maps/mvc/workflow/workflow-canvas.js.map A static/maps/mvc/workflow/workflow-forms.js.map A static/maps/mvc/workflow/workflow-icons.js.map M static/maps/mvc/workflow/workflow-manager.js.map M static/maps/mvc/workflow/workflow-node.js.map M static/maps/mvc/workflow/workflow-view-node.js.map M static/maps/mvc/workflow/workflow-view.js.map R static/maps/mvc/workflow/workflow.js.map A static/maps/nls/fr/locale.js.map M static/maps/nls/ja/locale.js.map M static/maps/nls/locale.js.map M static/maps/nls/zh/locale.js.map M static/maps/ui/autocom_tagging.js.map M static/maps/viz/trackster/tracks.js.map A static/scripts/analysis.js A static/scripts/app.js A static/scripts/app/analysis.js 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.interactive_environments.js M static/scripts/layout/menu.js M static/scripts/libs/jquery/jquery.autocomplete.js A static/scripts/libs/showdown.js A static/scripts/mvc/collection/base-creator.js M static/scripts/mvc/collection/collection-view-edit.js M static/scripts/mvc/collection/collection-view.js M static/scripts/mvc/collection/list-collection-creator.js M static/scripts/mvc/collection/list-of-pairs-collection-creator.js M static/scripts/mvc/collection/pair-collection-creator.js M static/scripts/mvc/dataset/dataset-li-edit.js M static/scripts/mvc/dataset/dataset-li.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/grid/grid-template.js M static/scripts/mvc/grid/grid-view.js M static/scripts/mvc/history/hda-li.js M static/scripts/mvc/history/hdca-li.js M static/scripts/mvc/history/history-contents.js M static/scripts/mvc/history/history-model.js M static/scripts/mvc/history/history-view-edit.js M static/scripts/mvc/history/history-view.js M static/scripts/mvc/history/options-menu.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/tag.js M static/scripts/mvc/tool/tool-form-base.js M static/scripts/mvc/tool/tool-form-composite.js R static/scripts/mvc/tool/tool-form-workflow.js M static/scripts/mvc/tool/tool-form.js M static/scripts/mvc/tool/tools.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-table.js A static/scripts/mvc/upload/collection/collection-row.js A static/scripts/mvc/upload/collection/collection-view.js M static/scripts/mvc/upload/upload-ftp.js M static/scripts/mvc/upload/upload-view.js A static/scripts/mvc/user/user-custom-builds.js M static/scripts/mvc/user/user-preferences.js M static/scripts/mvc/user/user-quotameter.js M static/scripts/mvc/workflow/workflow-canvas.js A static/scripts/mvc/workflow/workflow-forms.js A static/scripts/mvc/workflow/workflow-icons.js M static/scripts/mvc/workflow/workflow-manager.js M static/scripts/mvc/workflow/workflow-node.js M static/scripts/mvc/workflow/workflow-view-node.js M static/scripts/mvc/workflow/workflow-view.js A static/scripts/nls/fr/locale.js M static/scripts/nls/ja/locale.js M static/scripts/nls/locale.js M static/scripts/nls/zh/locale.js M static/scripts/ui/autocom_tagging.js M static/scripts/viz/trackster/tracks.js M static/style/blue/base.css M templates/admin/reload_tool.mako R templates/admin/tool_shed_repository/select_shed_tool_panel_config.mako M templates/admin/tool_shed_repository/select_tool_panel_section.mako M templates/grid_base.mako M templates/ind_share_base.mako M templates/show_params.mako R templates/user/dbkeys.mako M templates/webapps/galaxy/admin/index.mako A templates/webapps/galaxy/admin/manage_dependencies.mako M templates/webapps/galaxy/history/share.mako M templates/webapps/galaxy/workflow/editor.mako R templates/webapps/galaxy/workflow/editor_generic_form.mako R templates/webapps/galaxy/workflow/editor_tool_form.mako M templates/webapps/tool_shed/repository/common.mako M templates/webapps/tool_shed/repository/tool_form.mako A test-data/1.fastqsanger.bz2 A test-data/1.fastqsanger.gz A test-data/simple.xml M test/TESTING.md R test/api/helpers.py M test/api/test_dataset_collections.py M test/api/test_datasets.py M test/api/test_datatypes.py M test/api/test_histories.py M test/api/test_history_contents.py M test/api/test_history_contents_provenance.py M test/api/test_jobs.py M test/api/test_libraries.py M test/api/test_search.py M test/api/test_tools.py M test/api/test_users.py A test/api/test_visualizations.py A test/api/test_webhooks.py R test/api/test_workflow_1.ga R test/api/test_workflow_2.ga R test/api/test_workflow_batch.ga M test/api/test_workflow_extraction.py R test/api/test_workflow_map_reduce_pause.ga R test/api/test_workflow_matching_lists.ga R test/api/test_workflow_missing_tool.ga R test/api/test_workflow_pause.ga R test/api/test_workflow_topoambigouity.ga R test/api/test_workflow_topoambigouity_auto_laidout.ga R test/api/test_workflow_validation_1.ga R test/api/test_workflow_with_runtime_input.ga M test/api/test_workflows.py M test/api/test_workflows_from_yaml.py R test/api/workflows_format_2/README.txt R test/api/workflows_format_2/__init__.py R test/api/workflows_format_2/converter.py R test/api/workflows_format_2/interface.py R test/api/workflows_format_2/main.py M test/base/api_asserts.py A test/base/data/test_workflow_1.ga A test/base/data/test_workflow_2.ga A test/base/data/test_workflow_batch.ga A test/base/data/test_workflow_map_reduce_pause.ga A test/base/data/test_workflow_matching_lists.ga A test/base/data/test_workflow_missing_tool.ga A test/base/data/test_workflow_pause.ga A test/base/data/test_workflow_topoambigouity.ga A test/base/data/test_workflow_topoambigouity_auto_laidout.ga A test/base/data/test_workflow_validation_1.ga A test/base/data/test_workflow_with_runtime_input.ga M test/base/driver_util.py A test/base/populators.py A test/base/workflows_format_2/README.txt A test/base/workflows_format_2/__init__.py A test/base/workflows_format_2/converter.py A test/base/workflows_format_2/interface.py A test/base/workflows_format_2/main.py R test/casperjs/api-dataset-tests.js R test/casperjs/api-visualizations-tests.js M test/docker/README.md M test/docker/base/Dockerfile M test/docker/base/ansible_vars.yml M test/docker/base/run_test_wrapper.sh M test/functional/tools/checksum.xml M test/functional/tools/column_param.xml A test/functional/tools/compressed_bz2_fastq_conversion.xml A test/functional/tools/compressed_bz2_fastq_no_conversion.xml A test/functional/tools/compressed_gz_fastq_conversion.xml A test/functional/tools/compressed_gz_fastq_no_conversion.xml M test/functional/tools/create_10.xml A test/functional/tools/create_2.xml A test/functional/tools/explicit_conversion.xml A test/functional/tools/for_workflows/mapper2.xml A test/functional/tools/identifier_multiple_in_conditional.xml A test/functional/tools/identifier_multiple_in_repeat.xml A test/functional/tools/implicit_conversion.xml A test/functional/tools/is_valid_xml.xml A test/functional/tools/legacy_r.xml M test/functional/tools/md5sum.xml A test/functional/tools/mulled_example_conflict.xml A test/functional/tools/mulled_example_multi_incomplete.xml A test/functional/tools/output_format_deprecated_when.xml A test/functional/tools/paired_collection_map_over_structured_like.xml A test/functional/tools/param_text_option.xml A test/functional/tools/python_environment_problem.py A test/functional/tools/python_environment_problem.xml M test/functional/tools/sample_datatypes_conf.xml M test/functional/tools/samples_tool_conf.xml A test/functional/webhooks/history_test1/config/history_test1.yml A test/functional/webhooks/history_test2/config/history_test2.yml A test/functional/webhooks/masthead_test/config/masthead_test.yml A test/functional/webhooks/phdcomics/config/phdcomics.yaml A test/functional/webhooks/phdcomics/helper/__init__.py A test/functional/webhooks/phdcomics/static/script.js A test/functional/webhooks/phdcomics/static/styles.css A test/functional/webhooks/trans_object/config/trans_object.yaml A test/functional/webhooks/trans_object/helper/__init__.py A test/functional/webhooks/xkcd/config/xkcd.yml A test/functional/webhooks/xkcd/static/script.js A test/functional/webhooks/xkcd/static/styles.css R test/functional/workflow.py M test/galaxy_selenium/has_driver.py M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/navigation-data.yml M test/galaxy_selenium/sizzle.py A test/integration/resubmission_default_job_conf.xml M test/integration/resubmission_runners.py M test/integration/test_job_resubmission.py A test/integration/test_maximum_worklfow_invocation_duration.py M test/integration/test_resolvers.py A test/integration/test_workflow_handler_configuration.py A test/integration/workflow_handler_configuration_job_conf.xml M test/manual/workflows_scaling.py M test/qunit/package.json M test/qunit/test-data/paired-collection-creator.data.js M test/qunit/tests/form_tests.js M test/qunit/tests/workflow_editor_tests.js A test/selenium_tests/_workflow_fixtures.py M test/selenium_tests/framework.py A test/selenium_tests/test_collection_builders.py M test/selenium_tests/test_history_dataset_state.py M test/selenium_tests/test_history_sharing.py M test/selenium_tests/test_stock_tours.py A test/selenium_tests/test_tool_form.py M test/selenium_tests/test_uploads.py M test/selenium_tests/test_workflow_editor.py A test/selenium_tests/test_workflow_management.py A test/selenium_tests/test_workflow_run.py M test/shed_functional/functional/test_1090_repository_dependency_handling.py M test/shed_functional/functional/test_1150_datatype_converters.py M test/unit/jobs/test_command_factory.py M test/unit/jobs/test_job_configuration.py M test/unit/managers/test_HDAManager.py M test/unit/managers/test_HistoryManager.py M test/unit/tools/test_conda_resolution.py M test/unit/tools/test_data_parameters.py M test/unit/tools/test_execution.py M test/unit/tools/test_tool_deps.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_VisualizationsRegistry.py M test/unit/workflows/test_modules.py M test/unit/workflows/test_workflow_progress.py M test/unit/workflows/workflow_support.py M tool-data/shared/ucsc/builds.txt.sample M tool-data/shared/ucsc/ucsc_build_sites.txt.sample M tools/data_source/upload.py M tools/evolution/add_scores.xml M tools/extract/extract_genomic_dna.xml M tools/filters/gff/gff_filter_by_attribute.py M tools/filters/gff/gff_filter_by_feature_count.py R tools/filters/gff/sort_gtf.py M tools/filters/pasteWrapper.xml M tools/filters/trimmer.py M tools/filters/trimmer.xml M tools/maf/genebed_maf_to_fasta.xml M tools/maf/interval2maf.xml M tools/maf/interval2maf_pairwise.xml M tools/maf/interval_maf_to_merged_fasta.xml M tools/maf/macros.xml M tools/maf/maf_by_block_number.xml M tools/maf/maf_filter.xml M tools/maf/maf_limit_size.xml M tools/maf/maf_limit_to_species.xml M tools/maf/maf_reverse_complement.xml M tools/maf/maf_split_by_species.xml M tools/maf/maf_stats.xml M tools/maf/maf_thread_for_species.xml M tools/maf/maf_to_bed.xml M tools/maf/maf_to_fasta.xml M tools/maf/maf_to_interval.xml M tools/maf/vcf_to_maf_customtrack.xml M tools/metag_tools/shrimp_color_wrapper.xml M tools/metag_tools/shrimp_wrapper.xml M tools/next_gen_conversion/fastq_gen_conv.xml M tools/plotting/bar_chart.xml M tools/stats/aggregate_binned_scores_in_intervals.xml M tox.ini Log Message: ----------- Merge branch 'dev' into auto_tour_generation # Conflicts: # static/maps/mvc/tool/tool-form-base.js.map # static/maps/mvc/tool/tool-form.js.map # static/scripts/bundled/analysis.bundled.js # static/scripts/bundled/analysis.bundled.js.map # static/scripts/bundled/libs.bundled.js # static/scripts/bundled/libs.bundled.js.map # static/scripts/bundled/login.bundled.js # static/scripts/bundled/login.bundled.js.map # static/scripts/mvc/tool/tool-form-base.js # static/scripts/mvc/tool/tool-form.js Commit: a3037742cf0a6521651dad63b5c9c466d0031da4 https://github.com/galaxyproject/galaxy/commit/a3037742cf0a6521651dad63b5c9c... Author: Evgeny Anatskiy <evgeny.anatskiy@gmail.com> Date: 2017-04-08 (Sat, 08 Apr 2017) Changed paths: M config/plugins/webhooks/demo/tool_list/helper/__init__.py M config/plugins/webhooks/demo/tour_generator/static/script.js M static/maps/mvc/tool/tool-form-base.js.map M static/maps/mvc/tool/tool-form.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/tool/tool-form-base.js M static/scripts/mvc/tool/tool-form.js Log Message: ----------- bugfixes after the previous merge Commit: ebcb2627dfa920d0b491191a961374fb3d091248 https://github.com/galaxyproject/galaxy/commit/ebcb2627dfa920d0b491191a96137... Author: Evgeny Anatskiy <evgeny.anatskiy@gmail.com> Date: 2017-04-08 (Sat, 08 Apr 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/webhooks.js M static/maps/mvc/tool/tool-form-composite.js.map M static/maps/mvc/webhooks.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tool/tool-form-composite.js M static/scripts/mvc/webhooks.js Log Message: ----------- tiny changes Commit: ebf1f3903caeeae7e712666228c34958cbfc4094 https://github.com/galaxyproject/galaxy/commit/ebf1f3903caeeae7e712666228c34... Author: Evgeny Anatskiy <evgeny.anatskiy@gmail.com> Date: 2017-04-08 (Sat, 08 Apr 2017) Changed paths: M config/plugins/webhooks/demo/tour_generator/static/script.js M lib/galaxy/webapps/galaxy/api/webhooks.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- bugfixes and small improvements Commit: 934a26c195a983f64889bac6e25498ec16328e53 https://github.com/galaxyproject/galaxy/commit/934a26c195a983f64889bac6e2549... Author: Evgeny Anatskiy <evgeny.anatskiy@gmail.com> Date: 2017-04-20 (Thu, 20 Apr 2017) Changed paths: M client/galaxy/scripts/onload.js M config/plugins/webhooks/demo/tour_generator/helper/__init__.py M config/plugins/webhooks/demo/tour_generator/static/script.js M static/maps/onload.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.map M static/scripts/onload.js Log Message: ----------- improve the generator + bugfixes Commit: dc29a1a637c0274bceeb817ab64638a17464db6b https://github.com/galaxyproject/galaxy/commit/dc29a1a637c0274bceeb817ab6463... Author: Evgeny Anatskiy <evgeny.anatskiy@gmail.com> Date: 2017-04-20 (Thu, 20 Apr 2017) Changed paths: M config/plugins/webhooks/demo/tour_generator/helper/__init__.py M config/plugins/webhooks/demo/tour_generator/static/script.js Log Message: ----------- add support for the 'conditional' input type Commit: 68ab3cfcac72cb759fc7941624d5a8e6a9ddb23e https://github.com/galaxyproject/galaxy/commit/68ab3cfcac72cb759fc7941624d5a... Author: Evgeny Anatskiy <evgeny.anatskiy@gmail.com> Date: 2017-04-25 (Tue, 25 Apr 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/tool/tool-form.js M client/galaxy/scripts/mvc/webhooks.js M client/galaxy/scripts/onload.js M client/galaxy/scripts/utils/uploadbox.js M config/plugins/visualizations/charts/static/repository/utilities/jobs.js A config/plugins/webhooks/tour_generator/config/tour_generator.yml A config/plugins/webhooks/tour_generator/helper/__init__.py A config/plugins/webhooks/tour_generator/static/script.js A config/plugins/webhooks/tour_generator/static/styles.css M lib/galaxy/webapps/galaxy/api/webhooks.py M lib/galaxy/webapps/galaxy/buildapp.py M static/maps/mvc/webhooks.js.map M static/maps/onload.js.map M static/scripts/mvc/webhooks.js M static/scripts/onload.js M test/functional/webhooks/phdcomics/helper/__init__.py M test/functional/webhooks/trans_object/helper/__init__.py Log Message: ----------- upload tool's test data into the History panel Commit: bb2c467c379a2780578e44551d9a447259256437 https://github.com/galaxyproject/galaxy/commit/bb2c467c379a2780578e44551d9a4... Author: Evgeny Anatskiy <evgeny.anatskiy@gmail.com> Date: 2017-04-25 (Tue, 25 Apr 2017) Changed paths: M .gitignore A config/plugins/webhooks/demo/tour_generator/config/tour_generator.yml A config/plugins/webhooks/demo/tour_generator/helper/__init__.py A config/plugins/webhooks/demo/tour_generator/static/script.js A config/plugins/webhooks/demo/tour_generator/static/styles.css R config/plugins/webhooks/tour_generator/config/tour_generator.yml R config/plugins/webhooks/tour_generator/helper/__init__.py R config/plugins/webhooks/tour_generator/static/script.js R config/plugins/webhooks/tour_generator/static/styles.css Log Message: ----------- generate tool tours Commit: e9accf5459d0a311cec590dcdeb4f07533d3a9aa https://github.com/galaxyproject/galaxy/commit/e9accf5459d0a311cec590dcdeb4f... Author: Evgeny Anatskiy <evgeny.anatskiy@gmail.com> Date: 2017-04-25 (Tue, 25 Apr 2017) Changed paths: M config/plugins/webhooks/demo/tour_generator/helper/__init__.py M config/plugins/webhooks/demo/tour_generator/static/script.js Log Message: ----------- deal with different input types + bugfixes Commit: 5227e7b632ef3add1f8f0289c4caf6e926e53de6 https://github.com/galaxyproject/galaxy/commit/5227e7b632ef3add1f8f0289c4caf... Author: Evgeny Anatskiy <evgeny.anatskiy@gmail.com> Date: 2017-04-25 (Tue, 25 Apr 2017) Changed paths: M client/galaxy/scripts/onload.js M config/plugins/webhooks/demo/tour_generator/helper/__init__.py M config/plugins/webhooks/demo/tour_generator/static/script.js M static/maps/onload.js.map M static/scripts/onload.js Log Message: ----------- improve frontend script + bugfixes Commit: 31277edc6109aa97ab34ce6d851ade314b340dfa https://github.com/galaxyproject/galaxy/commit/31277edc6109aa97ab34ce6d851ad... Author: Evgeny Anatskiy <evgeny.anatskiy@gmail.com> Date: 2017-04-25 (Tue, 25 Apr 2017) Changed paths: M config/plugins/webhooks/demo/tool_list/helper/__init__.py M config/plugins/webhooks/demo/tour_generator/static/script.js M static/maps/mvc/tool/tool-form-base.js.map M static/maps/mvc/tool/tool-form.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/tool/tool-form-base.js M static/scripts/mvc/tool/tool-form.js Log Message: ----------- bugfixes after the previous merge Commit: e1f7875351c826bf503d00d6a43f3c415c601858 https://github.com/galaxyproject/galaxy/commit/e1f7875351c826bf503d00d6a43f3... Author: Evgeny Anatskiy <evgeny.anatskiy@gmail.com> Date: 2017-04-25 (Tue, 25 Apr 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/webhooks.js M static/maps/mvc/tool/tool-form-composite.js.map M static/maps/mvc/webhooks.js.map M static/scripts/mvc/tool/tool-form-composite.js M static/scripts/mvc/webhooks.js Log Message: ----------- tiny changes Commit: d6109ee1e81cb7b744309fca7cb7c0ef57ba6eb2 https://github.com/galaxyproject/galaxy/commit/d6109ee1e81cb7b744309fca7cb7c... Author: Evgeny Anatskiy <evgeny.anatskiy@gmail.com> Date: 2017-04-25 (Tue, 25 Apr 2017) Changed paths: M config/plugins/webhooks/demo/tour_generator/static/script.js M lib/galaxy/webapps/galaxy/api/webhooks.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- bugfixes and small improvements Commit: e64cff4647ec2806b9b548274c363b7d022b6730 https://github.com/galaxyproject/galaxy/commit/e64cff4647ec2806b9b548274c363... Author: Evgeny Anatskiy <evgeny.anatskiy@gmail.com> Date: 2017-04-25 (Tue, 25 Apr 2017) Changed paths: M client/galaxy/scripts/onload.js M config/plugins/webhooks/demo/tour_generator/helper/__init__.py M config/plugins/webhooks/demo/tour_generator/static/script.js M static/maps/onload.js.map M static/scripts/bundled/login.bundled.js.map M static/scripts/onload.js Log Message: ----------- improve the generator + bugfixes Commit: d253d7aa468bc9fe5d48ecea3be74059b9252300 https://github.com/galaxyproject/galaxy/commit/d253d7aa468bc9fe5d48ecea3be74... Author: Evgeny Anatskiy <evgeny.anatskiy@gmail.com> Date: 2017-04-25 (Tue, 25 Apr 2017) Changed paths: M config/plugins/webhooks/demo/tour_generator/helper/__init__.py M config/plugins/webhooks/demo/tour_generator/static/script.js Log Message: ----------- add support for the 'conditional' input type Commit: 65a31e0e5dd7efd7c69a434100ff7d93eabee91c https://github.com/galaxyproject/galaxy/commit/65a31e0e5dd7efd7c69a434100ff7... Author: Evgeny Anatskiy <evgeny.anatskiy@gmail.com> Date: 2017-04-25 (Tue, 25 Apr 2017) Changed paths: M config/plugins/webhooks/demo/tour_generator/helper/__init__.py M config/plugins/webhooks/demo/tour_generator/static/script.js M lib/galaxy/webapps/galaxy/api/webhooks.py Log Message: ----------- improve conditional input type message Commit: 17bb071721b83d63b3edf49ab1c509e4efb781ff https://github.com/galaxyproject/galaxy/commit/17bb071721b83d63b3edf49ab1c50... Author: Evgeny Anatskiy <evgeny.anatskiy@gmail.com> Date: 2017-04-25 (Tue, 25 Apr 2017) Changed paths: M client/galaxy/scripts/onload.js M config/plugins/webhooks/demo/tour_generator/helper/__init__.py M config/plugins/webhooks/demo/tour_generator/static/script.js M static/maps/onload.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/onload.js Log Message: ----------- improve and simplify the main script Commit: 19567f48b846219a48eceb8d1a58cd29a659d5ba https://github.com/galaxyproject/galaxy/commit/19567f48b846219a48eceb8d1a58c... Author: Evgeny Anatskiy <evgeny.anatskiy@gmail.com> Date: 2017-04-25 (Tue, 25 Apr 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/webhooks.py M static/scripts/bundled/login.bundled.js Log Message: ----------- make client Commit: 64e91ddb8f0baf7a63c015bb7438fe19bd40bc7d https://github.com/galaxyproject/galaxy/commit/64e91ddb8f0baf7a63c015bb7438f... Author: Evgeny Anatskiy <evgeny.anatskiy@gmail.com> Date: 2017-04-25 (Tue, 25 Apr 2017) Changed paths: 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 Log Message: ----------- make client Commit: ed4fa0425efc9b719e923f6d0959e8098fd9b8e7 https://github.com/galaxyproject/galaxy/commit/ed4fa0425efc9b719e923f6d0959e... Author: Evgeny Anatskiy <evgeny.anatskiy@gmail.com> Date: 2017-04-26 (Wed, 26 Apr 2017) Changed paths: M config/plugins/webhooks/demo/tour_generator/static/script.js Log Message: ----------- fix a bug when a tour coudn't be ended after executing a tool Commit: 47a5f17089b696208cb5f432ade866c1d953601d https://github.com/galaxyproject/galaxy/commit/47a5f17089b696208cb5f432ade86... Author: Evgeny Anatskiy <evgeny.anatskiy@gmail.com> Date: 2017-04-26 (Wed, 26 Apr 2017) Changed paths: M config/plugins/webhooks/demo/tour_generator/helper/__init__.py M config/plugins/webhooks/demo/tour_generator/static/script.js Log Message: ----------- many improvements - show warning messages (not errors) - upload test datasets with a correct type according to the tool's .xml file (no 'auto' detection) - add more checks to improve the overall stability - fix tour messages - other bugfixes Commit: 542e396ddf48a8d9159ee0aa1e5137f307a6b8f4 https://github.com/galaxyproject/galaxy/commit/542e396ddf48a8d9159ee0aa1e513... Author: Evgeny Anatskiy <evgeny.anatskiy@gmail.com> Date: 2017-04-26 (Wed, 26 Apr 2017) Changed paths: M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/onload.js M config/plugins/webhooks/demo/tour_generator/config/tour_generator.yml M static/maps/layout/menu.js.map M static/maps/mvc/tool/tool-form-base.js.map M static/maps/onload.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/menu.js M static/scripts/mvc/tool/tool-form-base.js M static/scripts/onload.js Log Message: ----------- introduce two new entry points: onload and tool-menu Commit: ce017c3fec9f1edd0d7858f408302b6962073657 https://github.com/galaxyproject/galaxy/commit/ce017c3fec9f1edd0d7858f408302... Author: Evgeny Anatskiy <evgeny.anatskiy@gmail.com> Date: 2017-05-01 (Mon, 01 May 2017) Changed paths: M config/plugins/webhooks/demo/tour_generator/helper/__init__.py M config/plugins/webhooks/demo/tour_generator/static/script.js Log Message: ----------- upload conditional test datasets Commit: c42941da04c94acec13598c8d6f8425c938ad548 https://github.com/galaxyproject/galaxy/commit/c42941da04c94acec13598c8d6f84... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-05-05 (Fri, 05 May 2017) Changed paths: M client/galaxy/scripts/onload.js M config/plugins/webhooks/demo/tour_generator/config/tour_generator.yml M config/plugins/webhooks/demo/tour_generator/static/script.js M static/maps/onload.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.map M static/scripts/onload.js M templates/js-app.mako Log Message: ----------- Remove global Toastr addition, allow external requires through standard js-app entrypoint. Commit: d90a30f5eaf57eb0e3a1ba370406f393a066f96d https://github.com/galaxyproject/galaxy/commit/d90a30f5eaf57eb0e3a1ba370406f... Author: Björn Grüning <bjoern@gruenings.eu> Date: 2017-05-05 (Fri, 05 May 2017) Changed paths: M client/galaxy/scripts/onload.js M config/plugins/webhooks/demo/tour_generator/config/tour_generator.yml M config/plugins/webhooks/demo/tour_generator/static/script.js M static/maps/onload.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.map M static/scripts/onload.js M templates/js-app.mako Log Message: ----------- Merge pull request #4 from dannon/auto_tour_generation Toastr Loading fixes. Commit: ef0809c2eb95fb9bd740718a287d6548ceea0f3a https://github.com/galaxyproject/galaxy/commit/ef0809c2eb95fb9bd740718a287d6... Author: Martin Cech <marten@bx.psu.edu> Date: 2017-05-05 (Fri, 05 May 2017) Changed paths: M client/galaxy/scripts/utils/uploadbox.js M config/plugins/visualizations/charts/static/repository/utilities/jobs.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.map Log Message: ----------- remove unnecessary whitespace fixes from otherwise untouched files Commit: 96d03c7c35eacb1d0e4bbf8675c51b3b429e53a1 https://github.com/galaxyproject/galaxy/commit/96d03c7c35eacb1d0e4bbf8675c51... Author: Evgeny Anatskiy <evgeny.anatskiy@gmail.com> Date: 2017-05-18 (Thu, 18 May 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/webhooks.js M config/plugins/webhooks/demo/tour_generator/config/tour_generator.yml M config/plugins/webhooks/demo/tour_generator/helper/__init__.py M config/plugins/webhooks/demo/tour_generator/static/script.js M static/maps/mvc/tool/tool-form-composite.js.map M static/maps/mvc/webhooks.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.map M static/scripts/mvc/tool/tool-form-composite.js M static/scripts/mvc/webhooks.js Log Message: ----------- pass tool version along with the id Commit: a8251fe656b3d7e1dabe98ad3fd2eff2cd2898d5 https://github.com/galaxyproject/galaxy/commit/a8251fe656b3d7e1dabe98ad3fd2e... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-06-13 (Tue, 13 Jun 2017) Changed paths: M .gitignore Log Message: ----------- Remove .idea and .vscode from .gitignore (these are editor specific files that contributors can add to their personal global .gitignores) Commit: d77962213872244daecc39ea6f9a1d130cce474b https://github.com/galaxyproject/galaxy/commit/d77962213872244daecc39ea6f9a1... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-06-14 (Wed, 14 Jun 2017) Changed paths: M .ci/flake8_lint_include_list.txt M .ci/flake8_wrapper_docstrings.sh M .ci/jenkins/selenium/run_tests.sh M .gitignore M .travis.yml M CITATION M CONTRIBUTORS.md M Makefile M README.rst A client/galaxy/scripts/admin.toolshed.js A client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/analysis.js R client/galaxy/scripts/apps/history-panel.js M client/galaxy/scripts/apps/login.js A client/galaxy/scripts/apps/panels/admin-panel.js A client/galaxy/scripts/apps/panels/history-panel.js A client/galaxy/scripts/apps/panels/tool-panel.js R client/galaxy/scripts/apps/tool-panel.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/layout/panel.js M client/galaxy/scripts/mvc/citation/citation-view.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-li.js M client/galaxy/scripts/mvc/dataset/dataset-model.js M client/galaxy/scripts/mvc/form/form-input.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/hda-li.js M client/galaxy/scripts/mvc/history/hdca-li.js M client/galaxy/scripts/mvc/library/library-folderlist-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/library/library-librarylist-view.js M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js A client/galaxy/scripts/mvc/page/page-list.js M client/galaxy/scripts/mvc/tag.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js A client/galaxy/scripts/mvc/toolshed/categories-view.js A client/galaxy/scripts/mvc/toolshed/repo-queue-view.js A client/galaxy/scripts/mvc/toolshed/repo-status-view.js A client/galaxy/scripts/mvc/toolshed/repositories-view.js A client/galaxy/scripts/mvc/toolshed/repository-queue-view.js A client/galaxy/scripts/mvc/toolshed/repository-view.js A client/galaxy/scripts/mvc/toolshed/shed-list-view.js A client/galaxy/scripts/mvc/toolshed/toolshed-model.js A client/galaxy/scripts/mvc/toolshed/util.js A client/galaxy/scripts/mvc/toolshed/workflows-view.js M client/galaxy/scripts/mvc/tours.js M client/galaxy/scripts/mvc/ui/ui-buttons.js M client/galaxy/scripts/mvc/ui/ui-select-content.js M client/galaxy/scripts/mvc/ui/ui-slider.js M client/galaxy/scripts/mvc/upload/collection/collection-view.js M client/galaxy/scripts/mvc/user/user-preferences.js A client/galaxy/scripts/mvc/workflow/workflow-configure-menu.js M client/galaxy/scripts/mvc/workflow/workflow-forms.js M client/galaxy/scripts/mvc/workflow/workflow-terminals.js A client/galaxy/scripts/mvc/workflow/workflow.js A client/galaxy/scripts/nls/de/locale.js A client/galaxy/scripts/nls/es/locale.js M client/galaxy/scripts/nls/fr/locale.js M client/galaxy/scripts/nls/locale.js M client/galaxy/scripts/viz/phyloviz.js M client/galaxy/style/less/base.less M client/galaxy/style/less/history.less M client/galaxy/style/less/ui.less M client/webpack.config.js M config/datatypes_conf.xml.sample M config/galaxy.ini.sample M config/job_conf.xml.sample_advanced M 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 M 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/static/js/rstudio.js M config/plugins/interactive_environments/rstudio/templates/rstudio.mako M config/plugins/tours/core.history.yaml M config/plugins/webhooks/demo/search/config/searchover.yaml M config/plugins/webhooks/demo/tool_list/config/tool_list.yml M contrib/galaxy.debian-init M contrib/galaxy_supervisor.conf M doc/Makefile R doc/patch.py M doc/source/admin/authentication.md M doc/source/admin/special_topics/mulled_containers.rst M doc/source/admin/special_topics/webhooks.rst R doc/source/api/api.rst R doc/source/api/ts_api.rst M doc/source/dev/build_a_job_runner.rst M doc/source/lib/galaxy.actions.rst M doc/source/lib/galaxy.auth.providers.rst M doc/source/lib/galaxy.auth.rst A doc/source/lib/galaxy.containers.rst M doc/source/lib/galaxy.dataset_collections.rst M doc/source/lib/galaxy.dataset_collections.types.rst M doc/source/lib/galaxy.datatypes.converters.rst M doc/source/lib/galaxy.datatypes.dataproviders.rst M doc/source/lib/galaxy.datatypes.display_applications.rst M doc/source/lib/galaxy.datatypes.rst M doc/source/lib/galaxy.datatypes.util.rst M doc/source/lib/galaxy.dependencies.rst M doc/source/lib/galaxy.eggs.rst M doc/source/lib/galaxy.exceptions.rst M doc/source/lib/galaxy.external_services.result_handlers.rst M doc/source/lib/galaxy.external_services.rst M doc/source/lib/galaxy.forms.rst M doc/source/lib/galaxy.jobs.actions.rst M doc/source/lib/galaxy.jobs.deferred.rst M doc/source/lib/galaxy.jobs.metrics.collectl.rst M doc/source/lib/galaxy.jobs.metrics.instrumenters.rst M doc/source/lib/galaxy.jobs.metrics.rst M doc/source/lib/galaxy.jobs.rst M doc/source/lib/galaxy.jobs.runners.rst M doc/source/lib/galaxy.jobs.runners.state_handlers.rst M doc/source/lib/galaxy.jobs.runners.util.cli.job.rst M doc/source/lib/galaxy.jobs.runners.util.cli.rst M doc/source/lib/galaxy.jobs.runners.util.cli.shell.rst M doc/source/lib/galaxy.jobs.runners.util.condor.rst A doc/source/lib/galaxy.jobs.runners.util.drmaa.rst M doc/source/lib/galaxy.jobs.runners.util.job_script.rst M doc/source/lib/galaxy.jobs.runners.util.rst M doc/source/lib/galaxy.jobs.splitters.rst M doc/source/lib/galaxy.managers.rst M doc/source/lib/galaxy.model.migrate.rst M doc/source/lib/galaxy.model.orm.rst M doc/source/lib/galaxy.model.rst M doc/source/lib/galaxy.model.tool_shed_install.migrate.rst M doc/source/lib/galaxy.model.tool_shed_install.rst M doc/source/lib/galaxy.objectstore.rst M doc/source/lib/galaxy.openid.rst M doc/source/lib/galaxy.quota.rst M doc/source/lib/galaxy.rst M doc/source/lib/galaxy.sample_tracking.rst M doc/source/lib/galaxy.security.rst R doc/source/lib/galaxy.tags.rst M doc/source/lib/galaxy.tools.actions.rst A doc/source/lib/galaxy.tools.cwl.rst M doc/source/lib/galaxy.tools.data.rst M doc/source/lib/galaxy.tools.data_manager.rst A doc/source/lib/galaxy.tools.deps.container_resolvers.rst A doc/source/lib/galaxy.tools.deps.mulled.rst M doc/source/lib/galaxy.tools.deps.resolvers.rst M doc/source/lib/galaxy.tools.deps.rst M doc/source/lib/galaxy.tools.filters.rst M doc/source/lib/galaxy.tools.imp_exp.rst M doc/source/lib/galaxy.tools.linters.rst A doc/source/lib/galaxy.tools.locations.rst M doc/source/lib/galaxy.tools.parameters.rst M doc/source/lib/galaxy.tools.parser.rst M doc/source/lib/galaxy.tools.rst M doc/source/lib/galaxy.tools.search.rst M doc/source/lib/galaxy.tools.toolbox.filters.rst M doc/source/lib/galaxy.tools.toolbox.lineages.rst M doc/source/lib/galaxy.tools.toolbox.rst M doc/source/lib/galaxy.tools.util.galaxyops.rst M doc/source/lib/galaxy.tools.util.rst A doc/source/lib/galaxy.tools.verify.asserts.rst A doc/source/lib/galaxy.tools.verify.rst A doc/source/lib/galaxy.tours.rst M doc/source/lib/galaxy.util.backports.rst M doc/source/lib/galaxy.util.log.rst M doc/source/lib/galaxy.util.pastescript.rst M doc/source/lib/galaxy.util.rst M doc/source/lib/galaxy.visualization.data_providers.phyloviz.rst M doc/source/lib/galaxy.visualization.data_providers.rst M doc/source/lib/galaxy.visualization.genome.rst M doc/source/lib/galaxy.visualization.plugins.rst M doc/source/lib/galaxy.visualization.rst M doc/source/lib/galaxy.visualization.tracks.rst M doc/source/lib/galaxy.web.base.controllers.rst M doc/source/lib/galaxy.web.base.rst M doc/source/lib/galaxy.web.framework.helpers.rst M doc/source/lib/galaxy.web.framework.middleware.rst M doc/source/lib/galaxy.web.framework.rst M doc/source/lib/galaxy.web.proxy.rst M doc/source/lib/galaxy.web.rst M doc/source/lib/galaxy.web.security.rst A doc/source/lib/galaxy.web.stack.rst A doc/source/lib/galaxy.webapps.galaxy.api.rst M doc/source/lib/galaxy.webapps.galaxy.controllers.rst M doc/source/lib/galaxy.webapps.galaxy.rst M doc/source/lib/galaxy.webapps.reports.controllers.rst M doc/source/lib/galaxy.webapps.reports.rst M doc/source/lib/galaxy.webapps.rst A doc/source/lib/galaxy.webapps.tool_shed.api.rst M doc/source/lib/galaxy.webapps.tool_shed.controllers.rst M doc/source/lib/galaxy.webapps.tool_shed.framework.middleware.rst M doc/source/lib/galaxy.webapps.tool_shed.framework.rst M doc/source/lib/galaxy.webapps.tool_shed.model.migrate.rst M doc/source/lib/galaxy.webapps.tool_shed.model.rst M doc/source/lib/galaxy.webapps.tool_shed.rst M doc/source/lib/galaxy.webapps.tool_shed.search.rst M doc/source/lib/galaxy.webapps.tool_shed.security.rst M doc/source/lib/galaxy.webapps.tool_shed.util.rst A doc/source/lib/galaxy.webhooks.rst M doc/source/lib/galaxy.work.rst M doc/source/lib/galaxy.workflow.rst M doc/source/lib/galaxy.workflow.schedulers.rst M doc/source/lib/galaxy_ext.metadata.rst M doc/source/lib/galaxy_ext.rst M doc/source/lib/log_tempfile.rst M doc/source/lib/psyco_full.rst M doc/source/lib/tool_shed.capsule.rst M doc/source/lib/tool_shed.dependencies.repository.rst M doc/source/lib/tool_shed.dependencies.rst M doc/source/lib/tool_shed.dependencies.tool.rst M doc/source/lib/tool_shed.galaxy_install.datatypes.rst M doc/source/lib/tool_shed.galaxy_install.grids.rst M doc/source/lib/tool_shed.galaxy_install.metadata.rst M doc/source/lib/tool_shed.galaxy_install.migrate.rst M doc/source/lib/tool_shed.galaxy_install.repository_dependencies.rst M doc/source/lib/tool_shed.galaxy_install.rst M doc/source/lib/tool_shed.galaxy_install.tool_dependencies.recipe.rst M doc/source/lib/tool_shed.galaxy_install.tool_dependencies.rst M doc/source/lib/tool_shed.galaxy_install.tools.rst M doc/source/lib/tool_shed.galaxy_install.utility_containers.rst M doc/source/lib/tool_shed.grids.rst M doc/source/lib/tool_shed.managers.rst M doc/source/lib/tool_shed.metadata.rst M doc/source/lib/tool_shed.repository_types.rst M doc/source/lib/tool_shed.rst M doc/source/lib/tool_shed.tools.rst M doc/source/lib/tool_shed.util.rst M doc/source/lib/tool_shed.utility_containers.rst M doc/source/releases/13.01_announce.rst M doc/source/releases/13.02_announce.rst M doc/source/releases/13.04_announce.rst M doc/source/releases/13.06_announce.rst M doc/source/releases/13.08_announce.rst M doc/source/releases/13.11_announce.rst M doc/source/releases/14.02_announce.rst M doc/source/releases/14.04_announce.rst M doc/source/releases/14.06_announce.rst M doc/source/releases/14.08_announce.rst M doc/source/releases/14.10_announce.rst M doc/source/releases/15.01_announce.rst M doc/source/releases/15.03_announce.rst M doc/source/releases/15.05.rst M doc/source/releases/15.05_announce.rst M doc/source/releases/15.07_announce.rst M doc/source/releases/15.10_announce.rst M doc/source/releases/16.01_announce.rst M doc/source/releases/16.04_announce.rst M doc/source/releases/16.07_announce.rst M doc/source/releases/16.10_announce.rst M doc/source/releases/17.01_announce.rst A doc/source/releases/17.05.rst M doc/source/releases/17.05_announce.rst A doc/source/releases/17.09_announce.rst M doc/source/releases/_thanks.rst M doc/source/releases/index.rst M doc/source/releases/older_releases.rst M doc/source/slideshow/architecture/galaxy_architecture.md M lib/galaxy/app.py M lib/galaxy/auth/__init__.py M lib/galaxy/config.py M lib/galaxy/containers/__init__.py M lib/galaxy/containers/docker_swarm.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/converters/cml_to_inchi_converter.xml M lib/galaxy/datatypes/converters/cml_to_mol2_converter.xml M lib/galaxy/datatypes/converters/cml_to_sdf_converter.xml M lib/galaxy/datatypes/converters/cml_to_smi_converter.xml M lib/galaxy/datatypes/converters/inchi_to_cml_converter.xml M lib/galaxy/datatypes/converters/inchi_to_mol2_converter.xml M lib/galaxy/datatypes/converters/inchi_to_mol_converter.xml M lib/galaxy/datatypes/converters/inchi_to_sdf_converter.xml M lib/galaxy/datatypes/converters/inchi_to_smi_converter.xml M lib/galaxy/datatypes/converters/mol2_to_cml_converter.xml M lib/galaxy/datatypes/converters/mol2_to_inchi_converter.xml M lib/galaxy/datatypes/converters/mol2_to_mol_converter.xml M lib/galaxy/datatypes/converters/mol2_to_sdf_converter.xml M lib/galaxy/datatypes/converters/mol2_to_smi_converter.xml M lib/galaxy/datatypes/converters/mol_to_cml_converter.xml M lib/galaxy/datatypes/converters/mol_to_inchi_converter.xml M lib/galaxy/datatypes/converters/mol_to_mol2_converter.xml M lib/galaxy/datatypes/converters/mol_to_smi_converter.xml M lib/galaxy/datatypes/converters/sdf_to_cml_converter.xml M lib/galaxy/datatypes/converters/sdf_to_inchi_converter.xml M lib/galaxy/datatypes/converters/sdf_to_mol2_converter.xml M lib/galaxy/datatypes/converters/sdf_to_smi_converter.xml M lib/galaxy/datatypes/converters/smi_to_cml_converter.xml M lib/galaxy/datatypes/converters/smi_to_inchi_converter.xml M lib/galaxy/datatypes/converters/smi_to_mol2_converter.xml M lib/galaxy/datatypes/converters/smi_to_mol_converter.xml M lib/galaxy/datatypes/converters/smi_to_sdf_converter.xml M lib/galaxy/datatypes/converters/smi_to_smi_converter.xml M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/dataproviders/hierarchy.py A lib/galaxy/datatypes/plant_tribes.py M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/text.py M lib/galaxy/dependencies/dev-requirements.txt M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/actions/post.py M lib/galaxy/jobs/rule_helper.py M lib/galaxy/jobs/runners/__init__.py A lib/galaxy/jobs/runners/chronos.py M lib/galaxy/jobs/runners/condor.py M lib/galaxy/jobs/runners/drmaa.py M lib/galaxy/jobs/runners/kubernetes.py M lib/galaxy/managers/collections.py M lib/galaxy/managers/collections_util.py M lib/galaxy/managers/configuration.py M lib/galaxy/managers/datasets.py M lib/galaxy/model/__init__.py M lib/galaxy/objectstore/azure_blob.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/model_operations.py A lib/galaxy/tools/cache.py M lib/galaxy/tools/data/__init__.py M lib/galaxy/tools/data_manager/manager.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/container_resolvers/explicit.py M lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/tools/deps/containers.py M lib/galaxy/tools/deps/docker_util.py M lib/galaxy/tools/deps/installable.py M lib/galaxy/tools/deps/mulled/invfile.lua M lib/galaxy/tools/deps/mulled/mulled_build.py M lib/galaxy/tools/deps/mulled/mulled_build_channel.py M lib/galaxy/tools/deps/mulled/mulled_build_files.py M lib/galaxy/tools/deps/mulled/mulled_search.py M lib/galaxy/tools/deps/mulled/util.py M lib/galaxy/tools/deps/resolvers/conda.py A lib/galaxy/tools/deps/singularity_util.py M lib/galaxy/tools/execute.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/parameters/validation.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/search/__init__.py M lib/galaxy/tools/toolbox/base.py R lib/galaxy/tools/toolbox/cache.py M lib/galaxy/tools/toolbox/lineages/tool_shed.py M lib/galaxy/tools/toolbox/parser.py M lib/galaxy/tools/xsd/README.md M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/util/__init__.py M lib/galaxy/util/compression_utils.py M lib/galaxy/util/plugin_config.py M lib/galaxy/version.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/framework/helpers/grids.py M lib/galaxy/web/framework/middleware/graphite.py M lib/galaxy/web/framework/middleware/remoteuser.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/web/proxy/js/package.json M lib/galaxy/webapps/galaxy/api/history_contents.py M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py A lib/galaxy/webapps/galaxy/api/toolshed.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/dataset.py M lib/galaxy/webapps/galaxy/controllers/page.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/webapps/reports/config.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/tools.py M lib/galaxy/webapps/tool_shed/buildapp.py M lib/galaxy/webapps/tool_shed/config.py M lib/tool_shed/galaxy_install/datatypes/custom_datatype_manager.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/tool_dependencies/env_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.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/metadata/metadata_generator.py M lib/tool_shed/util/repository_util.py M lib/tool_shed/util/tool_dependency_util.py M lib/tool_shed/util/tool_util.py M run_tests.sh M scripts/bootstrap_history.py M setup.cfg A static/maps/admin.toolshed.js.map M static/maps/layout/menu.js.map M static/maps/layout/page.js.map M static/maps/layout/panel.js.map M static/maps/mvc/citation/citation-view.js.map M static/maps/mvc/collection/collection-model.js.map M static/maps/mvc/collection/collection-view.js.map M static/maps/mvc/dataset/dataset-li.js.map M static/maps/mvc/dataset/dataset-model.js.map M static/maps/mvc/form/form-input.js.map M static/maps/mvc/grid/grid-template.js.map M static/maps/mvc/grid/grid-view.js.map M static/maps/mvc/history/hda-li.js.map M static/maps/mvc/history/hdca-li.js.map M static/maps/mvc/library/library-folderlist-view.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/maps/mvc/library/library-librarylist-view.js.map M static/maps/mvc/library/library-librarytoolbar-view.js.map A static/maps/mvc/page/page-list.js.map M static/maps/mvc/tag.js.map M static/maps/mvc/tool/tool-form-base.js.map M static/maps/mvc/tool/tool-form-composite.js.map A static/maps/mvc/toolshed/categories-view.js.map A static/maps/mvc/toolshed/repo-queue-view.js.map A static/maps/mvc/toolshed/repo-status-view.js.map A static/maps/mvc/toolshed/repositories-view.js.map A static/maps/mvc/toolshed/repository-queue-view.js.map A static/maps/mvc/toolshed/repository-view.js.map A static/maps/mvc/toolshed/shed-category-view.js.map A static/maps/mvc/toolshed/shed-list-view.js.map A static/maps/mvc/toolshed/shed-repo-details-view.js.map A static/maps/mvc/toolshed/shed-repo-list-view.js.map A static/maps/mvc/toolshed/sheds-list-view.js.map A static/maps/mvc/toolshed/toolshed-model.js.map A static/maps/mvc/toolshed/util.js.map A static/maps/mvc/toolshed/workflows-view.js.map M static/maps/mvc/tours.js.map M static/maps/mvc/ui/ui-buttons.js.map M static/maps/mvc/ui/ui-select-content.js.map M static/maps/mvc/ui/ui-slider.js.map M static/maps/mvc/upload/collection/collection-view.js.map M static/maps/mvc/user/user-preferences.js.map A static/maps/mvc/workflow/workflow-configure-menu.js.map M static/maps/mvc/workflow/workflow-forms.js.map M static/maps/mvc/workflow/workflow-terminals.js.map A static/maps/mvc/workflow/workflow.js.map A static/maps/nls/de/locale.js.map A static/maps/nls/es/locale.js.map M static/maps/nls/fr/locale.js.map M static/maps/nls/locale.js.map M static/maps/viz/phyloviz.js.map A static/scripts/admin.toolshed.js A static/scripts/bundled/admin.bundled.js A 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/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/panel.js M static/scripts/mvc/citation/citation-view.js M static/scripts/mvc/collection/collection-model.js M static/scripts/mvc/collection/collection-view.js M static/scripts/mvc/dataset/dataset-li.js M static/scripts/mvc/dataset/dataset-model.js M static/scripts/mvc/form/form-input.js M static/scripts/mvc/grid/grid-template.js M static/scripts/mvc/grid/grid-view.js M static/scripts/mvc/history/hda-li.js M static/scripts/mvc/history/hdca-li.js M static/scripts/mvc/library/library-folderlist-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/library/library-librarylist-view.js M static/scripts/mvc/library/library-librarytoolbar-view.js A static/scripts/mvc/page/page-list.js M static/scripts/mvc/tag.js M static/scripts/mvc/tool/tool-form-base.js M static/scripts/mvc/tool/tool-form-composite.js A static/scripts/mvc/toolshed/categories-view.js A static/scripts/mvc/toolshed/repo-queue-view.js A static/scripts/mvc/toolshed/repo-status-view.js A static/scripts/mvc/toolshed/repositories-view.js A static/scripts/mvc/toolshed/repository-queue-view.js A static/scripts/mvc/toolshed/repository-view.js A static/scripts/mvc/toolshed/shed-category-view.js A static/scripts/mvc/toolshed/shed-list-view.js A static/scripts/mvc/toolshed/shed-repo-details-view.js A static/scripts/mvc/toolshed/shed-repo-list-view.js A static/scripts/mvc/toolshed/sheds-list-view.js A static/scripts/mvc/toolshed/toolshed-model.js A static/scripts/mvc/toolshed/util.js A static/scripts/mvc/toolshed/workflows-view.js M static/scripts/mvc/tours.js M static/scripts/mvc/ui/ui-buttons.js M static/scripts/mvc/ui/ui-select-content.js M static/scripts/mvc/ui/ui-slider.js M static/scripts/mvc/upload/collection/collection-view.js M static/scripts/mvc/user/user-preferences.js A static/scripts/mvc/workflow/workflow-configure-menu.js M static/scripts/mvc/workflow/workflow-forms.js M static/scripts/mvc/workflow/workflow-terminals.js A static/scripts/mvc/workflow/workflow.js A static/scripts/nls/de/locale.js A static/scripts/nls/es/locale.js M static/scripts/nls/fr/locale.js M static/scripts/nls/locale.js M static/scripts/viz/phyloviz.js M static/style/blue/base.css M static/welcome.html.sample R templates/admin/tool_shed_repository/browse_toolsheds.mako M templates/admin/tool_shed_repository/select_tool_panel_section.mako M templates/grid_base.mako M templates/sharing_base.mako M templates/show_params.mako M templates/user/index.mako M templates/webapps/galaxy/admin/center.mako R templates/webapps/galaxy/admin/index.mako M templates/webapps/galaxy/data_manager/index.mako R templates/webapps/galaxy/dataset/grid.mako M templates/webapps/galaxy/galaxy.masthead.mako M templates/webapps/galaxy/page/editor.mako R templates/webapps/galaxy/page/index.mako R templates/webapps/galaxy/page/list_published.mako R templates/webapps/galaxy/workflow/configure_menu.mako R templates/webapps/galaxy/workflow/list.mako R templates/webapps/galaxy/workflow/list_for_run.mako M templates/webapps/tool_shed/base_panels.mako M test/api/test_dataset_collections.py M test/api/test_jobs.py M test/api/test_workflows.py M test/base/driver_util.py M test/base/populators.py A test/functional/tools/collection_creates_dynamic_nested_fail.xml A test/functional/tools/collection_creates_list_fail.xml A test/functional/tools/mulled_example_multi_versionless.xml M test/functional/tools/sample_datatypes_conf.xml M test/functional/tools/samples_tool_conf.xml M test/functional/webhooks/trans_object/config/trans_object.yaml M test/galaxy_selenium/navigates_galaxy.py M test/qunit/test-data/bootstrapped.js M test/qunit/tests/form_tests.js M test/qunit/tests/galaxy-app-base.js M test/qunit/tests/page_tests.js M test/qunit/tests/ui_tests.html M test/qunit/tests/ui_tests.js M test/selenium_tests/framework.py M test/selenium_tests/test_history_sharing.py M test/selenium_tests/test_login.py M test/selenium_tests/test_registration.py M test/selenium_tests/test_tool_form.py M test/selenium_tests/test_workflow_management.py M test/selenium_tests/test_workflow_run.py A test/unit/jobs/conditional_runners_job_conf.xml M test/unit/jobs/test_job_configuration.py M test/unit/tools/test_toolbox.py M tools/data_source/upload.py M tox.ini Log Message: ----------- Merge with current dev. Commit: 26f214257337c4546b9783bda8df9ac7e15b4444 https://github.com/galaxyproject/galaxy/commit/26f214257337c4546b9783bda8df9... Author: Björn Grüning <bjoern@gruenings.eu> Date: 2017-06-14 (Wed, 14 Jun 2017) Changed paths: M .ci/flake8_lint_include_list.txt M .ci/flake8_wrapper_docstrings.sh M .ci/jenkins/selenium/run_tests.sh M .gitignore M .travis.yml M CITATION M CONTRIBUTORS.md M Makefile M README.rst A client/galaxy/scripts/admin.toolshed.js A client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/analysis.js R client/galaxy/scripts/apps/history-panel.js M client/galaxy/scripts/apps/login.js A client/galaxy/scripts/apps/panels/admin-panel.js A client/galaxy/scripts/apps/panels/history-panel.js A client/galaxy/scripts/apps/panels/tool-panel.js R client/galaxy/scripts/apps/tool-panel.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/layout/panel.js M client/galaxy/scripts/mvc/citation/citation-view.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-li.js M client/galaxy/scripts/mvc/dataset/dataset-model.js M client/galaxy/scripts/mvc/form/form-input.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/hda-li.js M client/galaxy/scripts/mvc/history/hdca-li.js M client/galaxy/scripts/mvc/library/library-folderlist-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/library/library-librarylist-view.js M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js A client/galaxy/scripts/mvc/page/page-list.js M client/galaxy/scripts/mvc/tag.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js A client/galaxy/scripts/mvc/toolshed/categories-view.js A client/galaxy/scripts/mvc/toolshed/repo-queue-view.js A client/galaxy/scripts/mvc/toolshed/repo-status-view.js A client/galaxy/scripts/mvc/toolshed/repositories-view.js A client/galaxy/scripts/mvc/toolshed/repository-queue-view.js A client/galaxy/scripts/mvc/toolshed/repository-view.js A client/galaxy/scripts/mvc/toolshed/shed-list-view.js A client/galaxy/scripts/mvc/toolshed/toolshed-model.js A client/galaxy/scripts/mvc/toolshed/util.js A client/galaxy/scripts/mvc/toolshed/workflows-view.js M client/galaxy/scripts/mvc/tours.js M client/galaxy/scripts/mvc/ui/ui-buttons.js M client/galaxy/scripts/mvc/ui/ui-select-content.js M client/galaxy/scripts/mvc/ui/ui-slider.js M client/galaxy/scripts/mvc/upload/collection/collection-view.js M client/galaxy/scripts/mvc/user/user-preferences.js A client/galaxy/scripts/mvc/workflow/workflow-configure-menu.js M client/galaxy/scripts/mvc/workflow/workflow-forms.js M client/galaxy/scripts/mvc/workflow/workflow-terminals.js A client/galaxy/scripts/mvc/workflow/workflow.js A client/galaxy/scripts/nls/de/locale.js A client/galaxy/scripts/nls/es/locale.js M client/galaxy/scripts/nls/fr/locale.js M client/galaxy/scripts/nls/locale.js M client/galaxy/scripts/viz/phyloviz.js M client/galaxy/style/less/base.less M client/galaxy/style/less/history.less M client/galaxy/style/less/ui.less M client/webpack.config.js M config/datatypes_conf.xml.sample M config/galaxy.ini.sample M config/job_conf.xml.sample_advanced M 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 M 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/static/js/rstudio.js M config/plugins/interactive_environments/rstudio/templates/rstudio.mako M config/plugins/tours/core.history.yaml M config/plugins/webhooks/demo/search/config/searchover.yaml M config/plugins/webhooks/demo/tool_list/config/tool_list.yml M contrib/galaxy.debian-init M contrib/galaxy_supervisor.conf M doc/Makefile R doc/patch.py M doc/source/admin/authentication.md M doc/source/admin/special_topics/mulled_containers.rst M doc/source/admin/special_topics/webhooks.rst R doc/source/api/api.rst R doc/source/api/ts_api.rst M doc/source/dev/build_a_job_runner.rst M doc/source/lib/galaxy.actions.rst M doc/source/lib/galaxy.auth.providers.rst M doc/source/lib/galaxy.auth.rst A doc/source/lib/galaxy.containers.rst M doc/source/lib/galaxy.dataset_collections.rst M doc/source/lib/galaxy.dataset_collections.types.rst M doc/source/lib/galaxy.datatypes.converters.rst M doc/source/lib/galaxy.datatypes.dataproviders.rst M doc/source/lib/galaxy.datatypes.display_applications.rst M doc/source/lib/galaxy.datatypes.rst M doc/source/lib/galaxy.datatypes.util.rst M doc/source/lib/galaxy.dependencies.rst M doc/source/lib/galaxy.eggs.rst M doc/source/lib/galaxy.exceptions.rst M doc/source/lib/galaxy.external_services.result_handlers.rst M doc/source/lib/galaxy.external_services.rst M doc/source/lib/galaxy.forms.rst M doc/source/lib/galaxy.jobs.actions.rst M doc/source/lib/galaxy.jobs.deferred.rst M doc/source/lib/galaxy.jobs.metrics.collectl.rst M doc/source/lib/galaxy.jobs.metrics.instrumenters.rst M doc/source/lib/galaxy.jobs.metrics.rst M doc/source/lib/galaxy.jobs.rst M doc/source/lib/galaxy.jobs.runners.rst M doc/source/lib/galaxy.jobs.runners.state_handlers.rst M doc/source/lib/galaxy.jobs.runners.util.cli.job.rst M doc/source/lib/galaxy.jobs.runners.util.cli.rst M doc/source/lib/galaxy.jobs.runners.util.cli.shell.rst M doc/source/lib/galaxy.jobs.runners.util.condor.rst A doc/source/lib/galaxy.jobs.runners.util.drmaa.rst M doc/source/lib/galaxy.jobs.runners.util.job_script.rst M doc/source/lib/galaxy.jobs.runners.util.rst M doc/source/lib/galaxy.jobs.splitters.rst M doc/source/lib/galaxy.managers.rst M doc/source/lib/galaxy.model.migrate.rst M doc/source/lib/galaxy.model.orm.rst M doc/source/lib/galaxy.model.rst M doc/source/lib/galaxy.model.tool_shed_install.migrate.rst M doc/source/lib/galaxy.model.tool_shed_install.rst M doc/source/lib/galaxy.objectstore.rst M doc/source/lib/galaxy.openid.rst M doc/source/lib/galaxy.quota.rst M doc/source/lib/galaxy.rst M doc/source/lib/galaxy.sample_tracking.rst M doc/source/lib/galaxy.security.rst R doc/source/lib/galaxy.tags.rst M doc/source/lib/galaxy.tools.actions.rst A doc/source/lib/galaxy.tools.cwl.rst M doc/source/lib/galaxy.tools.data.rst M doc/source/lib/galaxy.tools.data_manager.rst A doc/source/lib/galaxy.tools.deps.container_resolvers.rst A doc/source/lib/galaxy.tools.deps.mulled.rst M doc/source/lib/galaxy.tools.deps.resolvers.rst M doc/source/lib/galaxy.tools.deps.rst M doc/source/lib/galaxy.tools.filters.rst M doc/source/lib/galaxy.tools.imp_exp.rst M doc/source/lib/galaxy.tools.linters.rst A doc/source/lib/galaxy.tools.locations.rst M doc/source/lib/galaxy.tools.parameters.rst M doc/source/lib/galaxy.tools.parser.rst M doc/source/lib/galaxy.tools.rst M doc/source/lib/galaxy.tools.search.rst M doc/source/lib/galaxy.tools.toolbox.filters.rst M doc/source/lib/galaxy.tools.toolbox.lineages.rst M doc/source/lib/galaxy.tools.toolbox.rst M doc/source/lib/galaxy.tools.util.galaxyops.rst M doc/source/lib/galaxy.tools.util.rst A doc/source/lib/galaxy.tools.verify.asserts.rst A doc/source/lib/galaxy.tools.verify.rst A doc/source/lib/galaxy.tours.rst M doc/source/lib/galaxy.util.backports.rst M doc/source/lib/galaxy.util.log.rst M doc/source/lib/galaxy.util.pastescript.rst M doc/source/lib/galaxy.util.rst M doc/source/lib/galaxy.visualization.data_providers.phyloviz.rst M doc/source/lib/galaxy.visualization.data_providers.rst M doc/source/lib/galaxy.visualization.genome.rst M doc/source/lib/galaxy.visualization.plugins.rst M doc/source/lib/galaxy.visualization.rst M doc/source/lib/galaxy.visualization.tracks.rst M doc/source/lib/galaxy.web.base.controllers.rst M doc/source/lib/galaxy.web.base.rst M doc/source/lib/galaxy.web.framework.helpers.rst M doc/source/lib/galaxy.web.framework.middleware.rst M doc/source/lib/galaxy.web.framework.rst M doc/source/lib/galaxy.web.proxy.rst M doc/source/lib/galaxy.web.rst M doc/source/lib/galaxy.web.security.rst A doc/source/lib/galaxy.web.stack.rst A doc/source/lib/galaxy.webapps.galaxy.api.rst M doc/source/lib/galaxy.webapps.galaxy.controllers.rst M doc/source/lib/galaxy.webapps.galaxy.rst M doc/source/lib/galaxy.webapps.reports.controllers.rst M doc/source/lib/galaxy.webapps.reports.rst M doc/source/lib/galaxy.webapps.rst A doc/source/lib/galaxy.webapps.tool_shed.api.rst M doc/source/lib/galaxy.webapps.tool_shed.controllers.rst M doc/source/lib/galaxy.webapps.tool_shed.framework.middleware.rst M doc/source/lib/galaxy.webapps.tool_shed.framework.rst M doc/source/lib/galaxy.webapps.tool_shed.model.migrate.rst M doc/source/lib/galaxy.webapps.tool_shed.model.rst M doc/source/lib/galaxy.webapps.tool_shed.rst M doc/source/lib/galaxy.webapps.tool_shed.search.rst M doc/source/lib/galaxy.webapps.tool_shed.security.rst M doc/source/lib/galaxy.webapps.tool_shed.util.rst A doc/source/lib/galaxy.webhooks.rst M doc/source/lib/galaxy.work.rst M doc/source/lib/galaxy.workflow.rst M doc/source/lib/galaxy.workflow.schedulers.rst M doc/source/lib/galaxy_ext.metadata.rst M doc/source/lib/galaxy_ext.rst M doc/source/lib/log_tempfile.rst M doc/source/lib/psyco_full.rst M doc/source/lib/tool_shed.capsule.rst M doc/source/lib/tool_shed.dependencies.repository.rst M doc/source/lib/tool_shed.dependencies.rst M doc/source/lib/tool_shed.dependencies.tool.rst M doc/source/lib/tool_shed.galaxy_install.datatypes.rst M doc/source/lib/tool_shed.galaxy_install.grids.rst M doc/source/lib/tool_shed.galaxy_install.metadata.rst M doc/source/lib/tool_shed.galaxy_install.migrate.rst M doc/source/lib/tool_shed.galaxy_install.repository_dependencies.rst M doc/source/lib/tool_shed.galaxy_install.rst M doc/source/lib/tool_shed.galaxy_install.tool_dependencies.recipe.rst M doc/source/lib/tool_shed.galaxy_install.tool_dependencies.rst M doc/source/lib/tool_shed.galaxy_install.tools.rst M doc/source/lib/tool_shed.galaxy_install.utility_containers.rst M doc/source/lib/tool_shed.grids.rst M doc/source/lib/tool_shed.managers.rst M doc/source/lib/tool_shed.metadata.rst M doc/source/lib/tool_shed.repository_types.rst M doc/source/lib/tool_shed.rst M doc/source/lib/tool_shed.tools.rst M doc/source/lib/tool_shed.util.rst M doc/source/lib/tool_shed.utility_containers.rst M doc/source/releases/13.01_announce.rst M doc/source/releases/13.02_announce.rst M doc/source/releases/13.04_announce.rst M doc/source/releases/13.06_announce.rst M doc/source/releases/13.08_announce.rst M doc/source/releases/13.11_announce.rst M doc/source/releases/14.02_announce.rst M doc/source/releases/14.04_announce.rst M doc/source/releases/14.06_announce.rst M doc/source/releases/14.08_announce.rst M doc/source/releases/14.10_announce.rst M doc/source/releases/15.01_announce.rst M doc/source/releases/15.03_announce.rst M doc/source/releases/15.05.rst M doc/source/releases/15.05_announce.rst M doc/source/releases/15.07_announce.rst M doc/source/releases/15.10_announce.rst M doc/source/releases/16.01_announce.rst M doc/source/releases/16.04_announce.rst M doc/source/releases/16.07_announce.rst M doc/source/releases/16.10_announce.rst M doc/source/releases/17.01_announce.rst A doc/source/releases/17.05.rst M doc/source/releases/17.05_announce.rst A doc/source/releases/17.09_announce.rst M doc/source/releases/_thanks.rst M doc/source/releases/index.rst M doc/source/releases/older_releases.rst M doc/source/slideshow/architecture/galaxy_architecture.md M lib/galaxy/app.py M lib/galaxy/auth/__init__.py M lib/galaxy/config.py M lib/galaxy/containers/__init__.py M lib/galaxy/containers/docker_swarm.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/converters/cml_to_inchi_converter.xml M lib/galaxy/datatypes/converters/cml_to_mol2_converter.xml M lib/galaxy/datatypes/converters/cml_to_sdf_converter.xml M lib/galaxy/datatypes/converters/cml_to_smi_converter.xml M lib/galaxy/datatypes/converters/inchi_to_cml_converter.xml M lib/galaxy/datatypes/converters/inchi_to_mol2_converter.xml M lib/galaxy/datatypes/converters/inchi_to_mol_converter.xml M lib/galaxy/datatypes/converters/inchi_to_sdf_converter.xml M lib/galaxy/datatypes/converters/inchi_to_smi_converter.xml M lib/galaxy/datatypes/converters/mol2_to_cml_converter.xml M lib/galaxy/datatypes/converters/mol2_to_inchi_converter.xml M lib/galaxy/datatypes/converters/mol2_to_mol_converter.xml M lib/galaxy/datatypes/converters/mol2_to_sdf_converter.xml M lib/galaxy/datatypes/converters/mol2_to_smi_converter.xml M lib/galaxy/datatypes/converters/mol_to_cml_converter.xml M lib/galaxy/datatypes/converters/mol_to_inchi_converter.xml M lib/galaxy/datatypes/converters/mol_to_mol2_converter.xml M lib/galaxy/datatypes/converters/mol_to_smi_converter.xml M lib/galaxy/datatypes/converters/sdf_to_cml_converter.xml M lib/galaxy/datatypes/converters/sdf_to_inchi_converter.xml M lib/galaxy/datatypes/converters/sdf_to_mol2_converter.xml M lib/galaxy/datatypes/converters/sdf_to_smi_converter.xml M lib/galaxy/datatypes/converters/smi_to_cml_converter.xml M lib/galaxy/datatypes/converters/smi_to_inchi_converter.xml M lib/galaxy/datatypes/converters/smi_to_mol2_converter.xml M lib/galaxy/datatypes/converters/smi_to_mol_converter.xml M lib/galaxy/datatypes/converters/smi_to_sdf_converter.xml M lib/galaxy/datatypes/converters/smi_to_smi_converter.xml M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/dataproviders/hierarchy.py A lib/galaxy/datatypes/plant_tribes.py M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/text.py M lib/galaxy/dependencies/dev-requirements.txt M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/actions/post.py M lib/galaxy/jobs/rule_helper.py M lib/galaxy/jobs/runners/__init__.py A lib/galaxy/jobs/runners/chronos.py M lib/galaxy/jobs/runners/condor.py M lib/galaxy/jobs/runners/drmaa.py M lib/galaxy/jobs/runners/kubernetes.py M lib/galaxy/managers/collections.py M lib/galaxy/managers/collections_util.py M lib/galaxy/managers/configuration.py M lib/galaxy/managers/datasets.py M lib/galaxy/model/__init__.py M lib/galaxy/objectstore/azure_blob.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/model_operations.py A lib/galaxy/tools/cache.py M lib/galaxy/tools/data/__init__.py M lib/galaxy/tools/data_manager/manager.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/container_resolvers/explicit.py M lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/tools/deps/containers.py M lib/galaxy/tools/deps/docker_util.py M lib/galaxy/tools/deps/installable.py M lib/galaxy/tools/deps/mulled/invfile.lua M lib/galaxy/tools/deps/mulled/mulled_build.py M lib/galaxy/tools/deps/mulled/mulled_build_channel.py M lib/galaxy/tools/deps/mulled/mulled_build_files.py M lib/galaxy/tools/deps/mulled/mulled_search.py M lib/galaxy/tools/deps/mulled/util.py M lib/galaxy/tools/deps/resolvers/conda.py A lib/galaxy/tools/deps/singularity_util.py M lib/galaxy/tools/execute.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/parameters/validation.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/search/__init__.py M lib/galaxy/tools/toolbox/base.py R lib/galaxy/tools/toolbox/cache.py M lib/galaxy/tools/toolbox/lineages/tool_shed.py M lib/galaxy/tools/toolbox/parser.py M lib/galaxy/tools/xsd/README.md M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/util/__init__.py M lib/galaxy/util/compression_utils.py M lib/galaxy/util/plugin_config.py M lib/galaxy/version.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/framework/helpers/grids.py M lib/galaxy/web/framework/middleware/graphite.py M lib/galaxy/web/framework/middleware/remoteuser.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/web/proxy/js/package.json M lib/galaxy/webapps/galaxy/api/history_contents.py M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py A lib/galaxy/webapps/galaxy/api/toolshed.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/dataset.py M lib/galaxy/webapps/galaxy/controllers/page.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/webapps/reports/config.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/tools.py M lib/galaxy/webapps/tool_shed/buildapp.py M lib/galaxy/webapps/tool_shed/config.py M lib/tool_shed/galaxy_install/datatypes/custom_datatype_manager.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/tool_dependencies/env_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.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/metadata/metadata_generator.py M lib/tool_shed/util/repository_util.py M lib/tool_shed/util/tool_dependency_util.py M lib/tool_shed/util/tool_util.py M run_tests.sh M scripts/bootstrap_history.py M setup.cfg A static/maps/admin.toolshed.js.map M static/maps/layout/menu.js.map M static/maps/layout/page.js.map M static/maps/layout/panel.js.map M static/maps/mvc/citation/citation-view.js.map M static/maps/mvc/collection/collection-model.js.map M static/maps/mvc/collection/collection-view.js.map M static/maps/mvc/dataset/dataset-li.js.map M static/maps/mvc/dataset/dataset-model.js.map M static/maps/mvc/form/form-input.js.map M static/maps/mvc/grid/grid-template.js.map M static/maps/mvc/grid/grid-view.js.map M static/maps/mvc/history/hda-li.js.map M static/maps/mvc/history/hdca-li.js.map M static/maps/mvc/library/library-folderlist-view.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/maps/mvc/library/library-librarylist-view.js.map M static/maps/mvc/library/library-librarytoolbar-view.js.map A static/maps/mvc/page/page-list.js.map M static/maps/mvc/tag.js.map M static/maps/mvc/tool/tool-form-base.js.map M static/maps/mvc/tool/tool-form-composite.js.map A static/maps/mvc/toolshed/categories-view.js.map A static/maps/mvc/toolshed/repo-queue-view.js.map A static/maps/mvc/toolshed/repo-status-view.js.map A static/maps/mvc/toolshed/repositories-view.js.map A static/maps/mvc/toolshed/repository-queue-view.js.map A static/maps/mvc/toolshed/repository-view.js.map A static/maps/mvc/toolshed/shed-category-view.js.map A static/maps/mvc/toolshed/shed-list-view.js.map A static/maps/mvc/toolshed/shed-repo-details-view.js.map A static/maps/mvc/toolshed/shed-repo-list-view.js.map A static/maps/mvc/toolshed/sheds-list-view.js.map A static/maps/mvc/toolshed/toolshed-model.js.map A static/maps/mvc/toolshed/util.js.map A static/maps/mvc/toolshed/workflows-view.js.map M static/maps/mvc/tours.js.map M static/maps/mvc/ui/ui-buttons.js.map M static/maps/mvc/ui/ui-select-content.js.map M static/maps/mvc/ui/ui-slider.js.map M static/maps/mvc/upload/collection/collection-view.js.map M static/maps/mvc/user/user-preferences.js.map A static/maps/mvc/workflow/workflow-configure-menu.js.map M static/maps/mvc/workflow/workflow-forms.js.map M static/maps/mvc/workflow/workflow-terminals.js.map A static/maps/mvc/workflow/workflow.js.map A static/maps/nls/de/locale.js.map A static/maps/nls/es/locale.js.map M static/maps/nls/fr/locale.js.map M static/maps/nls/locale.js.map M static/maps/viz/phyloviz.js.map A static/scripts/admin.toolshed.js A static/scripts/bundled/admin.bundled.js A 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/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/panel.js M static/scripts/mvc/citation/citation-view.js M static/scripts/mvc/collection/collection-model.js M static/scripts/mvc/collection/collection-view.js M static/scripts/mvc/dataset/dataset-li.js M static/scripts/mvc/dataset/dataset-model.js M static/scripts/mvc/form/form-input.js M static/scripts/mvc/grid/grid-template.js M static/scripts/mvc/grid/grid-view.js M static/scripts/mvc/history/hda-li.js M static/scripts/mvc/history/hdca-li.js M static/scripts/mvc/library/library-folderlist-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/library/library-librarylist-view.js M static/scripts/mvc/library/library-librarytoolbar-view.js A static/scripts/mvc/page/page-list.js M static/scripts/mvc/tag.js M static/scripts/mvc/tool/tool-form-base.js M static/scripts/mvc/tool/tool-form-composite.js A static/scripts/mvc/toolshed/categories-view.js A static/scripts/mvc/toolshed/repo-queue-view.js A static/scripts/mvc/toolshed/repo-status-view.js A static/scripts/mvc/toolshed/repositories-view.js A static/scripts/mvc/toolshed/repository-queue-view.js A static/scripts/mvc/toolshed/repository-view.js A static/scripts/mvc/toolshed/shed-category-view.js A static/scripts/mvc/toolshed/shed-list-view.js A static/scripts/mvc/toolshed/shed-repo-details-view.js A static/scripts/mvc/toolshed/shed-repo-list-view.js A static/scripts/mvc/toolshed/sheds-list-view.js A static/scripts/mvc/toolshed/toolshed-model.js A static/scripts/mvc/toolshed/util.js A static/scripts/mvc/toolshed/workflows-view.js M static/scripts/mvc/tours.js M static/scripts/mvc/ui/ui-buttons.js M static/scripts/mvc/ui/ui-select-content.js M static/scripts/mvc/ui/ui-slider.js M static/scripts/mvc/upload/collection/collection-view.js M static/scripts/mvc/user/user-preferences.js A static/scripts/mvc/workflow/workflow-configure-menu.js M static/scripts/mvc/workflow/workflow-forms.js M static/scripts/mvc/workflow/workflow-terminals.js A static/scripts/mvc/workflow/workflow.js A static/scripts/nls/de/locale.js A static/scripts/nls/es/locale.js M static/scripts/nls/fr/locale.js M static/scripts/nls/locale.js M static/scripts/viz/phyloviz.js M static/style/blue/base.css M static/welcome.html.sample R templates/admin/tool_shed_repository/browse_toolsheds.mako M templates/admin/tool_shed_repository/select_tool_panel_section.mako M templates/grid_base.mako M templates/sharing_base.mako M templates/show_params.mako M templates/user/index.mako M templates/webapps/galaxy/admin/center.mako R templates/webapps/galaxy/admin/index.mako M templates/webapps/galaxy/data_manager/index.mako R templates/webapps/galaxy/dataset/grid.mako M templates/webapps/galaxy/galaxy.masthead.mako M templates/webapps/galaxy/page/editor.mako R templates/webapps/galaxy/page/index.mako R templates/webapps/galaxy/page/list_published.mako R templates/webapps/galaxy/workflow/configure_menu.mako R templates/webapps/galaxy/workflow/list.mako R templates/webapps/galaxy/workflow/list_for_run.mako M templates/webapps/tool_shed/base_panels.mako M test/api/test_dataset_collections.py M test/api/test_jobs.py M test/api/test_workflows.py M test/base/driver_util.py M test/base/populators.py A test/functional/tools/collection_creates_dynamic_nested_fail.xml A test/functional/tools/collection_creates_list_fail.xml A test/functional/tools/mulled_example_multi_versionless.xml M test/functional/tools/sample_datatypes_conf.xml M test/functional/tools/samples_tool_conf.xml M test/functional/webhooks/trans_object/config/trans_object.yaml M test/galaxy_selenium/navigates_galaxy.py M test/qunit/test-data/bootstrapped.js M test/qunit/tests/form_tests.js M test/qunit/tests/galaxy-app-base.js M test/qunit/tests/page_tests.js M test/qunit/tests/ui_tests.html M test/qunit/tests/ui_tests.js M test/selenium_tests/framework.py M test/selenium_tests/test_history_sharing.py M test/selenium_tests/test_login.py M test/selenium_tests/test_registration.py M test/selenium_tests/test_tool_form.py M test/selenium_tests/test_workflow_management.py M test/selenium_tests/test_workflow_run.py A test/unit/jobs/conditional_runners_job_conf.xml M test/unit/jobs/test_job_configuration.py M test/unit/tools/test_toolbox.py M tools/data_source/upload.py M tox.ini Log Message: ----------- Merge pull request #5 from dannon/auto_tour_generation Fixes .gitignore, merges dev. Commit: 579b8b025cc5242f1e32563cfb78ac3c354703d6 https://github.com/galaxyproject/galaxy/commit/579b8b025cc5242f1e32563cfb78a... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-06-14 (Wed, 14 Jun 2017) Changed paths: M .gitignore M client/galaxy/scripts/layout/menu.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.js M client/galaxy/scripts/mvc/webhooks.js M client/galaxy/scripts/onload.js M config/plugins/webhooks/demo/tool_list/helper/__init__.py A config/plugins/webhooks/demo/tour_generator/config/tour_generator.yml A config/plugins/webhooks/demo/tour_generator/helper/__init__.py A config/plugins/webhooks/demo/tour_generator/static/script.js A config/plugins/webhooks/demo/tour_generator/static/styles.css M lib/galaxy/webapps/galaxy/api/webhooks.py M static/maps/layout/menu.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.js.map M static/maps/mvc/webhooks.js.map M static/maps/onload.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/menu.js M static/scripts/mvc/tool/tool-form-base.js M static/scripts/mvc/tool/tool-form-composite.js M static/scripts/mvc/tool/tool-form.js M static/scripts/mvc/webhooks.js M static/scripts/onload.js M templates/js-app.mako M test/functional/webhooks/phdcomics/helper/__init__.py M test/functional/webhooks/trans_object/helper/__init__.py Log Message: ----------- Merge pull request #4019 from anatskiy/auto_tour_generation Tool-Describing-Tours Compare: https://github.com/galaxyproject/galaxy/compare/f58f372a26c4...579b8b025cc5