- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 9356ff: Rulebuilder: Special case auto URL schema detectio...
by GitHub 16 Jul '18

16 Jul '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 9356ff88c3e6a786f494f2b2cba059fc24ea3f98 https://github.com/galaxyproject/galaxy/commit/9356ff88c3e6a786f494f2b2cba0… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-07-09 (Mon, 09 Jul 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue Log Message: ----------- Rulebuilder: Special case auto URL schema detection for SRA inputs. @mblue9 has runs some tests and this prefix seems to serve the files considerably faster. Commit: 6da93fc07102d98a5f996ec9694e1465e2d45c3c https://github.com/galaxyproject/galaxy/commit/6da93fc07102d98a5f996ec9694e… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-07-16 (Mon, 16 Jul 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue Log Message: ----------- Merge pull request #6476 from jmchilton/sra_special_case Rulebuilder: Special case auto URL schema detection for SRA inputs. Compare: https://github.com/galaxyproject/galaxy/compare/a72954dfba7c...6da93fc07102 **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 89c622: remove dead link
by GitHub 16 Jul '18

16 Jul '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 89c62229c5af00ecc05df596129a53473a96db38 https://github.com/galaxyproject/galaxy/commit/89c62229c5af00ecc05df596129a… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-07-12 (Thu, 12 Jul 2018) Changed paths: M tools/data_source/upload.py Log Message: ----------- remove dead link I did not find the original post Commit: a72954dfba7c69195a6845b4111d4a350e69d54f https://github.com/galaxyproject/galaxy/commit/a72954dfba7c69195a6845b4111d… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-07-16 (Mon, 16 Jul 2018) Changed paths: M tools/data_source/upload.py Log Message: ----------- Merge pull request #6496 from martenson/remove-dead-link remove dead link Compare: https://github.com/galaxyproject/galaxy/compare/bc90d0a43591...a72954dfba7c **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 59bd1b: Add unittest that catches https://github.com/galax...
by GitHub 13 Jul '18

13 Jul '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 59bd1ba20a16ecf50586abec4b637c133eefb2a7 https://github.com/galaxyproject/galaxy/commit/59bd1ba20a16ecf50586abec4b63… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-07-13 (Fri, 13 Jul 2018) Changed paths: M test/unit/managers/test_HistoryManager.py Log Message: ----------- Add unittest that catches https://github.com/galaxyproject/galaxy/issues/6495 Commit: 4610258b9c2fde78fb056bb9183eb67d12ec00a4 https://github.com/galaxyproject/galaxy/commit/4610258b9c2fde78fb056bb9183e… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-07-13 (Fri, 13 Jul 2018) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Fix job resume from history menu Commit: bc90d0a4359194fc79b5102f4e88a0cd9a36b1a8 https://github.com/galaxyproject/galaxy/commit/bc90d0a4359194fc79b5102f4e88… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-07-13 (Fri, 13 Jul 2018) Changed paths: M lib/galaxy/model/__init__.py M test/unit/managers/test_HistoryManager.py Log Message: ----------- Merge pull request #6498 from mvdbeek/fix_resume_from_history_panel Fix resume from history panel Compare: https://github.com/galaxyproject/galaxy/compare/4a8857e4f9da...bc90d0a43591 **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 4b0ae3: Added fix to ensure that original ftp files that h...
by GitHub 13 Jul '18

13 Jul '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: 4b0ae30a83aeb86a821ec15cfa87e6af7e160a03 https://github.com/galaxyproject/galaxy/commit/4b0ae30a83aeb86a821ec15cfa87… Author: takadonet <philipmabon(a)gmail.com> Date: 2018-07-12 (Thu, 12 Jul 2018) Changed paths: M tools/data_source/upload.py Log Message: ----------- Added fix to ensure that original ftp files that have been uploaded are purged if set in galaxy.yml with flag ftp_upload_purge. Address issue #6492 Commit: fd33c5c6d6aa2478654da74c7e80efdcf31e09a7 https://github.com/galaxyproject/galaxy/commit/fd33c5c6d6aa2478654da74c7e80… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-07-13 (Fri, 13 Jul 2018) Changed paths: M tools/data_source/upload.py Log Message: ----------- Merge pull request #6497 from martenson/backport-takadonet [18.05] backport ftp purge fix Compare: https://github.com/galaxyproject/galaxy/compare/dfc996c8d6b8...fd33c5c6d6aa **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 77c344: Add webapp mapper for cloud upload API.
by GitHub 13 Jul '18

13 Jul '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 77c34446728f414491dd7a14fc5992800d9ae32a https://github.com/galaxyproject/galaxy/commit/77c34446728f414491dd7a14fc59… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-05-07 (Mon, 07 May 2018) Changed paths: M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Add webapp mapper for cloud upload API. Commit: 92830a1c155450a68bdd5d214d3f432f00056a1c https://github.com/galaxyproject/galaxy/commit/92830a1c155450a68bdd5d214d3f… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-05-07 (Mon, 07 May 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/cloud.py Log Message: ----------- Implement cloud upload API. Commit: 4e23c5e67dbc57ff03512f65549d6ea097a70deb https://github.com/galaxyproject/galaxy/commit/4e23c5e67dbc57ff03512f65549d… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-05-07 (Mon, 07 May 2018) Changed paths: M lib/galaxy/managers/cloud.py Log Message: ----------- Implement logic of uploading dataset(s) to cloud in the cloud manager. Commit: 62d67c9c401c2c5c1547457fe82229cf97e7e0ff https://github.com/galaxyproject/galaxy/commit/62d67c9c401c2c5c1547457fe822… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-05-07 (Mon, 07 May 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/cloud.py Log Message: ----------- Check for missing arguments from payload in cloud upload api. Commit: 63be2dba410c1d1cc17e6e4a1030d100bf5eaf6b https://github.com/galaxyproject/galaxy/commit/63be2dba410c1d1cc17e6e4a1030… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-05-07 (Mon, 07 May 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/cloud.py Log Message: ----------- Assert the validity of provided history ID in cloud upload API. Commit: 6a9ce39a2147b0b2449e4eaf73fb6e54399b5976 https://github.com/galaxyproject/galaxy/commit/6a9ce39a2147b0b2449e4eaf73fb… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-05-07 (Mon, 07 May 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/cloud.py Log Message: ----------- Assert the validity of provided dataset ID(s). Commit: ff42cc7b0684c47191a94e4d1a016dcbc7ef21b1 https://github.com/galaxyproject/galaxy/commit/ff42cc7b0684c47191a94e4d1a01… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-05-07 (Mon, 07 May 2018) Changed paths: M lib/galaxy/managers/cloud.py M lib/galaxy/webapps/galaxy/api/cloud.py Log Message: ----------- In cloud upload API, handle overwriting an existing object. Commit: f1b9a23c939f20718b430916e5e5fdd4d9b2a330 https://github.com/galaxyproject/galaxy/commit/f1b9a23c939f20718b430916e5e5… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-05-07 (Mon, 07 May 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/cloud.py Log Message: ----------- Use named arguments in cloud upload API when calling its manager. Commit: 35a30219f652741e20f6810b42c21dbf3e74e0c0 https://github.com/galaxyproject/galaxy/commit/35a30219f652741e20f6810b42c2… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-05-07 (Mon, 07 May 2018) Changed paths: M lib/galaxy/managers/cloud.py Log Message: ----------- Fix a bug in cloud upload API. Commit: 17ab3e8d2dff82996264a3404fda800a707b8487 https://github.com/galaxyproject/galaxy/commit/17ab3e8d2dff82996264a3404fda… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-05-07 (Mon, 07 May 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/cloud.py Log Message: ----------- Update cloud upload API description. Commit: 0ed19ad7b0402c7be544a358386b80377d63d85c https://github.com/galaxyproject/galaxy/commit/0ed19ad7b0402c7be544a358386b… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-05-07 (Mon, 07 May 2018) Changed paths: M lib/galaxy/managers/cloud.py M lib/galaxy/webapps/galaxy/api/cloud.py Log Message: ----------- Update cloud upload API description. Commit: 3b74bd899c323f99135362a23f64726cd09ee331 https://github.com/galaxyproject/galaxy/commit/3b74bd899c323f99135362a23f64… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-05-07 (Mon, 07 May 2018) Changed paths: M lib/galaxy/managers/cloud.py Log Message: ----------- Fix bugs related to import order and boolean assert in cloud upload API. Commit: c7c7691c98b2ef2cdeee5bf7661b9415e6eebf86 https://github.com/galaxyproject/galaxy/commit/c7c7691c98b2ef2cdeee5bf7661b… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-07-12 (Thu, 12 Jul 2018) Changed paths: M .ci/flake8_blacklist.txt M .ci/jenkins/selenium/run_tests.sh M .gitignore M .travis.yml M Makefile M client/GruntFile.js M client/bower.json A client/galaxy/docs/bootstrap.md A client/galaxy/docs/galaxy-buttons.md A client/galaxy/docs/galaxy-forms.md A client/galaxy/docs/galaxy-masthead.md A client/galaxy/docs/galaxy-menus.md A client/galaxy/docs/galaxy-messages.md A client/galaxy/docs/galaxy-panels.md A client/galaxy/docs/galaxy-tables.md A client/galaxy/docs/galaxy-tabs.md M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/apps/extended.js M client/galaxy/scripts/apps/panels/admin-panel.js M client/galaxy/scripts/apps/panels/tool-panel.js M client/galaxy/scripts/components/Citations.vue A client/galaxy/scripts/components/DataDialog.vue M client/galaxy/scripts/components/HistoryImport.vue M client/galaxy/scripts/components/HistoryView.vue M client/galaxy/scripts/components/PluginList.vue M client/galaxy/scripts/components/RuleCollectionBuilder.vue A client/galaxy/scripts/components/RulesDisplay.vue A client/galaxy/scripts/components/Sharing.vue A client/galaxy/scripts/components/WorkflowImport.vue M client/galaxy/scripts/components/admin/DataTablesGrid.vue A client/galaxy/scripts/components/admin/DataTypes.vue R client/galaxy/scripts/components/admin/UserAPIKeys.vue M client/galaxy/scripts/galaxy.pages.js A client/galaxy/scripts/layout/communication-server-view.js A client/galaxy/scripts/layout/data.js R client/galaxy/scripts/layout/generic-nav-view.js M client/galaxy/scripts/layout/masthead.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/modal.js M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/layout/panel.js M client/galaxy/scripts/layout/scratchbook.js M client/galaxy/scripts/legacy/grid/grid-view.js R client/galaxy/scripts/libs/bootstrap-tour.js R client/galaxy/scripts/libs/bootstrap.js A client/galaxy/scripts/mocha/test.js A client/galaxy/scripts/mocha/tests/rules_dsl_spec.yml A client/galaxy/scripts/mocha/tests/rules_tests.js M client/galaxy/scripts/mvc/collection/collection-model.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.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/form/form-wrapper.js M client/galaxy/scripts/mvc/grid/grid-model.js M client/galaxy/scripts/mvc/grid/grid-shared.js M 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client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/library/library-library-view.js M client/galaxy/scripts/mvc/library/library-librarylist-view.js M client/galaxy/scripts/mvc/library/library-libraryrow-view.js M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js M client/galaxy/scripts/mvc/list/list-view.js A client/galaxy/scripts/mvc/rules/rule-definitions.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 M client/galaxy/scripts/mvc/tool/tool-form.js M client/galaxy/scripts/mvc/tool/tools.js M client/galaxy/scripts/mvc/tours.js M client/galaxy/scripts/mvc/ui/error-modal.js M client/galaxy/scripts/mvc/ui/ui-buttons.js M client/galaxy/scripts/mvc/ui/ui-drilldown.js M client/galaxy/scripts/mvc/ui/ui-frames.js M client/galaxy/scripts/mvc/ui/ui-list.js M client/galaxy/scripts/mvc/ui/ui-misc.js M client/galaxy/scripts/mvc/ui/ui-modal.js M 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M client/galaxy/scripts/mvc/visualization/chart/components/screenshot.js M client/galaxy/scripts/mvc/visualization/chart/utilities/jobs.js M client/galaxy/scripts/mvc/visualization/chart/utilities/series.js M client/galaxy/scripts/mvc/workflow/workflow-canvas.js M client/galaxy/scripts/mvc/workflow/workflow-connector.js M client/galaxy/scripts/mvc/workflow/workflow-forms.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-terminals.js M client/galaxy/scripts/mvc/workflow/workflow-view-data.js M client/galaxy/scripts/mvc/workflow/workflow-view-node.js M client/galaxy/scripts/mvc/workflow/workflow-view-terminals.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M client/galaxy/scripts/mvc/workflow/workflow.js M client/galaxy/scripts/qunit/test-app.js M client/galaxy/scripts/qunit/tests/form_tests.js M client/galaxy/scripts/qunit/tests/masthead_tests.js M 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lib/galaxy/datatypes/converters/bedgraph_to_bigwig_converter.xml A lib/galaxy/datatypes/converters/bz2_to_uncompressed.xml M lib/galaxy/datatypes/converters/fasta_to_2bit.xml M lib/galaxy/datatypes/converters/fasta_to_fai.xml R lib/galaxy/datatypes/converters/fastagz_to_fasta.xml R lib/galaxy/datatypes/converters/fastqbz2_to_fastq.xml R lib/galaxy/datatypes/converters/fastqcssangerbz2_to_fastqcssanger.xml R lib/galaxy/datatypes/converters/fastqcssangergz_to_fastqcssanger.xml R lib/galaxy/datatypes/converters/fastqgz_to_fastq.xml R lib/galaxy/datatypes/converters/fastqilluminabz2_to_fastqillumina.xml R lib/galaxy/datatypes/converters/fastqilluminagz_to_fastqillumina.xml R lib/galaxy/datatypes/converters/fastqsangerbz2_to_fastqsanger.xml R lib/galaxy/datatypes/converters/fastqsangergz_to_fastqsanger.xml R lib/galaxy/datatypes/converters/fastqsolexabz2_to_fastqsolexa.xml R lib/galaxy/datatypes/converters/fastqsolexagz_to_fastqsolexa.xml R 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M lib/galaxy/managers/sharable.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/custom_types.py M lib/galaxy/model/mapping.py M lib/galaxy/model/metadata.py M lib/galaxy/model/migrate/versions/0136_collection_and_workflow_state.py A lib/galaxy/model/migrate/versions/0141_add_oidc_tables.py A lib/galaxy/model/migrate/versions/0142_change_numeric_metric_precision.py M lib/galaxy/model/orm/scripts.py M lib/galaxy/queue_worker.py M lib/galaxy/security/__init__.py M lib/galaxy/security/passwords.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/actions/upload.py A lib/galaxy/tools/apply_rules.xml M lib/galaxy/tools/data/__init__.py M lib/galaxy/tools/data_fetch.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/mulled.py M 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lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/galaxy/webapps/tool_shed/controllers/repository_review.py M lib/galaxy/webapps/tool_shed/controllers/upload.py M lib/galaxy/webapps/tool_shed/model/__init__.py M lib/galaxy/workflow/modules.py M lib/galaxy_ext/metadata/set_metadata.py M lib/tool_shed/capsule/capsule_manager.py M lib/tool_shed/dependencies/attribute_handlers.py M lib/tool_shed/dependencies/repository/relation_builder.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py M lib/tool_shed/grids/repository_grids.py M lib/tool_shed/grids/repository_review_grids.py M lib/tool_shed/grids/util.py M lib/tool_shed/metadata/metadata_generator.py M lib/tool_shed/metadata/repository_metadata_manager.py M lib/tool_shed/repository_registry.py M lib/tool_shed/repository_types/metadata.py M lib/tool_shed/repository_types/repository_suite_definition.py M lib/tool_shed/repository_types/tool_dependency_definition.py M lib/tool_shed/tools/data_table_manager.py M lib/tool_shed/tools/tool_validator.py M lib/tool_shed/tools/tool_version_manager.py M lib/tool_shed/util/admin_util.py M lib/tool_shed/util/commit_util.py M lib/tool_shed/util/common_util.py M lib/tool_shed/util/encoding_util.py M lib/tool_shed/util/hg_util.py M lib/tool_shed/util/metadata_util.py M lib/tool_shed/util/readme_util.py M lib/tool_shed/util/repository_content_util.py M lib/tool_shed/util/repository_util.py M lib/tool_shed/util/review_util.py M lib/tool_shed/util/shed_util_common.py M lib/tool_shed/util/web_util.py M manage_db.sh M run.sh M run_reports.sh M run_tests.sh M run_tool_shed.sh M scripts/api/common.py M scripts/bootstrap_history.py M scripts/check_python.py M scripts/cleanup_datasets/delete_datasets.sh M scripts/cleanup_datasets/delete_userless_histories.sh M scripts/cleanup_datasets/purge_datasets.sh M scripts/cleanup_datasets/purge_folders.sh M scripts/cleanup_datasets/purge_histories.sh M scripts/cleanup_datasets/purge_libraries.sh M scripts/common_startup.sh M scripts/common_startup_functions.sh R scripts/common_startup_variables.sh A scripts/docker_swarm_manager.py M scripts/get_uwsgi_args.py M scripts/grt/export.py M scripts/grt/grt.yml.sample M scripts/grt/upload.py M scripts/maintenance.sh A scripts/plugin_staging.py A static/images/fonts/FontAwesome.otf M static/images/fonts/fontawesome-webfont.eot A static/images/fonts/fontawesome-webfont.svg M static/images/fonts/fontawesome-webfont.ttf M static/images/fonts/fontawesome-webfont.woff A static/images/fonts/fontawesome-webfont.woff2 M static/style/blue/autocomplete_tagging.css M static/style/blue/base.css M static/style/blue/circster.css M static/style/blue/embed_item.css M static/style/blue/library.css M static/style/blue/reports.css M static/style/blue/trackster.css M static/welcome.html.sample R templates/admin/impersonate.mako R templates/admin/view_data_tables_registry.mako R templates/admin/view_datatypes_registry.mako M templates/base/base_panels.mako M templates/display_common.mako M templates/ind_share_base.mako R templates/sharing_base.mako M templates/show_params.mako M templates/tagging_common.mako M templates/user/login.mako M templates/webapps/galaxy/admin/center.mako M templates/webapps/galaxy/admin/view_display_applications.mako M templates/webapps/galaxy/data_manager/index.mako M templates/webapps/galaxy/dataset/copy_view.mako M templates/webapps/galaxy/galaxy.panels.mako R templates/webapps/galaxy/history/structure.mako M templates/webapps/galaxy/workflow/editor.mako M templates/webapps/reports/index.mako M templates/webapps/tool_shed/base_panels.mako M templates/webapps/tool_shed/common/grid_common.mako M templates/webapps/tool_shed/repository/manage_repository.mako M templates/webapps/tool_shed/repository/view_repository.mako M templates/webapps/tool_shed/user/manage_email_alerts.mako A test-data/1.tiff A test-data/filter1_in6.bed A test-data/filter1_test6.bed A test-data/rules/treated1fb.txt A test-data/rules/treated2fb.txt A test-data/rules/treated3fb.txt M test-data/rules/uniprot.json A test-data/rules/untreated1fb.txt A test-data/rules/untreated2fb.txt A test-data/rules/untreated3fb.txt A test-data/rules/untreated4fb.txt A test-data/sort_out1.bed A test-data/sort_out2.bed A test-data/sort_out3.tab A test-data/sort_out4.sam M test/api/test_jobs.py M test/api/test_libraries.py M test/api/test_tools.py M test/api/test_tools_upload.py M test/api/test_workflows.py A test/base/data/rules_dsl_spec.yml M test/base/populators.py A test/base/rules_test_data.py A test/base/workflow_fixtures.py M test/base/workflows_format_2/main.py M test/docker/base/Dockerfile M test/docker/base/ansible_vars.yml M test/docker/base/run_test_wrapper.sh M test/functional/test_data_managers.py M test/functional/test_toolbox.py A test/functional/tools/collection_paired_conditional_structured_like.xml A test/functional/tools/collection_paired_structured_like.xml A test/functional/tools/collection_type_source_map_over.xml A test/functional/tools/empty_select.xml M test/functional/tools/for_workflows/cat_collection.xml A test/functional/tools/identifier_single_in_repeat.xml A test/functional/tools/inputs_as_json_with_paths.xml M test/functional/tools/job_properties.xml M test/functional/tools/multi_data_optional.xml A test/functional/tools/output_action_change_format_paired.xml R test/functional/tools/paired_collection_map_over_structured_like.xml M test/functional/tools/sample_datatypes_conf.xml M test/functional/tools/samples_tool_conf.xml M test/galaxy_selenium/components.py M test/galaxy_selenium/has_driver.py M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/navigation.yml M test/galaxy_selenium/smart_components.py M test/integration/test_scripts.py M test/integration/test_upload_configuration_options.py R test/selenium_tests/_workflow_fixtures.py M test/selenium_tests/framework.py A test/selenium_tests/test_admin_app.py M test/selenium_tests/test_library_landing.py M test/selenium_tests/test_registration.py M test/selenium_tests/test_saved_histories.py M test/selenium_tests/test_tool_form.py M test/selenium_tests/test_uploads.py M test/selenium_tests/test_workflow_editor.py M test/selenium_tests/test_workflow_management.py M test/selenium_tests/test_workflow_run.py M test/unit/config/1607_root_filters/config/galaxy.ini M test/unit/config/1607_root_samples/config/galaxy.ini M test/unit/datatypes/dataproviders/test_base_dataproviders.py M test/unit/datatypes/test_bam.py A test/unit/datatypes/test_datatypes_registry.py M test/unit/jobs/test_job_output_checker.py M test/unit/jobs/test_runner_params.py M test/unit/test_galaxy_mapping.py M test/unit/test_remote_shell.py A test/unit/test_rule_utils.py M test/unit/test_security_helper.py A test/unit/test_security_passwords.py M test/unit/tools/test_collect_primary_datasets.py M test/unit/tools/test_data_parameters.py M test/unit/tools/test_dataset_matcher.py M test/unit/tools/test_history_imp_exp.py M test/unit/tools/test_parsing.py M test/unit/tools/test_tool_dependency_description.py M test/unit/tools/test_tool_deps.py M test/unit/unittest_utils/galaxy_mock.py M test/unit/unittest_utils/tempfilecache.py M test/unit/visualizations/plugins/test_VisualizationPlugin.py M test/unit/visualizations/plugins/test_VisualizationsRegistry.py M test/unit/web/framework/test_webapp.py M test/unit/workflows/test_extract_summary.py M test/unit/workflows/test_modules.py A tool-data/intermine_simple_display.loc.sample A tools/data_source/intermine.xml M tools/data_source/upload.py M tools/evolution/codingSnps.xml M tools/extract/extract_genomic_dna.xml M tools/extract/liftOver_wrapper.xml M tools/filters/bed_to_bigbed.xml M tools/filters/cutWrapper.pl M tools/filters/sorter.py M tools/filters/sorter.xml M tools/filters/wig_to_bigwig.xml M tools/phenotype_association/gpass.xml M tools/phenotype_association/lps.xml M tools/phenotype_association/master2gd_snp.xml M tools/phenotype_association/master2pg.xml M tools/sr_mapping/bfast_wrapper.xml M tools/stats/filtering.py M tools/stats/filtering.xml M tox.ini Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into upload_to_cloud Commit: 5b1b4314a3ac140779146286f4dc2cfd5fad6807 https://github.com/galaxyproject/galaxy/commit/5b1b4314a3ac140779146286f4dc… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-07-12 (Thu, 12 Jul 2018) Changed paths: M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Refactor the API end point from `upload` to `copy_to`. Commit: 97fd2088faa0eda1275448d7552a47c801ab9a4b https://github.com/galaxyproject/galaxy/commit/97fd2088faa0eda1275448d7552a… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-07-12 (Thu, 12 Jul 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/cloud.py Log Message: ----------- Add cloud storage `copy_to` API. Commit: 7e8be2ff53e9f6f781618c2182d9b3d58675c47e https://github.com/galaxyproject/galaxy/commit/7e8be2ff53e9f6f781618c2182d9… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-07-12 (Thu, 12 Jul 2018) Changed paths: M lib/galaxy/managers/cloud.py Log Message: ----------- Add cloud-based storage `copy-to` manager. Commit: b3f1a7cf9cdc29bcc52a6d7f5c35fc6ecfa02878 https://github.com/galaxyproject/galaxy/commit/b3f1a7cf9cdc29bcc52a6d7f5c35… Author: Enis Afgan <afgane(a)gmail.com> Date: 2018-07-12 (Thu, 12 Jul 2018) Changed paths: M lib/galaxy/managers/cloud.py M lib/galaxy/webapps/galaxy/api/cloud.py Log Message: ----------- Doc style updates; copy-to return dict with copied datasets Commit: 4a8857e4f9daf15101270724375dad14c4897e6c https://github.com/galaxyproject/galaxy/commit/4a8857e4f9daf15101270724375d… Author: Enis Afgan <afgane(a)gmail.com> Date: 2018-07-12 (Thu, 12 Jul 2018) Changed paths: M lib/galaxy/managers/cloud.py M lib/galaxy/webapps/galaxy/api/cloud.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Merge pull request #6078 from VJalili/upload_to_cloud Upload data to a cloud-based storage Compare: https://github.com/galaxyproject/galaxy/compare/2abb01b6cbb1...4a8857e4f9da **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 603b23: Force standard HTTPTransport for sentry -- this pl...
by GitHub 13 Jul '18

13 Jul '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 603b2365b6a261e5603c618c637cf8458e667007 https://github.com/galaxyproject/galaxy/commit/603b2365b6a261e5603c618c637c… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-06-21 (Thu, 21 Jun 2018) Changed paths: M lib/galaxy/app.py M lib/galaxy/tools/error_reports/plugins/sentry.py Log Message: ----------- Force standard HTTPTransport for sentry -- this plays nicer with a wider array of uwsgi configurations Commit: f94a073e86be608916ec7ae79285da06ee82483b https://github.com/galaxyproject/galaxy/commit/f94a073e86be608916ec7ae79285… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-06-21 (Thu, 21 Jun 2018) Changed paths: M lib/galaxy/web/base/controller.py Log Message: ----------- Make sure that the workflow step has a proper state available Commit: 3fe88a9bfe1b010ca30ffac32e5c4e200398c48e https://github.com/galaxyproject/galaxy/commit/3fe88a9bfe1b010ca30ffac32e5c… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M lib/galaxy/visualization/plugins/interactive_environments.py Log Message: ----------- Merge pull request #6465 from dannon/backport-gie-static-again [18.05] Backport of IE static url fix (to actual 18.05) Commit: bc95f2563601635cfa1daa686b3d5c4e3ebb51ea https://github.com/galaxyproject/galaxy/commit/bc95f2563601635cfa1daa686b3d… Author: Devon Ryan <dpryan79(a)gmail.com> Date: 2018-07-09 (Mon, 09 Jul 2018) Changed paths: M lib/galaxy/config.py Log Message: ----------- Fix the --log-file option in the job handlers (cherry picked from commit 97c344a17a0188a687629103feefcdf03af8e768) Commit: 23666c94a22b816bc5238e4a22c759a11265f7aa https://github.com/galaxyproject/galaxy/commit/23666c94a22b816bc5238e4a22c7… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-07-11 (Wed, 11 Jul 2018) Changed paths: M lib/galaxy/config.py Log Message: ----------- Merge pull request #6477 from natefoo/backport-pr-6351 [18.01] Fix the --log-file option in the job handlers Commit: 93fc3a63507d6cd7c85a99ad62e71b14d4d6265e https://github.com/galaxyproject/galaxy/commit/93fc3a63507d6cd7c85a99ad62e7… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-07-11 (Wed, 11 Jul 2018) Changed paths: M lib/galaxy/web/base/controller.py Log Message: ----------- Merge pull request #6369 from guerler/pages [18.05] Make sure that the workflow step has a proper state available Commit: 20565a2b8517fbc4c54524fa0ae127c2f6aaefb0 https://github.com/galaxyproject/galaxy/commit/20565a2b8517fbc4c54524fa0ae1… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-07-11 (Wed, 11 Jul 2018) Changed paths: M lib/galaxy/app.py M lib/galaxy/tools/error_reports/plugins/sentry.py Log Message: ----------- Merge pull request #6375 from dannon/sentry_transport_fix [18.05] Specify standard HTTPTransport for Sentry Commit: dfc996c8d6b8e166ae17fe8502f9e4f9252b6106 https://github.com/galaxyproject/galaxy/commit/dfc996c8d6b8e166ae17fe8502f9… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-07-13 (Fri, 13 Jul 2018) Changed paths: M lib/galaxy/config.py Log Message: ----------- Merge branch 'release_18.01' into release_18.05 Commit: 2abb01b6cbb11f28a7f6a838c97b8540b62e45fb https://github.com/galaxyproject/galaxy/commit/2abb01b6cbb11f28a7f6a838c97b… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-07-13 (Fri, 13 Jul 2018) Changed paths: M lib/galaxy/app.py M lib/galaxy/tools/error_reports/plugins/sentry.py M lib/galaxy/web/base/controller.py Log Message: ----------- Merge branch 'release_18.05' into dev Compare: https://github.com/galaxyproject/galaxy/compare/fa43f2c2b2e7...2abb01b6cbb1 **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] bc95f2: Fix the --log-file option in the job handlers
by GitHub 13 Jul '18

13 Jul '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: bc95f2563601635cfa1daa686b3d5c4e3ebb51ea https://github.com/galaxyproject/galaxy/commit/bc95f2563601635cfa1daa686b3d… Author: Devon Ryan <dpryan79(a)gmail.com> Date: 2018-07-09 (Mon, 09 Jul 2018) Changed paths: M lib/galaxy/config.py Log Message: ----------- Fix the --log-file option in the job handlers (cherry picked from commit 97c344a17a0188a687629103feefcdf03af8e768) Commit: 23666c94a22b816bc5238e4a22c759a11265f7aa https://github.com/galaxyproject/galaxy/commit/23666c94a22b816bc5238e4a22c7… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-07-11 (Wed, 11 Jul 2018) Changed paths: M lib/galaxy/config.py Log Message: ----------- Merge pull request #6477 from natefoo/backport-pr-6351 [18.01] Fix the --log-file option in the job handlers Commit: dfc996c8d6b8e166ae17fe8502f9e4f9252b6106 https://github.com/galaxyproject/galaxy/commit/dfc996c8d6b8e166ae17fe8502f9… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-07-13 (Fri, 13 Jul 2018) Changed paths: M lib/galaxy/config.py Log Message: ----------- Merge branch 'release_18.01' into release_18.05 Compare: https://github.com/galaxyproject/galaxy/compare/20565a2b8517...dfc996c8d6b8 **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

1 0

[galaxyproject/galaxy] 29de69: Add period to the list of allowed characters in us...
by GitHub 12 Jul '18

12 Jul '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 29de694b1f272e58cf84c8998c6e6181e25b9fd2 https://github.com/galaxyproject/galaxy/commit/29de694b1f272e58cf84c8998c6e… Author: Oleksandr Moskalenko <om(a)rc.ufl.edu> Date: 2018-06-20 (Wed, 20 Jun 2018) Changed paths: M lib/galaxy/web/framework/webapp.py Log Message: ----------- Add period to the list of allowed characters in user names Commit: fa43f2c2b2e7f047b2d8a27b9bca313f67637c75 https://github.com/galaxyproject/galaxy/commit/fa43f2c2b2e7f047b2d8a27b9bca… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-07-12 (Thu, 12 Jul 2018) Changed paths: M lib/galaxy/web/framework/webapp.py Log Message: ----------- Merge pull request #6365 from moskalenko/dev Add period to the list of allowed characters in user names Compare: https://github.com/galaxyproject/galaxy/compare/30feac0c4ca4...fa43f2c2b2e7 **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

1 0

[galaxyproject/galaxy] 4da672: Added fix to ensure that original ftp files that h...
by GitHub 12 Jul '18

12 Jul '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4da67218c166374016c239397db2c10f3a388e66 https://github.com/galaxyproject/galaxy/commit/4da67218c166374016c239397db2… Author: takadonet <philipmabon(a)gmail.com> Date: 2018-07-12 (Thu, 12 Jul 2018) Changed paths: M tools/data_source/upload.py Log Message: ----------- Added fix to ensure that original ftp files that have been uploaded are purged if set in galaxy.yml with flag ftp_upload_purge. Address issue #6492 Commit: 30feac0c4ca4488caa4d7d00beee698a6e465cdf https://github.com/galaxyproject/galaxy/commit/30feac0c4ca4488caa4d7d00beee… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-07-12 (Thu, 12 Jul 2018) Changed paths: M tools/data_source/upload.py Log Message: ----------- Merge pull request #6494 from phac-nml/fix_ftp_upload_purge Fix ftp_upload_purge in galaxy.yml Compare: https://github.com/galaxyproject/galaxy/compare/2cccf7c23fc5...30feac0c4ca4 **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] b06932: Allow : in tag values for PJA setting.
by GitHub 12 Jul '18

12 Jul '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b0693203a1ed4d755f6fac261dd98bdddb6da6b2 https://github.com/galaxyproject/galaxy/commit/b0693203a1ed4d755f6fac261dd9… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-07-12 (Thu, 12 Jul 2018) Changed paths: M lib/galaxy/managers/tags.py Log Message: ----------- Allow : in tag values for PJA setting. Based on #5457, certain paths to creating tag values with : must already work - just not when parsing from a raw string I guess. Commit: b45ce119401b6ef36a19c1bd21c84856ebc074e2 https://github.com/galaxyproject/galaxy/commit/b45ce119401b6ef36a19c1bd21c8… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-07-12 (Thu, 12 Jul 2018) Changed paths: M lib/galaxy/managers/collections.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Centralize logic for determining which tags get auto-propagated. Commit: 0280713c43442a412cf6294b57caf1c12160322f https://github.com/galaxyproject/galaxy/commit/0280713c43442a412cf6294b57ca… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-07-12 (Thu, 12 Jul 2018) Changed paths: M lib/galaxy/model/__init__.py M test/api/test_workflows.py Log Message: ----------- Auto-propagate group tags - the way name tags are propagated. Commit: 2cccf7c23fc57e4e633af2b1703d7d4a034f5850 https://github.com/galaxyproject/galaxy/commit/2cccf7c23fc57e4e633af2b1703d… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2018-07-12 (Thu, 12 Jul 2018) Changed paths: M lib/galaxy/managers/collections.py M lib/galaxy/managers/tags.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/actions/__init__.py M test/api/test_workflows.py Log Message: ----------- Merge pull request #6491 from jmchilton/auto_group_tags Implement ``group:`` tags (toward multi-factor analysis with group tagging) Compare: https://github.com/galaxyproject/galaxy/compare/0674af824d2c...2cccf7c23fc5 **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] d91ad7: small improvement to the too xsd docs
by GitHub 12 Jul '18

12 Jul '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d91ad7d6275cf004b670a11a23a6258e51500c89 https://github.com/galaxyproject/galaxy/commit/d91ad7d6275cf004b670a11a23a6… Author: M Bernt <m.bernt(a)ufz.de> Date: 2018-07-12 (Thu, 12 Jul 2018) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- small improvement to the too xsd docs Commit: cabd6a11bed38eaa69175a8505c4f6071478bd5f https://github.com/galaxyproject/galaxy/commit/cabd6a11bed38eaa69175a8505c4… Author: M Bernt <m.bernt(a)ufz.de> Date: 2018-07-12 (Thu, 12 Jul 2018) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- added <output> to snippet Commit: 5bac0eff82d5fa4931834082baeb220c701fd5b5 https://github.com/galaxyproject/galaxy/commit/5bac0eff82d5fa4931834082baeb… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2018-07-12 (Thu, 12 Jul 2018) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- Update galaxy.xsd Commit: 0674af824d2ccfa8cdc924b6387e0112912bbb47 https://github.com/galaxyproject/galaxy/commit/0674af824d2ccfa8cdc924b6387e… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-07-12 (Thu, 12 Jul 2018) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- Merge pull request #6490 from bernt-matthias/topic/xsd-doc-discover-improvement small improvement to the too xsd docs regarding discovered_datasets Compare: https://github.com/galaxyproject/galaxy/compare/6fc937a3d8b4...0674af824d2c **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/usegalaxy-playbook] ac87a1: Install migmap version 1.0.2 for the pRESTO suite
by GitHub 11 Jul '18

11 Jul '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: ac87a19c3df23214462dfa85338a6b691a8e2dba https://github.com/galaxyproject/usegalaxy-playbook/commit/ac87a19c3df23214… Author: Dave B <dave(a)bx.psu.edu> Date: 2018-07-11 (Wed, 11 Jul 2018) Changed paths: M env/main/files/galaxy/var/integrated_tool_panel.xml M env/main/files/galaxy/var/shed_tool_conf.xml Log Message: ----------- Install migmap version 1.0.2 for the pRESTO suite **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 8ad57f: Fix for rendering multiple dependent dynamic selec...
by GitHub 11 Jul '18

11 Jul '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 8ad57fa1f18453c1cd94249b881b93a557639dfd https://github.com/galaxyproject/galaxy/commit/8ad57fa1f18453c1cd94249b881b… Author: greg <ghv2(a)psu.edu> Date: 2018-06-21 (Thu, 21 Jun 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Fix for rendering multiple dependent dynamic select lists where choosing an option in the first refreshes the options in the second Commit: 6fc937a3d8b46f3620b73f3e057d9b6ba5422540 https://github.com/galaxyproject/galaxy/commit/6fc937a3d8b46f3620b73f3e057d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-07-11 (Wed, 11 Jul 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Merge pull request #6374 from gregvonkuster/multi_dynamic_select Fix for rendering multiple dependent dynamic select lists Compare: https://github.com/galaxyproject/galaxy/compare/f33770096c03...6fc937a3d8b4 **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 603b23: Force standard HTTPTransport for sentry -- this pl...
by GitHub 11 Jul '18

11 Jul '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: 603b2365b6a261e5603c618c637cf8458e667007 https://github.com/galaxyproject/galaxy/commit/603b2365b6a261e5603c618c637c… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-06-21 (Thu, 21 Jun 2018) Changed paths: M lib/galaxy/app.py M lib/galaxy/tools/error_reports/plugins/sentry.py Log Message: ----------- Force standard HTTPTransport for sentry -- this plays nicer with a wider array of uwsgi configurations Commit: 20565a2b8517fbc4c54524fa0ae127c2f6aaefb0 https://github.com/galaxyproject/galaxy/commit/20565a2b8517fbc4c54524fa0ae1… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-07-11 (Wed, 11 Jul 2018) Changed paths: M lib/galaxy/app.py M lib/galaxy/tools/error_reports/plugins/sentry.py Log Message: ----------- Merge pull request #6375 from dannon/sentry_transport_fix [18.05] Specify standard HTTPTransport for Sentry Compare: https://github.com/galaxyproject/galaxy/compare/93fc3a63507d...20565a2b8517 **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] f94a07: Make sure that the workflow step has a proper stat...
by GitHub 11 Jul '18

11 Jul '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: f94a073e86be608916ec7ae79285da06ee82483b https://github.com/galaxyproject/galaxy/commit/f94a073e86be608916ec7ae79285… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-06-21 (Thu, 21 Jun 2018) Changed paths: M lib/galaxy/web/base/controller.py Log Message: ----------- Make sure that the workflow step has a proper state available Commit: 93fc3a63507d6cd7c85a99ad62e71b14d4d6265e https://github.com/galaxyproject/galaxy/commit/93fc3a63507d6cd7c85a99ad62e7… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-07-11 (Wed, 11 Jul 2018) Changed paths: M lib/galaxy/web/base/controller.py Log Message: ----------- Merge pull request #6369 from guerler/pages [18.05] Make sure that the workflow step has a proper state available Compare: https://github.com/galaxyproject/galaxy/compare/3fe88a9bfe1b...93fc3a63507d **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] bc95f2: Fix the --log-file option in the job handlers
by GitHub 11 Jul '18

11 Jul '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: bc95f2563601635cfa1daa686b3d5c4e3ebb51ea https://github.com/galaxyproject/galaxy/commit/bc95f2563601635cfa1daa686b3d… Author: Devon Ryan <dpryan79(a)gmail.com> Date: 2018-07-09 (Mon, 09 Jul 2018) Changed paths: M lib/galaxy/config.py Log Message: ----------- Fix the --log-file option in the job handlers (cherry picked from commit 97c344a17a0188a687629103feefcdf03af8e768) Commit: 23666c94a22b816bc5238e4a22c759a11265f7aa https://github.com/galaxyproject/galaxy/commit/23666c94a22b816bc5238e4a22c7… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-07-11 (Wed, 11 Jul 2018) Changed paths: M lib/galaxy/config.py Log Message: ----------- Merge pull request #6477 from natefoo/backport-pr-6351 [18.01] Fix the --log-file option in the job handlers Compare: https://github.com/galaxyproject/galaxy/compare/36706e9eb387...23666c94a22b **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 8077d5: Update common_startup_functions.sh
by GitHub 11 Jul '18

11 Jul '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 8077d59fd9772ef6d1d9175e8edef4c8f95ace5a https://github.com/galaxyproject/galaxy/commit/8077d59fd9772ef6d1d9175e8ede… Author: Nadia Goué <nadia.goue(a)gmail.com> Date: 2018-07-10 (Tue, 10 Jul 2018) Changed paths: M scripts/common_startup_functions.sh Log Message: ----------- Update common_startup_functions.sh Not to override tool_shed config file. Commit: f33770096c038d420696c822bd3ab8c397156f14 https://github.com/galaxyproject/galaxy/commit/f33770096c038d420696c822bd3a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-07-11 (Wed, 11 Jul 2018) Changed paths: M scripts/common_startup_functions.sh Log Message: ----------- Merge pull request #6481 from nagoue/patch-1 Update common_startup_functions.sh Compare: https://github.com/galaxyproject/galaxy/compare/f25af28f6667...f33770096c03 **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] fb449b: fix the logging init
by GitHub 11 Jul '18

11 Jul '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: fb449b49906197fbb611833acf06ee13e5b34e48 https://github.com/galaxyproject/galaxy/commit/fb449b49906197fbb611833acf06… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-07-09 (Mon, 09 Jul 2018) Changed paths: M scripts/grt/upload.py Log Message: ----------- fix the logging init - properly initialiaze the logger - change level for some of the logs - add some debug and critical logs Commit: 390aedf8c8c28db739a78dc7c41e9275a735369b https://github.com/galaxyproject/galaxy/commit/390aedf8c8c28db739a78dc7c41e… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-07-09 (Mon, 09 Jul 2018) Changed paths: M scripts/grt/grt.yml.sample M scripts/grt/upload.py Log Message: ----------- add all sample tool_conf data source tools to GRT sanitization Commit: ab760f5d27bb248a9c78d79a002b5ab2c68fa5d3 https://github.com/galaxyproject/galaxy/commit/ab760f5d27bb248a9c78d79a002b… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-07-10 (Tue, 10 Jul 2018) Changed paths: M scripts/grt/export.py M scripts/grt/grt.yml.sample Log Message: ----------- revert the datasource tool sanitation, set default # for export Commit: f25af28f6667fa3984fd64bd5c17d906c5e1510a https://github.com/galaxyproject/galaxy/commit/f25af28f6667fa3984fd64bd5c17… Author: Helena Rasche <erasche(a)users.noreply.github.com> Date: 2018-07-11 (Wed, 11 Jul 2018) Changed paths: M scripts/grt/export.py M scripts/grt/grt.yml.sample M scripts/grt/upload.py Log Message: ----------- Merge pull request #6478 from martenson/telescope-logging GRT: fix the upload logging init Compare: https://github.com/galaxyproject/galaxy/compare/038da2e3e65b...f25af28f6667 **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 6ca7db: Fix for show params server error for https://githu...
by GitHub 10 Jul '18

10 Jul '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 6ca7db806b953a183fa192bcc0739540599348fa https://github.com/galaxyproject/galaxy/commit/6ca7db806b953a183fa192bcc073… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2018-07-10 (Tue, 10 Jul 2018) Changed paths: M templates/show_params.mako Log Message: ----------- Fix for show params server error for https://github.com/galaxyproject/galaxy/pull/6480 Commit: 038da2e3e65b8bb21fcf77a186f02db1aae563f2 https://github.com/galaxyproject/galaxy/commit/038da2e3e65b8bb21fcf77a186f0… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-07-10 (Tue, 10 Jul 2018) Changed paths: M templates/show_params.mako Log Message: ----------- Merge pull request #6486 from blankenberg/show-param Fix for show params server error Compare: https://github.com/galaxyproject/galaxy/compare/0860fdf13497...038da2e3e65b **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/usegalaxy-playbook] aaf8aa: add intermine to Test configs
by GitHub 10 Jul '18

10 Jul '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: aaf8aae9226a9dac206dc28524b8a3ce1ce89c6f https://github.com/galaxyproject/usegalaxy-playbook/commit/aaf8aae9226a9dac… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-07-10 (Tue, 10 Jul 2018) Changed paths: M env/test/files/galaxy/config/tool_conf.xml M env/test/files/galaxy/config/tool_data_table_conf.xml M env/test/files/galaxy/var/integrated_tool_panel.xml Log Message: ----------- add intermine to Test configs **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/usegalaxy-playbook] 4a97ec: install imtermine exchange converter, update Test
by GitHub 10 Jul '18

10 Jul '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 4a97eced1ece9f8351168aa1d132c50d4628ad0e https://github.com/galaxyproject/usegalaxy-playbook/commit/4a97eced1ece9f83… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-07-10 (Tue, 10 Jul 2018) Changed paths: M env/test/files/galaxy/galaxy_version.yml M env/test/files/galaxy/var/integrated_tool_panel.xml M env/test/files/galaxy/var/shed_tool_conf.xml Log Message: ----------- install imtermine exchange converter, update Test **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 9f0018: Add more information to the dataset template
by GitHub 10 Jul '18

10 Jul '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 9f001807df651ec2792902aa82dd48ea0f937205 https://github.com/galaxyproject/galaxy/commit/9f001807df651ec2792902aa82dd… Author: Helena Rasche <hxr(a)hx42.org> Date: 2018-07-10 (Tue, 10 Jul 2018) Changed paths: M templates/show_params.mako Log Message: ----------- Add more information to the dataset template Commit: 04db42343ce9840a078f0f0178a667e20c982b17 https://github.com/galaxyproject/galaxy/commit/04db42343ce9840a078f0f0178a6… Author: Helena Rasche <hxr(a)hx42.org> Date: 2018-07-10 (Tue, 10 Jul 2018) Changed paths: M templates/show_params.mako Log Message: ----------- Address review comments Commit: 4bf2d60d6cdc1ef20a275aaf37d602c33005a865 https://github.com/galaxyproject/galaxy/commit/4bf2d60d6cdc1ef20a275aaf37d6… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2018-07-10 (Tue, 10 Jul 2018) Changed paths: M templates/show_params.mako Log Message: ----------- Use horizontal <th> Commit: 0860fdf134978f634707bf3f6aa18e1517f89bbb https://github.com/galaxyproject/galaxy/commit/0860fdf134978f634707bf3f6aa1… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2018-07-10 (Tue, 10 Jul 2018) Changed paths: M templates/show_params.mako Log Message: ----------- Merge pull request #6480 from erasche/more-job-info Add more information to the dataset template Compare: https://github.com/galaxyproject/galaxy/compare/ce09f53e24ff...0860fdf13497 **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 019f08: Allow including paths in inputs json files.
by GitHub 10 Jul '18

10 Jul '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 019f088543736cecf74febd414782d7a207acd9c https://github.com/galaxyproject/galaxy/commit/019f088543736cecf74febd41478… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/parameters/wrapped_json.py M lib/galaxy/tools/xsd/galaxy.xsd A test/functional/tools/inputs_as_json_with_paths.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Allow including paths in inputs json files. Commit: 6af48d90dbb64b9aa01b9876ae5b10cbe17e5f09 https://github.com/galaxyproject/galaxy/commit/6af48d90dbb64b9aa01b9876ae5b… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- data_stype to data_style Commit: ce09f53e24ff992d7f39fc94d01b75a1cbcee1fe https://github.com/galaxyproject/galaxy/commit/ce09f53e24ff992d7f39fc94d01b… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-07-09 (Mon, 09 Jul 2018) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/parameters/wrapped_json.py M lib/galaxy/tools/xsd/galaxy.xsd A test/functional/tools/inputs_as_json_with_paths.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge pull request #6468 from jmchilton/allow_including_paths_in_inputs_json Allow including paths in inputs json files. Compare: https://github.com/galaxyproject/galaxy/compare/60fc4baa4c3a...ce09f53e24ff **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/usegalaxy-playbook] f9cadc: Update SnpEff build to 4.3+T.galaxy3
by GitHub 10 Jul '18

10 Jul '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: f9cadc3a86a865fd95d60b4e4c6394156ce1df95 https://github.com/galaxyproject/usegalaxy-playbook/commit/f9cadc3a86a865fd… Author: Dave B <dave(a)bx.psu.edu> Date: 2018-07-09 (Mon, 09 Jul 2018) Changed paths: M env/main/files/galaxy/var/integrated_tool_panel.xml M env/main/files/galaxy/var/shed_tool_conf.xml M env/main/files/galaxy/var/shed_tool_data_table_conf.xml Log Message: ----------- Update SnpEff build to 4.3+T.galaxy3 **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/usegalaxy-playbook] 9454f7: Markdown missing code closing tag
by GitHub 09 Jul '18

09 Jul '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 9454f715b8c2c9797fee64379c86164504a0788e https://github.com/galaxyproject/usegalaxy-playbook/commit/9454f715b8c2c979… Author: Mark Esler <eslerm(a)umn.edu> Date: 2018-07-09 (Mon, 09 Jul 2018) Changed paths: M roles/galaxyproject.galaxy/README.md Log Message: ----------- Markdown missing code closing tag Commit: 39e34574fa086c1ad0745da177ebf401585c73eb https://github.com/galaxyproject/usegalaxy-playbook/commit/39e34574fa086c1a… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-07-09 (Mon, 09 Jul 2018) Changed paths: M roles/galaxyproject.galaxy/README.md Log Message: ----------- Merge pull request #148 from eslerm/patch-1 Markdown missing code closing tag Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/bd52ea967973...… **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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