Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 1a2cd725bb303e8db6fa07118f4714b7c0516e60 https://github.com/galaxyproject/galaxy/commit/1a2cd725bb303e8db6fa07118f471... Author: M Bernt <m.bernt@ufz.de> Date: 2018-06-20 (Wed, 20 Jun 2018) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py Log Message: ----------- added daa (diamond alignment) datatype Commit: 68dc4c26508087829150b8e5c6d3530a47202304 https://github.com/galaxyproject/galaxy/commit/68dc4c26508087829150b8e5c6d35... Author: M Bernt <m.bernt@ufz.de> Date: 2018-06-20 (Wed, 20 Jun 2018) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- removed try-except and used with Commit: 3b6ab3ecd087786113daa81e8cb0beda9a8eff82 https://github.com/galaxyproject/galaxy/commit/3b6ab3ecd087786113daa81e8cb0b... Author: M Bernt <m.bernt@ufz.de> Date: 2018-06-20 (Wed, 20 Jun 2018) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- shortened code Commit: e636bf00c64354bea8236cbfec81074f19b6a295 https://github.com/galaxyproject/galaxy/commit/e636bf00c64354bea8236cbfec810... Author: M Bernt <m.bernt@ufz.de> Date: 2018-06-20 (Wed, 20 Jun 2018) Changed paths: A lib/galaxy/datatypes/test/diamond.daa Log Message: ----------- added missing test file Commit: a651b6af1ea04041aa4fa4230786e255b5fb954a https://github.com/galaxyproject/galaxy/commit/a651b6af1ea04041aa4fa4230786e... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-06-20 (Wed, 20 Jun 2018) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- Minor cosmetics on diamond datatypes Commit: 46788b99b2386c165a9edc899d9a0a7fdafaba05 https://github.com/galaxyproject/galaxy/commit/46788b99b2386c165a9edc899d9a0... Author: M Bernt <m.bernt@ufz.de> Date: 2018-06-20 (Wed, 20 Jun 2018) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- added sniffer entry in data_types.conf.sample Commit: 891b8923bfbdd9c51e41f334185589b4ca87280d https://github.com/galaxyproject/galaxy/commit/891b8923bfbdd9c51e41f33418558... Author: M Bernt <m.bernt@ufz.de> Date: 2018-06-21 (Thu, 21 Jun 2018) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- fixed typo in test this commit introduces also debug output for DAA and DMND snifferes which needs to be removed before merging Commit: 116c7051c9f4cc8e4b36577a3477a1bfcdc4b7d9 https://github.com/galaxyproject/galaxy/commit/116c7051c9f4cc8e4b36577a3477a... Author: M Bernt <m.bernt@ufz.de> Date: 2018-06-22 (Fri, 22 Jun 2018) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- daa detection: fixed typo and removed debug output Commit: 14ef3b8643eb96a98b1f39391c1f385596d1cb42 https://github.com/galaxyproject/galaxy/commit/14ef3b8643eb96a98b1f39391c1f3... Author: Björn Grüning <bjoern@gruenings.eu> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M .ci/flake8_blacklist.txt M .travis.yml 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 R client/galaxy/docs/galaxy-styles.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/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 A client/galaxy/scripts/components/admin/DataTypes.vue M client/galaxy/scripts/galaxy.pages.js A client/galaxy/scripts/layout/data.js M client/galaxy/scripts/layout/masthead.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/mvc/collection/list-of-pairs-collection-creator.js M client/galaxy/scripts/mvc/history/history-view-edit.js M client/galaxy/scripts/mvc/history/job-dag.js M client/galaxy/scripts/mvc/library/library-folderlist-view.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/ui/ui-misc.js M client/galaxy/scripts/mvc/ui/ui-options.js M client/galaxy/scripts/mvc/visualization/chart/components/model.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-manager.js M client/galaxy/scripts/mvc/workflow/workflow-view-data.js M client/galaxy/scripts/mvc/workflow/workflow-view-terminals.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M client/galaxy/scripts/reports/run_stats.js M client/galaxy/scripts/utils/config.js M client/galaxy/scripts/utils/uploadbox.js M client/galaxy/scripts/viz/circster.js M client/galaxy/scripts/viz/sweepster.js M client/galaxy/scripts/viz/trackster/painters.js M client/galaxy/scripts/viz/trackster/tracks.js M client/galaxy/scripts/viz/visualization.js M client/galaxy/style/scss/base.scss M client/galaxy/style/scss/galaxy_bootstrap/variables.scss M client/galaxy/style/scss/galaxy_variables.scss M client/galaxy/style/scss/theme/blue.scss M client/galaxy/style/scss/ui.scss M client/galaxy/style/scss/upload.scss M client/package.json M client/styleguide.config.js M client/webpack.config.js M client/yarn.lock M config/datatypes_conf.xml.sample M config/plugins/visualizations/msa/config/msa.xml M lib/galaxy/datatypes/binary.py A lib/galaxy/datatypes/converters/bam_to_bai.xml M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/proteomics.py M lib/galaxy/datatypes/sniff.py A lib/galaxy/datatypes/test/empty.txt M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt M lib/galaxy/dependencies/pipfiles/develop/Pipfile.lock M lib/galaxy/dependencies/pipfiles/develop/pinned-requirements.txt M lib/galaxy/dependencies/pipfiles/flake8/Pipfile.lock M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/dynamic_tool_destination.py R lib/galaxy/jobs/error_level.py M lib/galaxy/jobs/output_checker.py M lib/galaxy/jobs/runners/chronos.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/managers/rbac_secured.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/metadata.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/tools/parser/cwl.py A lib/galaxy/tools/parser/error_level.py M lib/galaxy/tools/parser/interface.py M lib/galaxy/tools/parser/util.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/relabel_from_file.xml M lib/galaxy/tools/util/maf_utilities.py M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/util/__init__.py M lib/galaxy/util/checkers.py M lib/galaxy/util/json.py M lib/galaxy/visualization/plugins/interactive_environments.py M lib/galaxy/visualization/plugins/plugin.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py M scripts/grt/export.py M static/style/blue/base.css R templates/admin/view_datatypes_registry.mako M templates/base/base_panels.mako M templates/webapps/galaxy/galaxy.panels.mako M templates/webapps/galaxy/workflow/editor.mako M templates/webapps/tool_shed/base_panels.mako M test/api/test_tools.py M test/functional/test_data_managers.py M test/functional/test_toolbox.py M test/unit/datatypes/dataproviders/test_base_dataproviders.py M test/unit/datatypes/test_bam.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_security_helper.py M test/unit/tools/test_evaluation.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_VisualizationsRegistry.py M test/unit/workflows/test_extract_summary.py M tools/data_source/upload.py Log Message: ----------- Merge branch 'dev' into topic/daa Commit: 9a06474a30cb82122ee6a78c30eca601af9d6578 https://github.com/galaxyproject/galaxy/commit/9a06474a30cb82122ee6a78c30eca... Author: Björn Grüning <bjoern@gruenings.eu> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py A lib/galaxy/datatypes/test/diamond.daa Log Message: ----------- Merge pull request #6313 from bernt-matthias/topic/daa added daa (diamond alignment) datatype Compare: https://github.com/galaxyproject/galaxy/compare/1f57706abffb...9a06474a30cb **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.