[galaxy-commits] [galaxyproject/galaxy] 3ae47e: Merge remote-tracking branch 'galaxyproject/dev' i...

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 3ae47e611d2582c543d42a69d0c320634a70150f https://github.com/galaxyproject/galaxy/commit/3ae47e611d2582c543d42a69d0c32... Author: Jim Johnson <jj@umn.edu> Date: 2018-01-22 (Mon, 22 Jan 2018) Changed paths: A .ci/autopep8.sh A .ci/check_py3_compatibility.sh M .ci/first_startup.sh M .ci/flake8_blacklist.txt A .ci/flake8_docstrings_include_list.txt R .ci/flake8_lint_include_list.txt R .ci/flake8_py3_wrapper.sh M .ci/flake8_wrapper.sh A .ci/flake8_wrapper_docstrings.sh R .ci/flake8_wrapper_imports.sh A .ci/jenkins/api/run_tests.sh A .ci/jenkins/framework/run_tests.sh A .ci/jenkins/integration/run_tests.sh A .ci/jenkins/selenium-compose/Dockerfile A .ci/jenkins/selenium-compose/docker-compose.yml A .ci/jenkins/selenium-compose/galaxy.ini A .ci/jenkins/selenium-compose/run_galaxy.bash A .ci/jenkins/selenium-compose/run_tests.sh A .ci/jenkins/selenium/run_tests.sh A .ci/jenkins/toolshed/run_tests.sh R .ci/py3_sources.txt M .gitignore M .travis.yml M CITATION M CONTRIBUTING.md M CONTRIBUTORS.md M Makefile M README.rst A SECURITY_POLICY.md A client/.babelrc M client/GruntFile.js M client/README.md M client/bower.json A client/galaxy/scripts/admin.toolshed.js A client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/analysis.js A client/galaxy/scripts/apps/extended.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 A client/galaxy/scripts/components/Citations.vue A client/galaxy/scripts/components/HistoryImport.vue A client/galaxy/scripts/components/Message.vue A client/galaxy/scripts/components/admin/BaseGrid.vue A client/galaxy/scripts/components/admin/DataManagerGrid.vue A client/galaxy/scripts/components/admin/DataTables.vue A client/galaxy/scripts/components/admin/DataTablesGrid.vue A client/galaxy/scripts/components/admin/UserAPIKeys.vue M client/galaxy/scripts/galaxy.interactive_environments.js M client/galaxy/scripts/galaxy.js M client/galaxy/scripts/galaxy.library.js M client/galaxy/scripts/galaxy.pages.js M client/galaxy/scripts/i18n.js M 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 A client/galaxy/scripts/layout/router.js M client/galaxy/scripts/layout/scratchbook.js A client/galaxy/scripts/legacy/grid/grid-model.js A client/galaxy/scripts/legacy/grid/grid-template.js A client/galaxy/scripts/legacy/grid/grid-view.js R client/galaxy/scripts/libs/backbone.js R client/galaxy/scripts/libs/bibtex.js R client/galaxy/scripts/libs/d3.js R client/galaxy/scripts/libs/jquery.complexify.js R client/galaxy/scripts/libs/jquery/jqtouch.js M client/galaxy/scripts/libs/jquery/jquery.autocomplete.js R client/galaxy/scripts/libs/jquery/jquery.cookie.js R client/galaxy/scripts/libs/jquery/jquery.js R 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client/galaxy/scripts/mvc/ui/ui-select-ftp.js A client/galaxy/scripts/mvc/ui/ui-select-genomespace.js M client/galaxy/scripts/mvc/ui/ui-select-library.js M client/galaxy/scripts/mvc/ui/ui-select.js M client/galaxy/scripts/mvc/ui/ui-slider.js M client/galaxy/scripts/mvc/ui/ui-table.js M client/galaxy/scripts/mvc/ui/ui-tabs.js A client/galaxy/scripts/mvc/ui/ui-thumbnails.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/composite/composite-row.js M client/galaxy/scripts/mvc/upload/composite/composite-view.js M client/galaxy/scripts/mvc/upload/default/default-row.js M client/galaxy/scripts/mvc/upload/default/default-view.js M client/galaxy/scripts/mvc/upload/upload-button.js A client/galaxy/scripts/mvc/upload/upload-extension.js M client/galaxy/scripts/mvc/upload/upload-ftp.js M client/galaxy/scripts/mvc/upload/upload-model.js M 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client/toolshed/scripts/mvc/groups/group-model.js R client/toolshed/scripts/toolshed.groups.js M client/webpack.config.js A client/yarn.lock M config/auth_conf.xml.sample A config/build_sites.yml.sample A config/containers_conf.yml.sample M config/datatypes_conf.xml.sample M config/dependency_resolvers_conf.xml.sample A config/error_report.yml.sample R config/external_service_types_conf.xml.sample R config/galaxy.ini.sample A config/galaxy.yml.sample M config/job_conf.xml.sample_advanced A config/lmod_modules_mapping.yml.sample A config/local_conda_mapping.yml.sample M config/object_store_conf.xml.sample M config/openid_conf.xml.sample A config/plugins/interactive_environments/askomics/config/allowed_images.yml.sample A config/plugins/interactive_environments/askomics/config/askomics.ini.sample A config/plugins/interactive_environments/askomics/config/askomics.xml A config/plugins/interactive_environments/askomics/static/js/askomics.js A 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config/plugins/tours/core.scratchbook.yaml R config/plugins/visualizations/charts/Gruntfile.js M config/plugins/visualizations/charts/config/charts.xml M config/plugins/visualizations/charts/package.json R config/plugins/visualizations/charts/sample.txt R config/plugins/visualizations/charts/static/app.css R config/plugins/visualizations/charts/static/app.js R config/plugins/visualizations/charts/static/charts/jqplot/bar/config.js R config/plugins/visualizations/charts/static/charts/jqplot/bar/logo.png R config/plugins/visualizations/charts/static/charts/jqplot/bar/wrapper.js R config/plugins/visualizations/charts/static/charts/jqplot/boxplot/config.js R config/plugins/visualizations/charts/static/charts/jqplot/boxplot/logo.png R config/plugins/visualizations/charts/static/charts/jqplot/boxplot/wrapper.js R config/plugins/visualizations/charts/static/charts/jqplot/common/config.js R config/plugins/visualizations/charts/static/charts/jqplot/common/plot-config.js R 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test-data/random-file A test-data/sam_with_header.sam Log Message: ----------- Merge remote-tracking branch 'galaxyproject/dev' into dev Commit: 007e3cc2db247096cf06b59d4c7583112dacd7fa https://github.com/galaxyproject/galaxy/commit/007e3cc2db247096cf06b59d4c758... Author: Jim Johnson <jj@umn.edu> Date: 2018-01-22 (Mon, 22 Jan 2018) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/interval.py Log Message: ----------- Add Proteomics datatypes proBAM and proBED Add datatypes proBAM and proBED for genomic alignment and annotation of proteomic analysis results. Commit: 0367a356d528b3ca395eec1f3de57563cba19c2e https://github.com/galaxyproject/galaxy/commit/0367a356d528b3ca395eec1f3de57... Author: Björn Grüning <bjoern@gruenings.eu> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/interval.py Log Message: ----------- Merge pull request #5360 from jj-umn/dev Add Proteomics datatypes proBAM and proBED Compare: https://github.com/galaxyproject/galaxy/compare/587f20cf9c0b...0367a356d528