Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 1534d9d8b40c468ee0fa70342be4a83ff50bb2c8 https://github.com/galaxyproject/galaxy/commit/1534d9d8b40c468ee0fa70342be4a... Author: Matthias Bernt <bernt.matthias@gmail.com> Date: 2017-09-01 (Fri, 01 Sep 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/style/less/ui.less M lib/galaxy/datatypes/registry.py M lib/galaxy/jobs/actions/post.py M lib/galaxy/managers/tags.py M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/wrappers.py M static/maps/mvc/tool/tool-form-base.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-base.js M static/style/blue/base.css M test/functional/tools/sample_datatypes_conf.xml Log Message: ----------- Merge remote-tracking branch 'upstream/master' into dev Commit: 4de7f0efd136f355395a741c9a865df71967f676 https://github.com/galaxyproject/galaxy/commit/4de7f0efd136f355395a741c9a865... Author: Matthias Bernt <bernt.matthias@gmail.com> Date: 2017-09-07 (Thu, 07 Sep 2017) Changed paths: A .ci/autopep8.sh M .ci/flake8_lint_include_list.txt M .ci/jenkins/selenium/docker-compose.yml M .ci/py3_sources.txt M .gitignore M CONTRIBUTING.md M Makefile A SECURITY_POLICY.md M client/bower.json M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/apps/panels/admin-panel.js M client/galaxy/scripts/apps/panels/tool-panel.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/layout/menu.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 R client/galaxy/scripts/libs/jquery/jqtouch.js M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/collection/list-collection-creator.js M 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tools/filters/wiggle_to_simple.py M tools/genomespace/genomespace_exporter.py M tools/genomespace/genomespace_exporter.xml M tools/genomespace/genomespace_file_browser.py R tools/genomespace/genomespace_file_browser_dev.xml R tools/genomespace/genomespace_file_browser_prod.xml R tools/genomespace/genomespace_file_browser_test.xml M tools/genomespace/genomespace_importer.py M tools/genomespace/genomespace_importer.xml A tools/genomespace/genomespace_push.xml M tools/maf/interval2maf.py M tools/maf/interval_maf_to_merged_fasta.py M tools/maf/maf_by_block_number.py M tools/maf/maf_filter.py M tools/maf/maf_limit_size.py M tools/maf/maf_limit_to_species.py M tools/maf/maf_reverse_complement.py M tools/maf/maf_split_by_species.py M tools/maf/maf_stats.py M tools/maf/maf_thread_for_species.py M tools/maf/maf_to_bed.py M tools/maf/maf_to_bed_code.py M tools/maf/maf_to_fasta_concat.py M tools/maf/maf_to_fasta_multiple_sets.py M tools/maf/maf_to_interval.py M tools/maf/vcf_to_maf_customtrack.py M tools/meme/fimo_wrapper.py M tools/metag_tools/blat_wrapper.py M tools/metag_tools/shrimp_color_wrapper.py M tools/metag_tools/shrimp_wrapper.py M tools/next_gen_conversion/fastq_conversions.py M tools/next_gen_conversion/fastq_gen_conv.py M tools/next_gen_conversion/solid2fastq.py M tools/next_gen_conversion/solid_to_fastq.py M tools/ngs_simulation/ngs_simulation.py M tools/plotting/bar_chart.py M tools/solid_tools/maq_cs_wrapper.py M tools/solid_tools/solid_qual_stats.py M tools/sr_assembly/velvetg.xml M tools/sr_assembly/velvetg_wrapper.py M tools/sr_assembly/velveth_wrapper.py M tools/sr_mapping/bfast_wrapper.py M tools/sr_mapping/srma_wrapper.py M tools/stats/aggregate_scores_in_intervals.py M tools/stats/filtering.py M tools/stats/grouping.py M tools/stats/gsummary.py M tools/visualization/LAJ.py M tools/visualization/LAJ_code.py M tox.ini Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into dev Commit: 5a3ada59615d81907baad36699597a7d855d9d5c https://github.com/galaxyproject/galaxy/commit/5a3ada59615d81907baad36699597... Author: Matthias Bernt <bernt.matthias@gmail.com> Date: 2017-10-23 (Mon, 23 Oct 2017) Changed paths: M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/mvc/base/controlled-fetch-collection.js M client/galaxy/scripts/mvc/grid/grid-shared.js M client/galaxy/scripts/mvc/grid/grid-view.js M client/galaxy/scripts/mvc/history/history-list.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/options-menu.js M client/galaxy/scripts/mvc/library/library-dataset-view.js M client/galaxy/scripts/mvc/library/library-folder-view.js M client/galaxy/scripts/mvc/library/library-folderlist-view.js M client/galaxy/scripts/mvc/library/library-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/tours.js M client/galaxy/scripts/mvc/user/user-preferences.js M client/galaxy/scripts/mvc/workflow/workflow.js M client/galaxy/scripts/utils/uploadbox.js M client/galaxy/scripts/utils/utils.js M client/galaxy/style/less/library.less M client/toolshed/scripts/mvc/groups/group-list-view.js M config/datatypes_conf.xml.sample M config/galaxy.ini.sample A config/plugins/interactive_environments/hicbrowser/config/allowed_images.yml.sample A config/plugins/interactive_environments/hicbrowser/config/hicbrowser.ini.sample A config/plugins/interactive_environments/hicbrowser/config/hicbrowser.xml A config/plugins/interactive_environments/hicbrowser/static/js/hicbrowser.js A config/plugins/interactive_environments/hicbrowser/templates/hicbrowser.mako M lib/galaxy/app.py M lib/galaxy/config.py M lib/galaxy/datatypes/binary.py R lib/galaxy/datatypes/converters/bam_to_bai.xml A lib/galaxy/datatypes/converters/biom1_to_biom2.xml A lib/galaxy/datatypes/converters/biom2_to_biom1.xml M lib/galaxy/datatypes/dataproviders/base.py M lib/galaxy/datatypes/dataproviders/dataset.py M lib/galaxy/datatypes/dataproviders/external.py M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/sniff.py A lib/galaxy/datatypes/test/biom2_sparse_otu_table_hdf5.biom A lib/galaxy/datatypes/test/test.fast5.tar A lib/galaxy/datatypes/test/test.fast5.tar.bz2 A lib/galaxy/datatypes/test/test.fast5.tar.gz M lib/galaxy/datatypes/text.py M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/command_factory.py M lib/galaxy/jobs/runners/cli.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/jobs/runners/state_handlers/_safe_eval.py M lib/galaxy/jobs/runners/tasks.py M lib/galaxy/jobs/runners/util/cli/shell/rsh.py M lib/galaxy/model/metadata.py M lib/galaxy/objectstore/azure_blob.py M lib/galaxy/objectstore/pulsar.py M lib/galaxy/tools/actions/metadata.py M lib/galaxy/tools/actions/upload.py M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/tools/evaluation.py M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/galaxy/workflow/run.py M lib/galaxy_ext/metadata/set_metadata.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py M lib/tool_shed/grids/repository_grids.py M static/maps/layout/page.js.map M static/maps/mvc/base/controlled-fetch-collection.js.map M static/maps/mvc/grid/grid-shared.js.map M static/maps/mvc/grid/grid-view.js.map M static/maps/mvc/history/history-list.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/options-menu.js.map M static/maps/mvc/library/library-dataset-view.js.map M static/maps/mvc/library/library-folder-view.js.map M static/maps/mvc/library/library-folderlist-view.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/maps/mvc/library/library-library-view.js.map M static/maps/mvc/library/library-librarylist-view.js.map M static/maps/mvc/tours.js.map M static/maps/mvc/user/user-preferences.js.map M static/maps/mvc/workflow/workflow.js.map M static/maps/utils/uploadbox.js.map M static/maps/utils/utils.js.map M static/scripts/bundled/admin.bundled.js M 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/layout/page.js M static/scripts/mvc/base/controlled-fetch-collection.js M static/scripts/mvc/grid/grid-shared.js M static/scripts/mvc/grid/grid-view.js M static/scripts/mvc/history/history-list.js M static/scripts/mvc/history/history-view-edit.js M static/scripts/mvc/history/options-menu.js M static/scripts/mvc/library/library-dataset-view.js M static/scripts/mvc/library/library-folder-view.js M static/scripts/mvc/library/library-folderlist-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/library/library-library-view.js M static/scripts/mvc/library/library-librarylist-view.js M static/scripts/mvc/tours.js M static/scripts/mvc/user/user-preferences.js M static/scripts/mvc/workflow/workflow.js M static/scripts/utils/uploadbox.js M static/scripts/utils/utils.js M static/style/blue/base.css M static/style/blue/library.css M templates/webapps/galaxy/workflow/editor.mako M test/api/test_workflows.py M test/galaxy_selenium/has_driver.py M test/galaxy_selenium/navigates_galaxy.py M test/integration/test_upload_configuration_options.py M test/selenium_tests/test_history_panel.py M test/selenium_tests/test_history_sharing.py M test/selenium_tests/test_login.py M test/selenium_tests/test_published_histories_grid.py A test/selenium_tests/test_saved_histories.py M test/selenium_tests/test_workflow_editor.py M tools/data_source/upload.py Log Message: ----------- Merge branch 'dev' of https://github.com/bernt-matthias/galaxy into dev Commit: 496a10f0c1d0394f960f4a7405b2742609f6ad74 https://github.com/galaxyproject/galaxy/commit/496a10f0c1d0394f960f4a7405b27... Author: Matthias Bernt <bernt.matthias@gmail.com> Date: 2017-10-23 (Mon, 23 Oct 2017) Changed paths: M create_db.sh M extract_dataset_parts.sh M lib/galaxy/webhooks/__init__.py M manage_db.sh M manage_tools.sh M static/maps/mvc/base/controlled-fetch-collection.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/base/controlled-fetch-collection.js Log Message: ----------- Merge remote-tracking branch 'upstream/master' into dev Commit: 095a797548dab55b3af70c6be2c135de9f373aca https://github.com/galaxyproject/galaxy/commit/095a797548dab55b3af70c6be2c13... Author: Matthias Bernt <m.bernt@ufz.de> Date: 2017-10-24 (Tue, 24 Oct 2017) Changed paths: M .ci/flake8_lint_include_list.txt R .ci/flake8_py3_wrapper.sh M .ci/jenkins/selenium/Dockerfile M .ci/jenkins/selenium/docker-compose.yml M .ci/jenkins/selenium/galaxy.ini M .ci/jenkins/selenium/run_galaxy.bash M .ci/jenkins/selenium/run_tests.sh M .ci/py3_sources.txt M .gitignore M .travis.yml M CITATION M Makefile A client/.babelrc M client/GruntFile.js M client/README.md M client/bower.json M client/galaxy/scripts/admin.toolshed.js M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/apps/login.js M client/galaxy/scripts/apps/panels/admin-panel.js M client/galaxy/scripts/apps/panels/history-panel.js M client/galaxy/scripts/apps/panels/tool-panel.js 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 M client/galaxy/scripts/layout/router.js M client/galaxy/scripts/layout/scratchbook.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/jquery.cookie.js R client/galaxy/scripts/libs/jquery/jquery.js R client/galaxy/scripts/libs/jquery/jquery.migrate.js R client/galaxy/scripts/libs/jquery/jquery.mousewheel.js R client/galaxy/scripts/libs/raven.js R client/galaxy/scripts/libs/require.js R client/galaxy/scripts/libs/underscore.js M client/galaxy/scripts/mvc/annotation.js M client/galaxy/scripts/mvc/base-mvc.js M client/galaxy/scripts/mvc/base/controlled-fetch-collection.js M client/galaxy/scripts/mvc/citation/citation-model.js M client/galaxy/scripts/mvc/citation/citation-view.js M client/galaxy/scripts/mvc/collection/base-creator.js M client/galaxy/scripts/mvc/collection/collection-li-edit.js M client/galaxy/scripts/mvc/collection/collection-li.js M client/galaxy/scripts/mvc/collection/collection-model.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/data.js M client/galaxy/scripts/mvc/dataset/dataset-choice.js M client/galaxy/scripts/mvc/dataset/dataset-edit-attributes.js M client/galaxy/scripts/mvc/dataset/dataset-error.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/dataset/dataset-list.js M client/galaxy/scripts/mvc/dataset/dataset-model.js M client/galaxy/scripts/mvc/dataset/states.js M client/galaxy/scripts/mvc/form/form-data.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-repeat.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 client/galaxy/scripts/mvc/grid/grid-template.js M client/galaxy/scripts/mvc/grid/grid-view.js M client/galaxy/scripts/mvc/history/copy-dialog.js M client/galaxy/scripts/mvc/history/hda-li-edit.js M client/galaxy/scripts/mvc/history/hda-li.js M client/galaxy/scripts/mvc/history/hda-model.js M client/galaxy/scripts/mvc/history/hdca-li-edit.js M client/galaxy/scripts/mvc/history/hdca-li.js M client/galaxy/scripts/mvc/history/hdca-model.js M client/galaxy/scripts/mvc/history/history-content-model.js M client/galaxy/scripts/mvc/history/history-contents.js M client/galaxy/scripts/mvc/history/history-list.js M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/history-preferences.js M client/galaxy/scripts/mvc/history/history-structure-view.js M client/galaxy/scripts/mvc/history/history-view-annotated.js M client/galaxy/scripts/mvc/history/history-view-edit-current.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/job-dag.js M client/galaxy/scripts/mvc/history/multi-panel.js M client/galaxy/scripts/mvc/history/options-menu.js M client/galaxy/scripts/mvc/job/job-li.js M client/galaxy/scripts/mvc/job/job-model.js M client/galaxy/scripts/mvc/job/job-params.js A client/galaxy/scripts/mvc/lazy/lazy-limited.js M client/galaxy/scripts/mvc/library/library-dataset-view.js M client/galaxy/scripts/mvc/library/library-folder-view.js M client/galaxy/scripts/mvc/library/library-folderlist-view.js M client/galaxy/scripts/mvc/library/library-folderrow-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/library/library-library-view.js M client/galaxy/scripts/mvc/library/library-librarylist-view.js M client/galaxy/scripts/mvc/library/library-libraryrow-view.js M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js M client/galaxy/scripts/mvc/library/library-model.js M client/galaxy/scripts/mvc/list/list-item.js M client/galaxy/scripts/mvc/list/list-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 M client/galaxy/scripts/mvc/tool/tool-form.js M client/galaxy/scripts/mvc/tool/tool-genomespace.js M 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client/galaxy/scripts/mvc/ui/ui-misc.js M client/galaxy/scripts/mvc/ui/ui-modal.js M client/galaxy/scripts/mvc/ui/ui-options.js M client/galaxy/scripts/mvc/ui/ui-popover.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-select-ftp.js M 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 M client/galaxy/scripts/mvc/ui/ui-thumbnails.js M client/galaxy/scripts/mvc/upload/collection/collection-row.js M 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 client/galaxy/scripts/mvc/upload/upload-settings.js M client/galaxy/scripts/mvc/upload/upload-view.js M client/galaxy/scripts/mvc/user/user-custom-builds.js M client/galaxy/scripts/mvc/user/user-model.js M client/galaxy/scripts/mvc/user/user-preferences.js M client/galaxy/scripts/mvc/user/user-quotameter.js M client/galaxy/scripts/mvc/visualization/visualization-model.js M client/galaxy/scripts/mvc/webhooks.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-icons.js M client/galaxy/scripts/mvc/workflow/workflow-manager.js M client/galaxy/scripts/mvc/workflow/workflow-model.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/nls/de/locale.js M client/galaxy/scripts/nls/es/locale.js M 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/onload.js M client/galaxy/scripts/polyfills.js M client/galaxy/scripts/reports_webapp/run_stats.js M client/galaxy/scripts/ui/autocom_tagging.js M client/galaxy/scripts/ui/editable-text.js M 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client/webpack.config.js A client/yarn.lock M config/datatypes_conf.xml.sample M config/error_report.yml.sample M config/galaxy.ini.sample M config/plugins/interactive_environments/common/templates/ie.mako M config/plugins/interactive_environments/jupyter/static/js/jupyter.js M config/plugins/interactive_environments/jupyter/templates/jupyter.mako 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/webpack.config.js M config/plugins/webhooks/demo/tour_generator/static/script.js M contrib/galaxy_config_merger.py M cron/build_chrom_db.py M cron/parse_builds.py M cron/parse_builds_3_sites.py M doc/source/admin/reports.md M doc/source/slideshow/architecture/galaxy_architecture.md M lib/galaxy/__init__.py M lib/galaxy/app.py M lib/galaxy/config.py M lib/galaxy/containers/__init__.py M lib/galaxy/containers/docker_model.py M 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tools/filters/ucsc_gene_bed_to_exon_bed.py M tools/filters/ucsc_gene_bed_to_exon_bed.xml M tools/filters/ucsc_gene_bed_to_intron_bed.py M tools/filters/ucsc_gene_table_to_intervals.py M tools/metag_tools/shrimp_wrapper.py M tools/sr_assembly/velvetg_wrapper.py M tox.ini Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into dev Commit: c3911038a3c24e19544cf0f1f9f339ddcfcb954b https://github.com/galaxyproject/galaxy/commit/c3911038a3c24e19544cf0f1f9f33... Author: Matthias Bernt <m.bernt@ufz.de> Date: 2017-11-15 (Wed, 15 Nov 2017) Changed paths: R .ci/flake8_lint_include_list.txt R .ci/flake8_wrapper_imports.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 R .ci/jenkins/selenium/Dockerfile R .ci/jenkins/selenium/docker-compose.yml R .ci/jenkins/selenium/galaxy.ini R .ci/jenkins/selenium/run_galaxy.bash M .ci/jenkins/selenium/run_tests.sh M .travis.yml M Makefile M README.rst M client/.babelrc M client/galaxy/scripts/admin.toolshed.js M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/apps/login.js M client/galaxy/scripts/apps/panels/admin-panel.js M client/galaxy/scripts/apps/panels/history-panel.js M client/galaxy/scripts/apps/panels/tool-panel.js M client/galaxy/scripts/galaxy.interactive_environments.js M 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Author: Matthias Bernt <m.bernt@ufz.de> Date: 2017-11-20 (Mon, 20 Nov 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-forms.js M client/galaxy/scripts/mvc/workflow/workflow-node.js M config/datatypes_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 config/plugins/interactive_environments/askomics/templates/askomics.mako M lib/galaxy/datatypes/binary.py A lib/galaxy/datatypes/test/matrix.cool M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt M lib/galaxy/jobs/metrics/instrumenters/core.py M lib/galaxy/managers/collections.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/webapps/galaxy/api/configuration.py M lib/galaxy/webapps/galaxy/api/history_contents.py M lib/galaxy/webapps/galaxy/buildapp.py M static/maps/mvc/workflow/workflow-forms.js.map M static/maps/mvc/workflow/workflow-node.js.map M static/scripts/mvc/workflow/workflow-forms.js M static/scripts/mvc/workflow/workflow-node.js R templates/search/index.mako M templates/user/register.mako M test/api/test_configuration.py M test/api/test_history_contents.py M test/api/test_libraries.py M test/api/test_workflows.py M test/base/populators.py M test/functional/tools/create_2.xml M test/integration/test_data_manager_table_reload.py M tools/data_source/microbial_import.xml Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into dev Commit: bea258d957d28810c75fa6182687d46c0e3d8601 https://github.com/galaxyproject/galaxy/commit/bea258d957d28810c75fa6182687d... Author: Matthias Bernt <m.bernt@ufz.de> Date: 2018-01-02 (Tue, 02 Jan 2018) Changed paths: A .ci/check_py3_compatibility.sh M .ci/first_startup.sh R .ci/py3_sources.txt M .gitignore M .travis.yml M Makefile M client/GruntFile.js M client/README.md M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/analysis.js A client/galaxy/scripts/apps/extended.js M client/galaxy/scripts/apps/panels/admin-panel.js M client/galaxy/scripts/apps/panels/history-panel.js M client/galaxy/scripts/apps/panels/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 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Author: Matthias Bernt <m.bernt@ufz.de> Date: 2018-01-03 (Wed, 03 Jan 2018) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/tool/tool-form.js M config/datatypes_conf.xml.sample M config/user_preferences_extra_conf.yml.sample A lib/galaxy/datatypes/converters/neostorezip_to_neostore_converter.xml M lib/galaxy/datatypes/neo4j.py M lib/galaxy/datatypes/plant_tribes.py M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/conditional-requirements.txt M lib/galaxy/jobs/handler.py M lib/galaxy/managers/jobs.py M lib/galaxy/model/__init__.py M lib/galaxy/model/base.py M lib/galaxy/model/mapping.py A lib/galaxy/model/migrate/versions/0137_add_copied_from_job_id_column.py A lib/galaxy/model/migrate/versions/0138_add_hda_version.py A lib/galaxy/model/migrate/versions/0139_add_history_dataset_association_history_table.py A lib/galaxy/model/migrate/versions/0140_add_dataset_version_to_job_to_input_dataset_association_table.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/execute.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/webapps/galaxy/api/jobs.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/workflow/modules.py M lib/galaxy/workflow/run.py M lib/galaxy/workflow/run_request.py M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/libs.bundled.js A static/scripts/libs/vue.js M static/scripts/mvc/tool/tool-form-composite.js M static/scripts/mvc/tool/tool-form.js M test-data/neostore.zip M test/api/test_jobs.py M test/api/test_tools.py M test/api/test_workflows.py M test/base/api.py M test/base/data/test_workflow_1.ga M test/base/interactor.py A test/functional/tools/compressed_neostorezip_neostore_conversion.xml A test/functional/tools/compressed_neostorezip_neostore_no_conversion.xml Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into dev Commit: 92b2ac876d78a552b960c54bc95edae7514c5eaf https://github.com/galaxyproject/galaxy/commit/92b2ac876d78a552b960c54bc95ed... Author: Matthias Bernt <m.bernt@ufz.de> Date: 2018-01-16 (Tue, 16 Jan 2018) Changed paths: M .gitignore M Makefile M client/README.md M client/galaxy/scripts/components/Citations.vue M client/galaxy/scripts/components/HistoryImport.vue M client/galaxy/scripts/components/Message.vue M client/galaxy/scripts/components/admin/BaseGrid.vue M client/galaxy/scripts/components/admin/DataManagerGrid.vue M client/galaxy/scripts/components/admin/DataTables.vue M client/galaxy/scripts/components/admin/DataTablesGrid.vue M client/galaxy/scripts/mvc/dataset/dataset-error.js M client/galaxy/scripts/mvc/library/library-dataset-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/workflow/workflow-node.js M client/galaxy/scripts/nls/zh/locale.js M client/package.json M client/webpack.config.js M client/yarn.lock M config/datatypes_conf.xml.sample M config/galaxy.ini.sample M doc/source/admin/production.md M doc/source/admin/special_topics/nginx.md M doc/source/api/quickstart.rst M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/msa.py A lib/galaxy/datatypes/test/infernal_model.cm M lib/galaxy/managers/library_datasets.py M lib/galaxy/model/__init__.py M lib/galaxy/model/migrate/check.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/tools/sort_collection_list.xml M lib/galaxy/workflow/modules.py M scripts/common_startup.sh M scripts/db_shell.py M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/extended.bundled.js M static/scripts/bundled/libs.bundled.js R static/scripts/libs/vue.js M static/scripts/mvc/dataset/dataset-error.js M static/scripts/mvc/tool/tool-form-composite.js M static/scripts/mvc/workflow/workflow-node.js M static/scripts/nls/zh/locale.js A test-data/new_element_sort_order.txt M test/api/test_workflows.py M test/integration/test_upload_configuration_options.py M tools/data_source/upload.py Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into dev Commit: 8a06ffb3d1613ba1528d0bd400b3e19863623956 https://github.com/galaxyproject/galaxy/commit/8a06ffb3d1613ba1528d0bd400b3e... Author: Matthias Bernt <m.bernt@ufz.de> Date: 2018-01-18 (Thu, 18 Jan 2018) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form.js M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/tools/parser/output_collection_def.py M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M scripts/common_startup.sh M scripts/common_startup_functions.sh A test/functional/tools/multi_output_recurse.xml M test/functional/tools/samples_tool_conf.xml M test/unit/tools/test_collect_primary_datasets.py M tools/data_source/microbial_import_code.py Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into dev Commit: d4c7938ee233bfab6905babb5cc49c161d6a19aa https://github.com/galaxyproject/galaxy/commit/d4c7938ee233bfab6905babb5cc49... Author: Matthias Bernt <m.bernt@ufz.de> Date: 2018-01-20 (Sat, 20 Jan 2018) Changed paths: M .ci/jenkins/selenium/run_tests.sh M .gitignore M .travis.yml M Makefile M client/galaxy/scripts/mvc/tours.js M config/auth_conf.xml.sample M config/datatypes_conf.xml.sample R config/galaxy.ini.sample A config/galaxy.yml.sample M config/job_conf.xml.sample_advanced M doc/Makefile A doc/source/admin/_inc_proxy_prereq.rst A doc/source/admin/_inc_proxy_serving_root.rst A doc/source/admin/_inc_proxy_ssl.rst A doc/source/admin/apache.md M doc/source/admin/authentication.md M doc/source/admin/cluster.md M doc/source/admin/conda_faq.rst A doc/source/admin/config.rst A doc/source/admin/config_logging.rst M doc/source/admin/dependency_resolvers.rst A doc/source/admin/galaxy_options.rst M doc/source/admin/index.rst M doc/source/admin/jobs.md A doc/source/admin/nginx.md A doc/source/admin/options.rst M doc/source/admin/production.md A doc/source/admin/proxy_package_layout.rst M doc/source/admin/reports.md M doc/source/admin/reports.rst M doc/source/admin/scaling.md R doc/source/admin/special_topics/apache.md M doc/source/admin/special_topics/bug_reports.rst M doc/source/admin/special_topics/chat.rst M doc/source/admin/special_topics/ftp.md M doc/source/admin/special_topics/index.rst M doc/source/admin/special_topics/interactive_environments.rst R doc/source/admin/special_topics/nginx.md M doc/source/admin/special_topics/performance_tracking.rst M doc/source/admin/special_topics/webhooks.rst M doc/source/admin/tool_panel.rst M doc/source/conf.py M lib/galaxy/auth/__init__.py M lib/galaxy/auth/providers/ldap_ad.py A lib/galaxy/auth/util.py M lib/galaxy/config.py M lib/galaxy/datatypes/binary.py A lib/galaxy/datatypes/converters/bam_native_to_bam_converter.xml M lib/galaxy/datatypes/converters/bam_to_bigwig_converter.xml A lib/galaxy/datatypes/converters/sam_to_bam_native.xml M lib/galaxy/datatypes/sniff.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/rule_helper.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/pulsar.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/objectstore/__init__.py M lib/galaxy/security/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/data_manager/manager.py M lib/galaxy/tools/deps/containers.py M lib/galaxy/tools/deps/docker_util.py M lib/galaxy/tools/error_reports/plugins/sentry.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/parser/interface.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/toolbox/filters/__init__.py M lib/galaxy/tools/toolbox/watcher.py M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/util/path/__init__.py M lib/galaxy/web/stack/__init__.py M lib/galaxy/webapps/config_manage.py M lib/galaxy/webapps/galaxy/api/configuration.py M lib/galaxy/webapps/galaxy/api/histories.py A lib/galaxy/webapps/galaxy/config_schema.yml M lib/galaxy/webapps/galaxy/controllers/user.py A lib/galaxy/webapps/galaxy/uwsgi_schema.yml M lib/galaxy/webapps/reports/config.py M lib/galaxy/webapps/tool_shed/config.py M lib/tool_shed/util/admin_util.py M scripts/common_startup.sh M scripts/common_startup_functions.sh A scripts/common_startup_variables.sh M scripts/functional_tests.py M scripts/galaxy-main M scripts/get_uwsgi_args.py A scripts/maintenance.sh M scripts/tool_shed/bootstrap_tool_shed/bootstrap_tool_shed.sh M scripts/tool_shed/bootstrap_tool_shed/bootstrap_util.py M templates/user/register.mako M templates/webapps/galaxy/history/display_structured.mako A test-data/bam_native_from_sam.bam M test-data/sam_with_header.sam M test/base/driver_util.py M test/base/integration_util.py M test/docker/base/run_test_wrapper.sh A test/functional/tools/job_environment_default.xml A test/functional/tools/job_environment_default_legacy.xml A test/functional/tools/job_environment_explicit_shared_home.xml A test/functional/tools/mulled_example_explicit.xml A test/functional/tools/mulled_example_simple.xml A test/functional/tools/sam_to_bam_native.xml M test/functional/tools/sample_datatypes_conf.xml M test/functional/tools/samples_tool_conf.xml A test/integration/dockerized_job_conf.xml A test/integration/sets_tmp_dir_expression_job_conf.xml A test/integration/sets_tmp_dir_to_true_job_conf.xml A test/integration/simple_job_conf.xml A test/integration/test_dockerized_jobs.py A test/integration/test_job_environments.py A test/unit/config/1705_allow_path_paste/config/galaxy.ini A test/unit/config/__init__.py M test/unit/config/test_config_manage.py M test/unit/jobs/test_runner_local.py M test/unit/tools/test_evaluation.py Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into dev Commit: e47b2857b8cf5101ea8e9bdb7d20457ac6a08132 https://github.com/galaxyproject/galaxy/commit/e47b2857b8cf5101ea8e9bdb7d204... Author: Matthias Bernt <m.bernt@ufz.de> Date: 2018-01-30 (Tue, 30 Jan 2018) Changed paths: M .ci/jenkins/api/run_tests.sh M .ci/jenkins/selenium-compose/run_tests.sh M .ci/jenkins/selenium/run_tests.sh M client/galaxy/scripts/apps/extended.js M client/galaxy/scripts/mvc/base/controlled-fetch-collection.js M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/multi-panel.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/tool/tool-form.js M client/galaxy/style/less/base.less M client/galaxy/style/less/dataset.less M client/galaxy/style/less/history.less M config/datatypes_conf.xml.sample M config/galaxy.yml.sample M config/tool_shed.yml.sample M doc/Makefile M doc/source/admin/galaxy_options.rst M lib/galaxy/app.py M lib/galaxy/config.py A lib/galaxy/datatypes/phylip.py A lib/galaxy/datatypes/test/test.phylip M lib/galaxy/dependencies/conda-environment.txt M lib/galaxy/dependencies/conditional-requirements.txt M lib/galaxy/dependencies/pinned-hashed-requirements.txt M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/pipfiles/develop/Pipfile M lib/galaxy/dependencies/pipfiles/develop/Pipfile.lock M lib/galaxy/dependencies/pipfiles/develop/pinned-hashed-requirements.txt M lib/galaxy/dependencies/pipfiles/develop/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt M lib/galaxy/jobs/__init__.py M lib/galaxy/managers/configuration.py M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py M lib/galaxy/model/tool_shed_install/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/data/__init__.py M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/views.py M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/integrated_panel.py M lib/galaxy/util/dictifiable.py M lib/galaxy/util/handlers.py M lib/galaxy/version.py M lib/galaxy/web/framework/helpers/__init__.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/web/security/__init__.py M lib/galaxy/webapps/config_manage.py M lib/galaxy/webapps/galaxy/api/histories.py M lib/galaxy/webapps/galaxy/api/jobs.py M lib/galaxy/webapps/galaxy/config_schema.yml M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/tool_shed/config_schema.yml M lib/galaxy/webapps/tool_shed/model/__init__.py M lib/galaxy/workflow/scheduling_manager.py M lib/tool_shed/galaxy_install/migrate/common.py M run_tests.sh M scripts/cleanup_datasets/cleanup_datasets.py M scripts/common_startup.sh M scripts/db_shell.py M templates/admin/tool_shed_repository/deactivate_or_uninstall_repository.mako M templates/admin/tool_shed_repository/manage_repository_tool_dependencies.mako M templates/admin/tool_shed_repository/reset_metadata_on_selected_repositories.mako M templates/webapps/tool_shed/common/reset_metadata_on_selected_repositories.mako M test/manual/launch_and_run.sh M test/unit/jobs/test_mapper.py M test/unit/managers/test_HistoryManager.py Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into dev Commit: 242af28132da114d6b714d716e32b3350e3a9a88 https://github.com/galaxyproject/galaxy/commit/242af28132da114d6b714d716e32b... Author: Matthias Bernt <m.bernt@ufz.de> Date: 2018-02-01 (Thu, 01 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-node.js M config/galaxy.yml.sample M doc/source/admin/dependency_resolvers.rst M doc/source/admin/galaxy_options.rst M lib/galaxy/dataset_collections/structure.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/actions/post.py M lib/galaxy/tools/deps/commands.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/mulled/mulled_build.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/webapps/galaxy/config_schema.yml M test/api/test_tools.py M test/api/test_workflows.py M test/functional/tools/collection_creates_dynamic_list_of_pairs.xml Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into dev Commit: 9cbd7e32a4c0d90a77c6b7f008263481e4993085 https://github.com/galaxyproject/galaxy/commit/9cbd7e32a4c0d90a77c6b7f008263... Author: Matthias Bernt <m.bernt@ufz.de> Date: 2018-02-16 (Fri, 16 Feb 2018) Changed paths: M .ci/check_py3_compatibility.sh M .ci/flake8_blacklist.txt M .ci/flake8_wrapper.sh M .ci/flake8_wrapper_docstrings.sh M .gitignore M .travis.yml M Makefile M client/galaxy/scripts/apps/analysis.js A client/galaxy/scripts/apps/chart.js M client/galaxy/scripts/galaxy.js M client/galaxy/scripts/layout/masthead.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/layout/scratchbook.js M client/galaxy/scripts/mvc/collection/collection-model.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-parameters.js M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/history/hdca-li-edit.js M client/galaxy/scripts/mvc/history/history-contents.js M client/galaxy/scripts/mvc/history/history-list.js M 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static/scripts/viz/trackster/util.js R static/scripts/viz/visualization.js R static/scripts/viz/viz_views.js M static/style/blue/base.css M templates/galaxy_client_app.mako M templates/js-app.mako M templates/webapps/galaxy/dataset/security_common.mako M templates/webapps/galaxy/galaxy.masthead.mako M templates/webapps/galaxy/history/display_structured.mako M templates/webapps/galaxy/workflow/sharing.mako M templates/webapps/tool_shed/repository/tool_form.mako A test-data/new_tags_1.txt M test/api/test_tools.py M test/api/test_visualizations.py M test/api/test_webhooks.py M test/api/test_workflows.py M test/base/interactor.py M test/base/workflows_format_2/converter.py A test/functional/tools/fail_writing_work_dir_file.xml M test/functional/tools/samples_tool_conf.xml M test/functional/twilltestcase.py A test/functional/webhooks/history_test1/config.yml R test/functional/webhooks/history_test1/config/history_test1.yml A test/functional/webhooks/history_test2/config.yml R 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test/functional/webhooks/xkcd/static/script.js R test/functional/webhooks/xkcd/static/styles.css A test/functional/webhooks/xkcd/styles.css M test/selenium_tests/test_saved_histories.py M test/selenium_tests/test_tool_describing_tours.py M test/shed_functional/base/twilltestcase.py M test/unit/tools/test_tool_validation.py M tox.ini Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into dev Commit: fadafd413b2bc561c28e194f90c845e9b1d95908 https://github.com/galaxyproject/galaxy/commit/fadafd413b2bc561c28e194f90c84... Author: Matthias Bernt <m.bernt@ufz.de> Date: 2018-02-22 (Thu, 22 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/history/hdca-li-edit.js M client/galaxy/scripts/mvc/history/history-contents.js M client/galaxy/scripts/mvc/history/history-view-edit.js M config/datatypes_conf.xml.sample M config/galaxy.yml.sample M doc/source/admin/galaxy_options.rst M lib/galaxy/auth/__init__.py M lib/galaxy/auth/providers/ldap_ad.py M lib/galaxy/config.py A lib/galaxy/datatypes/converters/fastagz_to_fasta.xml M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/text.py M lib/galaxy/datatypes/util/gff_util.py M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt M lib/galaxy/jobs/__init__.py M lib/galaxy/model/mapping.py M lib/galaxy/model/orm/engine_factory.py M lib/galaxy/tools/toolbox/base.py A lib/galaxy/web/framework/middleware/sqldebug.py M lib/galaxy/web/proxy/js/package.json M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/config_schema.yml M run_tests.sh R test/casperjs/README.txt R test/casperjs/api-anon-history-permission-tests.js R test/casperjs/api-anon-history-tests.js R test/casperjs/api-hda-tests.js R test/casperjs/api-history-permission-tests.js R test/casperjs/casperjs_runner.py R test/casperjs/modules/api.js R test/casperjs/modules/historyoptions.js R test/casperjs/modules/historypanel.js R test/casperjs/modules/tools.js R test/casperjs/modules/user.js R test/casperjs/page-data/selectors.json R test/casperjs/server_env.py R test/casperjs/spaceghost.js R test/casperjs/test-data/simple_test.ga R test/casperjs/utils/simple-galaxy.js M test/galaxy_selenium/navigation.yml M test/selenium_tests/test_jupyter.py Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into dev Commit: c5f597f35345a1bdcf4f0633052b3cdc67a3556b https://github.com/galaxyproject/galaxy/commit/c5f597f35345a1bdcf4f0633052b3... Author: Matthias Bernt <m.bernt@ufz.de> Date: 2018-02-28 (Wed, 28 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/grid/grid-shared.js M client/galaxy/scripts/mvc/grid/grid-view.js M client/galaxy/scripts/mvc/history/history-list.js M client/galaxy/scripts/mvc/list/list-view.js M client/galaxy/scripts/mvc/workflow/workflow.js M client/galaxy/scripts/ui/loading-indicator.js M lib/galaxy/actions/library.py M lib/galaxy/datatypes/binary.py M lib/galaxy/model/migrate/versions/0137_add_copied_from_job_id_column.py M lib/galaxy/tools/actions/upload.py M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/tools/cwl/__init__.py M lib/galaxy/tools/cwl/parser.py M lib/galaxy/tools/cwl/representation.py M lib/galaxy/tools/cwl/runtime_actions.py M lib/galaxy/tools/cwl/schema.py A lib/galaxy/tools/cwl/util.py M lib/galaxy/tools/deps/commands.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_files.py M lib/galaxy/tools/deps/mulled/util.py M lib/galaxy/tools/deps/requirements.py M lib/galaxy/tools/linters/command.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/util/__init__.py M lib/galaxy/util/checkers.py M lib/galaxy/util/compression_utils.py M lib/galaxy/util/path/__init__.py M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M test/base/populators.py M test/integration/test_upload_configuration_options.py M tools/data_source/upload.py M tools/data_source/upload.xml Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into dev Commit: ee76c06da486e47c87fb4b8c236fa2191a403980 https://github.com/galaxyproject/galaxy/commit/ee76c06da486e47c87fb4b8c236fa... Author: Matthias Bernt <m.bernt@ufz.de> Date: 2018-03-01 (Thu, 01 Mar 2018) Changed paths: M lib/galaxy/jobs/runners/util/job_script/MEMORY_STATEMENT.sh Log Message: ----------- added GALAXY_MEMORY_MB_PERSLOT Commit: c6c47be0cbb7d29cefe3e1c0657f4b188286abb6 https://github.com/galaxyproject/galaxy/commit/c6c47be0cbb7d29cefe3e1c0657f4... Author: Matthias Bernt <m.bernt@ufz.de> Date: 2018-03-01 (Thu, 01 Mar 2018) Changed paths: M lib/galaxy/jobs/runners/util/job_script/MEMORY_STATEMENT.sh Log Message: ----------- added GALAXY_MEMORY_MB_PERSLOT Commit: 27a93fe8f463803e4d918a2f83e409bef8d404d8 https://github.com/galaxyproject/galaxy/commit/27a93fe8f463803e4d918a2f83e40... Author: Matthias Bernt <m.bernt@ufz.de> Date: 2018-03-01 (Thu, 01 Mar 2018) Log Message: ----------- Merge branch 'topic/memperslot' of https://github.com/bernt-matthias/galaxy into topic/memperslot Commit: 7316302ba385c329f458aa333994e6eeb6d5b97d https://github.com/galaxyproject/galaxy/commit/7316302ba385c329f458aa333994e... Author: Matthias Bernt <m.bernt@ufz.de> Date: 2018-03-05 (Mon, 05 Mar 2018) Changed paths: M lib/galaxy/jobs/runners/util/job_script/MEMORY_STATEMENT.sh Log Message: ----------- renamed variable to GALAXY_MEMORY_MB_PER_SLOT Commit: f54f3aa9e47141fa4b564ec56d37a97a129bea12 https://github.com/galaxyproject/galaxy/commit/f54f3aa9e47141fa4b564ec56d37a... Author: Matthias Bernt <m.bernt@ufz.de> Date: 2018-03-06 (Tue, 06 Mar 2018) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- added a bit of documentation Commit: 4a59f30209c9a9bee4e2ae70b56ff02f5248716c https://github.com/galaxyproject/galaxy/commit/4a59f30209c9a9bee4e2ae70b56ff... Author: Matthias Bernt <m.bernt@ufz.de> Date: 2018-03-13 (Tue, 13 Mar 2018) Changed paths: M doc/source/admin/cluster.md Log Message: ----------- added cluster admin docs for the new variables Commit: b92a5e1b470cbe3848e251c8c844cc652782d43d https://github.com/galaxyproject/galaxy/commit/b92a5e1b470cbe3848e251c8c844c... Author: Nicola Soranzo <nsoranzo@tiscali.it> Date: 2018-03-13 (Tue, 13 Mar 2018) Changed paths: M doc/source/admin/cluster.md Log Message: ----------- Small doc fixes Commit: 5f23f5da725199204950d89bb6b4b0af9e1d2f82 https://github.com/galaxyproject/galaxy/commit/5f23f5da725199204950d89bb6b4b... Author: John Chilton <jmchilton@gmail.com> Date: 2018-03-20 (Tue, 20 Mar 2018) Changed paths: M doc/source/admin/cluster.md M lib/galaxy/jobs/runners/util/job_script/MEMORY_STATEMENT.sh M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- Merge pull request #5625 from bernt-matthias/topic/memperslot added GALAXY_MEMORY_MB_PER_SLOT variable Compare: https://github.com/galaxyproject/galaxy/compare/11b32f38f46c...5f23f5da7251