August 2017 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 6d1397: Install tools and workflow
by GitHub 12 Aug '17

12 Aug '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 6d1397647fd6b185a639915a8f1ac929d78317d4 https://github.com/galaxyproject/galaxy/commit/6d1397647fd6b185a639915a8f1a… Author: Manabu ISHII <manabu.ishii.rb(a)gmail.com> Date: 2016-10-18 (Tue, 18 Oct 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Install tools and workflow import_tools is option and default is False. If import_tools is True, install tools in workflow. Commit: 30aa73e1974e1669984f0b6f242110451a8499ab https://github.com/galaxyproject/galaxy/commit/30aa73e1974e1669984f0b6f2421… Author: Manabu ISHII <manabu.ishii.rb(a)gmail.com> Date: 2016-10-18 (Tue, 18 Oct 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Remove unused variable Commit: 02924dece4653d476a2838e9b91bd2664d8bf518 https://github.com/galaxyproject/galaxy/commit/02924dece4653d476a2838e9b91b… Author: Manabu ISHII <manabu.ishii.rb(a)gmail.com> Date: 2016-10-19 (Wed, 19 Oct 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Fix lint Commit: 23db89ba3ddf54420b40e881bd92edbfeff869c6 https://github.com/galaxyproject/galaxy/commit/23db89ba3ddf54420b40e881bd92… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-10 (Thu, 10 Aug 2017) Changed paths: M .ci/flake8_blacklist.txt M .ci/flake8_docstrings_include_list.txt M .ci/flake8_lint_include_list.txt M .ci/flake8_wrapper_docstrings.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/Dockerfile A .ci/jenkins/selenium/docker-compose.yml A .ci/jenkins/selenium/galaxy.ini A .ci/jenkins/selenium/run_galaxy.bash A .ci/jenkins/selenium/run_tests.sh A .ci/jenkins/toolshed/run_tests.sh M .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/galaxy/scripts/admin.toolshed.js A client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/analysis.js R client/galaxy/scripts/apps/history-panel.js M client/galaxy/scripts/apps/login.js A client/galaxy/scripts/apps/panels/admin-panel.js A client/galaxy/scripts/apps/panels/history-panel.js A client/galaxy/scripts/apps/panels/tool-panel.js R client/galaxy/scripts/apps/tool-panel.js M client/galaxy/scripts/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/layout/masthead.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 M client/galaxy/scripts/libs/jquery/jquery.autocomplete.js M client/galaxy/scripts/mvc/citation/citation-view.js A client/galaxy/scripts/mvc/collection/base-creator.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 A client/galaxy/scripts/mvc/dataset/dataset-edit-attributes.js A 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-model.js M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/grid/grid-model.js A 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/hda-li.js M client/galaxy/scripts/mvc/history/hdca-li.js M client/galaxy/scripts/mvc/history/history-contents.js A 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-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/options-menu.js A client/galaxy/scripts/mvc/job/job-params.js M client/galaxy/scripts/mvc/library/library-dataset-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-librarylist-view.js M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js M client/galaxy/scripts/mvc/tag.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js R client/galaxy/scripts/mvc/tool/tool-form-workflow.js M client/galaxy/scripts/mvc/tool/tool-form.js M client/galaxy/scripts/mvc/tool/tools.js A client/galaxy/scripts/mvc/toolshed/categories-view.js A client/galaxy/scripts/mvc/toolshed/repo-queue-view.js A client/galaxy/scripts/mvc/toolshed/repo-status-view.js A client/galaxy/scripts/mvc/toolshed/repositories-view.js A client/galaxy/scripts/mvc/toolshed/repository-queue-view.js A client/galaxy/scripts/mvc/toolshed/repository-view.js A client/galaxy/scripts/mvc/toolshed/shed-list-view.js A client/galaxy/scripts/mvc/toolshed/toolshed-model.js A client/galaxy/scripts/mvc/toolshed/util.js A client/galaxy/scripts/mvc/toolshed/workflows-view.js M client/galaxy/scripts/mvc/tours.js M client/galaxy/scripts/mvc/ui/ui-buttons.js M client/galaxy/scripts/mvc/ui/ui-color-picker.js M client/galaxy/scripts/mvc/ui/ui-misc.js M client/galaxy/scripts/mvc/ui/ui-options.js M client/galaxy/scripts/mvc/ui/ui-portlet.js M client/galaxy/scripts/mvc/ui/ui-select-content.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/galaxy/scripts/mvc/ui/ui-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/default/default-row.js M client/galaxy/scripts/mvc/upload/upload-ftp.js M client/galaxy/scripts/mvc/upload/upload-view.js A client/galaxy/scripts/mvc/user/user-custom-builds.js A client/galaxy/scripts/mvc/user/user-preferences.js M client/galaxy/scripts/mvc/user/user-quotameter.js A client/galaxy/scripts/mvc/webhooks.js M client/galaxy/scripts/mvc/workflow/workflow-canvas.js A client/galaxy/scripts/mvc/workflow/workflow-forms.js A client/galaxy/scripts/mvc/workflow/workflow-icons.js M client/galaxy/scripts/mvc/workflow/workflow-manager.js M client/galaxy/scripts/mvc/workflow/workflow-node.js M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M client/galaxy/scripts/mvc/workflow/workflow-view-node.js M client/galaxy/scripts/mvc/workflow/workflow-view.js A client/galaxy/scripts/mvc/workflow/workflow.js A client/galaxy/scripts/nls/de/locale.js A client/galaxy/scripts/nls/es/locale.js A client/galaxy/scripts/nls/fr/locale.js M client/galaxy/scripts/nls/ja/locale.js M client/galaxy/scripts/nls/locale.js M client/galaxy/scripts/nls/zh/locale.js M client/galaxy/scripts/onload.js M client/galaxy/scripts/ui/autocom_tagging.js M client/galaxy/scripts/utils/utils.js M client/galaxy/scripts/viz/circster.js M client/galaxy/scripts/viz/phyloviz.js M client/galaxy/scripts/viz/trackster.js M client/galaxy/scripts/viz/trackster/tracks.js M client/galaxy/scripts/viz/visualization.js M client/galaxy/style/less/base.less M client/galaxy/style/less/dataset.less M client/galaxy/style/less/galaxy_bootstrap/overrides.less M client/galaxy/style/less/history.less M client/galaxy/style/less/ui.less M client/galaxy/style/less/ui/paired-collection-creator.less M client/galaxy/style/less/upload.less M client/galaxy/style/source_material/circle.py A client/package-lock.json M client/package.json M client/webpack.config.js 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 M config/galaxy.ini.sample M config/job_conf.xml.sample_advanced A config/local_conda_mapping.yml.sample M config/openid_conf.xml.sample M config/plugins/interactive_environments/bam_iobio/config/bam_iobio.ini.sample M config/plugins/interactive_environments/bam_iobio/static/js/bam_iobio.js M config/plugins/interactive_environments/bam_iobio/templates/bam_iobio.mako M config/plugins/interactive_environments/common/templates/ie.mako A config/plugins/interactive_environments/ethercalc/config/allowed_images.yml.sample A config/plugins/interactive_environments/ethercalc/config/ethercalc.ini.sample A config/plugins/interactive_environments/ethercalc/config/ethercalc.xml A config/plugins/interactive_environments/ethercalc/static/js/ethercalc.js A config/plugins/interactive_environments/ethercalc/templates/ethercalc.mako M config/plugins/interactive_environments/jupyter/config/allowed_images.yml.sample M config/plugins/interactive_environments/jupyter/config/jupyter.ini.sample M config/plugins/interactive_environments/jupyter/config/jupyter.xml M config/plugins/interactive_environments/jupyter/static/js/jupyter.js M config/plugins/interactive_environments/jupyter/templates/jupyter.mako M config/plugins/interactive_environments/neo/config/allowed_images.yml.sample M config/plugins/interactive_environments/neo/config/neo.ini.sample M config/plugins/interactive_environments/neo/config/neo.xml M config/plugins/interactive_environments/neo/static/js/neo.js M config/plugins/interactive_environments/neo/templates/neo.mako M config/plugins/interactive_environments/phinch/config/phinch.ini.sample M config/plugins/interactive_environments/phinch/static/js/phinch.js M config/plugins/interactive_environments/phinch/templates/phinch.mako M config/plugins/interactive_environments/rstudio/config/allowed_images.yml.sample M config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample M config/plugins/interactive_environments/rstudio/config/rstudio.xml M config/plugins/interactive_environments/rstudio/static/js/rstudio.js M config/plugins/interactive_environments/rstudio/templates/rstudio.mako M config/plugins/tours/core.galaxy_ui.yaml M config/plugins/tours/core.history.yaml M config/plugins/visualizations/charts/static/client/app.css M config/plugins/visualizations/charts/static/client/app.js M config/plugins/visualizations/charts/static/client/views/editor.js R config/plugins/visualizations/charts/static/client/views/types.js A config/plugins/visualizations/charts/static/repository/build/biojs_phylocanvas.js A config/plugins/visualizations/charts/static/repository/build/biojs_phylocanvas.js.map R config/plugins/visualizations/charts/static/repository/build/cytoscape_basic.js R config/plugins/visualizations/charts/static/repository/build/cytoscape_basic.js.map A config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js A config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js.map A config/plugins/visualizations/charts/static/repository/build/ngl_viewer.js A config/plugins/visualizations/charts/static/repository/build/ngl_viewer.js.map M config/plugins/visualizations/charts/static/repository/build/registry.js M config/plugins/visualizations/charts/static/repository/build/registry.js.map M config/plugins/visualizations/charts/static/repository/build/registry.tmp.js A config/plugins/visualizations/charts/static/repository/plugins/biojs/phylocanvas/phylocanvas.js A config/plugins/visualizations/charts/static/repository/plugins/ngl/viewer.js M config/plugins/visualizations/charts/static/repository/registry.json A config/plugins/visualizations/charts/static/repository/utilities/sifjson.js M config/plugins/visualizations/charts/static/repository/utilities/utils.js A config/plugins/visualizations/charts/static/repository/visualizations/biojs/phylocanvas/config.js A config/plugins/visualizations/charts/static/repository/visualizations/biojs/phylocanvas/logo.png A config/plugins/visualizations/charts/static/repository/visualizations/biojs/phylocanvas/wrapper.js R config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/basic/config.js R config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/basic/logo.png R config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/basic/wrapper.js A config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/config.js A config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/logo.png A config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/wrapper.js A config/plugins/visualizations/charts/static/repository/visualizations/ngl/viewer/config.js A config/plugins/visualizations/charts/static/repository/visualizations/ngl/viewer/logo.png A config/plugins/visualizations/charts/static/repository/visualizations/ngl/viewer/wrapper.js M config/plugins/visualizations/charts/static/repository/visualizations/utilities/tabular-form.js M config/plugins/visualizations/charts/templates/charts.mako M config/plugins/visualizations/charts/webpack.config.js M config/plugins/visualizations/csg/templates/csg.mako M config/plugins/visualizations/graphviz/templates/graphviz.mako M config/plugins/visualizations/scatterplot/templates/scatterplot.mako A config/plugins/visualizations/unipept/README.md A config/plugins/visualizations/unipept/config/unipept.xml A config/plugins/visualizations/unipept/static/style.css A config/plugins/visualizations/unipept/static/tooltip.css A config/plugins/visualizations/unipept/static/unipept-visualizations.es5.js A config/plugins/visualizations/unipept/static/unipept-visualizations.es5.js.map A config/plugins/visualizations/unipept/static/unipept_viz.js A config/plugins/visualizations/unipept/templates/glyphicons-86-repeat.png A config/plugins/visualizations/unipept/templates/unipept.mako A config/plugins/webhooks/demo/search/config/searchover.yaml A config/plugins/webhooks/demo/search/static/script.js A config/plugins/webhooks/demo/search/static/styles.css A config/plugins/webhooks/demo/tool_list/config/tool_list.yml A config/plugins/webhooks/demo/tool_list/helper/__init__.py A config/plugins/webhooks/demo/tour_generator/config/tour_generator.yml A config/plugins/webhooks/demo/tour_generator/helper/__init__.py A config/plugins/webhooks/demo/tour_generator/static/script.js A config/plugins/webhooks/demo/tour_generator/static/styles.css A config/swarm_manager_conf.yml.sample M config/tool_conf.xml.main M config/tool_conf.xml.sample M config/tool_data_table_conf.xml.sample M config/tool_destinations.yml.sample M config/tool_shed.ini.sample A config/user_preferences_extra_conf.yml.sample M contrib/galaxy.debian-init M contrib/galaxy_config_merger.py M contrib/galaxy_supervisor.conf M contrib/nagios/check_galaxy M contrib/nagios/check_galaxy.py M cron/add_manual_builds.py M cron/build_chrom_db.py M cron/parse_builds.py M cron/parse_builds_3_sites.py M cron/updateucsc.sh.sample M display_applications/igv/bigwig.xml A display_applications/igv/genome_fasta.xml M doc/Makefile A doc/fix_schema_rst.sh M doc/parse_gx_xsd.py R doc/patch.py M doc/schema_template.md A doc/source/admin/authentication.md R doc/source/admin/chat-0.png R doc/source/admin/chat-1.png R doc/source/admin/chat-2.png R doc/source/admin/chat-3.png R doc/source/admin/chat-4.png R doc/source/admin/chat.rst R doc/source/admin/communication_server.png R doc/source/admin/communication_server_rooms.png M doc/source/admin/conda_faq.rst M doc/source/admin/dependency_resolvers.rst M doc/source/admin/framework_dependencies.rst R doc/source/admin/grt.rst M doc/source/admin/index.rst R doc/source/admin/interactive_environments.png R doc/source/admin/interactive_environments.rst R doc/source/admin/interactive_environments.svg R doc/source/admin/interactive_environments_success.png R doc/source/admin/mulled_containers.rst A doc/source/admin/reports.md A doc/source/admin/special_topics/bug_reports.rst A doc/source/admin/special_topics/chat-0.png A doc/source/admin/special_topics/chat-1.png A doc/source/admin/special_topics/chat-2.png A doc/source/admin/special_topics/chat-3.png A doc/source/admin/special_topics/chat-4.png A doc/source/admin/special_topics/chat.rst A doc/source/admin/special_topics/communication_server.png A doc/source/admin/special_topics/communication_server_rooms.png A doc/source/admin/special_topics/grafana.png A doc/source/admin/special_topics/grt.rst A doc/source/admin/special_topics/images_webhooks/history-menu.png A doc/source/admin/special_topics/images_webhooks/masthead.png A doc/source/admin/special_topics/images_webhooks/masthead_trans_object.png A doc/source/admin/special_topics/images_webhooks/tool.png A doc/source/admin/special_topics/images_webhooks/workflow.png A doc/source/admin/special_topics/index.rst A doc/source/admin/special_topics/interactive_environments.png A doc/source/admin/special_topics/interactive_environments.rst A doc/source/admin/special_topics/interactive_environments.svg A doc/source/admin/special_topics/mulled_containers.rst A doc/source/admin/special_topics/performance_tracking.rst A doc/source/admin/special_topics/webhooks.rst A doc/source/admin/tool_panel.rst M doc/source/admin/useful_scripts.rst M doc/source/api/guidelines.rst M doc/source/api_doc.rst M doc/source/conf.py M doc/source/dev/build_a_job_runner.rst M doc/source/dev/faq.rst M doc/source/dev/index.rst A doc/source/dev/inherit.png M doc/source/dev/interactive_environments.rst A doc/source/dev/interactive_environments_success.png A doc/source/dev/queue.png A doc/source/dev/queue_b.png A doc/source/dev/runner_diag.png M doc/source/index.rst M doc/source/lib/galaxy.actions.rst M doc/source/lib/galaxy.auth.providers.rst M doc/source/lib/galaxy.auth.rst A doc/source/lib/galaxy.containers.rst M doc/source/lib/galaxy.dataset_collections.rst M doc/source/lib/galaxy.dataset_collections.types.rst M doc/source/lib/galaxy.datatypes.converters.rst M doc/source/lib/galaxy.datatypes.dataproviders.rst M doc/source/lib/galaxy.datatypes.display_applications.rst M doc/source/lib/galaxy.datatypes.rst M doc/source/lib/galaxy.datatypes.util.rst M doc/source/lib/galaxy.dependencies.rst M doc/source/lib/galaxy.eggs.rst M doc/source/lib/galaxy.exceptions.rst M doc/source/lib/galaxy.external_services.result_handlers.rst M doc/source/lib/galaxy.external_services.rst M doc/source/lib/galaxy.forms.rst M doc/source/lib/galaxy.jobs.actions.rst M doc/source/lib/galaxy.jobs.deferred.rst M doc/source/lib/galaxy.jobs.metrics.collectl.rst M doc/source/lib/galaxy.jobs.metrics.instrumenters.rst M doc/source/lib/galaxy.jobs.metrics.rst M doc/source/lib/galaxy.jobs.rst M doc/source/lib/galaxy.jobs.runners.rst M doc/source/lib/galaxy.jobs.runners.state_handlers.rst M doc/source/lib/galaxy.jobs.runners.util.cli.job.rst M doc/source/lib/galaxy.jobs.runners.util.cli.rst M doc/source/lib/galaxy.jobs.runners.util.cli.shell.rst M doc/source/lib/galaxy.jobs.runners.util.condor.rst A doc/source/lib/galaxy.jobs.runners.util.drmaa.rst M doc/source/lib/galaxy.jobs.runners.util.job_script.rst M doc/source/lib/galaxy.jobs.runners.util.rst M doc/source/lib/galaxy.jobs.splitters.rst M doc/source/lib/galaxy.managers.rst M doc/source/lib/galaxy.model.migrate.rst M doc/source/lib/galaxy.model.orm.rst M doc/source/lib/galaxy.model.rst M doc/source/lib/galaxy.model.tool_shed_install.migrate.rst M doc/source/lib/galaxy.model.tool_shed_install.rst M doc/source/lib/galaxy.objectstore.rst M doc/source/lib/galaxy.openid.rst M doc/source/lib/galaxy.quota.rst M doc/source/lib/galaxy.rst M doc/source/lib/galaxy.sample_tracking.rst M doc/source/lib/galaxy.security.rst R doc/source/lib/galaxy.tags.rst M doc/source/lib/galaxy.tools.actions.rst A doc/source/lib/galaxy.tools.cwl.rst M doc/source/lib/galaxy.tools.data.rst M doc/source/lib/galaxy.tools.data_manager.rst A doc/source/lib/galaxy.tools.deps.container_resolvers.rst A doc/source/lib/galaxy.tools.deps.mulled.rst M doc/source/lib/galaxy.tools.deps.resolvers.rst M doc/source/lib/galaxy.tools.deps.rst M doc/source/lib/galaxy.tools.filters.rst M doc/source/lib/galaxy.tools.imp_exp.rst M doc/source/lib/galaxy.tools.linters.rst A doc/source/lib/galaxy.tools.locations.rst M doc/source/lib/galaxy.tools.parameters.rst M doc/source/lib/galaxy.tools.parser.rst M doc/source/lib/galaxy.tools.rst M doc/source/lib/galaxy.tools.search.rst M doc/source/lib/galaxy.tools.toolbox.filters.rst M doc/source/lib/galaxy.tools.toolbox.lineages.rst M doc/source/lib/galaxy.tools.toolbox.rst M doc/source/lib/galaxy.tools.util.galaxyops.rst M doc/source/lib/galaxy.tools.util.rst A doc/source/lib/galaxy.tools.verify.asserts.rst A doc/source/lib/galaxy.tools.verify.rst A doc/source/lib/galaxy.tours.rst R doc/source/lib/galaxy.util.backports.importlib.rst M doc/source/lib/galaxy.util.backports.rst M doc/source/lib/galaxy.util.log.rst M doc/source/lib/galaxy.util.pastescript.rst M doc/source/lib/galaxy.util.rst M doc/source/lib/galaxy.visualization.data_providers.phyloviz.rst M doc/source/lib/galaxy.visualization.data_providers.rst M doc/source/lib/galaxy.visualization.genome.rst M doc/source/lib/galaxy.visualization.plugins.rst M doc/source/lib/galaxy.visualization.rst M doc/source/lib/galaxy.visualization.tracks.rst M doc/source/lib/galaxy.web.base.controllers.rst M doc/source/lib/galaxy.web.base.rst M doc/source/lib/galaxy.web.framework.helpers.rst M doc/source/lib/galaxy.web.framework.middleware.rst M doc/source/lib/galaxy.web.framework.rst M doc/source/lib/galaxy.web.proxy.rst M doc/source/lib/galaxy.web.rst M doc/source/lib/galaxy.web.security.rst A doc/source/lib/galaxy.web.stack.rst M doc/source/lib/galaxy.webapps.galaxy.api.rst M doc/source/lib/galaxy.webapps.galaxy.controllers.rst M doc/source/lib/galaxy.webapps.galaxy.rst M doc/source/lib/galaxy.webapps.reports.controllers.rst M doc/source/lib/galaxy.webapps.reports.rst M doc/source/lib/galaxy.webapps.rst M doc/source/lib/galaxy.webapps.tool_shed.api.rst M doc/source/lib/galaxy.webapps.tool_shed.controllers.rst M doc/source/lib/galaxy.webapps.tool_shed.framework.middleware.rst M doc/source/lib/galaxy.webapps.tool_shed.framework.rst M doc/source/lib/galaxy.webapps.tool_shed.model.migrate.rst M doc/source/lib/galaxy.webapps.tool_shed.model.rst M doc/source/lib/galaxy.webapps.tool_shed.rst M doc/source/lib/galaxy.webapps.tool_shed.search.rst M doc/source/lib/galaxy.webapps.tool_shed.security.rst M doc/source/lib/galaxy.webapps.tool_shed.util.rst A doc/source/lib/galaxy.webhooks.rst M doc/source/lib/galaxy.work.rst M doc/source/lib/galaxy.workflow.rst M doc/source/lib/galaxy.workflow.schedulers.rst M doc/source/lib/galaxy_ext.metadata.rst M doc/source/lib/galaxy_ext.rst R doc/source/lib/galaxy_utils.rst R doc/source/lib/galaxy_utils.sequence.rst M doc/source/lib/log_tempfile.rst M doc/source/lib/modules.rst M doc/source/lib/psyco_full.rst M doc/source/lib/tool_shed.capsule.rst M doc/source/lib/tool_shed.dependencies.repository.rst M doc/source/lib/tool_shed.dependencies.rst M doc/source/lib/tool_shed.dependencies.tool.rst M doc/source/lib/tool_shed.galaxy_install.datatypes.rst M doc/source/lib/tool_shed.galaxy_install.grids.rst M doc/source/lib/tool_shed.galaxy_install.metadata.rst M doc/source/lib/tool_shed.galaxy_install.migrate.rst M doc/source/lib/tool_shed.galaxy_install.repository_dependencies.rst M doc/source/lib/tool_shed.galaxy_install.rst M doc/source/lib/tool_shed.galaxy_install.tool_dependencies.recipe.rst M doc/source/lib/tool_shed.galaxy_install.tool_dependencies.rst M doc/source/lib/tool_shed.galaxy_install.tools.rst M doc/source/lib/tool_shed.galaxy_install.utility_containers.rst M doc/source/lib/tool_shed.grids.rst M doc/source/lib/tool_shed.managers.rst M doc/source/lib/tool_shed.metadata.rst M doc/source/lib/tool_shed.repository_types.rst M doc/source/lib/tool_shed.rst M doc/source/lib/tool_shed.tools.rst M doc/source/lib/tool_shed.util.rst M doc/source/lib/tool_shed.utility_containers.rst M doc/source/project/issues.rst M doc/source/project/organization.rst M doc/source/releases/13.01_announce.rst M doc/source/releases/13.02_announce.rst M doc/source/releases/13.04_announce.rst M doc/source/releases/13.06_announce.rst M doc/source/releases/13.08_announce.rst M doc/source/releases/13.11_announce.rst M doc/source/releases/14.02_announce.rst M doc/source/releases/14.04_announce.rst M doc/source/releases/14.06_announce.rst M doc/source/releases/14.08_announce.rst M doc/source/releases/14.10_announce.rst M doc/source/releases/15.01_announce.rst M doc/source/releases/15.03_announce.rst M doc/source/releases/15.05.rst M doc/source/releases/15.05_announce.rst M doc/source/releases/15.07_announce.rst M doc/source/releases/15.10_announce.rst M doc/source/releases/16.01_announce.rst M doc/source/releases/16.04.rst M doc/source/releases/16.04_announce.rst M doc/source/releases/16.07.rst M doc/source/releases/16.07_announce.rst A doc/source/releases/16.10.rst M doc/source/releases/16.10_announce.rst A doc/source/releases/17.01.rst A doc/source/releases/17.01_announce.rst A doc/source/releases/17.05.rst A doc/source/releases/17.05_announce.rst A doc/source/releases/17.09_announce.rst M doc/source/releases/_header.rst M doc/source/releases/_thanks.rst M doc/source/releases/index.rst M doc/source/releases/older_releases.rst A doc/source/slideshow/architecture/galaxy_architecture.md A doc/source/slideshow/architecture/images/backbone-model-view.svg A doc/source/slideshow/architecture/images/cluster_support.svg A doc/source/slideshow/architecture/images/data_managers.svg A doc/source/slideshow/architecture/images/docker-chart.png A doc/source/slideshow/architecture/images/family/team.png A doc/source/slideshow/architecture/images/galaxy_schema.png A doc/source/slideshow/architecture/images/hda.svg A doc/source/slideshow/architecture/images/hda_dataset.plantuml.svg A doc/source/slideshow/architecture/images/hda_dataset.plantuml.txt A doc/source/slideshow/architecture/images/hda_hdca.plantuml.svg A doc/source/slideshow/architecture/images/hda_hdca.plantuml.txt A doc/source/slideshow/architecture/images/jsload.png A doc/source/slideshow/architecture/images/libraries.svg A doc/source/slideshow/architecture/images/library_permissions.svg A doc/source/slideshow/architecture/images/objectstore.plantuml.svg A doc/source/slideshow/architecture/images/objectstore.plantuml.txt A doc/source/slideshow/architecture/images/objectstore_diagram.svg A doc/source/slideshow/architecture/images/plantuml_options.txt A doc/source/slideshow/architecture/images/sequence.json A doc/source/slideshow/architecture/images/server_client.plantuml.svg A doc/source/slideshow/architecture/images/server_client.plantuml.txt A doc/source/slideshow/architecture/images/server_client_old.plantuml.svg A doc/source/slideshow/architecture/images/server_client_old.plantuml.txt A doc/source/slideshow/architecture/images/sqla_arch_small.png A doc/source/slideshow/architecture/images/usegalaxy_webservers.svg A doc/source/slideshow/architecture/images/usegalaxyorg.svg A doc/source/slideshow/architecture/images/webapp.plantuml.svg A doc/source/slideshow/architecture/images/webapp.plantuml.txt A doc/source/slideshow/architecture/images/what-is-webpack.svg A doc/source/slideshow/architecture/images/workflow_definition.svg A doc/source/slideshow/architecture/images/workflow_run.svg A doc/source/slideshow/architecture/images/wsgi_app.svg A doc/source/slideshow/architecture/images/wsgi_request.svg A doc/source/slideshow/architecture/remark-latest.min.js A doc/source/slideshow/architecture/style.css M doc/source/ts_api_doc.rst M lib/galaxy/actions/admin.py M lib/galaxy/app.py M lib/galaxy/auth/__init__.py M lib/galaxy/auth/providers/__init__.py M lib/galaxy/auth/providers/alwaysreject.py M lib/galaxy/auth/providers/ldap_ad.py M lib/galaxy/auth/providers/localdb.py M lib/galaxy/auth/providers/pam_auth.py M lib/galaxy/config.py A lib/galaxy/containers/__init__.py A lib/galaxy/containers/docker.py A lib/galaxy/containers/docker_decorators.py A lib/galaxy/containers/docker_model.py A lib/galaxy/containers/docker_swarm.py A lib/galaxy/containers/docker_swarm_manager.py M lib/galaxy/dataset_collections/matching.py M lib/galaxy/dataset_collections/registry.py M lib/galaxy/dataset_collections/structure.py M lib/galaxy/dataset_collections/types/__init__.py M lib/galaxy/dataset_collections/types/list.py M lib/galaxy/dataset_collections/types/paired.py M lib/galaxy/datatypes/assembly.py M lib/galaxy/datatypes/binary.py A lib/galaxy/datatypes/blast.py M lib/galaxy/datatypes/checkers.py M lib/galaxy/datatypes/chrominfo.py M lib/galaxy/datatypes/constructive_solid_geometry.py M lib/galaxy/datatypes/converters/bam_to_bai.xml M lib/galaxy/datatypes/converters/bam_to_bigwig_converter.xml M lib/galaxy/datatypes/converters/bcf_bgzip_to_bcf_converter.xml M lib/galaxy/datatypes/converters/bcf_to_bcf_bgzip_converter.xml M lib/galaxy/datatypes/converters/bed_gff_or_vcf_to_bigwig_converter.xml M lib/galaxy/datatypes/converters/bed_to_bgzip_converter.xml M lib/galaxy/datatypes/converters/bed_to_fli_converter.xml M lib/galaxy/datatypes/converters/bed_to_gff_converter.py M lib/galaxy/datatypes/converters/bed_to_gff_converter.xml M lib/galaxy/datatypes/converters/bed_to_interval_index_converter.xml M lib/galaxy/datatypes/converters/bed_to_tabix_converter.xml M lib/galaxy/datatypes/converters/bedgraph_to_array_tree_converter.py M lib/galaxy/datatypes/converters/bedgraph_to_array_tree_converter.xml M lib/galaxy/datatypes/converters/bedgraph_to_bigwig_converter.xml M lib/galaxy/datatypes/converters/bgzip.py M lib/galaxy/datatypes/converters/cml_to_inchi_converter.xml M lib/galaxy/datatypes/converters/cml_to_mol2_converter.xml M lib/galaxy/datatypes/converters/cml_to_sdf_converter.xml M lib/galaxy/datatypes/converters/cml_to_smi_converter.xml M lib/galaxy/datatypes/converters/encodepeak_to_bgzip_converter.xml M lib/galaxy/datatypes/converters/encodepeak_to_tabix_converter.xml M lib/galaxy/datatypes/converters/fasta_to_2bit.xml M lib/galaxy/datatypes/converters/fasta_to_bowtie_base_index_converter.xml M lib/galaxy/datatypes/converters/fasta_to_bowtie_color_index_converter.xml A lib/galaxy/datatypes/converters/fasta_to_fai.xml M lib/galaxy/datatypes/converters/fasta_to_len.py M lib/galaxy/datatypes/converters/fasta_to_len.xml M lib/galaxy/datatypes/converters/fasta_to_tabular_converter.py M lib/galaxy/datatypes/converters/fasta_to_tabular_converter.xml M lib/galaxy/datatypes/converters/fastq_to_fqtoc.xml A lib/galaxy/datatypes/converters/fastqbz2_to_fastq.xml A lib/galaxy/datatypes/converters/fastqcssangerbz2_to_fastqcssanger.xml A lib/galaxy/datatypes/converters/fastqcssangergz_to_fastqcssanger.xml A lib/galaxy/datatypes/converters/fastqgz_to_fastq.xml A lib/galaxy/datatypes/converters/fastqilluminabz2_to_fastqillumina.xml A lib/galaxy/datatypes/converters/fastqilluminagz_to_fastqillumina.xml A lib/galaxy/datatypes/converters/fastqsangerbz2_to_fastqsanger.xml A lib/galaxy/datatypes/converters/fastqsangergz_to_fastqsanger.xml M lib/galaxy/datatypes/converters/fastqsolexa_to_fasta_converter.py M lib/galaxy/datatypes/converters/fastqsolexa_to_fasta_converter.xml M lib/galaxy/datatypes/converters/fastqsolexa_to_qual_converter.py M lib/galaxy/datatypes/converters/fastqsolexa_to_qual_converter.xml A lib/galaxy/datatypes/converters/fastqsolexabz2_to_fastqsolexa.xml A lib/galaxy/datatypes/converters/fastqsolexagz_to_fastqsolexa.xml M lib/galaxy/datatypes/converters/gff_to_bed_converter.py M lib/galaxy/datatypes/converters/gff_to_bed_converter.xml M lib/galaxy/datatypes/converters/gff_to_bgzip_converter.xml M lib/galaxy/datatypes/converters/gff_to_fli_converter.xml M lib/galaxy/datatypes/converters/gff_to_interval_index_converter.py M lib/galaxy/datatypes/converters/gff_to_interval_index_converter.xml M lib/galaxy/datatypes/converters/gff_to_tabix_converter.xml M lib/galaxy/datatypes/converters/inchi_to_cml_converter.xml M lib/galaxy/datatypes/converters/inchi_to_mol2_converter.xml M lib/galaxy/datatypes/converters/inchi_to_mol_converter.xml M lib/galaxy/datatypes/converters/inchi_to_sdf_converter.xml M lib/galaxy/datatypes/converters/inchi_to_smi_converter.xml M lib/galaxy/datatypes/converters/interval_to_bed12_converter.xml M lib/galaxy/datatypes/converters/interval_to_bed6_converter.xml M lib/galaxy/datatypes/converters/interval_to_bed_converter.py M lib/galaxy/datatypes/converters/interval_to_bed_converter.xml M lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.py M lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.xml M lib/galaxy/datatypes/converters/interval_to_bgzip_converter.xml M lib/galaxy/datatypes/converters/interval_to_bigwig_converter.xml M lib/galaxy/datatypes/converters/interval_to_coverage.py M lib/galaxy/datatypes/converters/interval_to_coverage.xml M lib/galaxy/datatypes/converters/interval_to_fli.py M lib/galaxy/datatypes/converters/interval_to_interval_index_converter.py M lib/galaxy/datatypes/converters/interval_to_interval_index_converter.xml M lib/galaxy/datatypes/converters/interval_to_tabix_converter.py M lib/galaxy/datatypes/converters/interval_to_tabix_converter.xml M lib/galaxy/datatypes/converters/len_to_linecount.xml M lib/galaxy/datatypes/converters/lped_to_fped_converter.py M lib/galaxy/datatypes/converters/lped_to_fped_converter.xml M lib/galaxy/datatypes/converters/lped_to_pbed_converter.py M lib/galaxy/datatypes/converters/lped_to_pbed_converter.xml M lib/galaxy/datatypes/converters/maf_to_fasta_converter.xml M lib/galaxy/datatypes/converters/maf_to_interval_converter.xml M lib/galaxy/datatypes/converters/mol2_to_cml_converter.xml M lib/galaxy/datatypes/converters/mol2_to_inchi_converter.xml M lib/galaxy/datatypes/converters/mol2_to_mol_converter.xml M lib/galaxy/datatypes/converters/mol2_to_sdf_converter.xml M lib/galaxy/datatypes/converters/mol2_to_smi_converter.xml M lib/galaxy/datatypes/converters/mol_to_cml_converter.xml M lib/galaxy/datatypes/converters/mol_to_inchi_converter.xml M lib/galaxy/datatypes/converters/mol_to_mol2_converter.xml M lib/galaxy/datatypes/converters/mol_to_smi_converter.xml M lib/galaxy/datatypes/converters/pbed_ldreduced_converter.py M lib/galaxy/datatypes/converters/pbed_ldreduced_converter.xml M lib/galaxy/datatypes/converters/pbed_to_lped_converter.py M lib/galaxy/datatypes/converters/pbed_to_lped_converter.xml M lib/galaxy/datatypes/converters/picard_interval_list_to_bed6_converter.py M lib/galaxy/datatypes/converters/picard_interval_list_to_bed6_converter.xml M lib/galaxy/datatypes/converters/pileup_to_interval_index_converter.py M lib/galaxy/datatypes/converters/pileup_to_interval_index_converter.xml M lib/galaxy/datatypes/converters/ref_to_seq_taxonomy_converter.py M lib/galaxy/datatypes/converters/ref_to_seq_taxonomy_converter.xml M lib/galaxy/datatypes/converters/sam_to_bam.py M lib/galaxy/datatypes/converters/sam_to_bam.xml M lib/galaxy/datatypes/converters/sam_to_bigwig_converter.xml M lib/galaxy/datatypes/converters/sdf_to_cml_converter.xml M lib/galaxy/datatypes/converters/sdf_to_inchi_converter.xml M lib/galaxy/datatypes/converters/sdf_to_mol2_converter.xml M lib/galaxy/datatypes/converters/sdf_to_smi_converter.xml M lib/galaxy/datatypes/converters/smi_to_cml_converter.xml M lib/galaxy/datatypes/converters/smi_to_inchi_converter.xml M lib/galaxy/datatypes/converters/smi_to_mol2_converter.xml M lib/galaxy/datatypes/converters/smi_to_mol_converter.xml M lib/galaxy/datatypes/converters/smi_to_sdf_converter.xml M lib/galaxy/datatypes/converters/smi_to_smi_converter.xml M lib/galaxy/datatypes/converters/tabular_to_dbnsfp.py M lib/galaxy/datatypes/converters/tabular_to_dbnsfp.xml M lib/galaxy/datatypes/converters/vcf_bgzip_to_tabix_converter.xml M lib/galaxy/datatypes/converters/vcf_to_bgzip_converter.xml M lib/galaxy/datatypes/converters/vcf_to_interval_index_converter.py M lib/galaxy/datatypes/converters/vcf_to_interval_index_converter.xml M lib/galaxy/datatypes/converters/vcf_to_tabix_converter.xml M lib/galaxy/datatypes/converters/vcf_to_vcf_bgzip.py M lib/galaxy/datatypes/converters/vcf_to_vcf_bgzip_converter.xml M lib/galaxy/datatypes/converters/wig_to_bigwig_converter.xml M lib/galaxy/datatypes/converters/wiggle_to_array_tree_converter.py M lib/galaxy/datatypes/converters/wiggle_to_array_tree_converter.xml M lib/galaxy/datatypes/converters/wiggle_to_simple_converter.py M lib/galaxy/datatypes/converters/wiggle_to_simple_converter.xml M lib/galaxy/datatypes/coverage.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/dataproviders/__init__.py M lib/galaxy/datatypes/dataproviders/chunk.py M lib/galaxy/datatypes/dataproviders/column.py M lib/galaxy/datatypes/dataproviders/dataset.py M lib/galaxy/datatypes/dataproviders/decorators.py M lib/galaxy/datatypes/dataproviders/external.py M lib/galaxy/datatypes/dataproviders/hierarchy.py M lib/galaxy/datatypes/dataproviders/line.py M lib/galaxy/datatypes/display_applications/application.py M lib/galaxy/datatypes/display_applications/parameters.py M lib/galaxy/datatypes/genetics.py M lib/galaxy/datatypes/graph.py M lib/galaxy/datatypes/images.py M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/metadata.py M lib/galaxy/datatypes/molecules.py M lib/galaxy/datatypes/mothur.py M lib/galaxy/datatypes/msa.py M lib/galaxy/datatypes/neo4j.py A lib/galaxy/datatypes/plant_tribes.py M lib/galaxy/datatypes/proteomics.py M lib/galaxy/datatypes/qualityscore.py M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/tabular.py A lib/galaxy/datatypes/test/1.ptkscmp A lib/galaxy/datatypes/test/1.smat A lib/galaxy/datatypes/test/diamond_db.dmnd A lib/galaxy/datatypes/test/tblastn_four_human_vs_rhodopsin.xml A lib/galaxy/datatypes/test/test.CEL M lib/galaxy/datatypes/text.py M lib/galaxy/datatypes/triples.py M lib/galaxy/datatypes/util/gff_util.py M lib/galaxy/datatypes/xml.py M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/conda-environment.txt M lib/galaxy/dependencies/conditional-requirements.txt M lib/galaxy/dependencies/dev-requirements.txt M lib/galaxy/dependencies/pinned-hashed-requirements.txt M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt M lib/galaxy/exceptions/__init__.py M lib/galaxy/exceptions/error_codes.json M lib/galaxy/exceptions/error_codes.py M lib/galaxy/external_services/actions.py M lib/galaxy/external_services/parameters.py M lib/galaxy/external_services/result_handlers/basic.py M lib/galaxy/external_services/service.py M lib/galaxy/forms/forms.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/actions/post.py M lib/galaxy/jobs/command_factory.py M lib/galaxy/jobs/datasets.py M lib/galaxy/jobs/deferred/__init__.py M lib/galaxy/jobs/deferred/data_transfer.py M lib/galaxy/jobs/deferred/manual_data_transfer.py M lib/galaxy/jobs/deferred/pacific_biosciences_smrt_portal.py M lib/galaxy/jobs/dynamic_tool_destination.py M lib/galaxy/jobs/handler.py M lib/galaxy/jobs/mapper.py M lib/galaxy/jobs/metrics/__init__.py M lib/galaxy/jobs/metrics/collectl/cli.py M lib/galaxy/jobs/metrics/collectl/processes.py M lib/galaxy/jobs/metrics/collectl/subsystems.py M lib/galaxy/jobs/metrics/instrumenters/__init__.py M lib/galaxy/jobs/metrics/instrumenters/collectl.py M lib/galaxy/jobs/metrics/instrumenters/core.py M lib/galaxy/jobs/metrics/instrumenters/cpuinfo.py M lib/galaxy/jobs/metrics/instrumenters/env.py M lib/galaxy/jobs/metrics/instrumenters/meminfo.py M lib/galaxy/jobs/metrics/instrumenters/uname.py M lib/galaxy/jobs/rule_helper.py M lib/galaxy/jobs/runners/__init__.py A lib/galaxy/jobs/runners/chronos.py M lib/galaxy/jobs/runners/cli.py M lib/galaxy/jobs/runners/condor.py M lib/galaxy/jobs/runners/drmaa.py M lib/galaxy/jobs/runners/godocker.py M lib/galaxy/jobs/runners/kubernetes.py M lib/galaxy/jobs/runners/local.py M lib/galaxy/jobs/runners/pbs.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/jobs/runners/slurm.py A lib/galaxy/jobs/runners/state_handlers/_safe_eval.py M lib/galaxy/jobs/runners/state_handlers/resubmit.py M lib/galaxy/jobs/runners/tasks.py M lib/galaxy/jobs/runners/util/__init__.py M lib/galaxy/jobs/runners/util/cli/__init__.py M lib/galaxy/jobs/runners/util/cli/job/__init__.py M lib/galaxy/jobs/runners/util/cli/job/slurm.py M lib/galaxy/jobs/runners/util/cli/job/slurm_torque.py M lib/galaxy/jobs/runners/util/cli/shell/__init__.py M lib/galaxy/jobs/runners/util/cli/shell/local.py M lib/galaxy/jobs/runners/util/cli/shell/rsh.py M lib/galaxy/jobs/runners/util/condor/__init__.py M lib/galaxy/jobs/runners/util/drmaa/__init__.py M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh M lib/galaxy/jobs/runners/util/job_script/__init__.py M lib/galaxy/jobs/runners/util/kill.py M lib/galaxy/jobs/runners/util/retry.py M lib/galaxy/jobs/runners/util/sudo.py M lib/galaxy/jobs/splitters/basic.py M lib/galaxy/managers/__init__.py M lib/galaxy/managers/base.py M lib/galaxy/managers/citations.py M lib/galaxy/managers/collections.py M lib/galaxy/managers/collections_util.py M lib/galaxy/managers/configuration.py M lib/galaxy/managers/datasets.py M lib/galaxy/managers/deletable.py M lib/galaxy/managers/hdas.py M lib/galaxy/managers/hdcas.py M lib/galaxy/managers/libraries.py M lib/galaxy/managers/rbac_secured.py M lib/galaxy/managers/roles.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/base.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/check.py M lib/galaxy/model/migrate/versions/0003_security_and_libraries.py M lib/galaxy/model/migrate/versions/0004_indexes_and_defaults.py M lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py M lib/galaxy/model/migrate/versions/0006_change_qual_datatype.py M lib/galaxy/model/migrate/versions/0007_sharing_histories.py M lib/galaxy/model/migrate/versions/0008_galaxy_forms.py M lib/galaxy/model/migrate/versions/0009_request_table.py M lib/galaxy/model/migrate/versions/0010_hda_display_at_authz_table.py M lib/galaxy/model/migrate/versions/0011_v0010_mysql_index_fix.py M lib/galaxy/model/migrate/versions/0012_user_address.py M lib/galaxy/model/migrate/versions/0013_change_lib_item_templates_to_forms.py M lib/galaxy/model/migrate/versions/0014_pages.py M lib/galaxy/model/migrate/versions/0015_tagging.py M lib/galaxy/model/migrate/versions/0016_v0015_mysql_index_fix.py M lib/galaxy/model/migrate/versions/0017_library_item_indexes.py M lib/galaxy/model/migrate/versions/0018_ordered_tags_and_page_tags.py M lib/galaxy/model/migrate/versions/0019_request_library_folder.py M lib/galaxy/model/migrate/versions/0020_library_upload_job.py M lib/galaxy/model/migrate/versions/0021_user_prefs.py M lib/galaxy/model/migrate/versions/0022_visualization_tables.py M lib/galaxy/model/migrate/versions/0024_page_slug_unique_constraint.py M lib/galaxy/model/migrate/versions/0025_user_info.py M lib/galaxy/model/migrate/versions/0026_cloud_tables.py M lib/galaxy/model/migrate/versions/0027_request_events.py M lib/galaxy/model/migrate/versions/0028_external_metadata_file_override.py M lib/galaxy/model/migrate/versions/0029_user_actions.py M lib/galaxy/model/migrate/versions/0031_community_and_workflow_tags.py M lib/galaxy/model/migrate/versions/0033_published_cols_for_histories_and_workflows.py M lib/galaxy/model/migrate/versions/0034_page_user_share_association.py M lib/galaxy/model/migrate/versions/0035_item_annotations_and_workflow_step_tags.py M lib/galaxy/model/migrate/versions/0036_add_deleted_column_to_library_template_assoc_tables.py M lib/galaxy/model/migrate/versions/0037_samples_library.py M lib/galaxy/model/migrate/versions/0038_add_inheritable_column_to_library_template_assoc_tables.py M lib/galaxy/model/migrate/versions/0039_add_synopsis_column_to_library_table.py M lib/galaxy/model/migrate/versions/0040_page_annotations.py M lib/galaxy/model/migrate/versions/0041_workflow_invocation.py M lib/galaxy/model/migrate/versions/0043_visualization_sharing_tagging_annotating.py M lib/galaxy/model/migrate/versions/0044_add_notify_column_to_request_table.py M lib/galaxy/model/migrate/versions/0045_request_type_permissions_table.py M lib/galaxy/model/migrate/versions/0046_post_job_actions.py M lib/galaxy/model/migrate/versions/0047_job_table_user_id_column.py M lib/galaxy/model/migrate/versions/0048_dataset_instance_state_column.py M lib/galaxy/model/migrate/versions/0049_api_keys_table.py M lib/galaxy/model/migrate/versions/0050_drop_cloud_tables.py M lib/galaxy/model/migrate/versions/0051_imported_col_for_jobs_table.py M lib/galaxy/model/migrate/versions/0052_sample_dataset_table.py M lib/galaxy/model/migrate/versions/0053_item_ratings.py M lib/galaxy/model/migrate/versions/0055_add_pja_assoc_for_jobs.py M lib/galaxy/model/migrate/versions/0057_request_notify.py M lib/galaxy/model/migrate/versions/0058_history_import_export.py M lib/galaxy/model/migrate/versions/0059_sample_dataset_file_path.py M lib/galaxy/model/migrate/versions/0060_history_archive_import.py M lib/galaxy/model/migrate/versions/0062_user_openid_table.py M lib/galaxy/model/migrate/versions/0063_sequencer_table.py M lib/galaxy/model/migrate/versions/0064_add_run_and_sample_run_association_tables.py M lib/galaxy/model/migrate/versions/0065_add_name_to_form_fields_and_values.py M lib/galaxy/model/migrate/versions/0066_deferred_job_and_transfer_job_tables.py M lib/galaxy/model/migrate/versions/0067_populate_sequencer_table.py M lib/galaxy/model/migrate/versions/0068_rename_sequencer_to_external_services.py M lib/galaxy/model/migrate/versions/0069_rename_sequencer_form_type.py M lib/galaxy/model/migrate/versions/0070_add_info_column_to_deferred_job_table.py M lib/galaxy/model/migrate/versions/0071_add_history_and_workflow_to_sample.py M lib/galaxy/model/migrate/versions/0072_add_pid_and_socket_columns_to_transfer_job_table.py M lib/galaxy/model/migrate/versions/0073_add_ldda_to_implicit_conversion_table.py M lib/galaxy/model/migrate/versions/0074_add_purged_column_to_library_dataset_table.py M lib/galaxy/model/migrate/versions/0075_add_subindex_column_to_run_table.py M lib/galaxy/model/migrate/versions/0077_create_tool_tag_association_table.py M lib/galaxy/model/migrate/versions/0078_add_columns_for_disk_usage_accounting.py M lib/galaxy/model/migrate/versions/0079_input_library_to_job_table.py M lib/galaxy/model/migrate/versions/0080_quota_tables.py M lib/galaxy/model/migrate/versions/0081_add_tool_version_to_hda_ldda.py M lib/galaxy/model/migrate/versions/0082_add_tool_shed_repository_table.py M lib/galaxy/model/migrate/versions/0083_add_prepare_files_to_task.py M lib/galaxy/model/migrate/versions/0084_add_ldda_id_to_implicit_conversion_table.py M lib/galaxy/model/migrate/versions/0085_add_task_info.py M lib/galaxy/model/migrate/versions/0086_add_tool_shed_repository_table_columns.py M lib/galaxy/model/migrate/versions/0087_tool_id_guid_map_table.py M lib/galaxy/model/migrate/versions/0088_add_installed_changeset_revison_column.py M lib/galaxy/model/migrate/versions/0089_add_object_store_id_columns.py M lib/galaxy/model/migrate/versions/0090_add_tool_shed_repository_table_columns.py M lib/galaxy/model/migrate/versions/0091_add_tool_version_tables.py M lib/galaxy/model/migrate/versions/0092_add_migrate_tools_table.py M lib/galaxy/model/migrate/versions/0093_add_job_params_col.py M lib/galaxy/model/migrate/versions/0094_add_job_handler_col.py M lib/galaxy/model/migrate/versions/0095_hda_subsets.py M lib/galaxy/model/migrate/versions/0096_openid_provider.py M lib/galaxy/model/migrate/versions/0097_add_ctx_rev_column.py M lib/galaxy/model/migrate/versions/0098_genome_index_tool_data_table.py M lib/galaxy/model/migrate/versions/0099_add_tool_dependency_table.py M lib/galaxy/model/migrate/versions/0100_alter_tool_dependency_table_version_column.py M lib/galaxy/model/migrate/versions/0101_drop_installed_changeset_revision_column.py M lib/galaxy/model/migrate/versions/0102_add_tool_dependency_status_columns.py M lib/galaxy/model/migrate/versions/0103_add_tool_shed_repository_status_columns.py M lib/galaxy/model/migrate/versions/0104_update_genome_downloader_job_parameters.py M lib/galaxy/model/migrate/versions/0105_add_cleanup_event_table.py M lib/galaxy/model/migrate/versions/0106_add_missing_indexes.py M lib/galaxy/model/migrate/versions/0107_add_exit_code_to_job_and_task.py M lib/galaxy/model/migrate/versions/0108_add_extended_metadata.py M lib/galaxy/model/migrate/versions/0109_add_repository_dependency_tables.py M lib/galaxy/model/migrate/versions/0110_add_dataset_uuid.py M lib/galaxy/model/migrate/versions/0111_add_job_destinations.py M lib/galaxy/model/migrate/versions/0112_add_data_manager_history_association_and_data_manager_job_association_tables.py M lib/galaxy/model/migrate/versions/0113_update_migrate_tools_table.py M lib/galaxy/model/migrate/versions/0114_update_migrate_tools_table_again.py M lib/galaxy/model/migrate/versions/0115_longer_user_password_field.py M lib/galaxy/model/migrate/versions/0116_drop_update_available_col_add_tool_shed_status_col.py M lib/galaxy/model/migrate/versions/0117_add_user_activation.py M lib/galaxy/model/migrate/versions/0118_add_hda_extended_metadata.py M lib/galaxy/model/migrate/versions/0119_job_metrics.py M lib/galaxy/model/migrate/versions/0120_dataset_collections.py M lib/galaxy/model/migrate/versions/0121_workflow_uuids.py M lib/galaxy/model/migrate/versions/0122_grow_mysql_blobs.py M lib/galaxy/model/migrate/versions/0123_add_workflow_request_tables.py M lib/galaxy/model/migrate/versions/0124_job_state_history.py M lib/galaxy/model/migrate/versions/0125_workflow_step_tracking.py M lib/galaxy/model/migrate/versions/0126_password_reset.py M lib/galaxy/model/migrate/versions/0127_output_collection_adjustments.py M lib/galaxy/model/migrate/versions/0128_session_timeout.py M lib/galaxy/model/migrate/versions/0129_job_external_output_metadata_validity.py M lib/galaxy/model/migrate/versions/0130_change_pref_datatype.py M lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_parameter_modules.py M lib/galaxy/model/migrate/versions/0132_add_lastpasswordchange_to_user.py M lib/galaxy/model/migrate/versions/0133_add_dependency_column_to_job.py A lib/galaxy/model/migrate/versions/0134_hda_set_deleted_if_purged.py A lib/galaxy/model/migrate/versions/0135_add_library_tags.py M lib/galaxy/model/orm/engine_factory.py M lib/galaxy/model/orm/scripts.py M lib/galaxy/model/search.py M lib/galaxy/model/tool_shed_install/__init__.py M lib/galaxy/model/tool_shed_install/mapping.py M lib/galaxy/model/tool_shed_install/migrate/check.py M lib/galaxy/objectstore/__init__.py M lib/galaxy/objectstore/azure_blob.py A lib/galaxy/objectstore/pithos.py M lib/galaxy/objectstore/pulsar.py M lib/galaxy/objectstore/rods.py M lib/galaxy/objectstore/s3.py M lib/galaxy/objectstore/s3_multipart_upload.py M lib/galaxy/queue_worker.py M lib/galaxy/queues.py M lib/galaxy/quota/__init__.py M lib/galaxy/sample_tracking/data_transfer.py M lib/galaxy/sample_tracking/external_service_types.py M lib/galaxy/sample_tracking/request_types.py M lib/galaxy/sample_tracking/sample.py M lib/galaxy/security/__init__.py M lib/galaxy/security/passwords.py R lib/galaxy/tags/__init__.py R lib/galaxy/tags/tag_handler.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/actions/data_manager.py M lib/galaxy/tools/actions/data_source.py M lib/galaxy/tools/actions/history_imp_exp.py M lib/galaxy/tools/actions/metadata.py M lib/galaxy/tools/actions/model_operations.py M lib/galaxy/tools/actions/upload.py M lib/galaxy/tools/actions/upload_common.py A lib/galaxy/tools/cache.py M lib/galaxy/tools/cwl/cwltool_deps.py M lib/galaxy/tools/cwl/parser.py M lib/galaxy/tools/cwl/representation.py M lib/galaxy/tools/cwl/runtime_actions.py M lib/galaxy/tools/cwl/schema.py M lib/galaxy/tools/data/__init__.py M lib/galaxy/tools/data_manager/manager.py M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/commands.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/container_resolvers/__init__.py M lib/galaxy/tools/deps/container_resolvers/explicit.py M lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/tools/deps/containers.py M lib/galaxy/tools/deps/dependencies.py M lib/galaxy/tools/deps/docker_util.py M lib/galaxy/tools/deps/installable.py M lib/galaxy/tools/deps/mulled/_cli.py M lib/galaxy/tools/deps/mulled/invfile.lua M lib/galaxy/tools/deps/mulled/mulled_build.py M lib/galaxy/tools/deps/mulled/mulled_build_channel.py M lib/galaxy/tools/deps/mulled/mulled_build_files.py M lib/galaxy/tools/deps/mulled/mulled_build_tool.py M lib/galaxy/tools/deps/mulled/mulled_search.py M lib/galaxy/tools/deps/mulled/util.py M lib/galaxy/tools/deps/requirements.py M lib/galaxy/tools/deps/resolvers/__init__.py M lib/galaxy/tools/deps/resolvers/brewed_tool_shed_packages.py M lib/galaxy/tools/deps/resolvers/conda.py A lib/galaxy/tools/deps/resolvers/default_conda_mapping.yml M lib/galaxy/tools/deps/resolvers/galaxy_packages.py M lib/galaxy/tools/deps/resolvers/homebrew.py M lib/galaxy/tools/deps/resolvers/modules.py M lib/galaxy/tools/deps/resolvers/resolver_mixins.py A lib/galaxy/tools/deps/singularity_util.py M lib/galaxy/tools/deps/views.py A lib/galaxy/tools/error_reports/__init__.py A lib/galaxy/tools/error_reports/plugins/__init__.py A lib/galaxy/tools/error_reports/plugins/biostars.py A lib/galaxy/tools/error_reports/plugins/email.py A lib/galaxy/tools/error_reports/plugins/json.py A lib/galaxy/tools/error_reports/plugins/sentry.py M lib/galaxy/tools/errors.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/execute.py A lib/galaxy/tools/fetcher.py M lib/galaxy/tools/filter_failed_collection.xml A lib/galaxy/tools/filter_from_file.xml M lib/galaxy/tools/flatten_collection.xml M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/tools/imp_exp/exp_history_to_archive.xml M lib/galaxy/tools/imp_exp/export_history.py M lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py M lib/galaxy/tools/lint.py M lib/galaxy/tools/linters/general.py M lib/galaxy/tools/linters/inputs.py M lib/galaxy/tools/linters/outputs.py M lib/galaxy/tools/linters/stdio.py M lib/galaxy/tools/linters/tests.py M lib/galaxy/tools/loader_directory.py A lib/galaxy/tools/locations/__init__.py A lib/galaxy/tools/locations/dockstore.py A lib/galaxy/tools/locations/file.py A lib/galaxy/tools/locations/http.py M lib/galaxy/tools/merge_collection.xml M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/dataset_matcher.py M lib/galaxy/tools/parameters/dynamic_options.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/tools/parameters/input_translation.py M lib/galaxy/tools/parameters/meta.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/tools/parameters/sanitize.py M lib/galaxy/tools/parameters/validation.py M lib/galaxy/tools/parameters/wrapped.py M lib/galaxy/tools/parser/cwl.py M lib/galaxy/tools/parser/factory.py M lib/galaxy/tools/parser/interface.py M lib/galaxy/tools/parser/output_actions.py M lib/galaxy/tools/parser/output_collection_def.py M lib/galaxy/tools/parser/output_objects.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/parser/yaml.py A lib/galaxy/tools/relabel_from_file.xml M lib/galaxy/tools/search/__init__.py A lib/galaxy/tools/sort_collection_list.xml M lib/galaxy/tools/test.py M lib/galaxy/tools/toolbox/base.py R lib/galaxy/tools/toolbox/cache.py M lib/galaxy/tools/toolbox/filters/__init__.py M lib/galaxy/tools/toolbox/filters/examples.py.sample M lib/galaxy/tools/toolbox/integrated_panel.py M lib/galaxy/tools/toolbox/lineages/__init__.py M lib/galaxy/tools/toolbox/lineages/factory.py M lib/galaxy/tools/toolbox/lineages/interface.py R lib/galaxy/tools/toolbox/lineages/stock.py R lib/galaxy/tools/toolbox/lineages/tool_shed.py M lib/galaxy/tools/toolbox/parser.py M lib/galaxy/tools/toolbox/tags.py M lib/galaxy/tools/toolbox/watcher.py M lib/galaxy/tools/unzip_collection.xml M lib/galaxy/tools/util/galaxyops/__init__.py M lib/galaxy/tools/util/maf_utilities.py M lib/galaxy/tools/verify/__init__.py M lib/galaxy/tools/verify/asserts/__init__.py M lib/galaxy/tools/verify/asserts/text.py M lib/galaxy/tools/verify/asserts/xml.py M lib/galaxy/tools/verify/test_data.py M lib/galaxy/tools/wrappers.py M lib/galaxy/tools/xsd/README.md M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/tools/zip_collection.xml M lib/galaxy/tours/__init__.py M lib/galaxy/util/__init__.py M lib/galaxy/util/aliaspickler.py M lib/galaxy/util/biostar.py M lib/galaxy/util/checkers.py A lib/galaxy/util/compression_utils.py M lib/galaxy/util/dbkeys.py A lib/galaxy/util/handlers.py M lib/galaxy/util/hash_util.py M lib/galaxy/util/json.py M lib/galaxy/util/object_wrapper.py A lib/galaxy/util/oset.py M lib/galaxy/util/pastescript/loadwsgi.py M lib/galaxy/util/pastescript/serve.py M lib/galaxy/util/plugin_config.py R lib/galaxy/util/postfork.py M lib/galaxy/util/properties.py M lib/galaxy/util/simplegraph.py M lib/galaxy/util/submodules.py A lib/galaxy/util/tool_version.py M lib/galaxy/util/topsort.py M lib/galaxy/version.py M lib/galaxy/visualization/genomes.py M lib/galaxy/visualization/plugins/plugin.py M lib/galaxy/visualization/plugins/registry.py M lib/galaxy/web/__init__.py M lib/galaxy/web/base/controller.py R lib/galaxy/web/base/controllers/__init__.py R lib/galaxy/web/base/controllers/admin.py M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/web/base/pluginframework.py M lib/galaxy/web/buildapp.py M lib/galaxy/web/form_builder.py M lib/galaxy/web/framework/__init__.py M lib/galaxy/web/framework/base.py M lib/galaxy/web/framework/decorators.py M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/web/framework/middleware/batch.py M lib/galaxy/web/framework/middleware/error.py A lib/galaxy/web/framework/middleware/graphite.py M lib/galaxy/web/framework/middleware/remoteuser.py M lib/galaxy/web/framework/middleware/sentry.py M lib/galaxy/web/framework/middleware/static.py M lib/galaxy/web/framework/middleware/statsd.py M lib/galaxy/web/framework/middleware/translogger.py M lib/galaxy/web/framework/openid_manager.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/web/proxy/__init__.py M lib/galaxy/web/proxy/js/Dockerfile M lib/galaxy/web/proxy/js/lib/mapper.js M lib/galaxy/web/proxy/js/package.json A lib/galaxy/web/stack/__init__.py M lib/galaxy/webapps/galaxy/api/configuration.py M lib/galaxy/webapps/galaxy/api/folder_contents.py M lib/galaxy/webapps/galaxy/api/histories.py M lib/galaxy/webapps/galaxy/api/history_contents.py M lib/galaxy/webapps/galaxy/api/jobs.py M lib/galaxy/webapps/galaxy/api/lda_datasets.py M lib/galaxy/webapps/galaxy/api/library_contents.py M lib/galaxy/webapps/galaxy/api/quotas.py M lib/galaxy/webapps/galaxy/api/tool_dependencies.py M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/api/tools.py A lib/galaxy/webapps/galaxy/api/toolshed.py M lib/galaxy/webapps/galaxy/api/tours.py M lib/galaxy/webapps/galaxy/api/users.py A lib/galaxy/webapps/galaxy/api/webhooks.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/buildapp.py A lib/galaxy/webapps/galaxy/config_watchers.py M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/async.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/external_services.py M lib/galaxy/webapps/galaxy/controllers/history.py A lib/galaxy/webapps/galaxy/controllers/interactive_environments.py M lib/galaxy/webapps/galaxy/controllers/library.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/galaxy/webapps/galaxy/controllers/page.py M lib/galaxy/webapps/galaxy/controllers/root.py R lib/galaxy/webapps/galaxy/controllers/search.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/webapps/galaxy/controllers/userskeys.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/webapps/reports/__init__.py M lib/galaxy/webapps/reports/app.py M lib/galaxy/webapps/reports/buildapp.py M lib/galaxy/webapps/reports/config.py M lib/galaxy/webapps/tool_shed/__init__.py M lib/galaxy/webapps/tool_shed/api/categories.py M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/api/tools.py M lib/galaxy/webapps/tool_shed/app.py M lib/galaxy/webapps/tool_shed/buildapp.py M lib/galaxy/webapps/tool_shed/config.py M lib/galaxy/webapps/tool_shed/controllers/admin.py M lib/galaxy/webapps/tool_shed/controllers/groups.py M lib/galaxy/webapps/tool_shed/controllers/user.py M lib/galaxy/webapps/tool_shed/framework/middleware/remoteuser.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0013_add_review_tables.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0024_password_reset.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0025_session_timeout.py M lib/galaxy/webapps/tool_shed/util/ratings_util.py M lib/galaxy/webapps/util.py A lib/galaxy/webhooks/__init__.py M lib/galaxy/work/context.py M lib/galaxy/workflow/extract.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/render.py M lib/galaxy/workflow/run.py M lib/galaxy/workflow/run_request.py M lib/galaxy/workflow/schedulers/__init__.py M lib/galaxy/workflow/schedulers/core.py M lib/galaxy/workflow/scheduling_manager.py M lib/galaxy/workflow/steps.py R lib/galaxy_utils/__init__.py R lib/galaxy_utils/sequence/__init__.py R lib/galaxy_utils/sequence/fasta.py R lib/galaxy_utils/sequence/fastq.py R lib/galaxy_utils/sequence/sequence.py R lib/galaxy_utils/sequence/transform.py R lib/galaxy_utils/sequence/vcf.py M lib/log_tempfile.py M lib/mimeparse.py M lib/tool_shed/capsule/capsule_manager.py M lib/tool_shed/galaxy_install/datatypes/custom_datatype_manager.py M lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/galaxy_install/installed_repository_manager.py M lib/tool_shed/galaxy_install/metadata/installed_repository_metadata_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/env_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/env_file_builder.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py M lib/tool_shed/galaxy_install/tool_migration_manager.py M lib/tool_shed/galaxy_install/tools/data_manager.py M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py M lib/tool_shed/galaxy_install/update_repository_manager.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/unrestricted.py M lib/tool_shed/tools/tool_validator.py M lib/tool_shed/tools/tool_version_manager.py A 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/readme_util.py M lib/tool_shed/util/repository_util.py M lib/tool_shed/util/shed_util_common.py M lib/tool_shed/util/tool_dependency_util.py M lib/tool_shed/util/tool_util.py M lib/tool_shed/util/web_util.py M lib/tool_shed/util/workflow_util.py M lib/tool_shed/utility_containers/__init__.py M lib/tool_shed/utility_containers/utility_container_manager.py R openid/google.xml M run.sh M run_tests.sh M run_tool_shed.sh M scripts/api/README M scripts/api/data_manager_example_execute.py M scripts/api/example_watch_folder.py M scripts/api/filter_failed_datasets_from_collection.py M scripts/api/form_create_from_xml.py M scripts/api/history_create_history.py M scripts/api/history_delete_history.py M scripts/api/import_library_dataset_to_history.py M scripts/api/import_workflows_from_installed_tool_shed_repository.py M scripts/api/install_tool_shed_repositories.py M scripts/api/library_create_folder.py M scripts/api/library_create_library.py M scripts/api/library_upload_dir.py M scripts/api/library_upload_from_import_dir.py M scripts/api/load_data_with_metadata.py M scripts/api/repair_tool_shed_repository.py M scripts/api/request_type_create_from_xml.py M scripts/api/requests_update_state.py M scripts/api/reset_metadata_on_installed_repositories.py M scripts/api/sample_dataset_update_status.py M scripts/api/sample_update_state.py M scripts/api/search.py M scripts/api/sequencer_configuration_create.py M scripts/api/upload_to_history.py M scripts/api/workflow_delete.py M scripts/api/workflow_execute.py M scripts/api/workflow_execute_parameters.py M scripts/api/workflow_import.py M scripts/api/workflow_import_from_file_rpark.py M scripts/auth/pam_auth_helper.py M scripts/bootstrap_history.py R scripts/bootstrap_history_announce_template.rst M scripts/build_toolbox.py M scripts/build_universe_config.py M scripts/check_galaxy.py M scripts/check_python.py M scripts/cleanup_datasets/admin_cleanup_datasets.py M scripts/cleanup_datasets/cleanup_datasets.py M scripts/cleanup_datasets/pgcleanup.py M scripts/cleanup_datasets/populate_uuid.py M scripts/cleanup_datasets/remove_renamed_datasets_from_disk.py M scripts/cleanup_datasets/rename_purged_datasets.py M scripts/cleanup_datasets/update_dataset_size.py M scripts/cleanup_datasets/update_metadata.py M scripts/common_startup.sh M scripts/communication/communication_server.py M scripts/create_db.py M scripts/data_libraries/build_lucene_index.py M scripts/data_libraries/build_whoosh_index.py M scripts/db_shell.py M scripts/drmaa_external_killer.py M scripts/drmaa_external_runner.py A scripts/dump_tour.py M scripts/external_chown_script.py M scripts/extract_dataset_part.py M scripts/extract_toolbox_sections.py M scripts/functional_tests.py M scripts/galaxy-main R scripts/grt.py R scripts/grt.yml.sample A scripts/grt/export.py A scripts/grt/grt.yml.sample A scripts/grt/upload.py M scripts/loc_files/create_all_fasta_loc.py M scripts/manage_db.py A scripts/manage_tool_dependencies.py M scripts/microbes/BeautifulSoup.py M scripts/microbes/create_bacteria_loc_file.py M scripts/microbes/create_bacteria_table.py M scripts/microbes/get_builds_lengths.py M scripts/microbes/harvest_bacteria.py M scripts/others/incorrect_gops_jobs.py M scripts/others/incorrect_gops_join_jobs.py R scripts/run_selenium_tests.sh M scripts/runtime_stats.py A scripts/secret_decoder_ring.py M scripts/set_dataset_sizes.py M scripts/set_user_disk_usage.py A scripts/slideshow/__init__.py A scripts/slideshow/build_slideshow.py A scripts/slideshow/example.md A scripts/slideshow/slideshow_template.html A scripts/slideshow/style.sample.css M scripts/summarize_timings.py M scripts/sync_reports_config.py M scripts/tool_shed/api/add_repository_registry_entry.py M scripts/tool_shed/api/create_categories.py M scripts/tool_shed/api/create_users.py M scripts/tool_shed/api/export.py M scripts/tool_shed/api/get_filtered_repository_revisions.py M scripts/tool_shed/api/import_capsule.py M scripts/tool_shed/api/remove_repository_registry_entry.py M scripts/tool_shed/api/reset_metadata_on_repositories.py M scripts/tool_shed/bootstrap_tool_shed/bootstrap_util.py M scripts/tool_shed/bootstrap_tool_shed/create_user_with_api_key.py M scripts/tool_shed/build_ts_whoosh_index.py M scripts/tool_shed/check_download_urls.py M scripts/tool_shed/check_filesystem_for_empty_tool_dependency_installation_paths.py M scripts/tool_shed/check_s3_for_empty_tool_dependency_installation_paths.py M scripts/tool_shed/clean_up_tool_dependency_directory.py M scripts/tool_shed/deprecate_repositories_without_metadata.py M scripts/tool_shed/migrate_tools_to_repositories.py M scripts/tool_shed/show_tool_dependency_installation_dir_contents.py M scripts/tools/maf/check_loc_file.py M scripts/tools/re_escape_output.py M scripts/transfer.py M scripts/update_shed_config_path.py M setup.cfg A static/GruntFile.js A static/GruntFile.js.map A static/maps/admin.toolshed.js.map A static/maps/analysis.js.map A static/maps/app.js.map A static/maps/app/analysis.js.map M static/maps/galaxy.interactive_environments.js.map M static/maps/galaxy.js.map M static/maps/galaxy.library.js.map M static/maps/galaxy.pages.js.map M static/maps/layout/menu.js.map M static/maps/layout/page.js.map M static/maps/layout/panel.js.map A static/maps/layout/router.js.map M static/maps/layout/scratchbook.js.map M static/maps/libs/jquery/jquery.autocomplete.js.map A static/maps/libs/showdown.js.map M static/maps/mvc/citation/citation-view.js.map A static/maps/mvc/collection/base-creator.js.map M static/maps/mvc/collection/collection-model.js.map M static/maps/mvc/collection/collection-view-edit.js.map M static/maps/mvc/collection/collection-view.js.map M static/maps/mvc/collection/list-collection-creator.js.map M static/maps/mvc/collection/list-of-pairs-collection-creator.js.map M static/maps/mvc/collection/pair-collection-creator.js.map M static/maps/mvc/dataset/data.js.map A static/maps/mvc/dataset/dataset-edit-attributes.js.map A static/maps/mvc/dataset/dataset-error.js.map M static/maps/mvc/dataset/dataset-li-edit.js.map M static/maps/mvc/dataset/dataset-li.js.map M static/maps/mvc/dataset/dataset-model.js.map M static/maps/mvc/form/form-input.js.map M static/maps/mvc/form/form-parameters.js.map M static/maps/mvc/form/form-section.js.map M static/maps/mvc/form/form-view.js.map M static/maps/mvc/grid/grid-model.js.map A static/maps/mvc/grid/grid-shared.js.map M static/maps/mvc/grid/grid-template.js.map M static/maps/mvc/grid/grid-view.js.map M static/maps/mvc/history/hda-li.js.map M static/maps/mvc/history/hdca-li.js.map M static/maps/mvc/history/history-contents.js.map A 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-current.js.map M static/maps/mvc/history/history-view-edit.js.map M static/maps/mvc/history/history-view.js.map M static/maps/mvc/history/options-menu.js.map A static/maps/mvc/job/job-params.js.map M static/maps/mvc/library/library-dataset-view.js.map M static/maps/mvc/library/library-folderlist-view.js.map M static/maps/mvc/library/library-folderrow-view.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/maps/mvc/library/library-librarylist-view.js.map M static/maps/mvc/library/library-librarytoolbar-view.js.map M static/maps/mvc/tag.js.map M static/maps/mvc/tool/tool-form-base.js.map M static/maps/mvc/tool/tool-form-composite.js.map R static/maps/mvc/tool/tool-form-workflow.js.map M static/maps/mvc/tool/tool-form.js.map A static/maps/mvc/tool/tool-webhooks.js.map M static/maps/mvc/tool/tools.js.map A static/maps/mvc/toolshed/categories-view.js.map A static/maps/mvc/toolshed/repo-queue-view.js.map A static/maps/mvc/toolshed/repo-status-view.js.map A static/maps/mvc/toolshed/repositories-view.js.map A static/maps/mvc/toolshed/repository-queue-view.js.map A static/maps/mvc/toolshed/repository-view.js.map A static/maps/mvc/toolshed/shed-category-view.js.map A static/maps/mvc/toolshed/shed-list-view.js.map A static/maps/mvc/toolshed/shed-repo-details-view.js.map A static/maps/mvc/toolshed/shed-repo-list-view.js.map A static/maps/mvc/toolshed/sheds-list-view.js.map A static/maps/mvc/toolshed/toolshed-model.js.map A static/maps/mvc/toolshed/util.js.map A static/maps/mvc/toolshed/workflows-view.js.map M static/maps/mvc/tours.js.map M static/maps/mvc/ui/ui-buttons.js.map M static/maps/mvc/ui/ui-color-picker.js.map M static/maps/mvc/ui/ui-misc.js.map M static/maps/mvc/ui/ui-options.js.map M static/maps/mvc/ui/ui-portlet.js.map M static/maps/mvc/ui/ui-select-content.js.map M static/maps/mvc/ui/ui-select-default.js.map M static/maps/mvc/ui/ui-slider.js.map M static/maps/mvc/ui/ui-table.js.map M static/maps/mvc/ui/ui-tabs.js.map A static/maps/mvc/ui/ui-thumbnails.js.map A static/maps/mvc/upload/collection/collection-row.js.map A static/maps/mvc/upload/collection/collection-view.js.map M static/maps/mvc/upload/composite/composite-row.js.map M static/maps/mvc/upload/default/default-row.js.map M static/maps/mvc/upload/upload-ftp.js.map M static/maps/mvc/upload/upload-view.js.map A static/maps/mvc/user/change-password.js.map A static/maps/mvc/user/extra-information.js.map A static/maps/mvc/user/manage-user-information.js.map A static/maps/mvc/user/user-custom-builds.js.map A static/maps/mvc/user/user-preferences.js.map M static/maps/mvc/user/user-quotameter.js.map A static/maps/mvc/webhooks.js.map M static/maps/mvc/workflow/workflow-canvas.js.map A static/maps/mvc/workflow/workflow-configure-menu.js.map A static/maps/mvc/workflow/workflow-forms.js.map A static/maps/mvc/workflow/workflow-icons.js.map M static/maps/mvc/workflow/workflow-manager.js.map M static/maps/mvc/workflow/workflow-node.js.map M static/maps/mvc/workflow/workflow-terminals.js.map M static/maps/mvc/workflow/workflow-view-node.js.map M static/maps/mvc/workflow/workflow-view.js.map M static/maps/mvc/workflow/workflow.js.map A static/maps/nls/de/locale.js.map A static/maps/nls/es/locale.js.map A static/maps/nls/fr/locale.js.map M static/maps/nls/ja/locale.js.map M static/maps/nls/locale.js.map M static/maps/nls/zh/locale.js.map M static/maps/onload.js.map M static/maps/ui/autocom_tagging.js.map M static/maps/utils/utils.js.map M static/maps/viz/circster.js.map M static/maps/viz/phyloviz.js.map M static/maps/viz/trackster.js.map M static/maps/viz/trackster/tracks.js.map M static/maps/viz/visualization.js.map A static/scripts/admin.toolshed.js A static/scripts/analysis.js A static/scripts/app.js A static/scripts/app/analysis.js A static/scripts/bundled/admin.bundled.js A static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/galaxy.interactive_environments.js M static/scripts/galaxy.js M static/scripts/galaxy.library.js M static/scripts/galaxy.pages.js M static/scripts/layout/menu.js M static/scripts/layout/page.js M static/scripts/layout/panel.js A static/scripts/layout/router.js M static/scripts/layout/scratchbook.js M static/scripts/libs/jquery/jquery.autocomplete.js A static/scripts/libs/showdown.js M static/scripts/mvc/citation/citation-view.js A static/scripts/mvc/collection/base-creator.js M static/scripts/mvc/collection/collection-model.js M static/scripts/mvc/collection/collection-view-edit.js M static/scripts/mvc/collection/collection-view.js M static/scripts/mvc/collection/list-collection-creator.js M static/scripts/mvc/collection/list-of-pairs-collection-creator.js M static/scripts/mvc/collection/pair-collection-creator.js M static/scripts/mvc/dataset/data.js A static/scripts/mvc/dataset/dataset-edit-attributes.js A static/scripts/mvc/dataset/dataset-error.js M static/scripts/mvc/dataset/dataset-li-edit.js M static/scripts/mvc/dataset/dataset-li.js M static/scripts/mvc/dataset/dataset-model.js M static/scripts/mvc/form/form-input.js M static/scripts/mvc/form/form-parameters.js M static/scripts/mvc/form/form-section.js M static/scripts/mvc/form/form-view.js A static/scripts/mvc/grid/grid-shared.js M static/scripts/mvc/grid/grid-template.js M static/scripts/mvc/grid/grid-view.js M static/scripts/mvc/history/hda-li.js M static/scripts/mvc/history/hdca-li.js M static/scripts/mvc/history/history-contents.js A static/scripts/mvc/history/history-list.js M static/scripts/mvc/history/history-model.js M static/scripts/mvc/history/history-view-edit-current.js M static/scripts/mvc/history/history-view-edit.js M static/scripts/mvc/history/history-view.js M static/scripts/mvc/history/options-menu.js A static/scripts/mvc/job/job-params.js M static/scripts/mvc/library/library-dataset-view.js M static/scripts/mvc/library/library-folderlist-view.js M static/scripts/mvc/library/library-folderrow-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/library/library-librarylist-view.js M static/scripts/mvc/library/library-librarytoolbar-view.js M static/scripts/mvc/tag.js M static/scripts/mvc/tool/tool-form-base.js M static/scripts/mvc/tool/tool-form-composite.js R static/scripts/mvc/tool/tool-form-workflow.js M static/scripts/mvc/tool/tool-form.js A static/scripts/mvc/tool/tool-webhooks.js M static/scripts/mvc/tool/tools.js A static/scripts/mvc/toolshed/categories-view.js A static/scripts/mvc/toolshed/repo-queue-view.js A static/scripts/mvc/toolshed/repo-status-view.js A static/scripts/mvc/toolshed/repositories-view.js A static/scripts/mvc/toolshed/repository-queue-view.js A static/scripts/mvc/toolshed/repository-view.js A static/scripts/mvc/toolshed/shed-category-view.js A static/scripts/mvc/toolshed/shed-list-view.js A static/scripts/mvc/toolshed/shed-repo-details-view.js A static/scripts/mvc/toolshed/shed-repo-list-view.js A static/scripts/mvc/toolshed/sheds-list-view.js A static/scripts/mvc/toolshed/toolshed-model.js A static/scripts/mvc/toolshed/util.js A static/scripts/mvc/toolshed/workflows-view.js M static/scripts/mvc/tours.js M static/scripts/mvc/ui/ui-buttons.js M static/scripts/mvc/ui/ui-color-picker.js M static/scripts/mvc/ui/ui-misc.js M static/scripts/mvc/ui/ui-options.js M static/scripts/mvc/ui/ui-portlet.js M static/scripts/mvc/ui/ui-select-content.js M static/scripts/mvc/ui/ui-select-default.js M static/scripts/mvc/ui/ui-slider.js M static/scripts/mvc/ui/ui-table.js M static/scripts/mvc/ui/ui-tabs.js A static/scripts/mvc/ui/ui-thumbnails.js A static/scripts/mvc/upload/collection/collection-row.js A static/scripts/mvc/upload/collection/collection-view.js M static/scripts/mvc/upload/composite/composite-row.js M static/scripts/mvc/upload/default/default-row.js M static/scripts/mvc/upload/upload-ftp.js M static/scripts/mvc/upload/upload-view.js A static/scripts/mvc/user/change-password.js A static/scripts/mvc/user/extra-information.js A static/scripts/mvc/user/manage-user-information.js A static/scripts/mvc/user/user-custom-builds.js A static/scripts/mvc/user/user-preferences.js M static/scripts/mvc/user/user-quotameter.js A static/scripts/mvc/webhooks.js M static/scripts/mvc/workflow/workflow-canvas.js A static/scripts/mvc/workflow/workflow-configure-menu.js A static/scripts/mvc/workflow/workflow-forms.js A static/scripts/mvc/workflow/workflow-icons.js M static/scripts/mvc/workflow/workflow-manager.js M static/scripts/mvc/workflow/workflow-node.js M static/scripts/mvc/workflow/workflow-terminals.js M static/scripts/mvc/workflow/workflow-view-node.js M static/scripts/mvc/workflow/workflow-view.js A static/scripts/mvc/workflow/workflow.js A static/scripts/nls/de/locale.js A static/scripts/nls/es/locale.js A static/scripts/nls/fr/locale.js M static/scripts/nls/ja/locale.js M static/scripts/nls/locale.js M static/scripts/nls/zh/locale.js M static/scripts/onload.js M static/scripts/ui/autocom_tagging.js M static/scripts/utils/utils.js M static/scripts/viz/circster.js M static/scripts/viz/phyloviz.js M static/scripts/viz/trackster.js M static/scripts/viz/trackster/tracks.js M static/scripts/viz/visualization.js M static/style/blue/base.css M static/welcome.html.sample M templates/admin/reload_tool.mako R templates/admin/tool_shed_repository/browse_toolsheds.mako M templates/admin/tool_shed_repository/common.mako R templates/admin/tool_shed_repository/select_shed_tool_panel_config.mako M templates/admin/tool_shed_repository/select_tool_panel_section.mako M templates/admin/user/reset_password.mako M templates/admin/user/user.mako M templates/base.mako M templates/base/base_panels.mako M templates/display_base.mako M templates/galaxy_client_app.mako M templates/grid_base.mako M templates/ind_share_base.mako M templates/js-app.mako M templates/sharing_base.mako M templates/show_params.mako R templates/user/change_password.mako R templates/user/communication_settings.mako R templates/user/dbkeys.mako R templates/user/edit_address.mako M templates/user/index.mako M templates/user/login.mako M templates/user/logout.mako R templates/user/new_address.mako R templates/user/permissions.mako M templates/user/register.mako R templates/user/toolbox_filters.mako R templates/user/username.mako M templates/webapps/galaxy/admin/center.mako R templates/webapps/galaxy/admin/index.mako A templates/webapps/galaxy/admin/manage_dependencies.mako M templates/webapps/galaxy/base_panels.mako M templates/webapps/galaxy/data_manager/index.mako M templates/webapps/galaxy/dataset/display.mako R templates/webapps/galaxy/dataset/edit_attributes.mako R templates/webapps/galaxy/dataset/errors.mako R templates/webapps/galaxy/dataset/grid.mako M templates/webapps/galaxy/galaxy.masthead.mako M templates/webapps/galaxy/galaxy.panels.mako M templates/webapps/galaxy/history/display_structured.mako R templates/webapps/galaxy/history/grid.mako R templates/webapps/galaxy/history/grid_js.mako R templates/webapps/galaxy/history/list_published.mako M templates/webapps/galaxy/history/share.mako R templates/webapps/galaxy/history/shared_grid.mako M templates/webapps/galaxy/mobile/form.mako M templates/webapps/galaxy/mobile/index.mako M templates/webapps/galaxy/page/editor.mako R templates/webapps/galaxy/page/index.mako R templates/webapps/galaxy/page/list_published.mako R templates/webapps/galaxy/page/select_items_grid.mako M templates/webapps/galaxy/requests/common/common.mako M templates/webapps/galaxy/root/tool_runner.mako R templates/webapps/galaxy/tracks/add_to_viz.mako R templates/webapps/galaxy/tracks/add_tracks.mako R templates/webapps/galaxy/tracks/history_datasets_select_grid.mako R templates/webapps/galaxy/tracks/history_select_grid.mako R templates/webapps/galaxy/tracks/library_datasets_select_grid.mako R templates/webapps/galaxy/user/api_keys.mako M templates/webapps/galaxy/user/list_users.mako R templates/webapps/galaxy/user/manage_info.mako R templates/webapps/galaxy/visualization/list.mako R templates/webapps/galaxy/visualization/list_published.mako M templates/webapps/galaxy/workflow/build_from_current_history.mako R templates/webapps/galaxy/workflow/configure_menu.mako M templates/webapps/galaxy/workflow/display.mako M templates/webapps/galaxy/workflow/editor.mako R templates/webapps/galaxy/workflow/editor_generic_form.mako R templates/webapps/galaxy/workflow/editor_tool_form.mako R templates/webapps/galaxy/workflow/import.mako R templates/webapps/galaxy/workflow/index.mako R templates/webapps/galaxy/workflow/list.mako R templates/webapps/galaxy/workflow/list_for_run.mako R templates/webapps/galaxy/workflow/list_published.mako R templates/webapps/galaxy/workflow/missing_tools.mako R templates/webapps/galaxy/workflow/myexp_export_content.mako R templates/webapps/galaxy/workflow/rename.mako R templates/webapps/galaxy/workflow/run.mako M templates/webapps/reports/base_panels.mako M templates/webapps/tool_shed/admin/center.mako M templates/webapps/tool_shed/base_panels.mako M templates/webapps/tool_shed/repository/common.mako M templates/webapps/tool_shed/repository/tool_form.mako A templates/webapps/tool_shed/user/api_keys.mako A templates/webapps/tool_shed/user/change_password.mako A templates/webapps/tool_shed/user/index.mako A templates/webapps/tool_shed/user/username.mako A test-data/1.fastqsanger.bz2 A test-data/1.fastqsanger.gz A test-data/5_Ig-like.gff A test-data/bam_from_sam.bam A test-data/filter_labels_1.txt A test-data/new_labels_1.txt A test-data/new_labels_2.txt A test-data/new_labels_bad_1.txt A test-data/new_labels_bad_2.txt A test-data/sam_with_header.sam A test-data/simple.xml A test-data/test.vcf.gz M test/TESTING.md R test/api/helpers.py M test/api/test_api_batch.py A test/api/test_configuration.py M test/api/test_dataset_collections.py M test/api/test_datasets.py M test/api/test_datatypes.py M test/api/test_histories.py M test/api/test_history_contents.py M test/api/test_history_contents_provenance.py M test/api/test_jobs.py M test/api/test_libraries.py M test/api/test_search.py M test/api/test_tools.py M test/api/test_users.py A test/api/test_visualizations.py A test/api/test_webhooks.py R test/api/test_workflow_1.ga R test/api/test_workflow_2.ga R test/api/test_workflow_batch.ga M test/api/test_workflow_extraction.py R test/api/test_workflow_map_reduce_pause.ga R test/api/test_workflow_matching_lists.ga R test/api/test_workflow_missing_tool.ga R test/api/test_workflow_pause.ga R test/api/test_workflow_topoambigouity.ga R test/api/test_workflow_topoambigouity_auto_laidout.ga R test/api/test_workflow_validation_1.ga R test/api/test_workflow_with_runtime_input.ga M test/api/test_workflows.py M test/api/test_workflows_from_yaml.py R test/api/workflows_format_2/README.txt R test/api/workflows_format_2/__init__.py R test/api/workflows_format_2/converter.py R test/api/workflows_format_2/interface.py R test/api/workflows_format_2/main.py M test/base/api.py M test/base/api_asserts.py A test/base/data/test_workflow_1.ga A test/base/data/test_workflow_2.ga A test/base/data/test_workflow_batch.ga A test/base/data/test_workflow_map_reduce_pause.ga A test/base/data/test_workflow_matching_lists.ga A test/base/data/test_workflow_missing_tool.ga A test/base/data/test_workflow_pause.ga A test/base/data/test_workflow_topoambigouity.ga A test/base/data/test_workflow_topoambigouity_auto_laidout.ga A test/base/data/test_workflow_validation_1.ga A test/base/data/test_workflow_with_runtime_input.ga M test/base/driver_util.py M test/base/integration_util.py M test/base/interactor.py A test/base/populators.py M test/base/twilltestcase.py A test/base/workflows_format_2/README.txt A test/base/workflows_format_2/__init__.py A test/base/workflows_format_2/converter.py A test/base/workflows_format_2/interface.py A test/base/workflows_format_2/main.py R test/casperjs/anon-history-tests.js R test/casperjs/api-batch-tests.js R test/casperjs/api-configuration-tests.js R test/casperjs/api-dataset-tests.js R test/casperjs/api-history-tests.js R test/casperjs/api-tool-tests.js R test/casperjs/api-user-tests.js R test/casperjs/api-visualizations-tests.js R test/casperjs/hda-state-tests.js R test/casperjs/history-options-tests.js R test/casperjs/history-panel-tests.js R test/casperjs/history-share-tests.js R test/casperjs/login-tests.js R test/casperjs/registration-tests.js R test/casperjs/upload-tests.js M test/docker/README.md M test/docker/base/Dockerfile M test/docker/base/ansible_vars.yml M test/docker/base/run_test_wrapper.sh M test/functional/test_library_templates.py M test/functional/test_toolbox.py M test/functional/tools/checksum.xml A test/functional/tools/collection_creates_dynamic_nested_fail.xml A test/functional/tools/collection_creates_list_fail.xml M test/functional/tools/column_param.xml A test/functional/tools/compressed_bz2_fastq_conversion.xml A test/functional/tools/compressed_bz2_fastq_no_conversion.xml A test/functional/tools/compressed_gz_fastq_conversion.xml A test/functional/tools/compressed_gz_fastq_no_conversion.xml M test/functional/tools/create_10.xml A test/functional/tools/create_2.xml A test/functional/tools/explicit_conversion.xml A test/functional/tools/for_tours/filtering.py A test/functional/tools/for_tours/filtering.xml A test/functional/tools/for_workflows/mapper2.xml A test/functional/tools/identifier_multiple_in_conditional.xml A test/functional/tools/identifier_multiple_in_repeat.xml A test/functional/tools/identifier_source.xml A test/functional/tools/implicit_conversion.xml A test/functional/tools/is_valid_xml.xml A test/functional/tools/legacy_r.xml M test/functional/tools/md5sum.xml A test/functional/tools/mulled_example_conflict.xml A test/functional/tools/mulled_example_multi_incomplete.xml A test/functional/tools/mulled_example_multi_versionless.xml A test/functional/tools/output_format_deprecated_when.xml A test/functional/tools/paired_collection_map_over_structured_like.xml A test/functional/tools/param_text_option.xml A test/functional/tools/python_environment_problem.py A test/functional/tools/python_environment_problem.xml A test/functional/tools/sam_to_bam.xml M test/functional/tools/sample_datatypes_conf.xml M test/functional/tools/samples_tool_conf.xml A test/functional/tools/vcf_bgzip.xml A test/functional/webhooks/history_test1/config/history_test1.yml A test/functional/webhooks/history_test2/config/history_test2.yml A test/functional/webhooks/masthead_test/config/masthead_test.yml A test/functional/webhooks/phdcomics/config/phdcomics.yaml A test/functional/webhooks/phdcomics/helper/__init__.py A test/functional/webhooks/phdcomics/static/script.js A test/functional/webhooks/phdcomics/static/styles.css A test/functional/webhooks/trans_object/config/trans_object.yaml A test/functional/webhooks/trans_object/helper/__init__.py A test/functional/webhooks/xkcd/config/xkcd.yml A test/functional/webhooks/xkcd/static/script.js A test/functional/webhooks/xkcd/static/styles.css R test/functional/workflow.py A test/galaxy_selenium/__init__.py A test/galaxy_selenium/cli.py A test/galaxy_selenium/data.py A test/galaxy_selenium/driver_factory.py A test/galaxy_selenium/has_driver.py A test/galaxy_selenium/navigates_galaxy.py A test/galaxy_selenium/navigation-data.yml A test/galaxy_selenium/sizzle.py A test/integration/resubmission_default_job_conf.xml A test/integration/resubmission_job_conf.xml A test/integration/resubmission_job_resource_parameters_conf.xml A test/integration/resubmission_rules/__init__.py A test/integration/resubmission_rules/rules.py A test/integration/resubmission_runners.py A test/integration/test_config_options_users.py A test/integration/test_job_resubmission.py A test/integration/test_maximum_worklfow_invocation_duration.py M test/integration/test_resolvers.py A test/integration/test_workflow_handler_configuration.py A test/integration/workflow_handler_configuration_job_conf.xml A test/integration/workflow_handler_configuration_workflow_scheduler_conf.xml M test/manual/workflows_scaling.py M test/qunit/package.json M test/qunit/test-data/bootstrapped.js M test/qunit/test-data/paired-collection-creator.data.js M test/qunit/tests/form_tests.js M test/qunit/tests/galaxy-app-base.js M test/qunit/tests/page_tests.js M test/qunit/tests/ui_tests.html M test/qunit/tests/ui_tests.js M test/qunit/tests/workflow_editor_tests.js A test/selenium_tests/__init__.py A test/selenium_tests/_workflow_fixtures.py A test/selenium_tests/framework.py A test/selenium_tests/test_anon_history.py A test/selenium_tests/test_collection_builders.py A test/selenium_tests/test_history_dataset_state.py A test/selenium_tests/test_history_options.py A test/selenium_tests/test_history_panel.py A test/selenium_tests/test_history_sharing.py A test/selenium_tests/test_login.py A test/selenium_tests/test_registration.py A test/selenium_tests/test_stock_tours.py A test/selenium_tests/test_tool_form.py A test/selenium_tests/test_uploads.py A test/selenium_tests/test_workflow_editor.py A test/selenium_tests/test_workflow_management.py A test/selenium_tests/test_workflow_run.py M test/shed_functional/base/twilltestcase.py M test/shed_functional/functional/test_1010_install_repository_with_tool_dependencies.py M test/shed_functional/functional/test_1090_repository_dependency_handling.py M test/shed_functional/functional/test_1140_simple_repository_dependency_multiple_owners.py M test/shed_functional/functional/test_1150_datatype_converters.py M test/shed_functional/functional/test_1210_uninstall_reinstall_repository_with_tool_dependencies.py M test/unit/dataset_collections/test_matching.py M test/unit/datatypes/dataproviders/test_base_dataproviders.py M test/unit/datatypes/dataproviders/test_line_dataproviders.py A test/unit/jobs/conditional_runners_job_conf.xml M test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py M test/unit/jobs/test_command_factory.py M test/unit/jobs/test_job_configuration.py M test/unit/jobs/test_job_output_checker.py M test/unit/jobs/test_job_wrapper.py M test/unit/jobs/test_mapper.py M test/unit/jobs/test_rule_helper.py M test/unit/jobs/test_runner_local.py M test/unit/managers/base.py M test/unit/managers/test_CollectionManager.py M test/unit/managers/test_DatasetManager.py M test/unit/managers/test_HDAManager.py M test/unit/managers/test_HDCAManager.py M test/unit/managers/test_HistoryContentsManager.py M test/unit/managers/test_HistoryManager.py M test/unit/managers/test_UserManager.py M test/unit/shed_unit/test_fabric_util.py A test/unit/shed_unit/test_installed_repository_manager.py M test/unit/shed_unit/test_td_common_util.py M test/unit/shed_unit/test_tool_panel_manager.py M test/unit/test_galaxy_transactions.py A test/unit/test_remote_shell.py M test/unit/test_routes.py M test/unit/test_sockets.py M test/unit/tools/test_actions.py M test/unit/tools/test_citations.py M test/unit/tools/test_collect_primary_datasets.py M test/unit/tools/test_column_parameters.py M test/unit/tools/test_conda_resolution.py M test/unit/tools/test_data_parameters.py M test/unit/tools/test_dataset_matcher.py M test/unit/tools/test_evaluation.py M test/unit/tools/test_execution.py M test/unit/tools/test_history_imp_exp.py M test/unit/tools/test_parameter_parsing.py M test/unit/tools/test_parsing.py M test/unit/tools/test_select_parameters.py M test/unit/tools/test_tool_dependency_description.py M test/unit/tools/test_tool_deps.py M test/unit/tools/test_tool_external_files.py M test/unit/tools/test_toolbox.py M test/unit/tools/test_watcher.py M test/unit/tools/test_wrappers.py M test/unit/tools_support.py M test/unit/unittest_utils/galaxy_mock.py M test/unit/unittest_utils/tempfilecache.py M test/unit/unittest_utils/utility.py M test/unit/visualizations/plugins/test_VisualizationPlugin.py M test/unit/visualizations/plugins/test_VisualizationsRegistry.py M test/unit/web/base/test_HookPluginManager.py M test/unit/web/base/test_PageServingPluginManager.py M test/unit/web/base/test_PluginManager.py M test/unit/web/framework/test_webapp.py M test/unit/workflows/test_modules.py M test/unit/workflows/test_run_parameters.py M test/unit/workflows/test_workflow_progress.py M test/unit/workflows/workflow_support.py A tool-data/blastdb.loc.sample A tool-data/blastdb_d.loc.sample A tool-data/blastdb_p.loc.sample M tool-data/shared/ucsc/builds.txt.sample M tool-data/shared/ucsc/ucsc_build_sites.txt.sample M tools/data_source/data_source.py M tools/data_source/fetch.py M tools/data_source/genbank.py M tools/data_source/upload.py M tools/evolution/add_scores.py M tools/evolution/add_scores.xml M tools/extract/extract_genomic_dna.py M tools/extract/extract_genomic_dna.xml M tools/extract/liftOver_wrapper.py M tools/filters/axt_to_fasta.py M tools/filters/bed_to_gff_converter.py M tools/filters/catWrapper.py M tools/filters/convert_characters.py M tools/filters/gff/extract_GFF_Features.py M tools/filters/gff/gff_filter_by_attribute.py M tools/filters/gff/gff_filter_by_attribute.xml M tools/filters/gff/gff_filter_by_feature_count.py M tools/filters/gff/gff_filter_by_feature_count.xml M tools/filters/gff/gtf_filter_by_attribute_values_list.py R tools/filters/gff/sort_gtf.py M tools/filters/gff_to_bed_converter.py M tools/filters/grep.py M tools/filters/gtf_to_bedgraph_converter.py M tools/filters/join.py M tools/filters/joinWrapper.py M tools/filters/lav_to_bed.py M tools/filters/mergeCols.py M tools/filters/pasteWrapper.xml M tools/filters/random_lines_two_pass.py M tools/filters/randomlines.py M tools/filters/secure_hash_message_digest.py M tools/filters/sorter.py M tools/filters/trimmer.py M tools/filters/trimmer.xml M tools/filters/ucsc_gene_bed_to_exon_bed.py M tools/filters/ucsc_gene_bed_to_intron_bed.py M tools/filters/ucsc_gene_table_to_intervals.py M tools/filters/uniq.py M tools/filters/wc_gnu.xml M tools/filters/wiggle_to_simple.py M tools/genomespace/genomespace_exporter.py M tools/genomespace/genomespace_file_browser.py M tools/genomespace/genomespace_importer.py M tools/maf/genebed_maf_to_fasta.xml M tools/maf/interval2maf.py M tools/maf/interval2maf.xml M tools/maf/interval2maf_pairwise.xml M tools/maf/interval_maf_to_merged_fasta.py M tools/maf/interval_maf_to_merged_fasta.xml M tools/maf/macros.xml M tools/maf/maf_by_block_number.py M tools/maf/maf_by_block_number.xml M tools/maf/maf_filter.py M tools/maf/maf_filter.xml M tools/maf/maf_limit_size.py M tools/maf/maf_limit_size.xml M tools/maf/maf_limit_to_species.py M tools/maf/maf_limit_to_species.xml M tools/maf/maf_reverse_complement.py M tools/maf/maf_reverse_complement.xml M tools/maf/maf_split_by_species.py M tools/maf/maf_split_by_species.xml M tools/maf/maf_stats.py M tools/maf/maf_stats.xml M tools/maf/maf_thread_for_species.py M tools/maf/maf_thread_for_species.xml M tools/maf/maf_to_bed.py M tools/maf/maf_to_bed.xml M tools/maf/maf_to_fasta.xml M tools/maf/maf_to_fasta_multiple_sets.py M tools/maf/maf_to_interval.py M tools/maf/maf_to_interval.xml M tools/maf/vcf_to_maf_customtrack.py M tools/maf/vcf_to_maf_customtrack.xml M tools/meme/fimo_wrapper.py M tools/metag_tools/blat_wrapper.py M tools/metag_tools/shrimp_color_wrapper.xml M tools/metag_tools/shrimp_wrapper.xml M tools/next_gen_conversion/fastq_conversions.py M tools/next_gen_conversion/fastq_gen_conv.py M tools/next_gen_conversion/fastq_gen_conv.xml 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/phenotype_association/pagetag.py M tools/phenotype_association/senatag.py M tools/plotting/bar_chart.xml M tools/solid_tools/maq_cs_wrapper.py M tools/solid_tools/solid_qual_stats.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_binned_scores_in_intervals.xml M tools/stats/aggregate_scores_in_intervals.py M tools/stats/filtering.py M tools/stats/grouping.py M tools/stats/gsummary.py M tox.ini Log Message: ----------- Merge remote-tracking branch 'jmchilton/dev' into install_workflow_and_tools Conflicts: lib/galaxy/webapps/galaxy/api/workflows.py Commit: 7dd3ddccafee8f5cc185f1b0dd711056576a92ce https://github.com/galaxyproject/galaxy/commit/7dd3ddccafee8f5cc185f1b0dd71… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-10 (Thu, 10 Aug 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py M test/api/test_workflows.py Log Message: ----------- Require admin for new import_tools function in workflows API. Includes test case. Commit: fc861cdf38d1d20fd611e8bcb042328eb905b3c4 https://github.com/galaxyproject/galaxy/commit/fc861cdf38d1d20fd611e8bcb042… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-12 (Sat, 12 Aug 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py M test/api/test_workflows.py Log Message: ----------- Merge pull request #3064 from manabuishii/install_workflow_and_tools Install tools and workflow Compare: https://github.com/galaxyproject/galaxy/compare/331851b0495d...fc861cdf38d1

1 0

[galaxyproject/galaxy] 6a7cc3: Bring Galaxy, reports, and shed run scripts in syn...
by GitHub 12 Aug '17

12 Aug '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 6a7cc34e1b1ade9580e464570fc6b83a488e941f https://github.com/galaxyproject/galaxy/commit/6a7cc34e1b1ade9580e464570fc6… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-10 (Thu, 10 Aug 2017) Changed paths: M run.sh M run_reports.sh M run_tool_shed.sh A scripts/common_startup_functions.sh Log Message: ----------- Bring Galaxy, reports, and shed run scripts in sync. - They now uniformly handle server option processing. - Reports and Tool Shed now respect many new and important options such as --skip_venv. - Reports and Tool Shed now do extra checking around Python version that Galaxy does. In addition to improving the reports and tool shed startup scripts and reducing cognative load with respect to option handling, this is an important pre-condition to us being able us to switch on uwsgi by default for all three services simultaneously without a bunch of copy and pasting. Commit: 72e5a00ba0ad9c1a8e56ad9544bec23c843d900d https://github.com/galaxyproject/galaxy/commit/72e5a00ba0ad9c1a8e56ad9544be… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-10 (Thu, 10 Aug 2017) Changed paths: M run_reports.sh M run_tool_shed.sh M scripts/common_startup_functions.sh Log Message: ----------- Centralize launching server for reports and tool shed. Initial outline of allowing launch via uwsgi. Commit: 1bdb99bbd76d0827cd3a7e617d288564584863ea https://github.com/galaxyproject/galaxy/commit/1bdb99bbd76d0827cd3a7e617d28… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-10 (Thu, 10 Aug 2017) Changed paths: M lib/galaxy/dependencies/__init__.py M lib/galaxy/util/properties.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/webapps/tool_shed/buildapp.py M scripts/manage_tools.py Log Message: ----------- Update galaxy.util.properties to allow YAML. Commit: 8189a1f1e289e14d362fcb8871b9339c3355e8b2 https://github.com/galaxyproject/galaxy/commit/8189a1f1e289e14d362fcb8871b9… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-10 (Thu, 10 Aug 2017) Changed paths: A lib/galaxy/webapps/config_manage.py A scripts/config_sample_to_kwalify.py A test/unit/config/1607_root_filters/config/galaxy.ini A test/unit/config/1607_root_filters/config/tool_shed.ini A test/unit/config/1607_root_samples/config/galaxy.ini A test/unit/config/1607_root_samples/config/reports.ini A test/unit/config/1607_root_samples/config/tool_shed.ini A test/unit/config/test_config_manage.py Log Message: ----------- Scripts to manage configuration infrastructure. This has been rebased several times and includes a variety of fixes (some thanks to martenson). Commit: 7973a914e0beef9680475d54947bd953c0b062cd https://github.com/galaxyproject/galaxy/commit/7973a914e0beef9680475d54947b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-10 (Thu, 10 Aug 2017) Changed paths: A lib/galaxy/webapps/uwsgi_schema.yml Log Message: ----------- Add uwsgi_schema.yml. Commit: 90e899d68fbf21effad1cf309efbd786c54be556 https://github.com/galaxyproject/galaxy/commit/90e899d68fbf21effad1cf309efb… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-10 (Thu, 10 Aug 2017) Changed paths: R config/tool_shed.ini.sample A config/tool_shed.yml.sample M lib/galaxy/webapps/tool_shed/buildapp.py A lib/galaxy/webapps/tool_shed/config_schema.yml A lib/galaxy/webapps/tool_shed/uwsgi_schema.yml M run_tool_shed.sh Log Message: ----------- Update tool shed to use newer configuration schema. - Implement kwalify schema to validate/define the schema. - Replace ini configuration with YAML (completely backward compatible). - Rebuild a sample configuration from the schema (config/tool_shed.yml.sample). Commit: 102566dd5e1c5903726057f1077a1d7fc614b815 https://github.com/galaxyproject/galaxy/commit/102566dd5e1c5903726057f1077a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-10 (Thu, 10 Aug 2017) Changed paths: R config/reports.ini.sample A config/reports.yml.sample M lib/galaxy/webapps/reports/buildapp.py A lib/galaxy/webapps/reports/config_schema.yml A lib/galaxy/webapps/reports/uwsgi_schema.yml M run_reports.sh Log Message: ----------- Update Galaxy Reports to use newer configuration schema. - Implement kwalify schema to validate/define the schema. - Replace ini configuration with YAML (completely backward compatible). - Rebuild a sample configuration from the schema (config/reports.yml.sample). Commit: 50d426ed2b9ae2aff8b243143478ce84c7731816 https://github.com/galaxyproject/galaxy/commit/50d426ed2b9ae2aff8b243143478… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-10 (Thu, 10 Aug 2017) Changed paths: A doc/source/admin/reports.rst A doc/source/admin/reports_options.rst Log Message: ----------- Add reports documentation to ``doc/``. - Automatically generate RST docs from config schema. - Describe older functionality as well as new YAML-based configuration. - Replace https://wiki.galaxyproject.org/Admin/UsageReports. Commit: 4945f55e4fe28842b58c025b37c4d6c96a07028f https://github.com/galaxyproject/galaxy/commit/4945f55e4fe28842b58c025b37c4… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-10 (Thu, 10 Aug 2017) Changed paths: M Makefile Log Message: ----------- Makefile shortcuts for configuration script. Commit: ef46a60a829e3dae44d935f6f886feef39b873e3 https://github.com/galaxyproject/galaxy/commit/ef46a60a829e3dae44d935f6f886… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-10 (Thu, 10 Aug 2017) Changed paths: M lib/galaxy/dependencies/pinned-requirements.txt Log Message: ----------- Add required dependency on uwsgi. Required for the new out-of-the-box configuration of tool shed and reports. Commit: 8191fd492819214b12c0aa28b35e5b6c4ea7bfa1 https://github.com/galaxyproject/galaxy/commit/8191fd492819214b12c0aa28b35e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-10 (Thu, 10 Aug 2017) Changed paths: M lib/galaxy/dependencies/pinned-requirements.txt Log Message: ----------- Add pykwalify as dependency for the new config validation stuff. xref https://github.com/galaxyproject/starforge/pull/110 Commit: ffe295e96dbd82615c987a2b9ba9bd15ea253826 https://github.com/galaxyproject/galaxy/commit/ffe295e96dbd82615c987a2b9ba9… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-10 (Thu, 10 Aug 2017) Changed paths: M test/unit/config/test_config_manage.py Log Message: ----------- Fix Python 3 linting problem with test_config_manage.py. Commit: 1ce93ccfdf7b54ec1efcf08b04c9f28b67ab0615 https://github.com/galaxyproject/galaxy/commit/1ce93ccfdf7b54ec1efcf08b04c9… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-10 (Thu, 10 Aug 2017) Changed paths: M lib/galaxy/dependencies/pinned-requirements.txt Log Message: ----------- Pin version of uWSGI to freshly released 2.0.15 available on wheels.galaxyproject.org. Commit: 539a62f642ada1f2d832f1f88ab339cafe672c1f https://github.com/galaxyproject/galaxy/commit/539a62f642ada1f2d832f1f88ab3… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-10 (Thu, 10 Aug 2017) Changed paths: M lib/galaxy/model/orm/scripts.py M lib/galaxy/util/properties.py Log Message: ----------- Fix ORM scripts for #3179. Commit: 98ca8ce7a68d18533f3bf85097490c5b66e9f876 https://github.com/galaxyproject/galaxy/commit/98ca8ce7a68d18533f3bf8509749… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-10 (Thu, 10 Aug 2017) Changed paths: M lib/galaxy/web/framework/webapp.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Update config overhaul branch for introduction of galaxy.web.stack package. Commit: 331851b0495d429220450ceb3a540fbba900143a https://github.com/galaxyproject/galaxy/commit/331851b0495d429220450ceb3a54… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-08-12 (Sat, 12 Aug 2017) Changed paths: M Makefile R config/reports.ini.sample A config/reports.yml.sample R config/tool_shed.ini.sample A config/tool_shed.yml.sample A doc/source/admin/reports.rst A doc/source/admin/reports_options.rst M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/model/orm/scripts.py M lib/galaxy/util/properties.py M lib/galaxy/web/framework/webapp.py A lib/galaxy/webapps/config_manage.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/reports/buildapp.py A lib/galaxy/webapps/reports/config_schema.yml A lib/galaxy/webapps/reports/uwsgi_schema.yml M lib/galaxy/webapps/tool_shed/buildapp.py A lib/galaxy/webapps/tool_shed/config_schema.yml A lib/galaxy/webapps/tool_shed/uwsgi_schema.yml A lib/galaxy/webapps/uwsgi_schema.yml M run.sh M run_reports.sh M run_tool_shed.sh A scripts/common_startup_functions.sh A scripts/config_sample_to_kwalify.py M scripts/manage_tools.py A test/unit/config/1607_root_filters/config/galaxy.ini A test/unit/config/1607_root_filters/config/tool_shed.ini A test/unit/config/1607_root_samples/config/galaxy.ini A test/unit/config/1607_root_samples/config/reports.ini A test/unit/config/1607_root_samples/config/tool_shed.ini A test/unit/config/test_config_manage.py Log Message: ----------- Merge pull request #3179 from jmchilton/web_config_overhaul_0 Configuration & Server Overhaul - Tool Shed and Reports Compare: https://github.com/galaxyproject/galaxy/compare/c6e45e7b0720...331851b0495d

1 0

[galaxyproject/galaxy] e72f5e: deals with .xls older file extension
by GitHub 11 Aug '17

11 Aug '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: e72f5e81a4baffcb4679d6e74837daedcfa65f67 https://github.com/galaxyproject/galaxy/commit/e72f5e81a4baffcb4679d6e74837… Author: Frederic Sapet <frederic.sapet(a)biogemma.com> Date: 2017-06-16 (Fri, 16 Jun 2017) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- deals with .xls older file extension Commit: 5fec6c87cba14dd7692d8239669a02d6b5586748 https://github.com/galaxyproject/galaxy/commit/5fec6c87cba14dd7692d8239669a… Author: Frederic Sapet <frederic.sapet(a)biogemma.com> Date: 2017-06-16 (Fri, 16 Jun 2017) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- indentation for Travis Commit: 9cd9c81279d1d7749af7d9c64f8329e8cfc7f6bf https://github.com/galaxyproject/galaxy/commit/9cd9c81279d1d7749af7d9c64f83… Author: Frederic Sapet <frederic.sapet(a)biogemma.com> Date: 2017-06-16 (Fri, 16 Jun 2017) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- deals with .xls older file extension Commit: 93dadd6db491700de46cafa4d52a0efe74cd6e94 https://github.com/galaxyproject/galaxy/commit/93dadd6db491700de46cafa4d52a… Author: Frederic Sapet <frederic.sapet(a)biogemma.com> Date: 2017-06-16 (Fri, 16 Jun 2017) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- use subprocess instead of os.popen Commit: 83b19889314a922ba3cf906f26fe7d3a34926533 https://github.com/galaxyproject/galaxy/commit/83b19889314a922ba3cf906f26fe… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-07-05 (Wed, 05 Jul 2017) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/sniff.py A lib/galaxy/datatypes/test/1.xls Log Message: ----------- Refine new Excel XLS datatype. - Call it excel.xls so we maintain backward compatiblity with older xls datatype. - Add an example file with a sniff test. - Correct variable name for Python styling. - Quote paths when using file command-line trick to sniff for the new type. - Switch file command-line flag to one that produces the Mimetype on both Linux and Mac OS X. Commit: 10285b8ecbbc6891a4954b5067198df2839a2957 https://github.com/galaxyproject/galaxy/commit/10285b8ecbbc6891a4954b506719… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-11 (Fri, 11 Aug 2017) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- Tweak Excel format phrasing based on review from @nsoranzo. Commit: fbde34f8c8e823badd0f565bce4922512448b532 https://github.com/galaxyproject/galaxy/commit/fbde34f8c8e823badd0f565bce49… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-11 (Fri, 11 Aug 2017) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- Add EDAM format for excel.xls datatype. Commit: c6e45e7b0720376886626393ae355e3398561035 https://github.com/galaxyproject/galaxy/commit/c6e45e7b0720376886626393ae35… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-08-11 (Fri, 11 Aug 2017) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/sniff.py A lib/galaxy/datatypes/test/1.xls Log Message: ----------- Merge pull request #4410 from jmchilton/excel97 Add Excel97 Datatype Compare: https://github.com/galaxyproject/galaxy/compare/cca00ea5d87f...c6e45e7b0720

1 0

[galaxyproject/galaxy] e49ba4: Generalize allow_library_path_paste to allow_path_...
by GitHub 11 Aug '17

11 Aug '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: e49ba40d771dae0d7056ed089c99f3d53a81b933 https://github.com/galaxyproject/galaxy/commit/e49ba40d771dae0d7056ed089c99… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-10 (Thu, 10 Aug 2017) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/tools/parameters/grouping.py Log Message: ----------- Generalize allow_library_path_paste to allow_path_paste. Enable pasting paths in the history upload GUI & general purpose tools API for admin users if enabled. Commit: f97efa6f90f80ced8bd0c794841e450813238710 https://github.com/galaxyproject/galaxy/commit/f97efa6f90f80ced8bd0c794841e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-10 (Thu, 10 Aug 2017) Changed paths: M lib/galaxy/tools/parameters/grouping.py Log Message: ----------- Remove unused dataset_info in parameters.grouping. Commit: cca00ea5d87fb0baba3ceca715038158cf2ceba0 https://github.com/galaxyproject/galaxy/commit/cca00ea5d87fb0baba3ceca71503… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-08-11 (Fri, 11 Aug 2017) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/tools/parameters/grouping.py Log Message: ----------- Merge pull request #4404 from jmchilton/allow_path_paste Generalize allow_library_path_paste to allow_path_paste. Compare: https://github.com/galaxyproject/galaxy/compare/33c794d27327...cca00ea5d87f

1 0

[galaxyproject/galaxy] 37a6c4: Remove unused template
by GitHub 11 Aug '17

11 Aug '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 37a6c488b0cb99450e2781656eee2462bf539900 https://github.com/galaxyproject/galaxy/commit/37a6c488b0cb99450e2781656eee… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-07-29 (Sat, 29 Jul 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- Remove unused template Commit: 4ccb3e3874e0548289d746fee03a96250df9f1e3 https://github.com/galaxyproject/galaxy/commit/4ccb3e3874e0548289d746fee03a… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-07-29 (Sat, 29 Jul 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- Return roles grid as dictionary Commit: 6c91bc287ef0846869f1604d2ebfd684fb550df4 https://github.com/galaxyproject/galaxy/commit/6c91bc287ef0846869f1604d2ebf… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-07-29 (Sat, 29 Jul 2017) Changed paths: M client/galaxy/scripts/apps/admin.js M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin.py 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/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map Log Message: ----------- Add client side routes Commit: b8396a961facd7dada8d8db837386b656855c3b1 https://github.com/galaxyproject/galaxy/commit/b8396a961facd7dada8d8db83738… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-07-30 (Sun, 30 Jul 2017) Changed paths: M client/galaxy/scripts/apps/panels/admin-panel.js M lib/galaxy/webapps/galaxy/controllers/admin.py 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/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map Log Message: ----------- Add admin role editing options Commit: 00432345ff20bbcf5023995b6cfb54937eb4be9e https://github.com/galaxyproject/galaxy/commit/00432345ff20bbcf5023995b6cfb… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-07-31 (Mon, 31 Jul 2017) Changed paths: M lib/tool_shed/util/admin_util.py M templates/admin/user/reset_password.mako M templates/admin/user/user.mako Log Message: ----------- Merge branch 'revise_page' into admin_grid_roles Commit: d7717cfa8b8562d82742ba285d54e7d7ab794d2d https://github.com/galaxyproject/galaxy/commit/d7717cfa8b8562d82742ba285d54… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-07-31 (Mon, 31 Jul 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- Remove unused galaxy role grid operations Commit: 8ee4c29a0579b2a9156f0cd4a70139758ed58b60 https://github.com/galaxyproject/galaxy/commit/8ee4c29a0579b2a9156f0cd4a701… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-01 (Tue, 01 Aug 2017) Changed paths: 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/galaxy.js M client/galaxy/scripts/layout/router.js A client/galaxy/scripts/mvc/dataset/dataset-edit-attributes.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/grid/grid-view.js M client/galaxy/scripts/nls/fr/locale.js M config/tool_shed.ini.sample M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/jobs/runners/cli.py M lib/galaxy/model/mapping.py M lib/galaxy/model/metadata.py M lib/galaxy/security/__init__.py M lib/galaxy/web/base/controller.py M lib/galaxy/webapps/galaxy/api/quotas.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/galaxy/webapps/tool_shed/buildapp.py M lib/galaxy/workflow/modules.py M static/maps/galaxy.js.map M static/maps/layout/router.js.map A static/maps/mvc/dataset/dataset-edit-attributes.js.map M static/maps/mvc/dataset/dataset-li-edit.js.map M static/maps/mvc/grid/grid-view.js.map M static/maps/nls/fr/locale.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/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/galaxy.js M static/scripts/layout/router.js A static/scripts/mvc/dataset/dataset-edit-attributes.js M static/scripts/mvc/dataset/dataset-li-edit.js M static/scripts/mvc/grid/grid-view.js M static/scripts/nls/fr/locale.js R templates/webapps/galaxy/dataset/edit_attributes.mako Log Message: ----------- Merge branch 'revise_page' into admin_grid_roles Commit: f76f9515a3b243bfb510f89aaa50e95a4990465f https://github.com/galaxyproject/galaxy/commit/f76f9515a3b243bfb510f89aaa50… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-01 (Tue, 01 Aug 2017) Changed paths: M client/galaxy/scripts/apps/admin.js M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Parse url parameters for message handling Commit: e32661301cef0815fdd36743d1ab9901d2576ef2 https://github.com/galaxyproject/galaxy/commit/e32661301cef0815fdd36743d1ab… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-02 (Wed, 02 Aug 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/mvc/user/user-preferences.js R client/galaxy/scripts/mvc/workflow/workflow-configure-menu.js M client/galaxy/scripts/mvc/workflow/workflow.js M client/galaxy/style/less/base.less M config/plugins/webhooks/demo/search/static/script.js M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/buildapp.py M static/maps/mvc/user/user-preferences.js.map M static/maps/mvc/workflow/workflow.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/mvc/user/user-preferences.js M static/scripts/mvc/workflow/workflow.js M static/style/blue/base.css Log Message: ----------- Merge branch 'dev' into admin_grid_roles Commit: 77608ac4105ee90e3323d74e2273618fd2d06ca7 https://github.com/galaxyproject/galaxy/commit/77608ac4105ee90e3323d74e2273… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-04 (Fri, 04 Aug 2017) Changed paths: M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/form/form-view.js A client/galaxy/scripts/mvc/form/form-wrapper.js M client/galaxy/scripts/mvc/grid/grid-template.js M client/galaxy/scripts/mvc/user/user-preferences.js M client/galaxy/scripts/mvc/workflow/workflow-forms.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M client/galaxy/scripts/utils/query-string-parsing.js M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/proteomics.py M lib/galaxy/jobs/actions/post.py M lib/galaxy/managers/tags.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/tool_shed/grids/admin_grids.py M lib/tool_shed/util/admin_util.py M static/maps/layout/menu.js.map M static/maps/mvc/form/form-view.js.map A static/maps/mvc/form/form-wrapper.js.map M static/maps/mvc/grid/grid-template.js.map M static/maps/mvc/user/user-preferences.js.map M static/maps/mvc/workflow/workflow-forms.js.map M static/maps/mvc/workflow/workflow-view.js.map M static/maps/utils/query-string-parsing.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/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/layout/menu.js M static/scripts/mvc/form/form-view.js A static/scripts/mvc/form/form-wrapper.js M static/scripts/mvc/grid/grid-template.js M static/scripts/mvc/user/user-preferences.js M static/scripts/mvc/workflow/workflow-forms.js M static/scripts/mvc/workflow/workflow-view.js M static/scripts/utils/query-string-parsing.js R templates/admin/dataset_security/group/grid.mako R templates/admin/dataset_security/role/grid.mako R templates/admin/quota/grid.mako R templates/admin/tool_version/grid.mako R templates/admin/user/grid.mako R templates/admin/user/reset_password.mako R templates/admin/user/user.mako A templates/webapps/tool_shed/admin/user/reset_password.mako A templates/webapps/tool_shed/admin/user/user.mako R templates/webapps/tool_shed/repository/grid.mako Log Message: ----------- Merge branch 'revise_grid_forms' into admin_grid_roles Commit: b46f4e4c84f042a3b668020d6767b6777e2babb4 https://github.com/galaxyproject/galaxy/commit/b46f4e4c84f042a3b668020d6767… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-04 (Fri, 04 Aug 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Remove unused routing message handler Commit: 44a339546b1849131b9c9f993aee332171217709 https://github.com/galaxyproject/galaxy/commit/44a339546b1849131b9c9f993aee… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-04 (Fri, 04 Aug 2017) Changed paths: M client/galaxy/scripts/apps/panels/admin-panel.js M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Fix menu link Commit: ffe3ac294d8a21a10546f45518e4d2c52e1bc966 https://github.com/galaxyproject/galaxy/commit/ffe3ac294d8a21a10546f45518e4… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-04 (Fri, 04 Aug 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- Do not parse empty messages Commit: 246e94ae8470e1ef78f1b136bcdc117f45e036ef https://github.com/galaxyproject/galaxy/commit/246e94ae8470e1ef78f1b136bcdc… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-04 (Fri, 04 Aug 2017) Changed paths: M client/galaxy/scripts/apps/admin.js M lib/galaxy/webapps/galaxy/controllers/admin.py M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Build role renaming in client Commit: 20ce574e3304af6cb09d98b9d8e17a7ff7c3c628 https://github.com/galaxyproject/galaxy/commit/20ce574e3304af6cb09d98b9d8e1… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-04 (Fri, 04 Aug 2017) Changed paths: M client/galaxy/scripts/apps/admin.js M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- Add role renaming feature to revised endpoint Commit: 99bf6809bebb621a33050164f2c7e2a2f203ae40 https://github.com/galaxyproject/galaxy/commit/99bf6809bebb621a33050164f2c7… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-04 (Fri, 04 Aug 2017) Changed paths: M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Repack scripts Commit: 5ab9ea4ffdb7c5359d32a0653f6ac59d9fc37d21 https://github.com/galaxyproject/galaxy/commit/5ab9ea4ffdb7c5359d32a0653f6a… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-04 (Fri, 04 Aug 2017) Changed paths: M client/galaxy/scripts/mvc/form/form-wrapper.js M static/maps/mvc/form/form-wrapper.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/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/form/form-wrapper.js Log Message: ----------- Use primary button Commit: 4d542820e70d02c0809d3bd8482746b90e68642d https://github.com/galaxyproject/galaxy/commit/4d542820e70d02c0809d3bd84827… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-04 (Fri, 04 Aug 2017) Changed paths: M client/galaxy/scripts/mvc/form/form-wrapper.js M lib/galaxy/webapps/galaxy/api/users.py M static/maps/mvc/form/form-wrapper.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/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/form/form-wrapper.js Log Message: ----------- Remove unused messages, set default message status Commit: 502b2a068c06e190484fda2adcdc43ffef7d07e2 https://github.com/galaxyproject/galaxy/commit/502b2a068c06e190484fda2adcdc… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-04 (Fri, 04 Aug 2017) Changed paths: M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/mvc/form/form-wrapper.js M client/galaxy/scripts/mvc/user/user-preferences.js M static/maps/mvc/form/form-wrapper.js.map M static/maps/mvc/user/user-preferences.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/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/form/form-wrapper.js M static/scripts/mvc/user/user-preferences.js Log Message: ----------- Use redirect option for user preferences Commit: b908e98e37de20aff2b18acd6b93b79b9020f4a8 https://github.com/galaxyproject/galaxy/commit/b908e98e37de20aff2b18acd6b93… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-04 (Fri, 04 Aug 2017) Changed paths: M client/galaxy/scripts/mvc/form/form-repeat.js M client/galaxy/scripts/mvc/form/form-wrapper.js M client/galaxy/scripts/mvc/tool/tool-form.js M client/galaxy/scripts/mvc/ui/ui-buttons.js M client/galaxy/style/less/ui.less M static/maps/mvc/form/form-repeat.js.map M static/maps/mvc/form/form-wrapper.js.map M static/maps/mvc/tool/tool-form.js.map M static/maps/mvc/ui/ui-buttons.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/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/form/form-repeat.js M static/scripts/mvc/form/form-wrapper.js M static/scripts/mvc/tool/tool-form.js M static/scripts/mvc/ui/ui-buttons.js M static/style/blue/base.css Log Message: ----------- Fix button and operations floating handling Commit: bf6e2d26bd128e773ae3c604216e7b939abf8c01 https://github.com/galaxyproject/galaxy/commit/bf6e2d26bd128e773ae3c604216e… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-04 (Fri, 04 Aug 2017) Changed paths: M client/galaxy/scripts/mvc/user/user-custom-builds.js M static/maps/mvc/user/user-custom-builds.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/user/user-custom-builds.js Log Message: ----------- Fix floating for custom build form button Commit: afa6964994fb6aa6acad44d03f4123f2f7726839 https://github.com/galaxyproject/galaxy/commit/afa6964994fb6aa6acad44d03f41… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-04 (Fri, 04 Aug 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-list.js M client/galaxy/style/less/ui.less M static/maps/mvc/ui/ui-list.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.map M static/scripts/mvc/ui/ui-list.js M static/style/blue/base.css Log Message: ----------- Fix style for list parameter Commit: d11fc568a41a3dba540457f9d861182acfbae117 https://github.com/galaxyproject/galaxy/commit/d11fc568a41a3dba540457f9d861… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-04 (Fri, 04 Aug 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py M lib/tool_shed/grids/repository_grids.py R templates/admin/tool_shed_repository/grid.mako Log Message: ----------- Merge branch 'revise_grid_forms' into admin_grid_roles Commit: 9d8bdc6f304d676157f8c0e5a76f6c49dd9e5d4b https://github.com/galaxyproject/galaxy/commit/9d8bdc6f304d676157f8c0e5a76f… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-05 (Sat, 05 Aug 2017) Changed paths: M lib/galaxy/web/base/controller.py M static/maps/galaxy.js.map M static/scripts/galaxy.js Log Message: ----------- Repack scripts Commit: 1675b9cca2cc1c5aa8a4e495e23c0877a781cf39 https://github.com/galaxyproject/galaxy/commit/1675b9cca2cc1c5aa8a4e495e23c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-05 (Sat, 05 Aug 2017) Changed paths: M client/galaxy/scripts/galaxy.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/user/user-preferences.js M lib/galaxy/jobs/rule_helper.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/web/base/controller.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/user.py M static/maps/galaxy.js.map M static/maps/layout/menu.js.map M static/maps/mvc/user/user-preferences.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/galaxy.js M static/scripts/layout/menu.js M static/scripts/mvc/user/user-preferences.js M templates/galaxy_client_app.mako M templates/user/login.mako M templates/user/register.mako M templates/webapps/galaxy/history/display_structured.mako M templates/webapps/galaxy/workflow/build_from_current_history.mako M test/shed_functional/base/twilltestcase.py Log Message: ----------- Merge branch 'revise_grid_forms' into admin_grid_roles Commit: d698d32ceb043fdb9820b68615748ca13e0825c8 https://github.com/galaxyproject/galaxy/commit/d698d32ceb043fdb9820b6861574… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-07 (Mon, 07 Aug 2017) Changed paths: M client/galaxy/scripts/apps/admin.js M lib/galaxy/webapps/galaxy/controllers/admin.py M static/maps/mvc/user/user-preferences.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/user/user-preferences.js Log Message: ----------- Manage users and groups for role Commit: 9ee062bd4622481165d4cb1e783454a49fcdd704 https://github.com/galaxyproject/galaxy/commit/9ee062bd4622481165d4cb1e7834… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-07 (Mon, 07 Aug 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- Show current name and description when renaming roles Commit: 183176a05c95e063a710ff469a368c463e18db2f https://github.com/galaxyproject/galaxy/commit/183176a05c95e063a710ff469a36… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-07 (Mon, 07 Aug 2017) Changed paths: M client/galaxy/scripts/apps/admin.js M lib/galaxy/webapps/galaxy/controllers/admin.py M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Add create role form Commit: 663c6c13975b01cf0472a083a68164d9bd010871 https://github.com/galaxyproject/galaxy/commit/663c6c13975b01cf0472a083a681… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-07 (Mon, 07 Aug 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py R templates/admin/dataset_security/role/role.mako R templates/admin/dataset_security/role/role_create.mako R templates/admin/dataset_security/role/role_rename.mako A templates/webapps/tool_shed/admin/dataset_security/role/role.mako A templates/webapps/tool_shed/admin/dataset_security/role/role_create.mako A templates/webapps/tool_shed/admin/dataset_security/role/role_rename.mako Log Message: ----------- Fix boolean title, and move unused role makos to toolshed Commit: e77fd47b034e6af5b19756bd778f5081332e7c85 https://github.com/galaxyproject/galaxy/commit/e77fd47b034e6af5b19756bd778f… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-07 (Mon, 07 Aug 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- Fix boolean handling Commit: 419f3db64fb3614d5a70ed9a9eea8a260b6f5865 https://github.com/galaxyproject/galaxy/commit/419f3db64fb3614d5a70ed9a9eea… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-07 (Mon, 07 Aug 2017) Changed paths: M lib/tool_shed/util/admin_util.py Log Message: ----------- Remove unused information feature for toolshed Commit: 733e225ec96b058dd159dda4e18ba1f7572573fd https://github.com/galaxyproject/galaxy/commit/733e225ec96b058dd159dda4e18b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-07 (Mon, 07 Aug 2017) Changed paths: M client/galaxy/scripts/utils/query-string-parsing.js M static/maps/utils/query-string-parsing.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/utils/query-string-parsing.js Log Message: ----------- Fix message handling in user preference main view Commit: a5d7c0fa84d8fe24fc94ac814b9f7502283de7c2 https://github.com/galaxyproject/galaxy/commit/a5d7c0fa84d8fe24fc94ac814b9f… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-07 (Mon, 07 Aug 2017) Changed paths: M client/galaxy/scripts/mvc/form/form-wrapper.js M static/maps/mvc/form/form-wrapper.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.map M static/scripts/mvc/form/form-wrapper.js Log Message: ----------- Scroll to highlight message Commit: 4b2eca373e936308b0550b9fabfc6494228b837a https://github.com/galaxyproject/galaxy/commit/4b2eca373e936308b0550b9fabfc… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-07 (Mon, 07 Aug 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/users.py Log Message: ----------- Remove duplicate roles from selection list Commit: 5a8adbf8b77dc985353803a724fc4344dcbbdc79 https://github.com/galaxyproject/galaxy/commit/5a8adbf8b77dc985353803a724fc… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-07 (Mon, 07 Aug 2017) Changed paths: M doc/source/admin/special_topics/grt.rst M lib/galaxy/dataset_collections/matching.py M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/jobs/runners/util/cli/__init__.py M lib/galaxy/jobs/runners/util/cli/shell/local.py M lib/galaxy/jobs/runners/util/cli/shell/rsh.py M lib/galaxy/objectstore/s3_multipart_upload.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/execute.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/parser/yaml.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/webapps/galaxy/api/users.py M lib/galaxy/webapps/galaxy/controllers/async.py M lib/galaxy/webapps/galaxy/controllers/history.py R scripts/grt.py R scripts/grt.yml.sample A scripts/grt/export.py A scripts/grt/grt.yml.sample A scripts/grt/upload.py M test/api/test_tools.py A test/functional/tools/identifier_source.xml M test/functional/tools/samples_tool_conf.xml A test/unit/test_remote_shell.py M test/unit/tools/test_toolbox.py M test/unit/tools_support.py M tox.ini Log Message: ----------- Merge branch 'remove_duplicates' into admin_grid_roles Commit: a7c6c69cbf6a6eeffdf53815144e623576c47b13 https://github.com/galaxyproject/galaxy/commit/a7c6c69cbf6a6eeffdf53815144e… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-08 (Tue, 08 Aug 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- Fix lint Commit: d3b8889c04ef22d740f8b668a8212c728ba5832c https://github.com/galaxyproject/galaxy/commit/d3b8889c04ef22d740f8b668a821… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-08 (Tue, 08 Aug 2017) Changed paths: M client/galaxy/scripts/apps/panels/admin-panel.js M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Fix second role link in admin panel Commit: c01023b5adc402a6a8662e9f319afcd9e4f5fc6e https://github.com/galaxyproject/galaxy/commit/c01023b5adc402a6a8662e9f319a… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-09 (Wed, 09 Aug 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- Fix indention Commit: d32a3a58a50bdbdbe6144a265ef3424a2f011ae2 https://github.com/galaxyproject/galaxy/commit/d32a3a58a50bdbdbe6144a265ef3… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-09 (Wed, 09 Aug 2017) Changed paths: M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt M config/datatypes_conf.xml.sample A config/user_preferences_extra_conf.yml.sample M lib/galaxy/config.py M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/molecules.py M lib/galaxy/datatypes/mothur.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/text.py M lib/galaxy/jobs/command_factory.py M lib/galaxy/managers/workflows.py M lib/galaxy/tools/parser/interface.py M lib/galaxy/tools/parser/output_objects.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/web/base/controller.py M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/web/base/pluginframework.py M lib/galaxy/webapps/galaxy/api/users.py M lib/galaxy/workflow/extract.py M lib/tool_shed/metadata/metadata_generator.py M lib/tool_shed/util/workflow_util.py M lib/tool_shed/utility_containers/utility_container_manager.py M templates/webapps/tool_shed/repository/common.mako M test/unit/tools/test_parsing.py Log Message: ----------- Merge branch 'revise_page' into admin_grid_roles Commit: 938bf525f46c8d3c7568d9b2a97edfa958ba900f https://github.com/galaxyproject/galaxy/commit/938bf525f46c8d3c7568d9b2a97e… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-10 (Thu, 10 Aug 2017) Changed paths: M client/galaxy/scripts/mvc/library/library-dataset-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M lib/galaxy/managers/tags.py M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py A lib/galaxy/model/migrate/versions/0135_add_library_tags.py M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/web/base/controller.py M lib/galaxy/webapps/galaxy/api/lda_datasets.py M lib/galaxy/webapps/galaxy/api/library_contents.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M static/maps/mvc/library/library-dataset-view.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/maps/mvc/user/user-preferences.js.map M static/scripts/mvc/library/library-dataset-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/user/user-preferences.js Log Message: ----------- Merge branch 'revise_grid_forms' into admin_grid_roles Commit: be19b36ecaab43dd9cbf2fd5f80995e7ac9ff507 https://github.com/galaxyproject/galaxy/commit/be19b36ecaab43dd9cbf2fd5f809… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-10 (Thu, 10 Aug 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js A client/galaxy/scripts/mvc/dataset/dataset-error.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js A client/galaxy/scripts/mvc/job/job-params.js M client/galaxy/style/less/galaxy_bootstrap/overrides.less M config/datatypes_conf.xml.sample A config/error_report.yml.sample M config/tool_conf.xml.sample A doc/source/admin/special_topics/bug_reports.rst M doc/source/admin/special_topics/index.rst M lib/galaxy/app.py M lib/galaxy/config.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/jobs/__init__.py M lib/galaxy/tools/__init__.py A lib/galaxy/tools/error_reports/__init__.py A lib/galaxy/tools/error_reports/plugins/__init__.py A lib/galaxy/tools/error_reports/plugins/biostars.py A lib/galaxy/tools/error_reports/plugins/email.py A lib/galaxy/tools/error_reports/plugins/json.py A lib/galaxy/tools/error_reports/plugins/sentry.py M lib/galaxy/tools/errors.py A lib/galaxy/tools/sort_collection_list.xml M lib/galaxy/util/biostar.py M lib/galaxy/util/plugin_config.py M lib/galaxy/webapps/galaxy/api/jobs.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M scripts/grt/export.py M scripts/grt/upload.py A static/maps/mvc/dataset/dataset-error.js.map M static/maps/mvc/dataset/dataset-li-edit.js.map A static/maps/mvc/job/job-params.js.map M static/maps/mvc/user/user-preferences.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 A static/scripts/mvc/dataset/dataset-error.js M static/scripts/mvc/dataset/dataset-li-edit.js A static/scripts/mvc/job/job-params.js M static/scripts/mvc/user/user-preferences.js M static/style/blue/base.css M templates/show_params.mako R templates/webapps/galaxy/dataset/errors.mako A test-data/test.vcf.gz M test/functional/tools/sample_datatypes_conf.xml M test/functional/tools/samples_tool_conf.xml A test/functional/tools/vcf_bgzip.xml Log Message: ----------- Merge branch 'revise_grid_forms' into admin_grid_roles Commit: 33c794d273271b14732fb8037c2ea8105a3c688e https://github.com/galaxyproject/galaxy/commit/33c794d273271b14732fb8037c2e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-11 (Fri, 11 Aug 2017) Changed paths: 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/mvc/form/form-repeat.js M client/galaxy/scripts/mvc/form/form-wrapper.js M client/galaxy/scripts/mvc/tool/tool-form.js M client/galaxy/scripts/mvc/ui/ui-buttons.js M client/galaxy/scripts/mvc/ui/ui-list.js M client/galaxy/scripts/mvc/user/user-custom-builds.js M client/galaxy/scripts/mvc/user/user-preferences.js M client/galaxy/scripts/utils/query-string-parsing.js M client/galaxy/style/less/ui.less M lib/galaxy/webapps/galaxy/api/users.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/tool_shed/util/admin_util.py M static/maps/mvc/form/form-repeat.js.map M static/maps/mvc/form/form-wrapper.js.map M static/maps/mvc/tool/tool-form.js.map M static/maps/mvc/ui/ui-buttons.js.map M static/maps/mvc/ui/ui-list.js.map M static/maps/mvc/user/user-custom-builds.js.map M static/maps/mvc/user/user-preferences.js.map M static/maps/utils/query-string-parsing.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/mvc/form/form-repeat.js M static/scripts/mvc/form/form-wrapper.js M static/scripts/mvc/tool/tool-form.js M static/scripts/mvc/ui/ui-buttons.js M static/scripts/mvc/ui/ui-list.js M static/scripts/mvc/user/user-custom-builds.js M static/scripts/mvc/user/user-preferences.js M static/scripts/utils/query-string-parsing.js M static/style/blue/base.css R templates/admin/dataset_security/role/role.mako R templates/admin/dataset_security/role/role_create.mako R templates/admin/dataset_security/role/role_rename.mako A templates/webapps/tool_shed/admin/dataset_security/role/role.mako A templates/webapps/tool_shed/admin/dataset_security/role/role_create.mako A templates/webapps/tool_shed/admin/dataset_security/role/role_rename.mako Log Message: ----------- Merge pull request #4385 from guerler/admin_grid_roles Admin grid roles revision Compare: https://github.com/galaxyproject/galaxy/compare/600b0aad7ce1...33c794d27327

1 0

[galaxyproject/galaxy] a7885e: Generalize how user preferences build forms
by GitHub 11 Aug '17

11 Aug '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a7885e0b6e195ecc1beaab6f526ce52e927053c2 https://github.com/galaxyproject/galaxy/commit/a7885e0b6e195ecc1beaab6f526c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-03 (Thu, 03 Aug 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js A client/galaxy/scripts/mvc/form/form-wrapper.js M client/galaxy/scripts/mvc/user/user-preferences.js A static/maps/mvc/form/form-wrapper.js.map M static/maps/mvc/user/user-preferences.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 A static/scripts/mvc/form/form-wrapper.js M static/scripts/mvc/user/user-preferences.js Log Message: ----------- Generalize how user preferences build forms Commit: ddcace7527d6fc20ce93c983d795ff3b35117191 https://github.com/galaxyproject/galaxy/commit/ddcace7527d6fc20ce93c983d795… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-03 (Thu, 03 Aug 2017) Changed paths: M client/galaxy/scripts/mvc/form/form-wrapper.js M static/maps/mvc/form/form-wrapper.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/form/form-wrapper.js Log Message: ----------- Remove unused options parsing Commit: 6c11ffbe84f2e279607a5dd16f6d0532d26dc1f9 https://github.com/galaxyproject/galaxy/commit/6c11ffbe84f2e279607a5dd16f6d… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-03 (Thu, 03 Aug 2017) Changed paths: M client/galaxy/scripts/apps/admin.js M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin.py 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/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map Log Message: ----------- User generic form wrapper to reset password Commit: cd8314808e67dc8a880c0bb16a1faf4e5a571456 https://github.com/galaxyproject/galaxy/commit/cd8314808e67dc8a880c0bb16a1f… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-03 (Thu, 03 Aug 2017) Changed paths: M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/utils/query-string-parsing.js M lib/galaxy/webapps/galaxy/controllers/admin.py M static/maps/utils/query-string-parsing.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/utils/query-string-parsing.js Log Message: ----------- Allow array parsing through url Commit: 06b5be23ddec4298cd78503e6e07f2949d882a6e https://github.com/galaxyproject/galaxy/commit/06b5be23ddec4298cd78503e6e07… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-03 (Thu, 03 Aug 2017) Changed paths: M client/galaxy/scripts/apps/admin.js M lib/galaxy/webapps/galaxy/controllers/admin.py 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/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map Log Message: ----------- Specify password reset form Commit: e0ccec46b3f4f4d8f13091fa2f5dcafd987c7b51 https://github.com/galaxyproject/galaxy/commit/e0ccec46b3f4f4d8f13091fa2f5d… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-03 (Thu, 03 Aug 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- Move help info Commit: c6dee98c55a46b23e9373ea53c4fa22e545978a3 https://github.com/galaxyproject/galaxy/commit/c6dee98c55a46b23e9373ea53c4f… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-04 (Fri, 04 Aug 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py 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/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map Log Message: ----------- Fix input types, repack scripts Commit: 23b141a2ec3e5ff865a8ea0718d41b9845e79d64 https://github.com/galaxyproject/galaxy/commit/23b141a2ec3e5ff865a8ea0718d4… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-04 (Fri, 04 Aug 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- Complete new controller endpoint to reset passwords Commit: 8312b07e60ee945fdde6ecc29eadcac9423ab3d5 https://github.com/galaxyproject/galaxy/commit/8312b07e60ee945fdde6ecc29ead… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-04 (Fri, 04 Aug 2017) Changed paths: M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/mvc/form/form-wrapper.js M client/galaxy/scripts/mvc/grid/grid-template.js M static/maps/mvc/form/form-wrapper.js.map M static/maps/mvc/grid/grid-template.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.map M static/scripts/mvc/form/form-wrapper.js M static/scripts/mvc/grid/grid-template.js Log Message: ----------- Allow form redirect to grid view Commit: 4e050282652ea3c3cbf20998653acb9a34a85415 https://github.com/galaxyproject/galaxy/commit/4e050282652ea3c3cbf20998653a… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-04 (Fri, 04 Aug 2017) Changed paths: M client/galaxy/scripts/apps/admin.js M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Create dictionary for form definitions Commit: f50e0ba5bba5fe6605bcbcc446ddb10f58ae898b https://github.com/galaxyproject/galaxy/commit/f50e0ba5bba5fe6605bcbcc446dd… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-04 (Fri, 04 Aug 2017) Changed paths: M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/form/form-wrapper.js M lib/galaxy/webapps/galaxy/controllers/admin.py M static/maps/mvc/form/form-view.js.map M static/maps/mvc/form/form-wrapper.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.map M static/scripts/mvc/form/form-view.js M static/scripts/mvc/form/form-wrapper.js Log Message: ----------- Revise endpoint to manage user roles and groups, add initial message support to form wrapper Commit: 7e1c40799efa67f43fe13b589ef2432b05fdebc3 https://github.com/galaxyproject/galaxy/commit/7e1c40799efa67f43fe13b589ef2… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-04 (Fri, 04 Aug 2017) Changed paths: M client/galaxy/scripts/mvc/form/form-wrapper.js M lib/galaxy/webapps/galaxy/controllers/admin.py M static/maps/mvc/form/form-wrapper.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.map M static/scripts/mvc/form/form-wrapper.js Log Message: ----------- Use initial method parsing for reset password info Commit: 63ebee1a415a9433b01164ef72e90e08c177fc18 https://github.com/galaxyproject/galaxy/commit/63ebee1a415a9433b01164ef72e9… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-04 (Fri, 04 Aug 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- Add put handling to revised manage_roles_and_groups_for_user controller endpoint Commit: e791ac29bb310cefcbcc8afd762c7c7ddec54586 https://github.com/galaxyproject/galaxy/commit/e791ac29bb310cefcbcc8afd762c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-04 (Fri, 04 Aug 2017) Changed paths: M lib/tool_shed/grids/admin_grids.py M lib/tool_shed/util/admin_util.py R templates/admin/user/grid.mako R templates/admin/user/reset_password.mako R templates/admin/user/user.mako A templates/webapps/tool_shed/admin/user/reset_password.mako A templates/webapps/tool_shed/admin/user/user.mako Log Message: ----------- Move user form grid makos to toolshed Commit: 3007122bd9c9e111ef8d0010707ddac51bff6387 https://github.com/galaxyproject/galaxy/commit/3007122bd9c9e111ef8d0010707d… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-04 (Fri, 04 Aug 2017) Changed paths: M templates/webapps/tool_shed/admin/user/reset_password.mako M templates/webapps/tool_shed/admin/user/user.mako Log Message: ----------- Remove custom case handling for galaxy app from makos, restoring previous state Commit: 146dd82f043c9adaa8f2891f03ab31f76b16af2e https://github.com/galaxyproject/galaxy/commit/146dd82f043c9adaa8f2891f03ab… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-04 (Fri, 04 Aug 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/tool_shed/grids/admin_grids.py R templates/admin/dataset_security/group/grid.mako R templates/admin/dataset_security/role/grid.mako R templates/admin/quota/grid.mako R templates/admin/tool_version/grid.mako R templates/webapps/tool_shed/repository/grid.mako Log Message: ----------- Remove unnecessary grid makos Commit: c2b98bce78366b4daf33b76c7a1fe2d465212274 https://github.com/galaxyproject/galaxy/commit/c2b98bce78366b4daf33b76c7a1f… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-04 (Fri, 04 Aug 2017) Changed paths: M lib/tool_shed/grids/repository_grids.py Log Message: ----------- Remove unused grid makos Commit: 010a7dfb9ce1e0002c2ea81d7ff88dbe3c1ecb38 https://github.com/galaxyproject/galaxy/commit/010a7dfb9ce1e0002c2ea81d7ff8… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-04 (Fri, 04 Aug 2017) Changed paths: M lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py R templates/admin/tool_shed_repository/grid.mako Log Message: ----------- Remove unused toolshed grid mako Commit: 96cc67a2caf6470c235d871878a86e6ebaca3b1c https://github.com/galaxyproject/galaxy/commit/96cc67a2caf6470c235d871878a8… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-04 (Fri, 04 Aug 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- Fix lint Commit: 9dc5ace31a5ec847e408baeaccb9dbd7433f02b7 https://github.com/galaxyproject/galaxy/commit/9dc5ace31a5ec847e408baeaccb9… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-04 (Fri, 04 Aug 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- Remove lines Commit: d2d250b847f22934a2f1d3c1d2256b40c52abc55 https://github.com/galaxyproject/galaxy/commit/d2d250b847f22934a2f1d3c1d225… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-05 (Sat, 05 Aug 2017) Changed paths: M client/galaxy/scripts/galaxy.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/user/user-preferences.js M lib/galaxy/jobs/rule_helper.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/web/base/controller.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/user.py M static/maps/galaxy.js.map M static/maps/layout/menu.js.map M static/maps/mvc/user/user-preferences.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/galaxy.js M static/scripts/layout/menu.js M static/scripts/mvc/user/user-preferences.js M templates/galaxy_client_app.mako M templates/user/login.mako M templates/user/register.mako M templates/webapps/galaxy/history/display_structured.mako M templates/webapps/galaxy/workflow/build_from_current_history.mako M test/shed_functional/base/twilltestcase.py Log Message: ----------- Merge branch 'dev' into revise_grid_forms Commit: f531d2c0c9810b2d0ee8f0482cb12e163bbc0de2 https://github.com/galaxyproject/galaxy/commit/f531d2c0c9810b2d0ee8f0482cb1… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-05 (Sat, 05 Aug 2017) Changed paths: M lib/galaxy/web/base/controller.py M static/maps/galaxy.js.map M static/maps/layout/menu.js.map M static/maps/mvc/user/user-preferences.js.map M static/scripts/galaxy.js M static/scripts/layout/menu.js M static/scripts/mvc/user/user-preferences.js Log Message: ----------- Repack scripts Commit: c49e749534f76c8bb2d0ea8bb629a6ee236ff5cc https://github.com/galaxyproject/galaxy/commit/c49e749534f76c8bb2d0ea8bb629… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-07 (Mon, 07 Aug 2017) Changed paths: M lib/tool_shed/util/admin_util.py Log Message: ----------- Fix user info link for toolshed Commit: e477cce9b68d90a313d1534c3ad156f9eb8cc6ec https://github.com/galaxyproject/galaxy/commit/e477cce9b68d90a313d1534c3ad1… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-10 (Thu, 10 Aug 2017) Changed paths: M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt M client/galaxy/scripts/mvc/library/library-dataset-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M config/datatypes_conf.xml.sample A config/user_preferences_extra_conf.yml.sample M doc/source/admin/special_topics/grt.rst M lib/galaxy/config.py M lib/galaxy/dataset_collections/matching.py M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/molecules.py M lib/galaxy/datatypes/mothur.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/text.py M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/jobs/command_factory.py M lib/galaxy/jobs/runners/util/cli/__init__.py M lib/galaxy/jobs/runners/util/cli/shell/local.py M lib/galaxy/jobs/runners/util/cli/shell/rsh.py M lib/galaxy/managers/tags.py M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py A lib/galaxy/model/migrate/versions/0135_add_library_tags.py M lib/galaxy/objectstore/s3_multipart_upload.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/tools/execute.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/tools/parser/interface.py M lib/galaxy/tools/parser/output_objects.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/parser/yaml.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/web/base/controller.py M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/web/base/pluginframework.py M lib/galaxy/webapps/galaxy/api/lda_datasets.py M lib/galaxy/webapps/galaxy/api/library_contents.py M lib/galaxy/webapps/galaxy/api/users.py M lib/galaxy/webapps/galaxy/controllers/async.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/galaxy/workflow/extract.py M lib/tool_shed/metadata/metadata_generator.py M lib/tool_shed/util/workflow_util.py M lib/tool_shed/utility_containers/utility_container_manager.py R scripts/grt.py R scripts/grt.yml.sample A scripts/grt/export.py A scripts/grt/grt.yml.sample A scripts/grt/upload.py M static/maps/mvc/library/library-dataset-view.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/scripts/mvc/library/library-dataset-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js M templates/webapps/tool_shed/repository/common.mako M test/api/test_tools.py A test/functional/tools/identifier_source.xml M test/functional/tools/samples_tool_conf.xml A test/unit/test_remote_shell.py M test/unit/tools/test_parsing.py M test/unit/tools/test_toolbox.py M test/unit/tools_support.py M tox.ini Log Message: ----------- Merge branch 'revise_page' into revise_grid_forms Commit: b8c05ede4dd188dce24c914912f8fa35963d9562 https://github.com/galaxyproject/galaxy/commit/b8c05ede4dd188dce24c914912f8… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-10 (Thu, 10 Aug 2017) Log Message: ----------- Merge branch 'dev' into revise_grid_forms Commit: 583765c7c087c77c6d1f2756e4233ce97a71240f https://github.com/galaxyproject/galaxy/commit/583765c7c087c77c6d1f2756e423… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-10 (Thu, 10 Aug 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js A client/galaxy/scripts/mvc/dataset/dataset-error.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js A client/galaxy/scripts/mvc/job/job-params.js M client/galaxy/style/less/galaxy_bootstrap/overrides.less M config/datatypes_conf.xml.sample A config/error_report.yml.sample M config/tool_conf.xml.sample A doc/source/admin/special_topics/bug_reports.rst M doc/source/admin/special_topics/index.rst M lib/galaxy/app.py M lib/galaxy/config.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/jobs/__init__.py M lib/galaxy/tools/__init__.py A lib/galaxy/tools/error_reports/__init__.py A lib/galaxy/tools/error_reports/plugins/__init__.py A lib/galaxy/tools/error_reports/plugins/biostars.py A lib/galaxy/tools/error_reports/plugins/email.py A lib/galaxy/tools/error_reports/plugins/json.py A lib/galaxy/tools/error_reports/plugins/sentry.py M lib/galaxy/tools/errors.py A lib/galaxy/tools/sort_collection_list.xml M lib/galaxy/util/biostar.py M lib/galaxy/util/plugin_config.py M lib/galaxy/webapps/galaxy/api/jobs.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M scripts/grt/export.py M scripts/grt/upload.py A static/maps/mvc/dataset/dataset-error.js.map M static/maps/mvc/dataset/dataset-li-edit.js.map A static/maps/mvc/job/job-params.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 A static/scripts/mvc/dataset/dataset-error.js M static/scripts/mvc/dataset/dataset-li-edit.js A static/scripts/mvc/job/job-params.js M static/style/blue/base.css M templates/show_params.mako R templates/webapps/galaxy/dataset/errors.mako A test-data/test.vcf.gz M test/functional/tools/sample_datatypes_conf.xml M test/functional/tools/samples_tool_conf.xml A test/functional/tools/vcf_bgzip.xml Log Message: ----------- Merge branch 'dev' into revise_grid_forms Commit: 600b0aad7ce10c1e427513684c4cd7423f5b52aa https://github.com/galaxyproject/galaxy/commit/600b0aad7ce10c1e427513684c4c… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-08-11 (Fri, 11 Aug 2017) Changed paths: M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/mvc/form/form-view.js A client/galaxy/scripts/mvc/form/form-wrapper.js M client/galaxy/scripts/mvc/grid/grid-template.js M client/galaxy/scripts/mvc/user/user-preferences.js M client/galaxy/scripts/utils/query-string-parsing.js M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py M lib/tool_shed/grids/admin_grids.py M lib/tool_shed/grids/repository_grids.py M lib/tool_shed/util/admin_util.py M static/maps/mvc/form/form-view.js.map A static/maps/mvc/form/form-wrapper.js.map M static/maps/mvc/grid/grid-template.js.map M static/maps/mvc/user/user-preferences.js.map M static/maps/utils/query-string-parsing.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/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/form/form-view.js A static/scripts/mvc/form/form-wrapper.js M static/scripts/mvc/grid/grid-template.js M static/scripts/mvc/user/user-preferences.js M static/scripts/utils/query-string-parsing.js R templates/admin/dataset_security/group/grid.mako R templates/admin/dataset_security/role/grid.mako R templates/admin/quota/grid.mako R templates/admin/tool_shed_repository/grid.mako R templates/admin/tool_version/grid.mako R templates/admin/user/grid.mako R templates/admin/user/reset_password.mako R templates/admin/user/user.mako A templates/webapps/tool_shed/admin/user/reset_password.mako A templates/webapps/tool_shed/admin/user/user.mako R templates/webapps/tool_shed/repository/grid.mako Log Message: ----------- Merge pull request #4377 from guerler/revise_grid_forms Remove makos of admin user grid forms Compare: https://github.com/galaxyproject/galaxy/compare/6353704e4b44...600b0aad7ce1

1 0

[galaxyproject/galaxy] aa1ce5: Updated missing parameters check for OpenID
by GitHub 10 Aug '17

10 Aug '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: aa1ce50689dd464c5c1e8b8b333397031914afb5 https://github.com/galaxyproject/galaxy/commit/aa1ce50689dd464c5c1e8b8b3333… Author: Vahid <VJalili(a)users.noreply.github.com> Date: 2017-05-05 (Fri, 05 May 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/user.py Log Message: ----------- Updated missing parameters check for OpenID When you have the OpenID URL, you don't need to recreate the provider. Only create the provider, if its not already created. Commit: dedc8eb1dc80804c7f43e08f8022f74edc2c91b3 https://github.com/galaxyproject/galaxy/commit/dedc8eb1dc80804c7f43e08f8022… Author: Vahid <VJalili(a)users.noreply.github.com> Date: 2017-05-12 (Fri, 12 May 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/user.py Log Message: ----------- Inform that the default provider is being used. Commit: a0e863f5706bfb7706e8dcb9e023a0f3c32a7629 https://github.com/galaxyproject/galaxy/commit/a0e863f5706bfb7706e8dcb9e023… Author: Vahid <VJalili(a)users.noreply.github.com> Date: 2017-05-12 (Fri, 12 May 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/user.py Log Message: ----------- Updated all `openid_url` and `openid_provider` checks Commit: a3c2ddff2b10a05eca6dfb460f8d539f2f595f19 https://github.com/galaxyproject/galaxy/commit/a3c2ddff2b10a05eca6dfb460f8d… Author: Vahid <VJalili(a)users.noreply.github.com> Date: 2017-05-12 (Fri, 12 May 2017) Changed paths: M openid/yahoo.xml Log Message: ----------- Corrected Yahoo OpenID endpoint At the time of making this change, Yahoo OpenID endpoint has issues--It's not accessible. This should be checked again later. Commit: 6353704e4b44e9eded6571b467f52a6dd288387d https://github.com/galaxyproject/galaxy/commit/6353704e4b44e9eded6571b467f5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-10 (Thu, 10 Aug 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/user.py M openid/yahoo.xml Log Message: ----------- Merge pull request #4039 from VJalili/patch-11 Updated parameters check for OpenID Compare: https://github.com/galaxyproject/galaxy/compare/bcdf2c84f6df...6353704e4b44

1 0

[galaxyproject/galaxy] 63865e: Add VcfGz datatype
by GitHub 10 Aug '17

10 Aug '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 63865e11935724a02ae641857d802f8650a7f97d https://github.com/galaxyproject/galaxy/commit/63865e11935724a02ae641857d80… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-07-07 (Fri, 07 Jul 2017) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/tabular.py Log Message: ----------- Add VcfGz datatype This adds support for uploading VcfGz files in the upload box. When a user does this, the file will not be uncompressed. Also adds uncompressed preview. TODO: - Move Vcf class to BaseVcf - Vcf and VcfGz should both inherit from BaseVcf - Add a metadata element for VcfGz indexes (vzf.gz.tbi) - Create index (in set_meta method of VcfGz class) - Write test tools This is a kcikstart to @ffinfo GCC hack project. Commit: 83f1e82e84a79673b2913f9f4a6c63dc6d6526f4 https://github.com/galaxyproject/galaxy/commit/83f1e82e84a79673b2913f9f4a6c… Author: Peter van 't Hof <p.j.van_t_hof(a)lumc.nl> Date: 2017-07-07 (Fri, 07 Jul 2017) Changed paths: M lib/galaxy/datatypes/tabular.py Log Message: ----------- Added index job to vcf.gz files Commit: f4e02700f5c27dfffab0034f2201b208533e42ba https://github.com/galaxyproject/galaxy/commit/f4e02700f5c27dfffab0034f2201… Author: Peter van 't Hof <p.j.van_t_hof(a)lumc.nl> Date: 2017-07-07 (Fri, 07 Jul 2017) Changed paths: M lib/galaxy/datatypes/tabular.py Log Message: ----------- Fixed some spacings Commit: e9daa0d74464534a490129476f027455dbf26a69 https://github.com/galaxyproject/galaxy/commit/e9daa0d74464534a490129476f02… Author: Peter van 't Hof <p.j.van_t_hof(a)lumc.nl> Date: 2017-07-07 (Fri, 07 Jul 2017) Changed paths: M lib/galaxy/datatypes/tabular.py Log Message: ----------- Fixed import order Commit: b96b5076cec2624cc1700bfcec43fd7745d0c0e5 https://github.com/galaxyproject/galaxy/commit/b96b5076cec2624cc1700bfcec43… Author: Peter van 't Hof <p.j.van_t_hof(a)lumc.nl> Date: 2017-07-07 (Fri, 07 Jul 2017) Changed paths: M lib/galaxy/datatypes/tabular.py Log Message: ----------- Fixed import order (again ;) ) Commit: 986379fd0d65c0e5d2d6bdcf1428ba5182713ae7 https://github.com/galaxyproject/galaxy/commit/986379fd0d65c0e5d2d6bdcf1428… Author: Peter van 't Hof <p.j.van_t_hof(a)lumc.nl> Date: 2017-07-07 (Fri, 07 Jul 2017) Changed paths: M lib/galaxy/datatypes/tabular.py Log Message: ----------- Fixed import order (again ;) ) Commit: 9d98f10767d7c43e979720ba8a9badee86501c78 https://github.com/galaxyproject/galaxy/commit/9d98f10767d7c43e979720ba8a9b… Author: Peter van 't Hof <p.j.van_t_hof(a)lumc.nl> Date: 2017-07-07 (Fri, 07 Jul 2017) Changed paths: M lib/galaxy/datatypes/tabular.py M test/functional/tools/samples_tool_conf.xml A test/functional/tools/vcf_bgzip.xml Log Message: ----------- Adding test tool Commit: 99703469c0a30348683190a894a0fc682f92ff68 https://github.com/galaxyproject/galaxy/commit/99703469c0a30348683190a894a0… Author: pjvan_thof <pjrvanthof(a)gmail.com> Date: 2017-07-07 (Fri, 07 Jul 2017) Changed paths: A test-data/test.vcf.gz Log Message: ----------- Added test file Commit: e29611f52dba5e44924b39009ee28c933f4ba7fd https://github.com/galaxyproject/galaxy/commit/e29611f52dba5e44924b39009ee2… Author: Peter van 't Hof <p.j.van_t_hof(a)lumc.nl> Date: 2017-07-07 (Fri, 07 Jul 2017) Changed paths: M test/functional/tools/vcf_bgzip.xml Log Message: ----------- Fixing formats in test Commit: ed2e71a8383698543d97f339bd2b1175a5c07986 https://github.com/galaxyproject/galaxy/commit/ed2e71a8383698543d97f339bd2b… Author: Peter van 't Hof <p.j.van_t_hof(a)lumc.nl> Date: 2017-07-07 (Fri, 07 Jul 2017) Changed paths: M test/functional/tools/vcf_bgzip.xml Log Message: ----------- Fixing tool format Commit: 77b948678d69769c3d6c117a4dc718b3b3cb8388 https://github.com/galaxyproject/galaxy/commit/77b948678d69769c3d6c117a4dc7… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-07-07 (Fri, 07 Jul 2017) Changed paths: M test/functional/tools/sample_datatypes_conf.xml Log Message: ----------- Add vcf_bgzip and dependent datatypes to test/functional/tools/sample_datatypes_conf.xml Commit: 5cc71d2e3c009841c96657d2c359dbe5182548b8 https://github.com/galaxyproject/galaxy/commit/5cc71d2e3c009841c96657d2c359… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-07-07 (Fri, 07 Jul 2017) Changed paths: M lib/galaxy/datatypes/tabular.py M test/functional/tools/vcf_bgzip.xml Log Message: ----------- Simplify vcf_bgzip.xml test wrapper and fix index file access Commit: ed67b117517920affeb71982f08bc355ed0a6cda https://github.com/galaxyproject/galaxy/commit/ed67b117517920affeb71982f08b… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-08-07 (Mon, 07 Aug 2017) Changed paths: M lib/galaxy/datatypes/tabular.py Log Message: ----------- Use with statement in VcfGz class Commit: bcdf2c84f6df020e81c8868b10bcf337e2d72630 https://github.com/galaxyproject/galaxy/commit/bcdf2c84f6df020e81c8868b10bc… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-10 (Thu, 10 Aug 2017) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/tabular.py A test-data/test.vcf.gz M test/functional/tools/sample_datatypes_conf.xml M test/functional/tools/samples_tool_conf.xml A test/functional/tools/vcf_bgzip.xml Log Message: ----------- Merge pull request #4254 from ffinfo/vcf_gz_datatype Vcf gz datatype Compare: https://github.com/galaxyproject/galaxy/compare/e3de5e250d02...bcdf2c84f6df

1 0

[galaxyproject/galaxy] e0d8db: Created alphabetic and numerical sort tool for col...
by GitHub 10 Aug '17

10 Aug '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: e0d8db05b8707b01a42a7be3e46df627bbdf0307 https://github.com/galaxyproject/galaxy/commit/e0d8db05b8707b01a42a7be3e46d… Author: Jorrit Boekel <jorrit.boekel(a)scilifelab.se> Date: 2017-07-21 (Fri, 21 Jul 2017) Changed paths: M config/tool_conf.xml.sample M lib/galaxy/tools/__init__.py A lib/galaxy/tools/sort_collection_list.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Created alphabetic and numerical sort tool for collection operations Commit: e3de5e250d02d105aff4265a0caf13553e3c3ade https://github.com/galaxyproject/galaxy/commit/e3de5e250d02d105aff4265a0caf… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-10 (Thu, 10 Aug 2017) Changed paths: M config/tool_conf.xml.sample M lib/galaxy/tools/__init__.py A lib/galaxy/tools/sort_collection_list.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge pull request #4329 from glormph/collection_list_sort Created alphabetic and numerical sort tool for collection operations Compare: https://github.com/galaxyproject/galaxy/compare/fcd06a96d613...e3de5e250d02

1 0

[galaxyproject/galaxy] bdbe36: fix pardir
by GitHub 10 Aug '17

10 Aug '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: bdbe3603059b84bb2a91646ebcad003477bb9590 https://github.com/galaxyproject/galaxy/commit/bdbe3603059b84bb2a91646ebcad… Author: E Rasche <hxr(a)hx42.org> Date: 2017-08-10 (Thu, 10 Aug 2017) Changed paths: M scripts/grt/export.py Log Message: ----------- fix pardir Commit: f4383bd983ee14d4e85ef610dba4b11266b196ed https://github.com/galaxyproject/galaxy/commit/f4383bd983ee14d4e85ef610dba4… Author: E Rasche <hxr(a)hx42.org> Date: 2017-08-10 (Thu, 10 Aug 2017) Changed paths: M scripts/grt/export.py Log Message: ----------- Fun things you find in production Commit: c5b36128644310e1ac52647df53f226c1457aaeb https://github.com/galaxyproject/galaxy/commit/c5b36128644310e1ac52647df53f… Author: E Rasche <hxr(a)hx42.org> Date: 2017-08-10 (Thu, 10 Aug 2017) Changed paths: M scripts/grt/upload.py Log Message: ----------- cleanup url in case Commit: 847df13fc0ea349ab2103099b696715a6d66b38f https://github.com/galaxyproject/galaxy/commit/847df13fc0ea349ab2103099b696… Author: E Rasche <hxr(a)hx42.org> Date: 2017-08-10 (Thu, 10 Aug 2017) Changed paths: M scripts/grt/upload.py Log Message: ----------- this should not have been missed Commit: 496169719465e18c899b991152a9e327d83e2446 https://github.com/galaxyproject/galaxy/commit/496169719465e18c899b991152a9… Author: E Rasche <hxr(a)hx42.org> Date: 2017-08-10 (Thu, 10 Aug 2017) Changed paths: M scripts/grt/upload.py Log Message: ----------- fix extension Commit: a177ccd0268805e0079f39d5d141ae4da39c0a00 https://github.com/galaxyproject/galaxy/commit/a177ccd0268805e0079f39d5d141… Author: E Rasche <hxr(a)hx42.org> Date: 2017-08-10 (Thu, 10 Aug 2017) Changed paths: M scripts/grt/upload.py Log Message: ----------- not needed Commit: fcd06a96d61342564febfaf652198bd009c9c76f https://github.com/galaxyproject/galaxy/commit/fcd06a96d61342564febfaf65219… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-10 (Thu, 10 Aug 2017) Changed paths: M scripts/grt/export.py M scripts/grt/upload.py Log Message: ----------- Merge pull request #4408 from erasche/grt-pardir Small GRT bugfixes Compare: https://github.com/galaxyproject/galaxy/compare/6d7d4e9e8e55...fcd06a96d613

1 0