Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 6d1397647fd6b185a639915a8f1ac929d78317d4 https://github.com/galaxyproject/galaxy/commit/6d1397647fd6b185a639915a8f1ac... Author: Manabu ISHII manabu.ishii.rb@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/30aa73e1974e1669984f0b6f24211... Author: Manabu ISHII manabu.ishii.rb@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/02924dece4653d476a2838e9b91bd... Author: Manabu ISHII manabu.ishii.rb@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/23db89ba3ddf54420b40e881bd92e... Author: John Chilton jmchilton@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 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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/7dd3ddccafee8f5cc185f1b0dd711... Author: John Chilton jmchilton@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/fc861cdf38d1d20fd611e8bcb0423... Author: John Chilton jmchilton@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