Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: afe5e0446ea3a943eb69616fda84fc9870c3b584 https://github.com/galaxyproject/galaxy/commit/afe5e0446ea3a943eb69616fda84f... Author: Dannon Baker dannon.baker@gmail.com Date: 2016-05-10 (Tue, 10 May 2016)

Changed paths: M lib/galaxy/jobs/runners/slurm.py M templates/show_params.mako M templates/webapps/galaxy/data_manager/view_job.mako

Log Message: ----------- Merge branch 'release_16.01'

Commit: f730f2d1abff763d35fa8514762d55f8a863c791 https://github.com/galaxyproject/galaxy/commit/f730f2d1abff763d35fa8514762d5... Author: John Chilton jmchilton@gmail.com Date: 2016-05-18 (Wed, 18 May 2016)

Changed paths: A .ci/first_startup.sh M .ci/flake8_blacklist.txt M .ci/flake8_wrapper.sh M .ci/py3_sources.txt M .gitignore M .travis.yml M Makefile M README.rst M client/GruntFile.js M client/README.md M client/bower.json M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/apps/tool-panel.js M client/galaxy/scripts/galaxy.library.js M client/galaxy/scripts/layout/masthead.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/layout/scratchbook.js R client/galaxy/scripts/libs/handlebars.runtime.js M client/galaxy/scripts/mvc/base-mvc.js M client/galaxy/scripts/mvc/collection/collection-li-edit.js M client/galaxy/scripts/mvc/collection/collection-li.js M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/collection/collection-view-edit.js M client/galaxy/scripts/mvc/collection/collection-view.js M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M client/galaxy/scripts/mvc/collection/pair-collection-creator.js M client/galaxy/scripts/mvc/dataset/dataset-choice.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/dataset/dataset-list.js M client/galaxy/scripts/mvc/dataset/dataset-model.js M client/galaxy/scripts/mvc/dataset/states.js M client/galaxy/scripts/mvc/form/form-data.js M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/form/form-repeat.js M client/galaxy/scripts/mvc/form/form-section.js R client/galaxy/scripts/mvc/form/form-select-content.js M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/history/copy-dialog.js M client/galaxy/scripts/mvc/history/hda-li-edit.js M client/galaxy/scripts/mvc/history/hda-li.js M client/galaxy/scripts/mvc/history/hda-model.js M client/galaxy/scripts/mvc/history/hdca-li-edit.js M client/galaxy/scripts/mvc/history/hdca-li.js M client/galaxy/scripts/mvc/history/hdca-model.js M client/galaxy/scripts/mvc/history/history-content-model.js M client/galaxy/scripts/mvc/history/history-contents.js M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/history-structure-view.js M client/galaxy/scripts/mvc/history/history-view-annotated.js M client/galaxy/scripts/mvc/history/history-view-edit-current.js M client/galaxy/scripts/mvc/history/history-view-edit.js M client/galaxy/scripts/mvc/history/history-view.js M client/galaxy/scripts/mvc/history/job-dag.js M client/galaxy/scripts/mvc/history/multi-panel.js M client/galaxy/scripts/mvc/history/options-menu.js M client/galaxy/scripts/mvc/library/library-dataset-view.js M client/galaxy/scripts/mvc/library/library-folder-view.js M client/galaxy/scripts/mvc/library/library-folderlist-view.js M client/galaxy/scripts/mvc/library/library-folderrow-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/library/library-library-view.js M client/galaxy/scripts/mvc/library/library-librarylist-view.js M client/galaxy/scripts/mvc/library/library-libraryrow-view.js M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js M client/galaxy/scripts/mvc/library/library-model.js M client/galaxy/scripts/mvc/list/list-item.js M client/galaxy/scripts/mvc/list/list-view.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M 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 M client/galaxy/scripts/mvc/tours.js M client/galaxy/scripts/mvc/ui/ui-list.js M client/galaxy/scripts/mvc/ui/ui-misc.js A client/galaxy/scripts/mvc/ui/ui-select-content.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/galaxy/scripts/mvc/upload/default/default-row.js M client/galaxy/scripts/mvc/upload/upload-settings.js M client/galaxy/scripts/mvc/user/user-model.js M client/galaxy/scripts/mvc/user/user-quotameter.js M client/galaxy/scripts/mvc/workflow/workflow-canvas.js M client/galaxy/scripts/mvc/workflow/workflow-view-node.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M client/galaxy/scripts/onload.js R client/galaxy/scripts/templates/compiled/panel_section.js R client/galaxy/scripts/templates/compiled/tool_form.js R client/galaxy/scripts/templates/compiled/tool_link.js R client/galaxy/scripts/templates/compiled/tool_search.js R client/galaxy/scripts/templates/panel_section.handlebars R client/galaxy/scripts/templates/tool_form.handlebars R client/galaxy/scripts/templates/tool_link.handlebars R client/galaxy/scripts/templates/tool_search.handlebars M client/galaxy/scripts/utils/utils.js M client/galaxy/style/less/base.less M client/galaxy/style/less/library.less A client/galaxy/style/less/tour.less M client/galaxy/style/less/ui.less M client/galaxy/style/less/upload.less M client/grunt-tasks/install-libs.js M client/grunt-tasks/style.js R client/grunt-tasks/templates.js A client/grunt-tasks/webpack.js M client/package.json M client/webpack.config.js M config/datatypes_conf.xml.sample M config/galaxy.ini.sample M config/job_conf.xml.sample_advanced R config/plugins/interactive_environments/ipython/config/ipython.ini.sample R config/plugins/interactive_environments/ipython/config/ipython.xml R config/plugins/interactive_environments/ipython/static/js/ipython.js R config/plugins/interactive_environments/ipython/templates/ipython.mako R config/plugins/interactive_environments/ipython/templates/notebook.ipynb A 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/templates/jupyter.mako A 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config/plugins/visualizations/scatterplot/src/scatterplot-config-editor.js M config/plugins/visualizations/scatterplot/static/scatterplot-edit.js M config/plugins/visualizations/scatterplot/templates/scatterplot.mako M config/tool_conf.xml.sample M config/tool_data_table_conf.xml.sample M contrib/galaxy.debian-init M contrib/galaxy.fedora-init A contrib/galaxy_reports.fedora-init A contrib/galaxy_supervisor.conf A display_applications/biom/biom_simple.xml A display_applications/iobio/bam.xml A display_applications/iobio/vcf.xml M doc/source/admin/framework_dependencies.rst M doc/source/lib/galaxy.datatypes.converters.rst M doc/source/lib/modules.rst R doc/source/lib/pulsar.client.rst R doc/source/lib/pulsar.client.staging.rst R doc/source/lib/pulsar.client.transport.rst R doc/source/lib/pulsar.rst M doc/source/project/issues.rst M doc/source/project/organization.rst M doc/source/releases/16.01.rst A doc/source/releases/16.04.rst M doc/source/releases/16.04_announce.rst A doc/source/releases/16.07_announce.rst M doc/source/releases/index.rst R install_and_test_tool_shed_repositories.sh M lib/galaxy/app.py M lib/galaxy/config.py M lib/galaxy/datatypes/assembly.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/chrominfo.py A lib/galaxy/datatypes/converters/bcf_bgzip_to_bcf_converter.py A lib/galaxy/datatypes/converters/bcf_bgzip_to_bcf_converter.xml A lib/galaxy/datatypes/converters/bcf_to_bcf_bgzip_converter.py A lib/galaxy/datatypes/converters/bcf_to_bcf_bgzip_converter.xml A lib/galaxy/datatypes/converters/cml_to_inchi_converter.xml A lib/galaxy/datatypes/converters/cml_to_mol2_converter.xml A lib/galaxy/datatypes/converters/cml_to_sdf_converter.xml A lib/galaxy/datatypes/converters/cml_to_smi_converter.xml A lib/galaxy/datatypes/converters/inchi_to_cml_converter.xml A lib/galaxy/datatypes/converters/inchi_to_mol2_converter.xml A lib/galaxy/datatypes/converters/inchi_to_mol_converter.xml A lib/galaxy/datatypes/converters/inchi_to_sdf_converter.xml A lib/galaxy/datatypes/converters/inchi_to_smi_converter.xml A lib/galaxy/datatypes/converters/mol2_to_cml_converter.xml A lib/galaxy/datatypes/converters/mol2_to_inchi_converter.xml A lib/galaxy/datatypes/converters/mol2_to_mol_converter.xml A lib/galaxy/datatypes/converters/mol2_to_sdf_converter.xml A lib/galaxy/datatypes/converters/mol2_to_smi_converter.xml A lib/galaxy/datatypes/converters/mol_to_cml_converter.xml A lib/galaxy/datatypes/converters/mol_to_inchi_converter.xml A lib/galaxy/datatypes/converters/mol_to_mol2_converter.xml A lib/galaxy/datatypes/converters/mol_to_smi_converter.xml A lib/galaxy/datatypes/converters/sdf_to_cml_converter.xml A lib/galaxy/datatypes/converters/sdf_to_inchi_converter.xml A lib/galaxy/datatypes/converters/sdf_to_mol2_converter.xml A lib/galaxy/datatypes/converters/sdf_to_smi_converter.xml A lib/galaxy/datatypes/converters/smi_to_cml_converter.xml A lib/galaxy/datatypes/converters/smi_to_inchi_converter.xml A lib/galaxy/datatypes/converters/smi_to_mol2_converter.xml A lib/galaxy/datatypes/converters/smi_to_mol_converter.xml A lib/galaxy/datatypes/converters/smi_to_sdf_converter.xml A lib/galaxy/datatypes/converters/smi_to_smi_converter.xml M lib/galaxy/datatypes/converters/wiggle_to_simple_converter.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/display_applications/application.py M lib/galaxy/datatypes/genetics.py M lib/galaxy/datatypes/images.py M lib/galaxy/datatypes/metadata.py A lib/galaxy/datatypes/molecules.py M lib/galaxy/datatypes/ngsindex.py M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/tabular.py A lib/galaxy/datatypes/test/5e5z.pdb A lib/galaxy/datatypes/test/drugbank_drugs.cml A lib/galaxy/datatypes/test/drugbank_drugs.inchi A lib/galaxy/datatypes/test/drugbank_drugs.mol2 A lib/galaxy/datatypes/test/drugbank_drugs.sdf A lib/galaxy/datatypes/test/drugbank_drugs.smi A lib/galaxy/datatypes/test/issue1818.tabular A lib/galaxy/datatypes/test/q.fps M lib/galaxy/datatypes/text.py M lib/galaxy/dependencies/conda-environment.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/external_services/result_handlers/basic.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/deferred/data_transfer.py M lib/galaxy/jobs/deferred/pacific_biosciences_smrt_portal.py M lib/galaxy/jobs/handler.py M lib/galaxy/jobs/runners/__init__.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/pbs.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/jobs/runners/slurm.py M lib/galaxy/jobs/runners/util/job_script/__init__.py M lib/galaxy/jobs/transfer_manager.py M lib/galaxy/managers/base.py M lib/galaxy/managers/configuration.py M lib/galaxy/managers/containers.py M lib/galaxy/managers/context.py M lib/galaxy/managers/datasets.py M lib/galaxy/managers/hdas.py A lib/galaxy/managers/hdcas.py M lib/galaxy/managers/histories.py A lib/galaxy/managers/history_contents.py M lib/galaxy/managers/ratable.py M lib/galaxy/managers/sharable.py M lib/galaxy/managers/taggable.py M lib/galaxy/managers/tags.py M lib/galaxy/managers/users.py M lib/galaxy/managers/visualizations.py M lib/galaxy/managers/workflows.py R lib/galaxy/metadata M lib/galaxy/model/__init__.py M lib/galaxy/model/custom_types.py M lib/galaxy/model/mapping.py A lib/galaxy/model/metadata.py M lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py M lib/galaxy/model/search.py M lib/galaxy/model/util.py M lib/galaxy/objectstore/__init__.py M lib/galaxy/queue_worker.py M lib/galaxy/security/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/actions/metadata.py M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/tools/cwl/__init__.py M lib/galaxy/tools/cwl/parser.py M lib/galaxy/tools/cwl/representation.py M lib/galaxy/tools/cwl/runtime_actions.py M lib/galaxy/tools/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/containers.py M lib/galaxy/tools/deps/resolvers/unlinked_tool_shed_packages.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/exception_handling.py M lib/galaxy/tools/execute.py M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/tools/imp_exp/export_history.py M lib/galaxy/tools/linters/inputs.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/dynamic_options.py M lib/galaxy/tools/parameters/grouping.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/parameters/wrapped_json.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/xml.py M lib/galaxy/tools/parser/yaml.py M lib/galaxy/tools/test.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/lineages/factory.py M lib/galaxy/tools/toolbox/panel.py M lib/galaxy/tools/toolbox/parser.py M lib/galaxy/tools/wrappers.py M lib/galaxy/util/__init__.py M lib/galaxy/util/dbkeys.py R lib/galaxy/util/dictobj.py M lib/galaxy/util/heartbeat.py M lib/galaxy/util/json.py M lib/galaxy/util/jstree.py M lib/galaxy/util/log/fluent_log.py M lib/galaxy/util/none_like.py M lib/galaxy/util/object_wrapper.py M lib/galaxy/util/pastescript/loadwsgi.py M lib/galaxy/util/sanitize_html.py A lib/galaxy/util/ucsc.py M lib/galaxy/util/validation.py M lib/galaxy/version.py M lib/galaxy/visualization/data_providers/basic.py M lib/galaxy/visualization/data_providers/genome.py M lib/galaxy/visualization/data_providers/registry.py M lib/galaxy/visualization/genomes.py M lib/galaxy/visualization/plugins/config_parser.py M lib/galaxy/visualization/plugins/plugin.py M lib/galaxy/visualization/plugins/registry.py M lib/galaxy/visualization/plugins/resource_parser.py M lib/galaxy/web/base/controller.py M lib/galaxy/web/base/controllers/admin.py M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/web/form_builder.py M lib/galaxy/web/framework/base.py M lib/galaxy/web/framework/decorators.py M lib/galaxy/web/framework/helpers/__init__.py M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/web/framework/middleware/sentry.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/webapps/galaxy/api/datasets.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/remote_files.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 M lib/galaxy/webapps/galaxy/api/visualizations.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/data_manager.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/galaxy/webapps/galaxy/controllers/page.py M lib/galaxy/webapps/galaxy/controllers/requests_common.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/galaxy/webapps/galaxy/controllers/tag.py M lib/galaxy/webapps/galaxy/controllers/tool_runner.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M lib/galaxy/webapps/galaxy/controllers/workflow.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/users.py M lib/galaxy/webapps/tool_shed/buildapp.py M lib/galaxy/webapps/tool_shed/config.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/galaxy/webapps/tool_shed/framework/middleware/hg.py M lib/galaxy/webapps/tool_shed/model/__init__.py M lib/galaxy/webapps/tool_shed/model/mapping.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_request.py M lib/galaxy/workflow/scheduling_manager.py M lib/galaxy_utils/sequence/fasta.py M lib/galaxy_utils/sequence/fastq.py R lib/pulsar/__init__.py R lib/pulsar/client/__init__.py R lib/pulsar/client/action_mapper.py R lib/pulsar/client/amqp_exchange.py R lib/pulsar/client/amqp_exchange_factory.py R lib/pulsar/client/client.py R lib/pulsar/client/config_util.py R lib/pulsar/client/decorators.py R lib/pulsar/client/destination.py R lib/pulsar/client/interface.py R lib/pulsar/client/job_directory.py R lib/pulsar/client/manager.py R lib/pulsar/client/object_client.py R lib/pulsar/client/path_mapper.py R lib/pulsar/client/setup_handler.py R lib/pulsar/client/staging/__init__.py R lib/pulsar/client/staging/down.py R lib/pulsar/client/staging/up.py R lib/pulsar/client/transport/__init__.py R lib/pulsar/client/transport/curl.py R lib/pulsar/client/transport/poster.py R lib/pulsar/client/transport/requests.py R lib/pulsar/client/transport/ssh.py R lib/pulsar/client/transport/standard.py R lib/pulsar/client/util.py M lib/tool_shed/capsule/capsule_manager.py M lib/tool_shed/dependencies/repository/relation_builder.py M lib/tool_shed/galaxy_install/dependency_display.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/galaxy_install/repair_repository_manager.py M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/env_file_builder.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/tool_panel_manager.py M lib/tool_shed/galaxy_install/update_repository_manager.py M lib/tool_shed/grids/repository_grids.py M lib/tool_shed/metadata/metadata_generator.py M lib/tool_shed/metadata/repository_metadata_manager.py R 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Log Message: ----------- Merge branch 'release_16.04'

Commit: ac5a328e5f56d395940e29532facc5655f79d8fe https://github.com/galaxyproject/galaxy/commit/ac5a328e5f56d395940e29532facc... Author: Dannon Baker dannon.baker@gmail.com Date: 2016-05-20 (Fri, 20 May 2016)

Changed paths: M doc/source/releases/index.rst M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/runners/pulsar.py M templates/webapps/galaxy/workflow/sharing.mako

Log Message: ----------- Merge branch 'release_16.04'

Commit: 5a97b8feac49df3f1e9fe0b2e0645b9240eb8291 https://github.com/galaxyproject/galaxy/commit/5a97b8feac49df3f1e9fe0b2e0645... Author: Dannon Baker dannon.baker@gmail.com Date: 2016-05-25 (Wed, 25 May 2016)

Changed paths: A lib/galaxy/datatypes/checkers.py M lib/galaxy/jobs/runners/slurm.py M lib/galaxy/managers/histories.py M lib/galaxy/util/checkers.py M test/unit/managers/test_HistoryManager.py

Log Message: ----------- Merge branch 'release_16.04'

Commit: 06eeb8bafec6f6262041cabe7b34e57d4e1aaa7c https://github.com/galaxyproject/galaxy/commit/06eeb8bafec6f6262041cabe7b34e... Author: Dannon Baker dannon.baker@gmail.com Date: 2016-06-15 (Wed, 15 Jun 2016)

Changed paths: M config/galaxy.ini.sample M config/job_conf.xml.sample_advanced M lib/galaxy/config.py M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/conditional-requirements.txt M lib/galaxy/external_services/actions.py M lib/galaxy/external_services/parameters.py M lib/galaxy/external_services/service.py M lib/galaxy/forms/forms.py M lib/galaxy/jobs/command_factory.py M lib/galaxy/jobs/runners/drmaa.py M lib/galaxy/jobs/runners/slurm.py M lib/galaxy/model/__init__.py M lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py M lib/galaxy/security/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/visualization/data_providers/genome.py M lib/galaxy/web/framework/middleware/statsd.py M lib/galaxy/web/security/__init__.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/external_services.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/webapps/tool_shed/security/__init__.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/repository_types/metadata.py M lib/tool_shed/util/basic_util.py M templates/webapps/galaxy/workflow/display.mako M templates/webapps/galaxy/workflow/sharing.mako A test-data/biom1_metadata_test.txt A test-data/input_taxonomy.biom1 A test/functional/tools/metadata_biom1.xml M test/functional/tools/sample_datatypes_conf.xml M test/functional/tools/samples_tool_conf.xml M test/unit/tools/test_select_parameters.py M tools/filters/axt_to_lav.py

Log Message: ----------- Merge branch 'release_16.04'

Commit: 9226e60fcc3c45434cdfdee80ff518c7ba94c20b https://github.com/galaxyproject/galaxy/commit/9226e60fcc3c45434cdfdee80ff51... Author: Dannon Baker dannon.baker@gmail.com Date: 2016-06-20 (Mon, 20 Jun 2016)

Changed paths: M client/galaxy/scripts/mvc/history/history-model.js M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/model/__init__.py M static/maps/mvc/history/history-model.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/history/history-model.js

Log Message: ----------- Merge branch 'release_16.04'

Commit: 0ba99fe246099cc1827f71f2722d253becee64ba https://github.com/galaxyproject/galaxy/commit/0ba99fe246099cc1827f71f2722d2... Author: Dannon Baker dannon.baker@gmail.com Date: 2016-06-21 (Tue, 21 Jun 2016)

Changed paths: M lib/galaxy/webapps/galaxy/api/visualizations.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M tools/filters/sff_extract.py

Log Message: ----------- Merge branch 'release_16.04'

Commit: a5b836e9eeead2eab752d79b0e15197b82cb0720 https://github.com/galaxyproject/galaxy/commit/a5b836e9eeead2eab752d79b0e151... Author: Dannon Baker dannon.baker@gmail.com Date: 2016-07-19 (Tue, 19 Jul 2016)

Changed paths: M client/galaxy/scripts/mvc/dataset/data.js M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/molecules.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/text.py M lib/galaxy/jobs/actions/post.py M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/web/proxy/js/lib/proxy.js M lib/galaxy/webapps/galaxy/api/datasets.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/tag.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M static/maps/mvc/dataset/data.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/dataset/data.js M templates/webapps/galaxy/history/grid.mako A test/unit/datatypes/test_data.py

Log Message: ----------- Merge branch 'release_16.04'

Commit: 5dfdf90dd09a53e9bc5108f22e439fae961102d5 https://github.com/galaxyproject/galaxy/commit/5dfdf90dd09a53e9bc5108f22e439... Author: anatskiy evgeny.anatskiy@gmail.com Date: 2016-07-30 (Sat, 30 Jul 2016)

Changed paths: M config/galaxy.ini.sample A config/plugins/plugin1.xml A config/plugins/plugin2.xml A config/plugins/webhooks/plugin1/config/plugin1.yaml A config/plugins/webhooks/plugin2/config/plugin2.yml M lib/galaxy/app.py M lib/galaxy/config.py A lib/galaxy/webapps/galaxy/api/webhooks.py A lib/galaxy/webhooks/__init__.py

Log Message: ----------- add Webhooks draft

Commit: 9551343c605f3f8895f75f7ba0fc295ee678ae1a https://github.com/galaxyproject/galaxy/commit/9551343c605f3f8895f75f7ba0fc2... Author: anatskiy evgeny.anatskiy@gmail.com Date: 2016-07-30 (Sat, 30 Jul 2016)

Changed paths: R config/plugins/plugin1.xml R config/plugins/plugin2.xml

Log Message: ----------- remove extra files

Commit: b00c18c26709483df26a0a2878b059e08d697c22 https://github.com/galaxyproject/galaxy/commit/b00c18c26709483df26a0a2878b05... Author: anatskiy evgeny.anatskiy@gmail.com Date: 2016-07-30 (Sat, 30 Jul 2016)

Changed paths: M config/galaxy.ini.sample A config/plugins/webhooks/plugin1/config/plugin1.yaml A config/plugins/webhooks/plugin2/config/plugin2.yml M lib/galaxy/app.py M lib/galaxy/config.py A lib/galaxy/webapps/galaxy/api/webhooks.py A lib/galaxy/webhooks/__init__.py

Log Message: ----------- add Webhooks draft

remove extra files

Commit: 05823a8d1499f5db150942039b31efce4ec97e6b https://github.com/galaxyproject/galaxy/commit/05823a8d1499f5db150942039b31e... Author: anatskiy evgeny.anatskiy@gmail.com Date: 2016-07-30 (Sat, 30 Jul 2016)

Log Message: ----------- Merge branch 'feature/plugin-system' of github.com:bgruening/galaxy into feature/plugin-system

Commit: fb76aa0a938a2498d3206e6039bc1d9906e6c2ce https://github.com/galaxyproject/galaxy/commit/fb76aa0a938a2498d3206e6039bc1... Author: Dannon Baker dannon.baker@gmail.com Date: 2016-08-08 (Mon, 08 Aug 2016)

Changed paths: M .ci/flake8_blacklist.txt M client/galaxy/scripts/mvc/collection/collection-li.js M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/collection/collection-view-edit.js M client/galaxy/scripts/mvc/collection/collection-view.js M client/galaxy/scripts/mvc/history/hdca-li-edit.js M client/galaxy/scripts/mvc/history/hdca-li.js M client/galaxy/scripts/mvc/history/hdca-model.js M client/galaxy/scripts/mvc/history/history-contents.js M config/job_conf.xml.sample_advanced M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/containers.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/wrappers.py M lib/galaxy/web/framework/helpers/__init__.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/workflow/render.py M static/maps/mvc/collection/collection-li.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/history/hdca-li-edit.js.map M static/maps/mvc/history/hdca-li.js.map M static/maps/mvc/history/hdca-model.js.map M static/maps/mvc/history/history-contents.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/collection/collection-li.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/history/hdca-li-edit.js M static/scripts/mvc/history/hdca-li.js M static/scripts/mvc/history/hdca-model.js M static/scripts/mvc/history/history-contents.js M test/base/driver_util.py M tool-data/shared/ucsc/ucsc_build_sites.txt.sample

Log Message: ----------- Merge branch 'release_16.04'

Commit: f8cf6f834bd92b82a05250b1c1f0e42957bffb15 https://github.com/galaxyproject/galaxy/commit/f8cf6f834bd92b82a05250b1c1f0e... Author: Dannon Baker dannon.baker@gmail.com Date: 2016-08-12 (Fri, 12 Aug 2016)

Changed paths: M .ci/flake8_blacklist.txt M lib/galaxy/tools/parameters/basic.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py M tox.ini

Log Message: ----------- Merge branch 'release_16.04'

Commit: bcfcd8184f297abc9f2e90fbf7504be08725600e https://github.com/galaxyproject/galaxy/commit/bcfcd8184f297abc9f2e90fbf7504... Author: Dannon Baker dannon.baker@gmail.com Date: 2016-08-16 (Tue, 16 Aug 2016)

Changed paths: M lib/galaxy/tools/deps/conda_util.py

Log Message: ----------- Merge branch 'release_16.04'

Commit: 12b020548689b973bc1b99379b35678317b412da https://github.com/galaxyproject/galaxy/commit/12b020548689b973bc1b99379b356... Author: anatskiy evgeny.anatskiy@gmail.com Date: 2016-08-18 (Thu, 18 Aug 2016)

Changed paths: M client/galaxy/scripts/mvc/tool/tool-form.js A client/galaxy/scripts/mvc/tool/tool-webhooks.js M config/plugins/webhooks/plugin2/config/plugin2.yml A config/plugins/webhooks/plugin2/static/style.css M lib/galaxy/webapps/galaxy/api/webhooks.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webhooks/__init__.py M static/maps/mvc/tool/tool-form.js.map A static/maps/mvc/tool/tool-webhooks.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/tool/tool-form.js A static/scripts/mvc/tool/tool-webhooks.js

Log Message: ----------- add very basic plugin system (for tools)

Commit: d01677618058a9ac7cb3758a4f6f1c3484790012 https://github.com/galaxyproject/galaxy/commit/d01677618058a9ac7cb3758a4f6f1... Author: anatskiy evgeny.anatskiy@gmail.com Date: 2016-08-19 (Fri, 19 Aug 2016)

Changed paths: M client/galaxy/scripts/mvc/tool/tool-webhooks.js R config/plugins/webhooks/plugin2/config/plugin2.yml R config/plugins/webhooks/plugin2/static/style.css A config/plugins/webhooks/xkcd/config/xkcd.yml A config/plugins/webhooks/xkcd/static/script.js A config/plugins/webhooks/xkcd/static/styles.css M lib/galaxy/webhooks/__init__.py M static/maps/mvc/tool/tool-webhooks.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/tool/tool-webhooks.js

Log Message: ----------- add first webhook

Commit: 08a2d275fa5f8b3713b28be52fcc78eea609a21d https://github.com/galaxyproject/galaxy/commit/08a2d275fa5f8b3713b28be52fcc7... Author: anatskiy evgeny.anatskiy@gmail.com Date: 2016-08-20 (Sat, 20 Aug 2016)

Changed paths: M client/galaxy/scripts/mvc/tool/tool-webhooks.js A config/plugins/webhooks/phdcomics/config/phdcomics.yaml A config/plugins/webhooks/phdcomics/helper/__init__.py A config/plugins/webhooks/phdcomics/static/script.js A config/plugins/webhooks/phdcomics/static/styles.css R config/plugins/webhooks/plugin1/config/plugin1.yaml M config/plugins/webhooks/xkcd/static/script.js M config/plugins/webhooks/xkcd/static/styles.css M lib/galaxy/webapps/galaxy/api/webhooks.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webhooks/__init__.py M static/maps/mvc/tool/tool-webhooks.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/tool/tool-webhooks.js

Log Message: ----------- add one more plugin

Commit: 3b9d1c96e0ea48e09c17c48fb9da8d1f65bbc791 https://github.com/galaxyproject/galaxy/commit/3b9d1c96e0ea48e09c17c48fb9da8... Author: anatskiy evgeny.anatskiy@gmail.com Date: 2016-08-20 (Sat, 20 Aug 2016)

Changed paths: M client/galaxy/scripts/layout/masthead.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/tool/tool-form.js R client/galaxy/scripts/mvc/tool/tool-webhooks.js A client/galaxy/scripts/mvc/webhooks.js A config/plugins/webhooks/topbar_test/config/topbar_test.yml M lib/galaxy/webhooks/__init__.py M static/maps/layout/menu.js.map M static/maps/mvc/tool/tool-form.js.map A static/maps/mvc/webhooks.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/menu.js M static/scripts/mvc/tool/tool-form.js A static/scripts/mvc/webhooks.js

Log Message: ----------- topbar webhooks testing

Commit: a4497004ac47a25d6f9cefbfcb08183c5b6b8564 https://github.com/galaxyproject/galaxy/commit/a4497004ac47a25d6f9cefbfcb081... Author: anatskiy evgeny.anatskiy@gmail.com Date: 2016-08-20 (Sat, 20 Aug 2016)

Changed paths: M config/galaxy.ini.sample A config/plugins/plugin1.xml A config/plugins/plugin2.xml A config/plugins/webhooks/plugin1/config/plugin1.yaml A config/plugins/webhooks/plugin2/config/plugin2.yml M lib/galaxy/app.py M lib/galaxy/config.py A lib/galaxy/webapps/galaxy/api/webhooks.py A lib/galaxy/webhooks/__init__.py

Log Message: ----------- add Webhooks draft

Commit: 356e7ad3982da9916da927c52dad29e86a1e0ceb https://github.com/galaxyproject/galaxy/commit/356e7ad3982da9916da927c52dad2... Author: anatskiy evgeny.anatskiy@gmail.com Date: 2016-08-20 (Sat, 20 Aug 2016)

Changed paths: R config/plugins/plugin1.xml R config/plugins/plugin2.xml

Log Message: ----------- remove extra files

Commit: 649bdd2aa947e11ab300152f4d9054be74229020 https://github.com/galaxyproject/galaxy/commit/649bdd2aa947e11ab300152f4d905... Author: anatskiy evgeny.anatskiy@gmail.com Date: 2016-08-20 (Sat, 20 Aug 2016)

Changed paths: M client/galaxy/scripts/mvc/tool/tool-form.js A client/galaxy/scripts/mvc/tool/tool-webhooks.js M config/plugins/webhooks/plugin2/config/plugin2.yml A config/plugins/webhooks/plugin2/static/style.css M lib/galaxy/webapps/galaxy/api/webhooks.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webhooks/__init__.py M static/maps/mvc/tool/tool-form.js.map A static/maps/mvc/tool/tool-webhooks.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/tool/tool-form.js A static/scripts/mvc/tool/tool-webhooks.js

Log Message: ----------- add very basic plugin system (for tools)

Commit: 6ea52120840ac0e89aa6b6cfbce414a81a1c42e7 https://github.com/galaxyproject/galaxy/commit/6ea52120840ac0e89aa6b6cfbce41... Author: anatskiy evgeny.anatskiy@gmail.com Date: 2016-08-20 (Sat, 20 Aug 2016)

Changed paths: M client/galaxy/scripts/mvc/tool/tool-webhooks.js R config/plugins/webhooks/plugin2/config/plugin2.yml R config/plugins/webhooks/plugin2/static/style.css A config/plugins/webhooks/xkcd/config/xkcd.yml A config/plugins/webhooks/xkcd/static/script.js A config/plugins/webhooks/xkcd/static/styles.css M lib/galaxy/webhooks/__init__.py M static/maps/mvc/tool/tool-webhooks.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/tool/tool-webhooks.js

Log Message: ----------- add first webhook

Commit: 4cbc8a0c0ce1587a52418d91e2918ecdc07cf7ca https://github.com/galaxyproject/galaxy/commit/4cbc8a0c0ce1587a52418d91e2918... Author: anatskiy evgeny.anatskiy@gmail.com Date: 2016-08-20 (Sat, 20 Aug 2016)

Changed paths: M client/galaxy/scripts/mvc/tool/tool-webhooks.js A config/plugins/webhooks/phdcomics/config/phdcomics.yaml A config/plugins/webhooks/phdcomics/helper/__init__.py A config/plugins/webhooks/phdcomics/static/script.js A config/plugins/webhooks/phdcomics/static/styles.css R config/plugins/webhooks/plugin1/config/plugin1.yaml M config/plugins/webhooks/xkcd/static/script.js M config/plugins/webhooks/xkcd/static/styles.css M lib/galaxy/webapps/galaxy/api/webhooks.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webhooks/__init__.py M static/maps/mvc/tool/tool-webhooks.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/tool/tool-webhooks.js

Log Message: ----------- add one more plugin

Commit: d2b58c80993c42b3add50a0266d4b8f9ca269a6d https://github.com/galaxyproject/galaxy/commit/d2b58c80993c42b3add50a0266d4b... Author: anatskiy evgeny.anatskiy@gmail.com Date: 2016-08-20 (Sat, 20 Aug 2016)

Changed paths: M client/galaxy/scripts/layout/masthead.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/tool/tool-form.js R client/galaxy/scripts/mvc/tool/tool-webhooks.js A client/galaxy/scripts/mvc/webhooks.js A config/plugins/webhooks/topbar_test/config/topbar_test.yml M lib/galaxy/webhooks/__init__.py M static/maps/layout/menu.js.map M static/maps/mvc/tool/tool-form.js.map A static/maps/mvc/webhooks.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/menu.js M static/scripts/mvc/tool/tool-form.js A static/scripts/mvc/webhooks.js

Log Message: ----------- topbar webhooks testing

Commit: 763aa1026dc6071cab0687859d5d764ac9f438ed https://github.com/galaxyproject/galaxy/commit/763aa1026dc6071cab0687859d5d7... Author: anatskiy evgeny.anatskiy@gmail.com Date: 2016-08-20 (Sat, 20 Aug 2016)

Log Message: ----------- Merge branch 'feature/plugin-system' of github.com:bgruening/galaxy into feature/plugin-system

Commit: bec41c889def0b012ec809d5e3e97fe2bc006492 https://github.com/galaxyproject/galaxy/commit/bec41c889def0b012ec809d5e3e97... Author: anatskiy evgeny.anatskiy@gmail.com Date: 2016-08-20 (Sat, 20 Aug 2016)

Changed paths: M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/tool/tool-form.js M client/galaxy/scripts/mvc/webhooks.js A config/plugins/webhooks/masthead_test/config/masthead_test.yml M config/plugins/webhooks/phdcomics/config/phdcomics.yaml R config/plugins/webhooks/topbar_test/config/topbar_test.yml M config/plugins/webhooks/xkcd/config/xkcd.yml M lib/galaxy/webhooks/__init__.py M static/maps/layout/menu.js.map M static/maps/mvc/tool/tool-form.js.map M static/maps/mvc/webhooks.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/menu.js M static/scripts/mvc/tool/tool-form.js M static/scripts/mvc/webhooks.js

Log Message: ----------- renamings and fixes

Commit: ddc9c647b2d2d910bdcc31579d0d1c1f54b6bdab https://github.com/galaxyproject/galaxy/commit/ddc9c647b2d2d910bdcc31579d0d1... Author: John Chilton jmchilton@gmail.com Date: 2016-08-25 (Thu, 25 Aug 2016)

Changed paths: M .ci/first_startup.sh A .ci/flake8_lint_include_list.txt A .ci/flake8_wrapper_imports.sh M .ci/py3_sources.txt M .gitignore M .travis.yml M CONTRIBUTORS.md M Makefile M README.rst R buildbot_setup.sh M client/README.md M client/bower.json A client/galaxy/scripts/layout/generic-nav-view.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/layout/scratchbook.js M client/galaxy/scripts/libs/backbone.js M client/galaxy/scripts/libs/bootstrap-tour.js M client/galaxy/scripts/libs/d3.js M client/galaxy/scripts/libs/jquery/jquery.js M client/galaxy/scripts/libs/jquery/jquery.migrate.js M client/galaxy/scripts/libs/raven.js M client/galaxy/scripts/libs/require.js R client/galaxy/scripts/libs/tracekit.js M client/galaxy/scripts/libs/underscore.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/dataset/dataset-model.js M client/galaxy/scripts/mvc/form/form-data.js M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/form/form-repeat.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/history/history-contents.js M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/history-view-annotated.js M client/galaxy/scripts/mvc/history/history-view-edit-current.js M client/galaxy/scripts/mvc/history/history-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/tool/tool-form.js R client/galaxy/scripts/mvc/tool/tool-template.js M client/galaxy/scripts/mvc/tool/tools.js M client/galaxy/scripts/mvc/ui/popup-menu.js M 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client/galaxy/scripts/utils/metrics-logger.js M client/galaxy/scripts/utils/utils.js M client/galaxy/scripts/viz/trackster/painters.js M client/galaxy/scripts/viz/trackster/tracks.js M client/galaxy/style/less/base.less M client/galaxy/style/less/frame.less M client/galaxy/style/less/library.less M client/galaxy/style/less/ui.less M client/grunt-tasks/install-libs.js M client/grunt-tasks/scripts.js M client/grunt-tasks/style.js M config/datatypes_conf.xml.sample M config/galaxy.ini.sample M config/job_conf.xml.sample_advanced M config/object_store_conf.xml.sample M config/plugins/interactive_environments/jupyter/config/jupyter.xml A config/plugins/interactive_environments/neo/config/allowed_images.yml.sample A config/plugins/interactive_environments/neo/config/neo.ini.sample A config/plugins/interactive_environments/neo/config/neo.xml A config/plugins/interactive_environments/neo/static/js/neo.js A config/plugins/interactive_environments/neo/templates/neo.mako M 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test/unit/jobs/dynamic_tool_destination/data/test_no_verbose.yml A test/unit/jobs/dynamic_tool_destination/data/test_num_input_datasets.yml A test/unit/jobs/dynamic_tool_destination/data/test_users.yml A test/unit/jobs/dynamic_tool_destination/data/tool_destination.yml A test/unit/jobs/dynamic_tool_destination/mockGalaxy.py A test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py A test/unit/jobs/dynamic_tool_destination/ymltests.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/test_galaxy_mapping.py M test/unit/test_objectstore.py M test/unit/tools/test_actions.py M test/unit/tools/test_conda_resolution.py M test/unit/tools/test_data_parameters.py M 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tools/extract/liftOver_wrapper.py M tools/filters/axt_to_concat_fasta.xml M tools/filters/axt_to_fasta.xml M tools/filters/axt_to_lav.py M tools/filters/axt_to_lav.xml M tools/filters/bed2gff.xml M tools/filters/bed_to_bigbed.xml M tools/filters/bed_to_gff_converter.py M tools/filters/gff/extract_GFF_Features.py M tools/filters/gff/gff_filter_by_attribute.py M tools/filters/gff2bed.xml M tools/filters/gff_to_bed_converter.py M tools/filters/gtf2bedgraph.xml 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/sff_extract.py M tools/filters/sorter.py M tools/filters/trimmer.xml M tools/filters/wiggle_to_simple.py M tools/genomespace/genomespace_exporter.py M tools/genomespace/genomespace_file_browser.py M tools/maf/interval_maf_to_merged_fasta.py M tools/maf/maf_split_by_species.py M tools/maf/maf_thread_for_species.py M tools/maf/maf_to_fasta_concat.py M tools/maf/maf_to_fasta_multiple_sets.py M tools/metag_tools/blat_wrapper.py M tools/metag_tools/shrimp_color_wrapper.py M tools/metag_tools/shrimp_wrapper.py M tools/next_gen_conversion/fastq_conversions.py M tools/next_gen_conversion/fastq_gen_conv.py M tools/next_gen_conversion/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/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/stats/aggregate_scores_in_intervals.py M tools/stats/filtering.py M tools/stats/filtering.xml M tools/stats/grouping.py M tools/stats/gsummary.py M tools/stats/gsummary.xml M tox.ini

Log Message: ----------- Merge branch 'release_16.07'

Commit: 9ff882944ee1fd78b6244dad5893ac7390eb76fa https://github.com/galaxyproject/galaxy/commit/9ff882944ee1fd78b6244dad5893a... Author: anatskiy evgeny.anatskiy@gmail.com Date: 2016-08-29 (Mon, 29 Aug 2016)

Changed paths: M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/tool/tool-form.js M client/galaxy/scripts/mvc/webhooks.js M config/plugins/webhooks/masthead_test/config/masthead_test.yml A config/plugins/webhooks/masthead_test/static/script.js M config/plugins/webhooks/phdcomics/helper/__init__.py M lib/galaxy/webapps/galaxy/api/webhooks.py M lib/galaxy/webhooks/__init__.py M static/maps/layout/menu.js.map M static/maps/mvc/tool/tool-form.js.map M static/maps/mvc/webhooks.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/menu.js M static/scripts/mvc/tool/tool-form.js M static/scripts/mvc/webhooks.js

Log Message: ----------- - unify webhooks entry point - simlify webhooks code (on load) - improve code readability - clean up

Commit: d2ec87548a22273a2e0d94bbe1b415fbf6352b36 https://github.com/galaxyproject/galaxy/commit/d2ec87548a22273a2e0d94bbe1b41... Author: anatskiy evgeny.anatskiy@gmail.com Date: 2016-08-30 (Tue, 30 Aug 2016)

Changed paths: M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/tool/tool-form.js M client/galaxy/scripts/mvc/webhooks.js M config/plugins/webhooks/masthead_test/config/masthead_test.yml M config/plugins/webhooks/phdcomics/config/phdcomics.yaml M config/plugins/webhooks/xkcd/config/xkcd.yml M lib/galaxy/webapps/galaxy/api/webhooks.py M static/maps/mvc/tool/tool-form.js.map M static/maps/mvc/webhooks.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/tool/tool-form.js M static/scripts/mvc/webhooks.js M templates/webapps/galaxy/workflow/run_complete.mako

Log Message: ----------- - add new entry point (Workflow) - temporarily hide masthead webhook (due to instability)

Commit: e320b1aaa70aea38b7108ca6ae372b1d06fd30bc https://github.com/galaxyproject/galaxy/commit/e320b1aaa70aea38b7108ca6ae372... Author: Dannon Baker dannon.baker@gmail.com Date: 2016-09-07 (Wed, 07 Sep 2016)

Changed paths: M config/galaxy.ini.sample M doc/source/releases/16.07.rst M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/watcher.py

Log Message: ----------- Merge branch 'release_16.07'

Commit: b46d55e30fd3f8a2832130dd3f917082f442836f https://github.com/galaxyproject/galaxy/commit/b46d55e30fd3f8a2832130dd3f917... Author: Evgeny Anatskiy evgeny.anatskiy@gmail.com Date: 2016-10-04 (Tue, 04 Oct 2016)

Changed paths: M client/galaxy/scripts/apps/history-panel.js M client/galaxy/scripts/mvc/history/options-menu.js M client/galaxy/scripts/mvc/webhooks.js A config/plugins/webhooks/history_test1/config/history_test1.yml A config/plugins/webhooks/history_test2/config/history_test2.yml M lib/galaxy/webapps/galaxy/api/webhooks.py M lib/galaxy/webapps/galaxy/buildapp.py M static/maps/mvc/history/options-menu.js.map M static/maps/mvc/webhooks.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/history/options-menu.js M static/scripts/mvc/webhooks.js

Log Message: ----------- add new entry point for History Panel menu

Commit: b98e49f2bc88e62b4835aa8d23f8d3386f81f66a https://github.com/galaxyproject/galaxy/commit/b98e49f2bc88e62b4835aa8d23f8d... Author: Evgeny Anatskiy evgeny.anatskiy@gmail.com Date: 2016-10-05 (Wed, 05 Oct 2016)

Changed paths: M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/history/options-menu.js M client/galaxy/scripts/mvc/tool/tool-form.js M client/galaxy/scripts/mvc/webhooks.js M config/plugins/webhooks/history_test1/config/history_test1.yml M config/plugins/webhooks/history_test2/config/history_test2.yml M config/plugins/webhooks/masthead_test/config/masthead_test.yml M config/plugins/webhooks/phdcomics/config/phdcomics.yaml M config/plugins/webhooks/xkcd/config/xkcd.yml M lib/galaxy/webhooks/__init__.py M static/maps/layout/menu.js.map M static/maps/mvc/history/options-menu.js.map M static/maps/mvc/tool/tool-form.js.map M static/maps/mvc/webhooks.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/menu.js M static/scripts/mvc/history/options-menu.js M static/scripts/mvc/tool/tool-form.js M static/scripts/mvc/webhooks.js

Log Message: ----------- bug fixes and improvements

Commit: 58e0d6e1a61b06c444b2086d7725e1100d49441a https://github.com/galaxyproject/galaxy/commit/58e0d6e1a61b06c444b2086d7725e... Author: anatskiy evgeny.anatskiy@gmail.com Date: 2016-10-05 (Wed, 05 Oct 2016)

Changed paths: M config/galaxy.ini.sample A config/plugins/plugin1.xml A config/plugins/plugin2.xml A config/plugins/webhooks/plugin1/config/plugin1.yaml A config/plugins/webhooks/plugin2/config/plugin2.yml M lib/galaxy/app.py M lib/galaxy/config.py A lib/galaxy/webapps/galaxy/api/webhooks.py A lib/galaxy/webhooks/__init__.py

Log Message: ----------- add Webhooks draft

Commit: cbbcf3d625a1625e89bbe7c59997d3658d23ea55 https://github.com/galaxyproject/galaxy/commit/cbbcf3d625a1625e89bbe7c59997d... Author: anatskiy evgeny.anatskiy@gmail.com Date: 2016-10-05 (Wed, 05 Oct 2016)

Changed paths: R config/plugins/plugin1.xml R config/plugins/plugin2.xml

Log Message: ----------- remove extra files

Commit: cf1fde577e9b918bacfe2d78d9f2b632a81ee20b https://github.com/galaxyproject/galaxy/commit/cf1fde577e9b918bacfe2d78d9f2b... Author: anatskiy evgeny.anatskiy@gmail.com Date: 2016-10-05 (Wed, 05 Oct 2016)

Changed paths: A client/galaxy/scripts/mvc/tool/tool-webhooks.js A client/galaxy/scripts/mvc/webhooks.js M config/plugins/webhooks/plugin2/config/plugin2.yml A config/plugins/webhooks/plugin2/static/style.css M lib/galaxy/webapps/galaxy/api/webhooks.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webhooks/__init__.py A static/maps/mvc/tool/tool-webhooks.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map A static/scripts/mvc/tool/tool-webhooks.js

Log Message: ----------- add very basic plugin system (for tools)

Commit: ac5a0f5a6adea3493549d69627d1d2223b97c09e https://github.com/galaxyproject/galaxy/commit/ac5a0f5a6adea3493549d69627d1d... Author: anatskiy evgeny.anatskiy@gmail.com Date: 2016-10-05 (Wed, 05 Oct 2016)

Changed paths: M client/galaxy/scripts/mvc/tool/tool-webhooks.js R config/plugins/webhooks/plugin2/config/plugin2.yml R config/plugins/webhooks/plugin2/static/style.css A config/plugins/webhooks/xkcd/config/xkcd.yml A config/plugins/webhooks/xkcd/static/script.js A config/plugins/webhooks/xkcd/static/styles.css M lib/galaxy/webhooks/__init__.py M static/maps/mvc/tool/tool-webhooks.js.map M static/scripts/mvc/tool/tool-webhooks.js

Log Message: ----------- add first webhook

Commit: fecf493ecde3590e9da4629a063d5885dde99502 https://github.com/galaxyproject/galaxy/commit/fecf493ecde3590e9da4629a063d5... Author: anatskiy evgeny.anatskiy@gmail.com Date: 2016-10-05 (Wed, 05 Oct 2016)

Changed paths: M client/galaxy/scripts/mvc/tool/tool-webhooks.js A config/plugins/webhooks/phdcomics/config/phdcomics.yaml A config/plugins/webhooks/phdcomics/helper/__init__.py A config/plugins/webhooks/phdcomics/static/script.js A config/plugins/webhooks/phdcomics/static/styles.css R config/plugins/webhooks/plugin1/config/plugin1.yaml M config/plugins/webhooks/xkcd/static/script.js M config/plugins/webhooks/xkcd/static/styles.css M lib/galaxy/webapps/galaxy/api/webhooks.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webhooks/__init__.py M static/maps/mvc/tool/tool-webhooks.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/tool/tool-webhooks.js

Log Message: ----------- add one more plugin

Commit: 239731d45aa5019eecc4d65a771102bb38a79851 https://github.com/galaxyproject/galaxy/commit/239731d45aa5019eecc4d65a77110... Author: anatskiy evgeny.anatskiy@gmail.com Date: 2016-10-05 (Wed, 05 Oct 2016)

Changed paths: M client/galaxy/scripts/layout/masthead.js R client/galaxy/scripts/mvc/tool/tool-webhooks.js A config/plugins/webhooks/topbar_test/config/topbar_test.yml M lib/galaxy/webhooks/__init__.py A static/maps/mvc/webhooks.js.map A static/scripts/mvc/webhooks.js

Log Message: ----------- topbar webhooks testing

Commit: d35d99727b76ab71173ad7cccca1a4d66aa9ce70 https://github.com/galaxyproject/galaxy/commit/d35d99727b76ab71173ad7cccca1a... Author: anatskiy evgeny.anatskiy@gmail.com Date: 2016-10-05 (Wed, 05 Oct 2016)

Changed paths: A config/plugins/plugin1.xml A config/plugins/plugin2.xml A config/plugins/webhooks/plugin1/config/plugin1.yaml A config/plugins/webhooks/plugin2/config/plugin2.yml

Log Message: ----------- add Webhooks draft

Commit: 1f7a4135318f0d6940e2a65a2b9f7ab29cdb0a41 https://github.com/galaxyproject/galaxy/commit/1f7a4135318f0d6940e2a65a2b9f7... Author: anatskiy evgeny.anatskiy@gmail.com Date: 2016-10-05 (Wed, 05 Oct 2016)

Changed paths: R config/plugins/plugin1.xml R config/plugins/plugin2.xml

Log Message: ----------- remove extra files

Commit: adc92fd31740ebe4fe66bfec32fe14ef5b736c72 https://github.com/galaxyproject/galaxy/commit/adc92fd31740ebe4fe66bfec32fe1... Author: anatskiy evgeny.anatskiy@gmail.com Date: 2016-10-05 (Wed, 05 Oct 2016)

Changed paths: A client/galaxy/scripts/mvc/tool/tool-webhooks.js M config/plugins/webhooks/plugin2/config/plugin2.yml A config/plugins/webhooks/plugin2/static/style.css

Log Message: ----------- add very basic plugin system (for tools)

Commit: d490415b0500dcbadca9a1f959cf0b996abe326e https://github.com/galaxyproject/galaxy/commit/d490415b0500dcbadca9a1f959cf0... Author: anatskiy evgeny.anatskiy@gmail.com Date: 2016-10-05 (Wed, 05 Oct 2016)

Changed paths: M client/galaxy/scripts/mvc/tool/tool-webhooks.js R config/plugins/webhooks/plugin2/config/plugin2.yml R config/plugins/webhooks/plugin2/static/style.css

Log Message: ----------- add first webhook

Commit: 86af65a7d6889086e1f16ef3ef4fcfa77ba3c88e https://github.com/galaxyproject/galaxy/commit/86af65a7d6889086e1f16ef3ef4fc... Author: anatskiy evgeny.anatskiy@gmail.com Date: 2016-10-05 (Wed, 05 Oct 2016)

Changed paths: M client/galaxy/scripts/mvc/tool/tool-webhooks.js R config/plugins/webhooks/plugin1/config/plugin1.yaml

Log Message: ----------- add one more plugin

Commit: 4635ff4575ea1a47fac8da2bbb50092cc3352c3f https://github.com/galaxyproject/galaxy/commit/4635ff4575ea1a47fac8da2bbb500... Author: anatskiy evgeny.anatskiy@gmail.com Date: 2016-10-05 (Wed, 05 Oct 2016)

Changed paths: R client/galaxy/scripts/mvc/tool/tool-webhooks.js

Log Message: ----------- topbar webhooks testing

Commit: 482e0b2bffe992c329f22e4f9b50a34cfd835518 https://github.com/galaxyproject/galaxy/commit/482e0b2bffe992c329f22e4f9b50a... Author: anatskiy evgeny.anatskiy@gmail.com Date: 2016-10-05 (Wed, 05 Oct 2016)

Changed paths: A config/plugins/webhooks/masthead_test/config/masthead_test.yml M config/plugins/webhooks/phdcomics/config/phdcomics.yaml R config/plugins/webhooks/topbar_test/config/topbar_test.yml M config/plugins/webhooks/xkcd/config/xkcd.yml M lib/galaxy/webhooks/__init__.py M static/maps/mvc/webhooks.js.map M static/scripts/mvc/webhooks.js

Log Message: ----------- renamings and fixes

Commit: 6e534213e12820f69bb849b74aa8924787d9023e https://github.com/galaxyproject/galaxy/commit/6e534213e12820f69bb849b74aa89... Author: anatskiy evgeny.anatskiy@gmail.com Date: 2016-10-05 (Wed, 05 Oct 2016)

Changed paths: M config/plugins/webhooks/masthead_test/config/masthead_test.yml A config/plugins/webhooks/masthead_test/static/script.js M config/plugins/webhooks/phdcomics/helper/__init__.py M lib/galaxy/webapps/galaxy/api/webhooks.py M lib/galaxy/webhooks/__init__.py M static/maps/mvc/webhooks.js.map M static/scripts/mvc/webhooks.js

Log Message: ----------- - unify webhooks entry point - simlify webhooks code (on load) - improve code readability - clean up

Commit: fce44d257b9d05e68ca4323036e7e509d329e789 https://github.com/galaxyproject/galaxy/commit/fce44d257b9d05e68ca4323036e7e... Author: anatskiy evgeny.anatskiy@gmail.com Date: 2016-10-05 (Wed, 05 Oct 2016)

Changed paths: M config/plugins/webhooks/masthead_test/config/masthead_test.yml M config/plugins/webhooks/phdcomics/config/phdcomics.yaml M config/plugins/webhooks/xkcd/config/xkcd.yml M lib/galaxy/webapps/galaxy/api/webhooks.py M static/maps/mvc/webhooks.js.map M static/scripts/mvc/webhooks.js M templates/webapps/galaxy/workflow/run_complete.mako

Log Message: ----------- - add new entry point (Workflow) - temporarily hide masthead webhook (due to instability)

Commit: 3c3819900fd293de1532a4c0a15685927a8fd2dd https://github.com/galaxyproject/galaxy/commit/3c3819900fd293de1532a4c0a1568... Author: Evgeny Anatskiy evgeny.anatskiy@gmail.com Date: 2016-10-05 (Wed, 05 Oct 2016)

Changed paths: M client/galaxy/scripts/apps/history-panel.js M client/galaxy/scripts/mvc/history/options-menu.js A config/plugins/webhooks/history_test1/config/history_test1.yml A config/plugins/webhooks/history_test2/config/history_test2.yml M lib/galaxy/webapps/galaxy/api/webhooks.py M lib/galaxy/webapps/galaxy/buildapp.py M static/maps/mvc/history/options-menu.js.map M static/maps/mvc/webhooks.js.map M static/scripts/mvc/history/options-menu.js M static/scripts/mvc/webhooks.js

Log Message: ----------- add new entry point for History Panel menu

Commit: 6f109176d16a162b9f5a132927eef13e096bdce4 https://github.com/galaxyproject/galaxy/commit/6f109176d16a162b9f5a132927eef... Author: Evgeny Anatskiy evgeny.anatskiy@gmail.com Date: 2016-10-05 (Wed, 05 Oct 2016)

Changed paths: M client/galaxy/scripts/mvc/history/options-menu.js M config/plugins/webhooks/history_test1/config/history_test1.yml M config/plugins/webhooks/history_test2/config/history_test2.yml M config/plugins/webhooks/masthead_test/config/masthead_test.yml M config/plugins/webhooks/phdcomics/config/phdcomics.yaml M config/plugins/webhooks/xkcd/config/xkcd.yml M lib/galaxy/webhooks/__init__.py M static/maps/mvc/history/options-menu.js.map M static/maps/mvc/webhooks.js.map M static/scripts/mvc/history/options-menu.js M static/scripts/mvc/webhooks.js

Log Message: ----------- bug fixes and improvements

Commit: 31674ef5b789b9c9557bb78efaa5d13961744c1d https://github.com/galaxyproject/galaxy/commit/31674ef5b789b9c9557bb78efaa5d... Author: Evgeny Anatskiy evgeny.anatskiy@gmail.com Date: 2016-10-05 (Wed, 05 Oct 2016)

Changed paths: M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/tool/tool-form.js M static/maps/layout/menu.js.map M static/maps/mvc/tool/tool-form.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/menu.js M static/scripts/mvc/tool/tool-form.js

Log Message: ----------- Merge branch 'feature/plugin-system' of github.com:bgruening/galaxy into feature/plugin-system

# Conflicts: # client/galaxy/scripts/layout/menu.js # client/galaxy/scripts/mvc/tool/tool-form.js # static/maps/layout/menu.js.map # static/maps/mvc/tool/tool-form.js.map # static/scripts/bundled/analysis.bundled.js # static/scripts/bundled/analysis.bundled.js.map # static/scripts/bundled/libs.bundled.js # static/scripts/bundled/libs.bundled.js.map # static/scripts/layout/menu.js # static/scripts/mvc/tool/tool-form.js

Commit: 2bf0549a371a1a3f683d375233b9b3f5b1e37944 https://github.com/galaxyproject/galaxy/commit/2bf0549a371a1a3f683d375233b9b... Author: Evgeny Anatskiy evgeny.anatskiy@gmail.com Date: 2016-10-05 (Wed, 05 Oct 2016)

Changed paths: M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/tool/tool-form.js M config/plugins/webhooks/xkcd/config/xkcd.yml M static/maps/layout/menu.js.map M static/maps/mvc/tool/tool-form.js.map M static/maps/mvc/webhooks.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/menu.js M static/scripts/mvc/tool/tool-form.js

Log Message: ----------- fix bugs after previous commit

Commit: d821c2745c014bc0e2e2cc31eac8d70bb576ea7e https://github.com/galaxyproject/galaxy/commit/d821c2745c014bc0e2e2cc31eac8d... Author: Evgeny Anatskiy evgeny.anatskiy@gmail.com Date: 2016-10-09 (Sun, 09 Oct 2016)

Changed paths: M client/galaxy/scripts/mvc/webhooks.js M config/plugins/webhooks/masthead_test/config/masthead_test.yml R config/plugins/webhooks/masthead_test/static/script.js M config/plugins/webhooks/phdcomics/helper/__init__.py M lib/galaxy/webapps/galaxy/api/webhooks.py M static/maps/mvc/webhooks.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/webhooks.js

Log Message: ----------- pass trans object into the helper function

Commit: 1a80a0df7f371347976f0b9fb3ff1cb651d4170b https://github.com/galaxyproject/galaxy/commit/1a80a0df7f371347976f0b9fb3ff1... Author: Björn Grüning bjoern@gruenings.eu Date: 2016-10-09 (Sun, 09 Oct 2016)

Changed paths: A doc/source/admin/webhooks.rst

Log Message: ----------- Add initial docs

Commit: 5361d7c03d23ed4fe4701b2e126f56114673cf7f https://github.com/galaxyproject/galaxy/commit/5361d7c03d23ed4fe4701b2e126f5... Author: anatskiy evgeny.anatskiy@gmail.com Date: 2016-10-09 (Sun, 09 Oct 2016)

Changed paths: M config/galaxy.ini.sample A config/plugins/plugin1.xml A config/plugins/plugin2.xml A config/plugins/webhooks/plugin1/config/plugin1.yaml A config/plugins/webhooks/plugin2/config/plugin2.yml M lib/galaxy/app.py M lib/galaxy/config.py A lib/galaxy/webapps/galaxy/api/webhooks.py A lib/galaxy/webhooks/__init__.py

Log Message: ----------- add Webhooks draft

Commit: a34a1201fc72abff092ccb8c0366b07dfde31987 https://github.com/galaxyproject/galaxy/commit/a34a1201fc72abff092ccb8c0366b... Author: anatskiy evgeny.anatskiy@gmail.com Date: 2016-10-09 (Sun, 09 Oct 2016)

Changed paths: R config/plugins/plugin1.xml R config/plugins/plugin2.xml

Log Message: ----------- remove extra files

Commit: 6e66fbeca8741748aa823e34432bd62527096491 https://github.com/galaxyproject/galaxy/commit/6e66fbeca8741748aa823e34432bd... Author: anatskiy evgeny.anatskiy@gmail.com Date: 2016-10-09 (Sun, 09 Oct 2016)

Changed paths: M client/galaxy/scripts/mvc/tool/tool-form.js A client/galaxy/scripts/mvc/tool/tool-webhooks.js M config/plugins/webhooks/plugin2/config/plugin2.yml A config/plugins/webhooks/plugin2/static/style.css M lib/galaxy/webapps/galaxy/api/webhooks.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webhooks/__init__.py A static/maps/mvc/tool/tool-webhooks.js.map A static/scripts/mvc/tool/tool-webhooks.js

Log Message: ----------- add very basic plugin system (for tools)

Commit: eb46e70206ba43a5e191153df74aa47dc441ed19 https://github.com/galaxyproject/galaxy/commit/eb46e70206ba43a5e191153df74aa... Author: anatskiy evgeny.anatskiy@gmail.com Date: 2016-10-09 (Sun, 09 Oct 2016)

Changed paths: M client/galaxy/scripts/mvc/tool/tool-webhooks.js R config/plugins/webhooks/plugin2/config/plugin2.yml R config/plugins/webhooks/plugin2/static/style.css A config/plugins/webhooks/xkcd/config/xkcd.yml A config/plugins/webhooks/xkcd/static/script.js A config/plugins/webhooks/xkcd/static/styles.css M lib/galaxy/webhooks/__init__.py M static/maps/mvc/tool/tool-webhooks.js.map M static/scripts/mvc/tool/tool-webhooks.js

Log Message: ----------- add first webhook

Commit: 40bcaaecf531920275d8f9f82d5e57bac60c43ae https://github.com/galaxyproject/galaxy/commit/40bcaaecf531920275d8f9f82d5e5... Author: anatskiy evgeny.anatskiy@gmail.com Date: 2016-10-09 (Sun, 09 Oct 2016)

Changed paths: M client/galaxy/scripts/mvc/tool/tool-webhooks.js A config/plugins/webhooks/phdcomics/config/phdcomics.yaml A config/plugins/webhooks/phdcomics/helper/__init__.py A config/plugins/webhooks/phdcomics/static/script.js A config/plugins/webhooks/phdcomics/static/styles.css R config/plugins/webhooks/plugin1/config/plugin1.yaml M config/plugins/webhooks/xkcd/static/script.js M config/plugins/webhooks/xkcd/static/styles.css M lib/galaxy/webapps/galaxy/api/webhooks.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webhooks/__init__.py M static/maps/mvc/tool/tool-webhooks.js.map M static/scripts/mvc/tool/tool-webhooks.js

Log Message: ----------- add one more plugin

Commit: bf4a1aa1a87050e030ead0e5ff8922bcb7338d98 https://github.com/galaxyproject/galaxy/commit/bf4a1aa1a87050e030ead0e5ff892... Author: anatskiy evgeny.anatskiy@gmail.com Date: 2016-10-09 (Sun, 09 Oct 2016)

Changed paths: M client/galaxy/scripts/layout/masthead.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/tool/tool-form.js R client/galaxy/scripts/mvc/tool/tool-webhooks.js A client/galaxy/scripts/mvc/webhooks.js A config/plugins/webhooks/topbar_test/config/topbar_test.yml M lib/galaxy/webhooks/__init__.py A static/maps/mvc/webhooks.js.map A static/scripts/mvc/webhooks.js

Log Message: ----------- topbar webhooks testing

Commit: 17440d7b11b5013e52033efe4668115a466115b0 https://github.com/galaxyproject/galaxy/commit/17440d7b11b5013e52033efe46681... Author: anatskiy evgeny.anatskiy@gmail.com Date: 2016-10-09 (Sun, 09 Oct 2016)

Changed paths: A config/plugins/plugin1.xml A config/plugins/plugin2.xml A config/plugins/webhooks/plugin1/config/plugin1.yaml A config/plugins/webhooks/plugin2/config/plugin2.yml M lib/galaxy/webapps/galaxy/api/webhooks.py M lib/galaxy/webhooks/__init__.py

Log Message: ----------- add Webhooks draft

Commit: 143a740dc38fec9f92211d26364cb0b40235a24e https://github.com/galaxyproject/galaxy/commit/143a740dc38fec9f92211d26364cb... Author: anatskiy evgeny.anatskiy@gmail.com Date: 2016-10-09 (Sun, 09 Oct 2016)

Changed paths: R config/plugins/plugin1.xml R config/plugins/plugin2.xml

Log Message: ----------- remove extra files

Commit: 117c5263acdfb8853cc6771810ef87c755b006ce https://github.com/galaxyproject/galaxy/commit/117c5263acdfb8853cc6771810ef8... Author: anatskiy evgeny.anatskiy@gmail.com Date: 2016-10-09 (Sun, 09 Oct 2016)

Changed paths: A client/galaxy/scripts/mvc/tool/tool-webhooks.js M config/plugins/webhooks/plugin2/config/plugin2.yml A config/plugins/webhooks/plugin2/static/style.css M lib/galaxy/webhooks/__init__.py

Log Message: ----------- add very basic plugin system (for tools)

Commit: ed2282d60b3f41c653e61be13d24ace6e83215ca https://github.com/galaxyproject/galaxy/commit/ed2282d60b3f41c653e61be13d24a... Author: anatskiy evgeny.anatskiy@gmail.com Date: 2016-10-09 (Sun, 09 Oct 2016)

Changed paths: M client/galaxy/scripts/mvc/tool/tool-webhooks.js R config/plugins/webhooks/plugin2/config/plugin2.yml R config/plugins/webhooks/plugin2/static/style.css M lib/galaxy/webhooks/__init__.py

Log Message: ----------- add first webhook

Commit: 29129463a0be1778c69fce6e783dd75da05d53c0 https://github.com/galaxyproject/galaxy/commit/29129463a0be1778c69fce6e783dd... Author: anatskiy evgeny.anatskiy@gmail.com Date: 2016-10-09 (Sun, 09 Oct 2016)

Changed paths: M client/galaxy/scripts/mvc/tool/tool-webhooks.js R config/plugins/webhooks/plugin1/config/plugin1.yaml

Log Message: ----------- add one more plugin

Commit: 411674521cf1d9d3c5479ae334fbead783d737fe https://github.com/galaxyproject/galaxy/commit/411674521cf1d9d3c5479ae334fbe... Author: anatskiy evgeny.anatskiy@gmail.com Date: 2016-10-09 (Sun, 09 Oct 2016)

Changed paths: R client/galaxy/scripts/mvc/tool/tool-webhooks.js

Log Message: ----------- topbar webhooks testing

Commit: b215de947c007dfc84ae4325d1a6b0be846986b5 https://github.com/galaxyproject/galaxy/commit/b215de947c007dfc84ae4325d1a6b... Author: anatskiy evgeny.anatskiy@gmail.com Date: 2016-10-09 (Sun, 09 Oct 2016)

Changed paths: M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/tool/tool-form.js M client/galaxy/scripts/mvc/webhooks.js A config/plugins/webhooks/masthead_test/config/masthead_test.yml M config/plugins/webhooks/phdcomics/config/phdcomics.yaml R config/plugins/webhooks/topbar_test/config/topbar_test.yml M config/plugins/webhooks/xkcd/config/xkcd.yml M lib/galaxy/webhooks/__init__.py M static/maps/mvc/webhooks.js.map M static/scripts/mvc/webhooks.js

Log Message: ----------- renamings and fixes

Commit: bb9dc0560ade3f44037a4d03a24651b91af36dbd https://github.com/galaxyproject/galaxy/commit/bb9dc0560ade3f44037a4d03a2465... Author: anatskiy evgeny.anatskiy@gmail.com Date: 2016-10-09 (Sun, 09 Oct 2016)

Changed paths: M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/tool/tool-form.js M client/galaxy/scripts/mvc/webhooks.js M config/plugins/webhooks/masthead_test/config/masthead_test.yml A config/plugins/webhooks/masthead_test/static/script.js M config/plugins/webhooks/phdcomics/helper/__init__.py M lib/galaxy/webapps/galaxy/api/webhooks.py M static/maps/mvc/webhooks.js.map M static/scripts/mvc/webhooks.js

Log Message: ----------- - unify webhooks entry point - simlify webhooks code (on load) - improve code readability - clean up

Commit: e95392b4b62b5ff803390287d0eac4f385504ef1 https://github.com/galaxyproject/galaxy/commit/e95392b4b62b5ff803390287d0eac... Author: anatskiy evgeny.anatskiy@gmail.com Date: 2016-10-09 (Sun, 09 Oct 2016)

Changed paths: M client/galaxy/scripts/mvc/tool/tool-form.js M client/galaxy/scripts/mvc/webhooks.js M config/plugins/webhooks/masthead_test/config/masthead_test.yml M config/plugins/webhooks/phdcomics/config/phdcomics.yaml M config/plugins/webhooks/xkcd/config/xkcd.yml M lib/galaxy/webapps/galaxy/api/webhooks.py M static/maps/mvc/webhooks.js.map M static/scripts/mvc/webhooks.js

Log Message: ----------- - add new entry point (Workflow) - temporarily hide masthead webhook (due to instability)

Commit: f3b1232bdb46e9ccb4f27b3a1fc668d987d650cc https://github.com/galaxyproject/galaxy/commit/f3b1232bdb46e9ccb4f27b3a1fc66... Author: Evgeny Anatskiy evgeny.anatskiy@gmail.com Date: 2016-10-09 (Sun, 09 Oct 2016)

Changed paths: M client/galaxy/scripts/apps/history-panel.js M client/galaxy/scripts/mvc/history/options-menu.js M client/galaxy/scripts/mvc/webhooks.js A config/plugins/webhooks/history_test1/config/history_test1.yml A config/plugins/webhooks/history_test2/config/history_test2.yml M lib/galaxy/webapps/galaxy/api/webhooks.py M lib/galaxy/webapps/galaxy/buildapp.py M static/maps/mvc/webhooks.js.map M static/scripts/mvc/webhooks.js

Log Message: ----------- add new entry point for History Panel menu

Commit: 578bdf679f0575e98922ddea004248de9b8b965c https://github.com/galaxyproject/galaxy/commit/578bdf679f0575e98922ddea00424... Author: Evgeny Anatskiy evgeny.anatskiy@gmail.com Date: 2016-10-09 (Sun, 09 Oct 2016)

Changed paths: M client/galaxy/scripts/mvc/history/options-menu.js M client/galaxy/scripts/mvc/tool/tool-form.js M client/galaxy/scripts/mvc/webhooks.js M config/plugins/webhooks/history_test1/config/history_test1.yml M config/plugins/webhooks/history_test2/config/history_test2.yml M config/plugins/webhooks/masthead_test/config/masthead_test.yml M config/plugins/webhooks/phdcomics/config/phdcomics.yaml M config/plugins/webhooks/xkcd/config/xkcd.yml M lib/galaxy/webhooks/__init__.py M static/maps/mvc/webhooks.js.map M static/scripts/mvc/webhooks.js

Log Message: ----------- bug fixes and improvements

Commit: 42adc9c7dfa1485162b78742f5ac3a7e8935902f https://github.com/galaxyproject/galaxy/commit/42adc9c7dfa1485162b78742f5ac3... Author: anatskiy evgeny.anatskiy@gmail.com Date: 2016-10-09 (Sun, 09 Oct 2016)

Changed paths: A config/plugins/plugin1.xml A config/plugins/plugin2.xml A config/plugins/webhooks/plugin1/config/plugin1.yaml A config/plugins/webhooks/plugin2/config/plugin2.yml

Log Message: ----------- add Webhooks draft

Commit: 6bc57ec0209f22970c4303870ba48cfea528e0ff https://github.com/galaxyproject/galaxy/commit/6bc57ec0209f22970c4303870ba48... Author: anatskiy evgeny.anatskiy@gmail.com Date: 2016-10-09 (Sun, 09 Oct 2016)

Changed paths: R config/plugins/plugin1.xml R config/plugins/plugin2.xml

Log Message: ----------- remove extra files

Commit: ca769ab848209be8e4e48a6b28c13ecf52744e0f https://github.com/galaxyproject/galaxy/commit/ca769ab848209be8e4e48a6b28c13... Author: anatskiy evgeny.anatskiy@gmail.com Date: 2016-10-09 (Sun, 09 Oct 2016)

Changed paths: A client/galaxy/scripts/mvc/tool/tool-webhooks.js M config/plugins/webhooks/plugin2/config/plugin2.yml A config/plugins/webhooks/plugin2/static/style.css

Log Message: ----------- add very basic plugin system (for tools)

Commit: 1a8a82370bcfd157f1d82ee6f6634bfcbcfb62af https://github.com/galaxyproject/galaxy/commit/1a8a82370bcfd157f1d82ee6f6634... Author: anatskiy evgeny.anatskiy@gmail.com Date: 2016-10-09 (Sun, 09 Oct 2016)

Changed paths: M client/galaxy/scripts/mvc/tool/tool-webhooks.js R config/plugins/webhooks/plugin2/config/plugin2.yml R config/plugins/webhooks/plugin2/static/style.css M config/plugins/webhooks/xkcd/config/xkcd.yml

Log Message: ----------- add first webhook

Commit: 454a88b45174cfddae5ad79c31d92edffb07cabe https://github.com/galaxyproject/galaxy/commit/454a88b45174cfddae5ad79c31d92... Author: anatskiy evgeny.anatskiy@gmail.com Date: 2016-10-09 (Sun, 09 Oct 2016)

Changed paths: M client/galaxy/scripts/mvc/tool/tool-webhooks.js R config/plugins/webhooks/plugin1/config/plugin1.yaml

Log Message: ----------- add one more plugin

Commit: 53f56c3426714b3531dd1c49ecca431f73b77de9 https://github.com/galaxyproject/galaxy/commit/53f56c3426714b3531dd1c49ecca4... Author: anatskiy evgeny.anatskiy@gmail.com Date: 2016-10-09 (Sun, 09 Oct 2016)

Changed paths: R client/galaxy/scripts/mvc/tool/tool-webhooks.js A config/plugins/webhooks/topbar_test/config/topbar_test.yml M lib/galaxy/webhooks/__init__.py

Log Message: ----------- topbar webhooks testing

Commit: c7f35c41d72a6131bfd0a4a7b3525518ed29d78a https://github.com/galaxyproject/galaxy/commit/c7f35c41d72a6131bfd0a4a7b3525... Author: anatskiy evgeny.anatskiy@gmail.com Date: 2016-10-09 (Sun, 09 Oct 2016)

Changed paths: A config/plugins/plugin1.xml A config/plugins/plugin2.xml A config/plugins/webhooks/plugin1/config/plugin1.yaml A config/plugins/webhooks/plugin2/config/plugin2.yml

Log Message: ----------- add Webhooks draft

Commit: a73d00fc04695b1f27a3cdf6091d352ee61f8f45 https://github.com/galaxyproject/galaxy/commit/a73d00fc04695b1f27a3cdf6091d3... Author: anatskiy evgeny.anatskiy@gmail.com Date: 2016-10-09 (Sun, 09 Oct 2016)

Changed paths: R config/plugins/plugin1.xml R config/plugins/plugin2.xml

Log Message: ----------- remove extra files

Commit: 2b2be226ee9425742e0a629459e126b0c90e5e86 https://github.com/galaxyproject/galaxy/commit/2b2be226ee9425742e0a629459e12... Author: anatskiy evgeny.anatskiy@gmail.com Date: 2016-10-09 (Sun, 09 Oct 2016)

Changed paths: A client/galaxy/scripts/mvc/tool/tool-webhooks.js M config/plugins/webhooks/plugin2/config/plugin2.yml A config/plugins/webhooks/plugin2/static/style.css

Log Message: ----------- add very basic plugin system (for tools)

Commit: 211491fdf31a814590250edd4447916a5213120b https://github.com/galaxyproject/galaxy/commit/211491fdf31a814590250edd44479... Author: anatskiy evgeny.anatskiy@gmail.com Date: 2016-10-09 (Sun, 09 Oct 2016)

Changed paths: M client/galaxy/scripts/mvc/tool/tool-webhooks.js R config/plugins/webhooks/plugin2/config/plugin2.yml R config/plugins/webhooks/plugin2/static/style.css

Log Message: ----------- add first webhook

Commit: 060df24ff5b329c37103f9c90caf65c4889c964d https://github.com/galaxyproject/galaxy/commit/060df24ff5b329c37103f9c90caf6... Author: anatskiy evgeny.anatskiy@gmail.com Date: 2016-10-09 (Sun, 09 Oct 2016)

Changed paths: M client/galaxy/scripts/mvc/tool/tool-webhooks.js R config/plugins/webhooks/plugin1/config/plugin1.yaml

Log Message: ----------- add one more plugin

Commit: 00cf0cb85ec2cca9091de22fcaa6579d611530f1 https://github.com/galaxyproject/galaxy/commit/00cf0cb85ec2cca9091de22fcaa65... Author: anatskiy evgeny.anatskiy@gmail.com Date: 2016-10-09 (Sun, 09 Oct 2016)

Changed paths: R client/galaxy/scripts/mvc/tool/tool-webhooks.js

Log Message: ----------- topbar webhooks testing

Commit: 27e0302ea3926e0a3ce6955317f6d1f38bc6f8b4 https://github.com/galaxyproject/galaxy/commit/27e0302ea3926e0a3ce6955317f6d... Author: anatskiy evgeny.anatskiy@gmail.com Date: 2016-10-09 (Sun, 09 Oct 2016)

Changed paths: R config/plugins/webhooks/topbar_test/config/topbar_test.yml M config/plugins/webhooks/xkcd/config/xkcd.yml M lib/galaxy/webhooks/__init__.py

Log Message: ----------- renamings and fixes

Commit: 29a57ba0fdd9ab066e19110715bbb091014e3f7a https://github.com/galaxyproject/galaxy/commit/29a57ba0fdd9ab066e19110715bbb... Author: anatskiy evgeny.anatskiy@gmail.com Date: 2016-10-09 (Sun, 09 Oct 2016)

Changed paths: M config/plugins/webhooks/xkcd/config/xkcd.yml

Log Message: ----------- - add new entry point (Workflow) - temporarily hide masthead webhook (due to instability)

Commit: e58fe7ca49f7b01244d1e6f4bfc92586459c799d https://github.com/galaxyproject/galaxy/commit/e58fe7ca49f7b01244d1e6f4bfc92... Author: Evgeny Anatskiy evgeny.anatskiy@gmail.com Date: 2016-10-09 (Sun, 09 Oct 2016)

Changed paths: M config/plugins/webhooks/xkcd/config/xkcd.yml

Log Message: ----------- bug fixes and improvements

Commit: 8b5716ddfda7d8d4bc604cf6d396d59fa45498c7 https://github.com/galaxyproject/galaxy/commit/8b5716ddfda7d8d4bc604cf6d396d... Author: Evgeny Anatskiy evgeny.anatskiy@gmail.com Date: 2016-10-09 (Sun, 09 Oct 2016)

Changed paths: M config/plugins/webhooks/xkcd/config/xkcd.yml M static/maps/mvc/webhooks.js.map

Log Message: ----------- fix bugs after previous commit

Commit: ce346b6ad4482a1e6a0e8e9f92e79ea1d90a33b4 https://github.com/galaxyproject/galaxy/commit/ce346b6ad4482a1e6a0e8e9f92e79... Author: Evgeny Anatskiy evgeny.anatskiy@gmail.com Date: 2016-10-09 (Sun, 09 Oct 2016)

Changed paths: M client/galaxy/scripts/mvc/webhooks.js M config/plugins/webhooks/masthead_test/config/masthead_test.yml R config/plugins/webhooks/masthead_test/static/script.js M config/plugins/webhooks/phdcomics/helper/__init__.py M static/maps/mvc/webhooks.js.map M static/scripts/mvc/webhooks.js

Log Message: ----------- pass trans object into the helper function

Commit: 2cc133f32507cd2aec8784e247106cef540a1c17 https://github.com/galaxyproject/galaxy/commit/2cc133f32507cd2aec8784e247106... Author: Björn Grüning bjoern@gruenings.eu Date: 2016-10-09 (Sun, 09 Oct 2016)

Changed paths: A doc/source/admin/webhooks.rst

Log Message: ----------- Add initial docs

Commit: 69a9344c529e34cdb70fdd71634ba2944bf0a7e8 https://github.com/galaxyproject/galaxy/commit/69a9344c529e34cdb70fdd71634ba... Author: Evgeny Anatskiy evgeny.anatskiy@gmail.com Date: 2016-10-09 (Sun, 09 Oct 2016)

Changed paths: M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/history/options-menu.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/tool/tool-form.js A config/plugins/webhooks/trans_object/config/trans_object.yaml A config/plugins/webhooks/trans_object/helper/__init__.py M lib/galaxy/webapps/galaxy/api/webhooks.py M lib/galaxy/webhooks/__init__.py M static/maps/layout/menu.js.map M static/maps/mvc/history/options-menu.js.map M static/maps/mvc/tool/tool-form-composite.js.map M static/maps/mvc/tool/tool-form.js.map M static/maps/mvc/webhooks.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/history/options-menu.js M static/scripts/mvc/tool/tool-form-composite.js M static/scripts/mvc/tool/tool-form.js

Log Message: ----------- - show Webhook on a workflow page - fix merge errors

Commit: ef304a2223ca080c9181fad4117919c71d539211 https://github.com/galaxyproject/galaxy/commit/ef304a2223ca080c9181fad411791... Author: Evgeny Anatskiy evgeny.anatskiy@gmail.com Date: 2016-10-09 (Sun, 09 Oct 2016)

Changed paths: M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/history/options-menu.js M client/galaxy/scripts/mvc/tool/tool-form.js M lib/galaxy/webapps/galaxy/api/webhooks.py M static/maps/layout/menu.js.map M static/maps/mvc/history/options-menu.js.map M static/maps/mvc/tool/tool-form.js.map M static/maps/mvc/webhooks.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/history/options-menu.js M static/scripts/mvc/tool/tool-form.js A templates/webapps/galaxy/workflow/run_complete.mako

Log Message: ----------- - merge

Commit: a3627b98ab8f5940af529e1387c8da8a4595a9e0 https://github.com/galaxyproject/galaxy/commit/a3627b98ab8f5940af529e1387c8d... Author: Evgeny Anatskiy evgeny.anatskiy@gmail.com Date: 2016-10-09 (Sun, 09 Oct 2016)

Changed paths: M static/maps/mvc/webhooks.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: ----------- make client

Commit: cc36793cd0d249fd2794c5de54af6ff10695b88e https://github.com/galaxyproject/galaxy/commit/cc36793cd0d249fd2794c5de54af6... Author: Evgeny Anatskiy evgeny.anatskiy@gmail.com Date: 2016-10-12 (Wed, 12 Oct 2016)

Changed paths: M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/history/options-menu.js M client/galaxy/scripts/mvc/webhooks.js M lib/galaxy/webapps/galaxy/api/webhooks.py M static/maps/layout/menu.js.map M static/maps/mvc/history/options-menu.js.map M static/maps/mvc/webhooks.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/menu.js M static/scripts/mvc/history/options-menu.js M static/scripts/mvc/webhooks.js

Log Message: ----------- - remove separate functions for adding masthead/history-menu plugins - choose a random tool/workflow plugin only among active ones

Commit: 812aca5b34df584a09d3f82f9d938e89d396b2bd https://github.com/galaxyproject/galaxy/commit/812aca5b34df584a09d3f82f9d938... Author: Evgeny Anatskiy evgeny.anatskiy@gmail.com Date: 2016-10-12 (Wed, 12 Oct 2016)

Changed paths: M lib/galaxy/webapps/galaxy/api/webhooks.py

Log Message: ----------- bug fix

Commit: 5f9154a6179f194a8186d0f91a375d449cb26ea2 https://github.com/galaxyproject/galaxy/commit/5f9154a6179f194a8186d0f91a375... Author: Evgeny Anatskiy evgeny.anatskiy@gmail.com Date: 2016-10-12 (Wed, 12 Oct 2016)

Changed paths: M doc/source/admin/webhooks.rst

Log Message: ----------- tiny fixes

Commit: cd92be8802e520a2f53eceb385f018ded4aea218 https://github.com/galaxyproject/galaxy/commit/cd92be8802e520a2f53eceb385f01... Author: Björn Grüning bjoern@gruenings.eu Date: 2016-10-12 (Wed, 12 Oct 2016)

Changed paths: M doc/source/admin/webhooks.rst

Log Message: ----------- Include a section about plugin dependencies.

Commit: 0ad7c99ea20ba49725fffe5a356ab39bf601111d https://github.com/galaxyproject/galaxy/commit/0ad7c99ea20ba49725fffe5a356ab... Author: Joachim Wolff wolffj@informatik.uni-freiburg.de Date: 2016-10-12 (Wed, 12 Oct 2016)

Changed paths: M doc/source/admin/webhooks.rst

Log Message: ----------- Extended the documentation of webhooks and added an images directory.

Commit: f29b003a8cd6a277ee67cb553653063fbc53dbfe https://github.com/galaxyproject/galaxy/commit/f29b003a8cd6a277ee67cb5536530... Author: Joachim Wolff wolffj@informatik.uni-freiburg.de Date: 2016-10-12 (Wed, 12 Oct 2016)

Changed paths: A doc/source/admin/images_webhooks/history-menu.png A doc/source/admin/images_webhooks/masthead.png A doc/source/admin/images_webhooks/masthead_trans_object.png A doc/source/admin/images_webhooks/tool.png A doc/source/admin/images_webhooks/workflow.png

Log Message: ----------- Added images directory for webhooks documentation

Commit: 95c1f186935a77ee71de59a3a616dc5d7f11c8c2 https://github.com/galaxyproject/galaxy/commit/95c1f186935a77ee71de59a3a616d... Author: Joachim Wolff wolffj@informatik.uni-freiburg.de Date: 2016-10-12 (Wed, 12 Oct 2016)

Changed paths: M doc/source/admin/webhooks.rst

Log Message: ----------- Fixed formatting errors

Commit: eb32ad229f5f22c8b2cb497344fd545f14f6eae3 https://github.com/galaxyproject/galaxy/commit/eb32ad229f5f22c8b2cb497344fd5... Author: Joachim Wolff wolffj@informatik.uni-freiburg.de Date: 2016-10-12 (Wed, 12 Oct 2016)

Changed paths: M doc/source/admin/webhooks.rst

Log Message: ----------- Fixed formatting errors

Commit: d1737110bf2d870346df43d5969b329cea1b16d8 https://github.com/galaxyproject/galaxy/commit/d1737110bf2d870346df43d5969b3... Author: Joachim Wolff wolffj@informatik.uni-freiburg.de Date: 2016-10-12 (Wed, 12 Oct 2016)

Changed paths: M doc/source/admin/webhooks.rst

Log Message: ----------- Fixing errors

Commit: 76b9e004d204b6569ef6d19b6e808b77db9984f2 https://github.com/galaxyproject/galaxy/commit/76b9e004d204b6569ef6d19b6e808... Author: Joachim Wolff wolffj@informatik.uni-freiburg.de Date: 2016-10-12 (Wed, 12 Oct 2016)

Changed paths: M doc/source/admin/webhooks.rst

Log Message: ----------- Fixing errors

Commit: 8030d2025ddaa0ca5f5d58f12a24f85e860f9339 https://github.com/galaxyproject/galaxy/commit/8030d2025ddaa0ca5f5d58f12a24f... Author: Joachim Wolff wolffj@informatik.uni-freiburg.de Date: 2016-10-12 (Wed, 12 Oct 2016)

Changed paths: M doc/source/admin/webhooks.rst

Log Message: ----------- Fixing errors

Commit: acd99f76fc967445cc9b8cd1317793a6074997b7 https://github.com/galaxyproject/galaxy/commit/acd99f76fc967445cc9b8cd131779... Author: Joachim Wolff wolffj@informatik.uni-freiburg.de Date: 2016-10-12 (Wed, 12 Oct 2016)

Changed paths: M doc/source/admin/webhooks.rst

Log Message: ----------- Fixing errors

Commit: 6684fd4e262f97c313d907bf44409d94172338c8 https://github.com/galaxyproject/galaxy/commit/6684fd4e262f97c313d907bf44409... Author: Joachim Wolff wolffj@informatik.uni-freiburg.de Date: 2016-10-12 (Wed, 12 Oct 2016)

Changed paths: M doc/source/admin/webhooks.rst

Log Message: ----------- Fixing errors

Commit: fafeedc286035d78d1033220717b346e4c0d3c99 https://github.com/galaxyproject/galaxy/commit/fafeedc286035d78d1033220717b3... Author: Joachim Wolff wolffj@informatik.uni-freiburg.de Date: 2016-10-12 (Wed, 12 Oct 2016)

Changed paths: M doc/source/admin/webhooks.rst

Log Message: ----------- Fixing errors

Commit: af8a3f11048c86f91f17044344211a5cdba98b13 https://github.com/galaxyproject/galaxy/commit/af8a3f11048c86f91f17044344211... Author: Joachim Wolff wolffj@informatik.uni-freiburg.de Date: 2016-10-12 (Wed, 12 Oct 2016)

Changed paths: M doc/source/admin/webhooks.rst

Log Message: ----------- Fixing errors

Commit: d5dc39ab0f034d79252a9fb0875824cbf8b02e04 https://github.com/galaxyproject/galaxy/commit/d5dc39ab0f034d79252a9fb087582... Author: Björn Grüning bjoern@gruenings.eu Date: 2016-10-12 (Wed, 12 Oct 2016)

Changed paths: A doc/source/admin/images_webhooks/history-menu.png A doc/source/admin/images_webhooks/masthead.png A doc/source/admin/images_webhooks/masthead_trans_object.png A doc/source/admin/images_webhooks/tool.png A doc/source/admin/images_webhooks/workflow.png M doc/source/admin/webhooks.rst

Log Message: ----------- Merge pull request #21 from joachimwolff/feature/plugin-system

Feature/plugin system

Commit: 0a15289d31a189df71490bba5392726ac0f6db47 https://github.com/galaxyproject/galaxy/commit/0a15289d31a189df71490bba53927... Author: Evgeny Anatskiy evgeny.anatskiy@gmail.com Date: 2016-10-12 (Wed, 12 Oct 2016)

Changed paths: M config/plugins/webhooks/phdcomics/helper/__init__.py

Log Message: ----------- added missing dependencies check

Commit: bc51dc3ec72dc7a5bbcc42bcd4f1cc834c1a69b6 https://github.com/galaxyproject/galaxy/commit/bc51dc3ec72dc7a5bbcc42bcd4f1c... Author: Evgeny Anatskiy evgeny.anatskiy@gmail.com Date: 2016-10-12 (Wed, 12 Oct 2016)

Changed paths: M doc/source/admin/webhooks.rst

Log Message: ----------- Update webhooks.rst

escape missing dependencies

Commit: 95d6990cf3f6f1e4ade87b6ba6557c99471ff924 https://github.com/galaxyproject/galaxy/commit/95d6990cf3f6f1e4ade87b6ba6557... Author: Evgeny Anatskiy evgeny.anatskiy@gmail.com Date: 2016-10-12 (Wed, 12 Oct 2016)

Changed paths: M doc/source/admin/webhooks.rst

Log Message: ----------- Update webhooks.rst

Commit: 4f89528c94d33f1e3eca8df9dd34c06965e7beec https://github.com/galaxyproject/galaxy/commit/4f89528c94d33f1e3eca8df9dd34c... Author: Björn Grüning bjoern@gruenings.eu Date: 2016-10-12 (Wed, 12 Oct 2016)

Changed paths: M doc/source/admin/webhooks.rst

Log Message: ----------- make activation procedure more clear

Commit: 2d915a42f6329bd31dfdc76b5bfa56376a57c841 https://github.com/galaxyproject/galaxy/commit/2d915a42f6329bd31dfdc76b5bfa5... Author: Björn Grüning bjoern@gruenings.eu Date: 2016-10-13 (Thu, 13 Oct 2016)

Changed paths: M doc/source/admin/webhooks.rst

Log Message: ----------- tense changes

Commit: b52d5be75b3f2bf9cae86d4a278689cb614095be https://github.com/galaxyproject/galaxy/commit/b52d5be75b3f2bf9cae86d4a27868... Author: Björn Grüning bjoern@gruenings.eu Date: 2016-10-13 (Thu, 13 Oct 2016)

Changed paths: M client/galaxy/scripts/layout/menu.js

Log Message: ----------- Change according to Aysam's review

Commit: 290c48b16c54fab54ec35601e04d6877071a78db https://github.com/galaxyproject/galaxy/commit/290c48b16c54fab54ec35601e04d6... Author: Björn Grüning bjoern@gruenings.eu Date: 2016-10-13 (Thu, 13 Oct 2016)

Changed paths: M client/galaxy/scripts/layout/menu.js

Log Message: ----------- Change according to Aysam's review

Commit: a231e240ed1a8002318678dde5979c3febb11770 https://github.com/galaxyproject/galaxy/commit/a231e240ed1a8002318678dde5979... Author: Björn Grüning bjoern@gruenings.eu Date: 2016-10-13 (Thu, 13 Oct 2016)

Changed paths: M client/galaxy/scripts/layout/menu.js

Log Message: ----------- remove obsolete code

Commit: 6a62dbc91a0f2ed282c2cc1e3c4227faed870ace https://github.com/galaxyproject/galaxy/commit/6a62dbc91a0f2ed282c2cc1e3c422... Author: Bjoern Gruening bjoern.gruening@gmail.com Date: 2016-10-13 (Thu, 13 Oct 2016)

Changed paths: M .ci/flake8_blacklist.txt M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt M .travis.yml M client/galaxy/style/source_material/circle.py M config/galaxy.ini.sample M config/job_conf.xml.sample_advanced M doc/parse_gx_xsd.py M doc/source/admin/dependency_resolvers.rst M doc/source/admin/index.rst A doc/source/admin/mulled_containers.rst M lib/galaxy/config.py M lib/galaxy/datatypes/registry.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/tools/deps/__init__.py A lib/galaxy/tools/deps/conda_compat.py M lib/galaxy/tools/deps/conda_util.py A lib/galaxy/tools/deps/container_resolvers/__init__.py A lib/galaxy/tools/deps/container_resolvers/explicit.py A lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/tools/deps/containers.py A lib/galaxy/tools/deps/installable.py A lib/galaxy/tools/deps/mulled/__init__.py A lib/galaxy/tools/deps/mulled/_cli.py A lib/galaxy/tools/deps/mulled/invfile.lua A lib/galaxy/tools/deps/mulled/mulled_build.py A lib/galaxy/tools/deps/mulled/mulled_build_channel.py A lib/galaxy/tools/deps/mulled/mulled_build_files.py A lib/galaxy/tools/deps/mulled/mulled_build_tool.py A lib/galaxy/tools/deps/mulled/mulled_search.py A lib/galaxy/tools/deps/mulled/util.py M lib/galaxy/tools/deps/resolvers/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/xsd/galaxy.xsd M test/api/helpers.py M test/api/test_api_batch.py M test/api/test_authenticate.py M test/api/test_dataset_collections.py M test/api/test_history_contents.py M test/api/test_page_revisions.py M test/api/test_pages.py M test/api/test_tool_data.py M test/api/test_tools.py M test/api/test_users.py M test/api/test_workflow_extraction.py M test/api/test_workflows.py M test/api/workflows_format_2/__init__.py M test/api/workflows_format_2/converter.py M test/base/api.py M test/base/driver_util.py M test/base/integration_util.py M test/base/interactor.py M test/base/test_logging.py M test/base/twilltestcase.py M test/functional/test_data_managers.py M test/functional/test_library_templates.py M test/functional/test_toolbox.py A test/functional/tools/mulled_example_multi_1.xml M test/functional/tools/samples_tool_conf.xml M test/functional/workflow.py M test/integration/test_resolvers.py M test/manual/workflows_scaling.py M test/shed_functional/base/test_db_util.py M test/shed_functional/functional/test_0300_reset_all_metadata.py M test/shed_functional/functional/test_1300_reset_all_metadata.py M test/shed_functional/functional_tests.py M test/unit/jobs/test_runner_local.py

Log Message: ----------- Merge branch 'dev' into feature/plugin-system

Commit: 8f5b54141dd2b46d3b532915b082c4bd5eeff44c https://github.com/galaxyproject/galaxy/commit/8f5b54141dd2b46d3b532915b082c... Author: Björn Grüning bjoern@gruenings.eu Date: 2016-10-13 (Thu, 13 Oct 2016)

Changed paths: M client/galaxy/scripts/layout/menu.js

Log Message: ----------- code optimization, thanks Sam

Commit: 773d85453f965712cdd8bcc209b9a05897959994 https://github.com/galaxyproject/galaxy/commit/773d85453f965712cdd8bcc209b9a... Author: Bjoern Gruening bjoern.gruening@gmail.com Date: 2016-10-13 (Thu, 13 Oct 2016)

Changed paths: A config/plugins/webhooks/demo/history_test1/config/history_test1.yml A config/plugins/webhooks/demo/history_test2/config/history_test2.yml A config/plugins/webhooks/demo/masthead_test/config/masthead_test.yml A config/plugins/webhooks/demo/phdcomics/config/phdcomics.yaml A config/plugins/webhooks/demo/phdcomics/helper/__init__.py A config/plugins/webhooks/demo/phdcomics/static/script.js A config/plugins/webhooks/demo/phdcomics/static/styles.css A config/plugins/webhooks/demo/trans_object/config/trans_object.yaml A config/plugins/webhooks/demo/trans_object/helper/__init__.py A config/plugins/webhooks/demo/xkcd/config/xkcd.yml A config/plugins/webhooks/demo/xkcd/static/script.js A config/plugins/webhooks/demo/xkcd/static/styles.css R config/plugins/webhooks/history_test1/config/history_test1.yml R config/plugins/webhooks/history_test2/config/history_test2.yml R config/plugins/webhooks/masthead_test/config/masthead_test.yml R config/plugins/webhooks/phdcomics/config/phdcomics.yaml R config/plugins/webhooks/phdcomics/helper/__init__.py R config/plugins/webhooks/phdcomics/static/script.js R config/plugins/webhooks/phdcomics/static/styles.css R config/plugins/webhooks/trans_object/config/trans_object.yaml R config/plugins/webhooks/trans_object/helper/__init__.py R config/plugins/webhooks/xkcd/config/xkcd.yml R config/plugins/webhooks/xkcd/static/script.js R config/plugins/webhooks/xkcd/static/styles.css

Log Message: ----------- move all plugins into a demo folder

Commit: a676d6e8234dd9db59376df7f54633a78e503f86 https://github.com/galaxyproject/galaxy/commit/a676d6e8234dd9db59376df7f5463... Author: Bjoern Gruening bjoern.gruening@gmail.com Date: 2016-10-13 (Thu, 13 Oct 2016)

Changed paths: M lib/galaxy/app.py M lib/galaxy/config.py M lib/galaxy/webhooks/__init__.py

Log Message: ----------- allow multiple webhook dirs

Commit: 6894df3dcb0f308724331bceceff46dba23156a1 https://github.com/galaxyproject/galaxy/commit/6894df3dcb0f308724331bceceff4... Author: Evgeny Anatskiy evgeny.anatskiy@gmail.com Date: 2016-10-13 (Thu, 13 Oct 2016)

Changed paths: M .ci/flake8_blacklist.txt M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt M .travis.yml M client/galaxy/scripts/layout/menu.js M client/galaxy/style/source_material/circle.py M config/galaxy.ini.sample M config/job_conf.xml.sample_advanced A config/plugins/webhooks/demo/history_test1/config/history_test1.yml A config/plugins/webhooks/demo/history_test2/config/history_test2.yml A config/plugins/webhooks/demo/masthead_test/config/masthead_test.yml A config/plugins/webhooks/demo/phdcomics/config/phdcomics.yaml A config/plugins/webhooks/demo/phdcomics/helper/__init__.py A config/plugins/webhooks/demo/phdcomics/static/script.js A config/plugins/webhooks/demo/phdcomics/static/styles.css A config/plugins/webhooks/demo/trans_object/config/trans_object.yaml A config/plugins/webhooks/demo/trans_object/helper/__init__.py A config/plugins/webhooks/demo/xkcd/config/xkcd.yml A config/plugins/webhooks/demo/xkcd/static/script.js A config/plugins/webhooks/demo/xkcd/static/styles.css R config/plugins/webhooks/history_test1/config/history_test1.yml R config/plugins/webhooks/history_test2/config/history_test2.yml R config/plugins/webhooks/masthead_test/config/masthead_test.yml R config/plugins/webhooks/phdcomics/config/phdcomics.yaml R config/plugins/webhooks/phdcomics/helper/__init__.py R config/plugins/webhooks/phdcomics/static/script.js R config/plugins/webhooks/phdcomics/static/styles.css R config/plugins/webhooks/trans_object/config/trans_object.yaml R config/plugins/webhooks/trans_object/helper/__init__.py R config/plugins/webhooks/xkcd/config/xkcd.yml R config/plugins/webhooks/xkcd/static/script.js R config/plugins/webhooks/xkcd/static/styles.css M doc/parse_gx_xsd.py M doc/source/admin/dependency_resolvers.rst A doc/source/admin/images_webhooks/history-menu.png A doc/source/admin/images_webhooks/masthead.png A doc/source/admin/images_webhooks/masthead_trans_object.png A doc/source/admin/images_webhooks/tool.png A doc/source/admin/images_webhooks/workflow.png M doc/source/admin/index.rst A doc/source/admin/mulled_containers.rst M doc/source/admin/webhooks.rst M lib/galaxy/app.py M lib/galaxy/config.py M lib/galaxy/datatypes/registry.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/tools/deps/__init__.py A lib/galaxy/tools/deps/conda_compat.py M lib/galaxy/tools/deps/conda_util.py A lib/galaxy/tools/deps/container_resolvers/__init__.py A lib/galaxy/tools/deps/container_resolvers/explicit.py A lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/tools/deps/containers.py A lib/galaxy/tools/deps/installable.py A lib/galaxy/tools/deps/mulled/__init__.py A lib/galaxy/tools/deps/mulled/_cli.py A lib/galaxy/tools/deps/mulled/invfile.lua A lib/galaxy/tools/deps/mulled/mulled_build.py A lib/galaxy/tools/deps/mulled/mulled_build_channel.py A lib/galaxy/tools/deps/mulled/mulled_build_files.py A lib/galaxy/tools/deps/mulled/mulled_build_tool.py A lib/galaxy/tools/deps/mulled/mulled_search.py A lib/galaxy/tools/deps/mulled/util.py M lib/galaxy/tools/deps/resolvers/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/webhooks/__init__.py M test/api/helpers.py M test/api/test_api_batch.py M test/api/test_authenticate.py M test/api/test_dataset_collections.py M test/api/test_history_contents.py M test/api/test_page_revisions.py M test/api/test_pages.py M test/api/test_tool_data.py M test/api/test_tools.py M test/api/test_users.py M test/api/test_workflow_extraction.py M test/api/test_workflows.py M test/api/workflows_format_2/__init__.py M test/api/workflows_format_2/converter.py M test/base/api.py M test/base/driver_util.py M test/base/integration_util.py M test/base/interactor.py M test/base/test_logging.py M test/base/twilltestcase.py M test/functional/test_data_managers.py M test/functional/test_library_templates.py M test/functional/test_toolbox.py A test/functional/tools/mulled_example_multi_1.xml M test/functional/tools/samples_tool_conf.xml M test/functional/workflow.py M test/integration/test_resolvers.py M test/manual/workflows_scaling.py M test/shed_functional/base/test_db_util.py M test/shed_functional/functional/test_0300_reset_all_metadata.py M test/shed_functional/functional/test_1300_reset_all_metadata.py M test/shed_functional/functional_tests.py M test/unit/jobs/test_runner_local.py

Log Message: ----------- Merge branch 'feature/plugin-system' of github.com:bgruening/galaxy into feature/plugin-system

Commit: 3f8d45b388e5788b23c39c2b544e4c98eae8018f https://github.com/galaxyproject/galaxy/commit/3f8d45b388e5788b23c39c2b544e4... Author: Evgeny Anatskiy evgeny.anatskiy@gmail.com Date: 2016-10-13 (Thu, 13 Oct 2016)

Changed paths: M lib/galaxy/webhooks/__init__.py

Log Message: ----------- PEP8

Commit: fb516d9387a2df9a1ccdd2c7a1a1ce162f7e52fc https://github.com/galaxyproject/galaxy/commit/fb516d9387a2df9a1ccdd2c7a1a1c... Author: Evgeny Anatskiy evgeny.anatskiy@gmail.com Date: 2016-10-13 (Thu, 13 Oct 2016)

Changed paths: M lib/galaxy/webhooks/__init__.py

Log Message: ----------- remove blank line

Commit: e220ed097067124f5ab616d0ece35d0af4cb2539 https://github.com/galaxyproject/galaxy/commit/e220ed097067124f5ab616d0ece35... Author: Bjoern Gruening bjoern.gruening@gmail.com Date: 2016-10-13 (Thu, 13 Oct 2016)

Changed paths: M lib/galaxy/config.py M lib/galaxy/webhooks/__init__.py

Log Message: ----------- use config_directories_from_setting

Commit: b0b5157f36ec26090c9c11c0a133513083015735 https://github.com/galaxyproject/galaxy/commit/b0b5157f36ec26090c9c11c0a1335... Author: Bjoern Gruening bjoern.gruening@gmail.com Date: 2016-10-13 (Thu, 13 Oct 2016)

Changed paths: M config/plugins/webhooks/demo/phdcomics/helper/__init__.py

Log Message: ----------- merge

Commit: f4dc38a54da3539f4d63f7e33708bcc2e33012fb https://github.com/galaxyproject/galaxy/commit/f4dc38a54da3539f4d63f7e33708b... Author: Bjoern Gruening bjoern.gruening@gmail.com Date: 2016-10-13 (Thu, 13 Oct 2016)

Changed paths: M config/plugins/webhooks/demo/history_test1/config/history_test1.yml M config/plugins/webhooks/demo/history_test2/config/history_test2.yml M config/plugins/webhooks/demo/masthead_test/config/masthead_test.yml M config/plugins/webhooks/demo/phdcomics/config/phdcomics.yaml M config/plugins/webhooks/demo/trans_object/config/trans_object.yaml M config/plugins/webhooks/demo/xkcd/config/xkcd.yml

Log Message: ----------- activate all plugins in the demo folder

Commit: 2703ba1a0cc3a28314018299b8f1a686dfb6e995 https://github.com/galaxyproject/galaxy/commit/2703ba1a0cc3a28314018299b8f1a... Author: Evgeny Anatskiy evgeny.anatskiy@gmail.com Date: 2016-10-13 (Thu, 13 Oct 2016)

Changed paths: M config/galaxy.ini.sample

Log Message: ----------- activate all demo plugins in testing purposes

Commit: 8694356ab7057c47164a92f8d4e47a800fca2f4d https://github.com/galaxyproject/galaxy/commit/8694356ab7057c47164a92f8d4e47... Author: Björn Grüning bjoern@gruenings.eu Date: 2016-10-13 (Thu, 13 Oct 2016)

Changed paths: M doc/source/admin/webhooks.rst

Log Message: ----------- Adopt help to the latest changes

Commit: 3aadd84b80bca7fc588ffccaa27f01c1d599b9d8 https://github.com/galaxyproject/galaxy/commit/3aadd84b80bca7fc588ffccaa27f0... Author: Bjoern Gruening bjoern.gruening@gmail.com Date: 2016-10-13 (Thu, 13 Oct 2016)

Changed paths: M config/plugins/webhooks/demo/trans_object/helper/__init__.py

Log Message: ----------- add case where no user is logged in

Commit: 0dc2c95bd07e2a53dec27c8d0d4fc86747aa8878 https://github.com/galaxyproject/galaxy/commit/0dc2c95bd07e2a53dec27c8d0d4fc... Author: Bjoern Gruening bjoern.gruening@gmail.com Date: 2016-10-13 (Thu, 13 Oct 2016)

Changed paths: M doc/source/admin/webhooks.rst

Log Message: ----------- Merge branch 'feature/plugin-system' of https://github.com/bgruening/galaxy into feature/plugin-system

Commit: 3cb8189e1fa48c58afaf609691a0801e784484b7 https://github.com/galaxyproject/galaxy/commit/3cb8189e1fa48c58afaf609691a08... Author: Bjoern Gruening bjoern.gruening@gmail.com Date: 2016-10-13 (Thu, 13 Oct 2016)

Changed paths: M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt M config/galaxy.ini.sample M lib/galaxy/managers/collections_util.py M lib/galaxy/model/item_attrs.py M lib/galaxy/model/metadata.py M lib/galaxy/model/orm/now.py M lib/galaxy/tools/cwl/__init__.py M lib/galaxy/tools/cwl/cwltool_deps.py M lib/galaxy/tools/cwl/parser.py M lib/galaxy/tools/cwl/runtime_actions.py M lib/galaxy/tools/deps/commands.py M lib/galaxy/tools/deps/conda_compat.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/tools/deps/docker_util.py M lib/galaxy/tools/deps/mulled/_cli.py 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/util.py M lib/galaxy/tools/deps/resolvers/brewed_tool_shed_packages.py M lib/galaxy/tools/deps/resolvers/conda.py 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/tool_shed_packages.py M lib/galaxy/tools/deps/resolvers/unlinked_tool_shed_packages.py M lib/galaxy/tools/exception_handling.py M lib/galaxy/tools/execute.py M lib/galaxy/tools/loader.py M lib/galaxy/tools/loader_directory.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/parameters/dataset_matcher.py M lib/galaxy/tools/parameters/wrapped.py M lib/galaxy/tools/parameters/wrapped_json.py M lib/galaxy/tools/parser/__init__.py M lib/galaxy/tools/parser/factory.py M lib/galaxy/tools/toolbox/__init__.py M lib/galaxy/tools/toolbox/lineages/__init__.py M lib/galaxy/tools/toolbox/lineages/factory.py M lib/galaxy/tools/toolbox/lineages/tool_shed.py M lib/galaxy/tools/toolbox/parser.py M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/workflow/extract.py M lib/galaxy/workflow/run.py M lib/galaxy/workflow/schedulers/core.py M test/api/test_workflow_extraction.py M test/api/workflows_format_2/__init__.py M test/api/workflows_format_2/converter.py M test/api/workflows_format_2/main.py M test/base/driver_util.py A test/functional/tools/multi_data_optional.xml M test/functional/tools/samples_tool_conf.xml M test/unit/tools_support.py M test/unit/unittest_utils/utility.py M tools/filters/gff/gff_filter_by_attribute.py M tools/stats/filtering.py

Log Message: ----------- Merge branch 'dev' into feature/plugin-system

Commit: 37702392817107dfd12cbb54f0af1dcb18bd848e https://github.com/galaxyproject/galaxy/commit/37702392817107dfd12cbb54f0af1... Author: Evgeny Anatskiy evgeny.anatskiy@gmail.com Date: 2016-10-14 (Fri, 14 Oct 2016)

Changed paths: M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt M config/galaxy.ini.sample M config/plugins/webhooks/demo/trans_object/helper/__init__.py M doc/source/admin/webhooks.rst M lib/galaxy/managers/collections_util.py M lib/galaxy/model/item_attrs.py M lib/galaxy/model/metadata.py M lib/galaxy/model/orm/now.py M lib/galaxy/tools/cwl/__init__.py M lib/galaxy/tools/cwl/cwltool_deps.py M lib/galaxy/tools/cwl/parser.py M lib/galaxy/tools/cwl/runtime_actions.py M lib/galaxy/tools/deps/commands.py M lib/galaxy/tools/deps/conda_compat.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/tools/deps/docker_util.py M lib/galaxy/tools/deps/mulled/_cli.py 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/util.py M lib/galaxy/tools/deps/resolvers/brewed_tool_shed_packages.py M lib/galaxy/tools/deps/resolvers/conda.py 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/tool_shed_packages.py M lib/galaxy/tools/deps/resolvers/unlinked_tool_shed_packages.py M lib/galaxy/tools/exception_handling.py M lib/galaxy/tools/execute.py M lib/galaxy/tools/loader.py M lib/galaxy/tools/loader_directory.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/parameters/dataset_matcher.py M lib/galaxy/tools/parameters/wrapped.py M lib/galaxy/tools/parameters/wrapped_json.py M lib/galaxy/tools/parser/__init__.py M lib/galaxy/tools/parser/factory.py M lib/galaxy/tools/toolbox/__init__.py M lib/galaxy/tools/toolbox/lineages/__init__.py M lib/galaxy/tools/toolbox/lineages/factory.py M lib/galaxy/tools/toolbox/lineages/tool_shed.py M lib/galaxy/tools/toolbox/parser.py M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/workflow/extract.py M lib/galaxy/workflow/run.py M lib/galaxy/workflow/schedulers/core.py M test/api/test_workflow_extraction.py M test/api/workflows_format_2/__init__.py M test/api/workflows_format_2/converter.py M test/api/workflows_format_2/main.py M test/base/driver_util.py A test/functional/tools/multi_data_optional.xml M test/functional/tools/samples_tool_conf.xml M test/unit/tools_support.py M test/unit/unittest_utils/utility.py M tools/filters/gff/gff_filter_by_attribute.py M tools/stats/filtering.py

Log Message: ----------- Merge branch 'feature/plugin-system' of github.com:bgruening/galaxy into feature/plugin-system

Commit: bd20ab1aa57381b36e16dc08c20b6b176a7ed724 https://github.com/galaxyproject/galaxy/commit/bd20ab1aa57381b36e16dc08c20b6... Author: Evgeny Anatskiy evgeny.anatskiy@gmail.com Date: 2016-10-14 (Fri, 14 Oct 2016)

Changed paths: M lib/galaxy/webhooks/__init__.py

Log Message: ----------- pep8

Commit: 3d4f302c4734e9afc7e065645c915dfd8f37566e https://github.com/galaxyproject/galaxy/commit/3d4f302c4734e9afc7e065645c915... Author: Bjoern Gruening bjoern.gruening@gmail.com Date: 2016-10-14 (Fri, 14 Oct 2016)

Changed paths: M config/galaxy.ini.sample

Log Message: ----------- change default settings in galaxy.ini.sample

Commit: 4bbab51c0500922c9a191d022de295daa48f0dd5 https://github.com/galaxyproject/galaxy/commit/4bbab51c0500922c9a191d022de29... Author: Björn Grüning bjoern@gruenings.eu Date: 2016-10-14 (Fri, 14 Oct 2016)

Changed paths: M doc/source/admin/webhooks.rst

Log Message: ----------- Add note about interface stability.

Commit: ebaffa2e0d6a030dfc3c78a3b9515093b14f7103 https://github.com/galaxyproject/galaxy/commit/ebaffa2e0d6a030dfc3c78a3b9515... Author: Evgeny Anatskiy evgeny.anatskiy@gmail.com Date: 2016-10-14 (Fri, 14 Oct 2016)

Changed paths: M config/plugins/webhooks/demo/phdcomics/helper/__init__.py M lib/galaxy/webapps/galaxy/api/webhooks.py

Log Message: ----------- fix failing Travis tests #2 (TOX_ENV=py27-lint) and #6 (TOX_ENV=py27-lint-imports)

Commit: a6d52cdbdc837c427c0971c6586eb5169a786752 https://github.com/galaxyproject/galaxy/commit/a6d52cdbdc837c427c0971c6586eb... Author: Dannon Baker dannon.baker@gmail.com Date: 2016-10-23 (Sun, 23 Oct 2016)

Changed paths: M client/galaxy/scripts/apps/history-panel.js M client/galaxy/scripts/layout/masthead.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/history/options-menu.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/tool/tool-form.js A client/galaxy/scripts/mvc/webhooks.js M config/galaxy.ini.sample A config/plugins/webhooks/demo/history_test1/config/history_test1.yml A config/plugins/webhooks/demo/history_test2/config/history_test2.yml A config/plugins/webhooks/demo/masthead_test/config/masthead_test.yml A config/plugins/webhooks/demo/phdcomics/config/phdcomics.yaml A config/plugins/webhooks/demo/phdcomics/helper/__init__.py A config/plugins/webhooks/demo/phdcomics/static/script.js A config/plugins/webhooks/demo/phdcomics/static/styles.css A config/plugins/webhooks/demo/trans_object/config/trans_object.yaml A config/plugins/webhooks/demo/trans_object/helper/__init__.py A config/plugins/webhooks/demo/xkcd/config/xkcd.yml A config/plugins/webhooks/demo/xkcd/static/script.js A config/plugins/webhooks/demo/xkcd/static/styles.css A doc/source/admin/images_webhooks/history-menu.png A doc/source/admin/images_webhooks/masthead.png A doc/source/admin/images_webhooks/masthead_trans_object.png A doc/source/admin/images_webhooks/tool.png A doc/source/admin/images_webhooks/workflow.png A doc/source/admin/webhooks.rst M lib/galaxy/app.py M lib/galaxy/config.py A lib/galaxy/webapps/galaxy/api/webhooks.py M lib/galaxy/webapps/galaxy/buildapp.py A lib/galaxy/webhooks/__init__.py M static/maps/layout/menu.js.map M static/maps/mvc/history/options-menu.js.map M static/maps/mvc/tool/tool-form-composite.js.map M static/maps/mvc/tool/tool-form.js.map A static/maps/mvc/tool/tool-webhooks.js.map A static/maps/mvc/webhooks.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/history/options-menu.js M static/scripts/mvc/tool/tool-form-composite.js M static/scripts/mvc/tool/tool-form.js A static/scripts/mvc/tool/tool-webhooks.js A static/scripts/mvc/webhooks.js A templates/webapps/galaxy/workflow/run_complete.mako

Log Message: ----------- Merge remote-tracking branch 'bgruening/feature/plugin-system' into dev

Compare: https://github.com/galaxyproject/galaxy/compare/cfeb0135ac5f...a6d52cdbdc83