Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a407a99ae3b8a83879b5f4629c8c07d7cfa3945b https://github.com/galaxyproject/galaxy/commit/a407a99ae3b8a83879b5f4629c8c0... Author: anuprulez anup.rulez@gmail.com Date: 2017-05-29 (Mon, 29 May 2017)

Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/apps/panels/tool-panel.js M client/galaxy/scripts/mvc/workflow/workflow.js M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M static/maps/mvc/workflow/workflow.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/workflow/workflow.js R templates/webapps/galaxy/workflow/run.mako

Log Message: ----------- Removing run mako from workflows

Commit: 094dbe92c3e33d0184cc3691f3d9f66cb7e2b697 https://github.com/galaxyproject/galaxy/commit/094dbe92c3e33d0184cc3691f3d9f... Author: anuprulez anup.rulez@gmail.com Date: 2017-05-30 (Tue, 30 May 2017)

Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/mvc/workflow/workflow.js M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M static/maps/mvc/workflow/workflow.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/workflow/workflow.js

Log Message: ----------- Adding basic elements for import workflow

Commit: 6dba0c74f266483ef0a67d5d8f25f5ced1bbed37 https://github.com/galaxyproject/galaxy/commit/6dba0c74f266483ef0a67d5d8f25f... Author: anuprulez anup.rulez@gmail.com Date: 2017-05-30 (Tue, 30 May 2017)

Changed paths: M client/galaxy/scripts/apps/analysis.js A client/galaxy/scripts/mvc/workflow/workflow-configure-menu.js M client/galaxy/scripts/mvc/workflow/workflow.js M client/galaxy/style/less/base.less M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/drmaa.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/workflow.py A static/maps/mvc/workflow/workflow-configure-menu.js.map M static/maps/mvc/workflow/workflow.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map A static/scripts/mvc/workflow/workflow-configure-menu.js M static/scripts/mvc/workflow/workflow.js M static/style/blue/base.css R templates/webapps/galaxy/workflow/configure_menu.mako

Log Message: ----------- Merging with dev

Commit: 764933bf3417c734ee2f5554ae122ddca1f3655a https://github.com/galaxyproject/galaxy/commit/764933bf3417c734ee2f5554ae122... Author: anuprulez anup.rulez@gmail.com Date: 2017-06-01 (Thu, 01 Jun 2017)

Changed paths: M client/galaxy/scripts/mvc/workflow/workflow.js M lib/galaxy/webapps/galaxy/controllers/workflow.py M static/maps/mvc/workflow/workflow.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/workflow/workflow.js

Log Message: ----------- Adding import functionality

Commit: 62bd742808e5c45a00cb64ac7ef962f936e57351 https://github.com/galaxyproject/galaxy/commit/62bd742808e5c45a00cb64ac7ef96... Author: anuprulez anup.rulez@gmail.com Date: 2017-06-01 (Thu, 01 Jun 2017)

Changed paths: M client/galaxy/scripts/mvc/workflow/workflow.js M lib/galaxy/webapps/galaxy/controllers/workflow.py M static/maps/mvc/workflow/workflow.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/workflow/workflow.js

Log Message: ----------- Moving common functions out of view and adding messages for client actions for importing workflow

Commit: 07ea4c04347956fd5e177b052c86a63568aa28a7 https://github.com/galaxyproject/galaxy/commit/07ea4c04347956fd5e177b052c86a... Author: anuprulez anup.rulez@gmail.com Date: 2017-06-06 (Tue, 06 Jun 2017)

Changed paths: M .ci/flake8_lint_include_list.txt M README.rst M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/collection/collection-view.js M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/grid/grid-template.js M client/galaxy/scripts/mvc/grid/grid-view.js M client/galaxy/scripts/mvc/history/hda-li.js M client/galaxy/scripts/mvc/history/hdca-li.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/workflow/workflow.js M client/galaxy/style/less/base.less M client/webpack.config.js M config/job_conf.xml.sample_advanced M contrib/galaxy.debian-init M contrib/galaxy_supervisor.conf M doc/Makefile R doc/patch.py M doc/source/admin/authentication.md M doc/source/admin/special_topics/mulled_containers.rst R doc/source/api/api.rst R doc/source/api/ts_api.rst M doc/source/dev/build_a_job_runner.rst M doc/source/lib/galaxy.actions.rst M doc/source/lib/galaxy.auth.providers.rst M doc/source/lib/galaxy.auth.rst A doc/source/lib/galaxy.containers.rst M doc/source/lib/galaxy.dataset_collections.rst M doc/source/lib/galaxy.dataset_collections.types.rst M doc/source/lib/galaxy.datatypes.converters.rst M doc/source/lib/galaxy.datatypes.dataproviders.rst M doc/source/lib/galaxy.datatypes.display_applications.rst M doc/source/lib/galaxy.datatypes.rst M doc/source/lib/galaxy.datatypes.util.rst M doc/source/lib/galaxy.dependencies.rst M doc/source/lib/galaxy.eggs.rst M doc/source/lib/galaxy.exceptions.rst M doc/source/lib/galaxy.external_services.result_handlers.rst M doc/source/lib/galaxy.external_services.rst M doc/source/lib/galaxy.forms.rst M doc/source/lib/galaxy.jobs.actions.rst M doc/source/lib/galaxy.jobs.deferred.rst M doc/source/lib/galaxy.jobs.metrics.collectl.rst M doc/source/lib/galaxy.jobs.metrics.instrumenters.rst M doc/source/lib/galaxy.jobs.metrics.rst M doc/source/lib/galaxy.jobs.rst M doc/source/lib/galaxy.jobs.runners.rst M doc/source/lib/galaxy.jobs.runners.state_handlers.rst M doc/source/lib/galaxy.jobs.runners.util.cli.job.rst M doc/source/lib/galaxy.jobs.runners.util.cli.rst M doc/source/lib/galaxy.jobs.runners.util.cli.shell.rst M doc/source/lib/galaxy.jobs.runners.util.condor.rst A doc/source/lib/galaxy.jobs.runners.util.drmaa.rst M doc/source/lib/galaxy.jobs.runners.util.job_script.rst M doc/source/lib/galaxy.jobs.runners.util.rst M doc/source/lib/galaxy.jobs.splitters.rst M doc/source/lib/galaxy.managers.rst M doc/source/lib/galaxy.model.migrate.rst M doc/source/lib/galaxy.model.orm.rst M doc/source/lib/galaxy.model.rst M doc/source/lib/galaxy.model.tool_shed_install.migrate.rst M doc/source/lib/galaxy.model.tool_shed_install.rst M doc/source/lib/galaxy.objectstore.rst M doc/source/lib/galaxy.openid.rst M doc/source/lib/galaxy.quota.rst M doc/source/lib/galaxy.rst M doc/source/lib/galaxy.sample_tracking.rst M doc/source/lib/galaxy.security.rst R doc/source/lib/galaxy.tags.rst M doc/source/lib/galaxy.tools.actions.rst A doc/source/lib/galaxy.tools.cwl.rst M doc/source/lib/galaxy.tools.data.rst M doc/source/lib/galaxy.tools.data_manager.rst A doc/source/lib/galaxy.tools.deps.container_resolvers.rst A doc/source/lib/galaxy.tools.deps.mulled.rst M doc/source/lib/galaxy.tools.deps.resolvers.rst M doc/source/lib/galaxy.tools.deps.rst M doc/source/lib/galaxy.tools.filters.rst M doc/source/lib/galaxy.tools.imp_exp.rst M doc/source/lib/galaxy.tools.linters.rst A doc/source/lib/galaxy.tools.locations.rst M doc/source/lib/galaxy.tools.parameters.rst M doc/source/lib/galaxy.tools.parser.rst M doc/source/lib/galaxy.tools.rst M doc/source/lib/galaxy.tools.search.rst M doc/source/lib/galaxy.tools.toolbox.filters.rst M doc/source/lib/galaxy.tools.toolbox.lineages.rst M doc/source/lib/galaxy.tools.toolbox.rst M doc/source/lib/galaxy.tools.util.galaxyops.rst M doc/source/lib/galaxy.tools.util.rst A doc/source/lib/galaxy.tools.verify.asserts.rst A doc/source/lib/galaxy.tools.verify.rst A doc/source/lib/galaxy.tours.rst M doc/source/lib/galaxy.util.backports.rst M doc/source/lib/galaxy.util.log.rst M doc/source/lib/galaxy.util.pastescript.rst M doc/source/lib/galaxy.util.rst M doc/source/lib/galaxy.visualization.data_providers.phyloviz.rst M doc/source/lib/galaxy.visualization.data_providers.rst M doc/source/lib/galaxy.visualization.genome.rst M doc/source/lib/galaxy.visualization.plugins.rst M doc/source/lib/galaxy.visualization.rst M doc/source/lib/galaxy.visualization.tracks.rst M doc/source/lib/galaxy.web.base.controllers.rst M doc/source/lib/galaxy.web.base.rst M doc/source/lib/galaxy.web.framework.helpers.rst M doc/source/lib/galaxy.web.framework.middleware.rst M doc/source/lib/galaxy.web.framework.rst M doc/source/lib/galaxy.web.proxy.rst M doc/source/lib/galaxy.web.rst M doc/source/lib/galaxy.web.security.rst A doc/source/lib/galaxy.web.stack.rst A doc/source/lib/galaxy.webapps.galaxy.api.rst M doc/source/lib/galaxy.webapps.galaxy.controllers.rst M doc/source/lib/galaxy.webapps.galaxy.rst M doc/source/lib/galaxy.webapps.reports.controllers.rst M doc/source/lib/galaxy.webapps.reports.rst M doc/source/lib/galaxy.webapps.rst A doc/source/lib/galaxy.webapps.tool_shed.api.rst M doc/source/lib/galaxy.webapps.tool_shed.controllers.rst M doc/source/lib/galaxy.webapps.tool_shed.framework.middleware.rst M doc/source/lib/galaxy.webapps.tool_shed.framework.rst M doc/source/lib/galaxy.webapps.tool_shed.model.migrate.rst M doc/source/lib/galaxy.webapps.tool_shed.model.rst M doc/source/lib/galaxy.webapps.tool_shed.rst M doc/source/lib/galaxy.webapps.tool_shed.search.rst M doc/source/lib/galaxy.webapps.tool_shed.security.rst M doc/source/lib/galaxy.webapps.tool_shed.util.rst A doc/source/lib/galaxy.webhooks.rst M doc/source/lib/galaxy.work.rst M doc/source/lib/galaxy.workflow.rst M doc/source/lib/galaxy.workflow.schedulers.rst M doc/source/lib/galaxy_ext.metadata.rst M doc/source/lib/galaxy_ext.rst M doc/source/lib/log_tempfile.rst M doc/source/lib/psyco_full.rst M doc/source/lib/tool_shed.capsule.rst M doc/source/lib/tool_shed.dependencies.repository.rst M doc/source/lib/tool_shed.dependencies.rst M doc/source/lib/tool_shed.dependencies.tool.rst M doc/source/lib/tool_shed.galaxy_install.datatypes.rst M doc/source/lib/tool_shed.galaxy_install.grids.rst M doc/source/lib/tool_shed.galaxy_install.metadata.rst M doc/source/lib/tool_shed.galaxy_install.migrate.rst M doc/source/lib/tool_shed.galaxy_install.repository_dependencies.rst M doc/source/lib/tool_shed.galaxy_install.rst M doc/source/lib/tool_shed.galaxy_install.tool_dependencies.recipe.rst M doc/source/lib/tool_shed.galaxy_install.tool_dependencies.rst M doc/source/lib/tool_shed.galaxy_install.tools.rst M doc/source/lib/tool_shed.galaxy_install.utility_containers.rst M doc/source/lib/tool_shed.grids.rst M doc/source/lib/tool_shed.managers.rst M doc/source/lib/tool_shed.metadata.rst M doc/source/lib/tool_shed.repository_types.rst M doc/source/lib/tool_shed.rst M doc/source/lib/tool_shed.tools.rst M doc/source/lib/tool_shed.util.rst M doc/source/lib/tool_shed.utility_containers.rst M doc/source/releases/13.01_announce.rst M doc/source/releases/13.02_announce.rst M doc/source/releases/13.04_announce.rst M doc/source/releases/13.06_announce.rst M doc/source/releases/13.08_announce.rst M doc/source/releases/13.11_announce.rst M doc/source/releases/14.02_announce.rst M doc/source/releases/14.04_announce.rst M doc/source/releases/14.06_announce.rst M doc/source/releases/14.08_announce.rst M doc/source/releases/14.10_announce.rst M doc/source/releases/15.01_announce.rst M doc/source/releases/15.03_announce.rst M doc/source/releases/15.05.rst M doc/source/releases/15.05_announce.rst M doc/source/releases/15.07_announce.rst M doc/source/releases/15.10_announce.rst M doc/source/releases/16.01_announce.rst M doc/source/releases/16.04_announce.rst M doc/source/releases/16.07_announce.rst M doc/source/releases/16.10_announce.rst M doc/source/releases/17.01_announce.rst M doc/source/slideshow/architecture/galaxy_architecture.md M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/data.py M lib/galaxy/jobs/actions/post.py M lib/galaxy/jobs/runners/chronos.py M lib/galaxy/managers/collections.py M lib/galaxy/managers/collections_util.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/data/__init__.py M lib/galaxy/tools/xsd/README.md M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/util/compression_utils.py M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/webapps/galaxy/api/history_contents.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/page.py M scripts/bootstrap_history.py M static/maps/layout/menu.js.map M static/maps/mvc/collection/collection-view.js.map M static/maps/mvc/dataset/dataset-li.js.map M static/maps/mvc/form/form-input.js.map M static/maps/mvc/grid/grid-template.js.map M static/maps/mvc/grid/grid-view.js.map M static/maps/mvc/history/hda-li.js.map M static/maps/mvc/history/hdca-li.js.map M static/maps/mvc/tool/tool-form-composite.js.map M static/maps/mvc/workflow/workflow.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/menu.js M static/scripts/mvc/collection/collection-view.js M static/scripts/mvc/dataset/dataset-li.js M static/scripts/mvc/form/form-input.js M static/scripts/mvc/grid/grid-template.js M static/scripts/mvc/grid/grid-view.js M static/scripts/mvc/history/hda-li.js M static/scripts/mvc/history/hdca-li.js M static/scripts/mvc/tool/tool-form-composite.js M static/scripts/mvc/workflow/workflow.js M static/style/blue/base.css M static/welcome.html.sample M templates/grid_base.mako R templates/webapps/galaxy/page/list_published.mako M test/api/test_dataset_collections.py M test/base/populators.py M test/functional/tools/sample_datatypes_conf.xml M test/qunit/test-data/bootstrapped.js M test/qunit/tests/galaxy-app-base.js

Log Message: ----------- Resolving conflicts and merging with dev

Commit: 207249a4665470288fe77ae9d532e3cb07d4ce32 https://github.com/galaxyproject/galaxy/commit/207249a4665470288fe77ae9d532e... Author: anuprulez anup.rulez@gmail.com Date: 2017-06-06 (Tue, 06 Jun 2017)

Changed paths: M client/galaxy/scripts/mvc/user/user-preferences.js M client/galaxy/scripts/mvc/workflow/workflow-configure-menu.js M client/galaxy/scripts/mvc/workflow/workflow.js M static/maps/mvc/user/user-preferences.js.map M static/maps/mvc/workflow/workflow-configure-menu.js.map M static/maps/mvc/workflow/workflow.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/user/user-preferences.js M static/scripts/mvc/workflow/workflow-configure-menu.js M static/scripts/mvc/workflow/workflow.js

Log Message: ----------- Moving configure menu call to user preferences

Commit: 77327d27b5f526f0b1ddd4375d32e57e83453169 https://github.com/galaxyproject/galaxy/commit/77327d27b5f526f0b1ddd4375d32e... Author: anuprulez anup.rulez@gmail.com Date: 2017-06-07 (Wed, 07 Jun 2017)

Changed paths: R templates/webapps/galaxy/workflow/import.mako

Log Message: ----------- Removing import.mako file

Commit: f2efc6e5f77c4116a3ae28f8d83c3a9962d42f19 https://github.com/galaxyproject/galaxy/commit/f2efc6e5f77c4116a3ae28f8d83c3... Author: anuprulez anup.rulez@gmail.com Date: 2017-06-07 (Wed, 07 Jun 2017)

Changed paths: M client/galaxy/scripts/mvc/ui/ui-slider.js M client/galaxy/style/less/ui.less M config/job_conf.xml.sample_advanced M config/plugins/webhooks/demo/search/config/searchover.yaml M config/plugins/webhooks/demo/tool_list/config/tool_list.yml M lib/galaxy/app.py M lib/galaxy/datatypes/text.py M lib/galaxy/jobs/__init__.py A lib/galaxy/tools/cache.py R lib/galaxy/tools/toolbox/cache.py M static/maps/mvc/ui/ui-slider.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/ui/ui-slider.js M static/style/blue/base.css M test/api/test_dataset_collections.py M test/functional/webhooks/trans_object/config/trans_object.yaml M test/qunit/tests/ui_tests.html M test/qunit/tests/ui_tests.js A test/unit/jobs/conditional_runners_job_conf.xml M test/unit/jobs/test_job_configuration.py M test/unit/tools/test_toolbox.py

Log Message: ----------- Merging with dev

Commit: 1caf29d7591ff3787de330de58003fd9f0c0b6e1 https://github.com/galaxyproject/galaxy/commit/1caf29d7591ff3787de330de58003... Author: anuprulez anup.rulez@gmail.com Date: 2017-06-07 (Wed, 07 Jun 2017)

Changed paths: M client/galaxy/scripts/apps/analysis.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map

Log Message: ----------- Removing extra link for custom_builds in analysis.js

Commit: 3573f4d59f3d177a0b91b06ce192e1711aaf4a0d https://github.com/galaxyproject/galaxy/commit/3573f4d59f3d177a0b91b06ce192e... Author: anuprulez anup.rulez@gmail.com Date: 2017-06-07 (Wed, 07 Jun 2017)

Changed paths: M client/galaxy/scripts/mvc/workflow/workflow.js M static/maps/mvc/workflow/workflow.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/workflow/workflow.js

Log Message: ----------- Removing usused imports in workflow.js

Commit: 785e3e557aeee7071905f1aa3d88c1ae1653ec9b https://github.com/galaxyproject/galaxy/commit/785e3e557aeee7071905f1aa3d88c... Author: anuprulez anup.rulez@gmail.com Date: 2017-06-09 (Fri, 09 Jun 2017)

Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/apps/panels/tool-panel.js M client/galaxy/scripts/mvc/workflow/workflow.js M client/galaxy/scripts/utils/utils.js M lib/galaxy/webapps/galaxy/controllers/workflow.py M static/maps/mvc/workflow/workflow.js.map M static/maps/utils/utils.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/workflow/workflow.js M static/scripts/utils/utils.js

Log Message: ----------- Fixing PR review comments

Commit: b52042ef8ebe250a1124071a98f4de486e5dc737 https://github.com/galaxyproject/galaxy/commit/b52042ef8ebe250a1124071a98f4d... Author: anuprulez anup.rulez@gmail.com Date: 2017-06-09 (Fri, 09 Jun 2017)

Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/grid/grid-view.js A client/galaxy/scripts/mvc/page/page-list.js M config/datatypes_conf.xml.sample M config/galaxy.ini.sample M lib/galaxy/datatypes/data.py A lib/galaxy/datatypes/plant_tribes.py M lib/galaxy/datatypes/text.py M lib/galaxy/webapps/galaxy/controllers/page.py M static/maps/layout/menu.js.map M static/maps/mvc/grid/grid-view.js.map A static/maps/mvc/page/page-list.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/menu.js M static/scripts/mvc/grid/grid-view.js A static/scripts/mvc/page/page-list.js M templates/sharing_base.mako M templates/webapps/galaxy/page/editor.mako R templates/webapps/galaxy/page/index.mako

Log Message: ----------- Merging with dev

Commit: 5cc46a95c9c9a54ae390496b52c7efc8ac25cf0d https://github.com/galaxyproject/galaxy/commit/5cc46a95c9c9a54ae390496b52c7e... Author: anuprulez anup.rulez@gmail.com Date: 2017-06-10 (Sat, 10 Jun 2017)

Changed paths: M client/galaxy/scripts/apps/analysis.js M lib/galaxy/webapps/galaxy/controllers/workflow.py M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map

Log Message: ----------- Fixing PR review comments

Commit: 6d9a911ea9200d3339635c0f4370f18001271f8b https://github.com/galaxyproject/galaxy/commit/6d9a911ea9200d3339635c0f4370f... Author: anuprulez anup.rulez@gmail.com Date: 2017-06-10 (Sat, 10 Jun 2017)

Changed paths: M lib/galaxy/webapps/galaxy/controllers/workflow.py

Log Message: ----------- Removing usused imports in workflow controller

Commit: 050ff3b159b7309609423c37cbf5d47a261c2944 https://github.com/galaxyproject/galaxy/commit/050ff3b159b7309609423c37cbf5d... Author: anuprulez anup.rulez@gmail.com Date: 2017-06-12 (Mon, 12 Jun 2017)

Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/layout/menu.js M config/job_conf.xml.sample_advanced M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/tools/deps/containers.py M lib/galaxy/tools/deps/docker_util.py M lib/galaxy/tools/deps/mulled/invfile.lua M lib/galaxy/tools/deps/mulled/mulled_build.py M lib/galaxy/tools/deps/mulled/mulled_build_channel.py M lib/galaxy/tools/deps/mulled/mulled_build_files.py M lib/galaxy/tools/deps/mulled/mulled_search.py M lib/galaxy/tools/deps/mulled/util.py A lib/galaxy/tools/deps/singularity_util.py M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M static/maps/layout/menu.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 R templates/webapps/galaxy/dataset/grid.mako A test/functional/tools/mulled_example_multi_versionless.xml M test/functional/tools/samples_tool_conf.xml

Log Message: ----------- Merging with dev

Commit: 659c039601a474eba86156a6957dd48560630fa1 https://github.com/galaxyproject/galaxy/commit/659c039601a474eba86156a6957dd... Author: guerler aysam.guerler@gmail.com Date: 2017-06-19 (Mon, 19 Jun 2017)

Changed paths: M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/layout/panel.js M client/galaxy/scripts/mvc/history/history-view-edit-current.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/style/less/base.less M static/maps/layout/page.js.map M static/maps/layout/panel.js.map M static/maps/mvc/history/history-view-edit-current.js.map M static/maps/mvc/tool/tool-form-base.js.map M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map M static/scripts/layout/page.js M static/scripts/layout/panel.js M static/scripts/mvc/history/history-view-edit-current.js M static/scripts/mvc/tool/tool-form-base.js M static/style/blue/base.css

Log Message: ----------- Revise panel/iframe handling, align naming, rely on empty to trigger removal of previous view

Repack

Move inline styles, use consistent naming

Commit: 2c4c7147e075f036ee703a89eb6de7f39c4e10dd https://github.com/galaxyproject/galaxy/commit/2c4c7147e075f036ee703a89eb6de... Author: guerler aysam.guerler@gmail.com Date: 2017-06-19 (Mon, 19 Jun 2017)

Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M static/maps/mvc/tool/tool-form-composite.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-form-composite.js

Log Message: ----------- Revise and fix resize handler

Commit: 21312138a47cb0c3f958c318500937b11df31d49 https://github.com/galaxyproject/galaxy/commit/21312138a47cb0c3f958c31850093... Author: guerler aysam.guerler@gmail.com Date: 2017-06-19 (Mon, 19 Jun 2017)

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

Log Message: ----------- Fix deferred form destructor

Commit: 71498cabfdb9e988e3035915a8be647b88db1ef8 https://github.com/galaxyproject/galaxy/commit/71498cabfdb9e988e3035915a8be6... Author: guerler aysam.guerler@gmail.com Date: 2017-06-19 (Mon, 19 Jun 2017)

Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js M static/maps/mvc/tool/tool-form-base.js.map M static/scripts/mvc/tool/tool-form-base.js

Log Message: ----------- Fix log statement

Commit: d031758d7323c39ed3176c158355f9d697266ef1 https://github.com/galaxyproject/galaxy/commit/d031758d7323c39ed3176c158355f... Author: guerler aysam.guerler@gmail.com Date: 2017-06-19 (Mon, 19 Jun 2017)

Changed paths: M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map

Log Message: ----------- Pack scripts

Commit: f4e4c08bab6b8ecf39a69844a904e2fa1c3e4459 https://github.com/galaxyproject/galaxy/commit/f4e4c08bab6b8ecf39a69844a904e... Author: Björn Grüning bjoern@gruenings.eu Date: 2017-06-19 (Mon, 19 Jun 2017)

Changed paths: M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/layout/panel.js M client/galaxy/scripts/mvc/history/history-view-edit-current.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/style/less/base.less M static/maps/layout/page.js.map M static/maps/layout/panel.js.map M static/maps/mvc/history/history-view-edit-current.js.map M static/maps/mvc/tool/tool-form-base.js.map M static/maps/mvc/tool/tool-form-composite.js.map M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map M static/scripts/layout/page.js M static/scripts/layout/panel.js M static/scripts/mvc/history/history-view-edit-current.js M static/scripts/mvc/tool/tool-form-base.js M static/scripts/mvc/tool/tool-form-composite.js M static/style/blue/base.css

Log Message: ----------- Merge pull request #36 from guerler/fix_cleanup

Fixes deferred removal of previous views, augments center panel handling

Commit: 837a5c85fcf9c6906843fe413aaf10f27ef21af4 https://github.com/galaxyproject/galaxy/commit/837a5c85fcf9c6906843fe413aaf1... Author: anuprulez anup.rulez@gmail.com Date: 2017-06-19 (Mon, 19 Jun 2017)

Changed paths: M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map

Log Message: ----------- Merging changes with static files

Commit: 8a09836ba79e7f7b08f51a8d7db7c416b03bd44f https://github.com/galaxyproject/galaxy/commit/8a09836ba79e7f7b08f51a8d7db7c... Author: anuprulez anup.rulez@gmail.com Date: 2017-06-19 (Mon, 19 Jun 2017)

Changed paths: M .gitignore M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/tool/tool-form.js M client/galaxy/scripts/mvc/webhooks.js M client/galaxy/scripts/onload.js M config/plugins/webhooks/demo/tool_list/helper/__init__.py A config/plugins/webhooks/demo/tour_generator/config/tour_generator.yml A config/plugins/webhooks/demo/tour_generator/helper/__init__.py A config/plugins/webhooks/demo/tour_generator/static/script.js A config/plugins/webhooks/demo/tour_generator/static/styles.css M cron/updateucsc.sh.sample M lib/galaxy/config.py M lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/tools/deps/containers.py M lib/galaxy/tools/deps/mulled/invfile.lua M lib/galaxy/tools/deps/mulled/mulled_build.py M lib/galaxy/tools/deps/mulled/mulled_build_files.py M lib/galaxy/tools/deps/mulled/mulled_build_tool.py M lib/galaxy/webapps/galaxy/api/webhooks.py M scripts/api/library_upload_dir.py M static/maps/layout/menu.js.map M static/maps/mvc/tool/tool-form-base.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/maps/onload.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-base.js M static/scripts/mvc/tool/tool-form-composite.js M static/scripts/mvc/tool/tool-form.js M static/scripts/mvc/webhooks.js M static/scripts/onload.js M templates/js-app.mako M test/functional/webhooks/phdcomics/helper/__init__.py M test/functional/webhooks/trans_object/helper/__init__.py

Log Message: ----------- Merging with dev

Commit: 9b9e2aa2274202c9afe336724c78142408c94a77 https://github.com/galaxyproject/galaxy/commit/9b9e2aa2274202c9afe336724c781... Author: Dannon Baker dannon.baker@gmail.com Date: 2017-06-20 (Tue, 20 Jun 2017)

Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/apps/panels/tool-panel.js M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/layout/panel.js M client/galaxy/scripts/mvc/history/history-view-edit-current.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/user/user-preferences.js M client/galaxy/scripts/mvc/workflow/workflow-configure-menu.js M client/galaxy/scripts/mvc/workflow/workflow.js M client/galaxy/scripts/utils/utils.js M client/galaxy/style/less/base.less M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M static/maps/layout/page.js.map M static/maps/layout/panel.js.map M static/maps/mvc/history/history-view-edit-current.js.map M static/maps/mvc/tool/tool-form-base.js.map M static/maps/mvc/tool/tool-form-composite.js.map M static/maps/mvc/user/user-preferences.js.map M static/maps/mvc/workflow/workflow-configure-menu.js.map M static/maps/mvc/workflow/workflow.js.map M static/maps/utils/utils.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/layout/page.js M static/scripts/layout/panel.js M static/scripts/mvc/history/history-view-edit-current.js M static/scripts/mvc/tool/tool-form-base.js M static/scripts/mvc/tool/tool-form-composite.js M static/scripts/mvc/user/user-preferences.js M static/scripts/mvc/workflow/workflow-configure-menu.js M static/scripts/mvc/workflow/workflow.js M static/scripts/utils/utils.js M static/style/blue/base.css R templates/webapps/galaxy/workflow/import.mako R templates/webapps/galaxy/workflow/run.mako

Log Message: ----------- Merge remote-tracking branch 'bgruening/convertworkflowmako' into dev

Compare: https://github.com/galaxyproject/galaxy/compare/6a0401e08ebc...9b9e2aa22742