Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 788886e1cec7abe9b7e50de76a93117c4b64ca2e https://github.com/galaxyproject/galaxy/commit/788886e1cec7abe9b7e50de76a931... Author: Pablo Moreno pablo.a.moreno@gmail.com Date: 2017-04-25 (Tue, 25 Apr 2017)

Changed paths: M config/job_conf.xml.sample_advanced M lib/galaxy/jobs/runners/kubernetes.py

Log Message: ----------- Adds supplemental group support for the Kubernetes runner.

Commit: aa2465db8684f807e5fdd6a8ae60079c37bf5723 https://github.com/galaxyproject/galaxy/commit/aa2465db8684f807e5fdd6a8ae600... Author: Pablo Moreno pablo.a.moreno@gmail.com Date: 2017-04-25 (Tue, 25 Apr 2017)

Changed paths: M lib/galaxy/jobs/runners/kubernetes.py

Log Message: ----------- Improves handling of supplemental group.

Commit: 528ea5c74831c3bc9e36e6a236956b784a3642ce https://github.com/galaxyproject/galaxy/commit/528ea5c74831c3bc9e36e6a236956... Author: Pablo Moreno pablo.a.moreno@gmail.com Date: 2017-04-25 (Tue, 25 Apr 2017)

Changed paths: M config/job_conf.xml.sample_advanced M lib/galaxy/jobs/runners/kubernetes.py

Log Message: ----------- Adds Kubernetes fsGroup id support.

Commit: bc96a0c267410fa229126512bb016dc17581d242 https://github.com/galaxyproject/galaxy/commit/bc96a0c267410fa229126512bb016... Author: Pablo Moreno pablo.a.moreno@gmail.com Date: 2017-04-25 (Tue, 25 Apr 2017)

Changed paths: M config/job_conf.xml.sample_advanced M lib/galaxy/jobs/runners/kubernetes.py

Log Message: ----------- Adds support for job api version setting, and changes default to batch/v1

Commit: cc4a37d22b5e7cd3274ead8314f41a0ac419ebbc https://github.com/galaxyproject/galaxy/commit/cc4a37d22b5e7cd3274ead8314f41... Author: Pablo Moreno pablo.a.moreno@gmail.com Date: 2017-04-25 (Tue, 25 Apr 2017)

Changed paths: M config/job_conf.xml.sample_advanced M lib/galaxy/jobs/runners/kubernetes.py

Log Message: ----------- Adds pull policy support

Commit: 9ffbcddb3918af2d55cd1383d6a8a148c4da179e https://github.com/galaxyproject/galaxy/commit/9ffbcddb3918af2d55cd1383d6a8a... Author: Pablo Moreno pablo.a.moreno@gmail.com Date: 2017-04-26 (Wed, 26 Apr 2017)

Changed paths: M config/job_conf.xml.sample_advanced M lib/galaxy/jobs/runners/kubernetes.py

Log Message: ----------- Style improvements

Commit: 8afcfa4ec926e589ea94dd2d84ada824ed2d7578 https://github.com/galaxyproject/galaxy/commit/8afcfa4ec926e589ea94dd2d84ada... Author: John Chilton jmchilton@gmail.com Date: 2017-05-01 (Mon, 01 May 2017)

Changed paths: M .ci/jenkins/selenium/run_tests.sh M .travis.yml M CITATION M Makefile M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/mvc/citation/citation-view.js M client/galaxy/scripts/mvc/library/library-folderlist-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/library/library-librarylist-view.js M client/galaxy/scripts/mvc/library/library-librarytoolbar-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/ui/ui-color-picker.js M client/galaxy/scripts/mvc/ui/ui-select-content.js M client/galaxy/scripts/mvc/user/user-preferences.js M client/galaxy/scripts/mvc/workflow/workflow-forms.js M client/galaxy/scripts/viz/phyloviz.js M client/galaxy/style/less/ui.less M config/galaxy.ini.sample M config/plugins/interactive_environments/rstudio/config/allowed_images.yml.sample M config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample M config/plugins/interactive_environments/rstudio/static/js/rstudio.js M config/plugins/interactive_environments/rstudio/templates/rstudio.mako A doc/source/admin/special_topics/grafana.png M doc/source/admin/special_topics/index.rst A doc/source/admin/special_topics/performance_tracking.rst M lib/galaxy/config.py M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/conditional-requirements.txt M lib/galaxy/dependencies/dev-requirements.txt M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/managers/configuration.py M lib/galaxy/model/__init__.py M lib/galaxy/objectstore/azure_blob.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/model_operations.py M lib/galaxy/tools/data_manager/manager.py M lib/galaxy/tools/execute.py M lib/galaxy/tools/parameters/validation.py M lib/galaxy/web/base/controllers/admin.py M lib/galaxy/web/base/interactive_environments.py A lib/galaxy/web/framework/middleware/graphite.py M lib/galaxy/web/framework/middleware/remoteuser.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/web/proxy/js/package.json M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/reports/config.py M lib/galaxy/webapps/tool_shed/config.py M lib/tool_shed/galaxy_install/tools/data_manager.py M run_tests.sh M static/maps/mvc/citation/citation-view.js.map M static/maps/mvc/library/library-folderlist-view.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/maps/mvc/library/library-librarylist-view.js.map M static/maps/mvc/library/library-librarytoolbar-view.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/ui/ui-color-picker.js.map M static/maps/mvc/ui/ui-select-content.js.map M static/maps/mvc/user/user-preferences.js.map M static/maps/mvc/workflow/workflow-forms.js.map M static/maps/viz/phyloviz.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/citation/citation-view.js M static/scripts/mvc/library/library-folderlist-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/library/library-librarylist-view.js M static/scripts/mvc/library/library-librarytoolbar-view.js M static/scripts/mvc/tool/tool-form-base.js M static/scripts/mvc/tool/tool-form-composite.js M static/scripts/mvc/ui/ui-color-picker.js M static/scripts/mvc/ui/ui-select-content.js M static/scripts/mvc/user/user-preferences.js M static/scripts/mvc/workflow/workflow-forms.js M static/scripts/viz/phyloviz.js M static/style/blue/base.css M templates/admin/tool_shed_repository/select_tool_panel_section.mako M templates/user/index.mako M templates/webapps/galaxy/admin/center.mako M templates/webapps/galaxy/data_manager/index.mako M templates/webapps/galaxy/galaxy.masthead.mako M templates/webapps/tool_shed/base_panels.mako M test/api/test_jobs.py M test/api/test_workflows.py M test/galaxy_selenium/navigates_galaxy.py M test/qunit/tests/form_tests.js M test/qunit/tests/ui_tests.js M test/selenium_tests/framework.py M test/selenium_tests/test_workflow_run.py M tox.ini

Log Message: ----------- Merge remote-tracking branch 'jmchilton/dev' into feature/pr_fs_access_job_version

Commit: 8fcf46d31c731eb5198305d1a8b5fd37d1d1c20b https://github.com/galaxyproject/galaxy/commit/8fcf46d31c731eb5198305d1a8b5f... Author: John Chilton jmchilton@gmail.com Date: 2017-05-01 (Mon, 01 May 2017)

Changed paths: M config/job_conf.xml.sample_advanced

Log Message: ----------- Touch up k8 options in job_conf sample.

Optional options should be commented out - I guess only the two claim options need to have non-default values specified?

Commit: 8a1cc7a7eb0627907b404e7ad69e5e4aaf279d69 https://github.com/galaxyproject/galaxy/commit/8a1cc7a7eb0627907b404e7ad69e5... Author: Pablo Moreno pcm32@users.noreply.github.com Date: 2017-05-03 (Wed, 03 May 2017)

Changed paths: M .ci/jenkins/selenium/run_tests.sh M .travis.yml M CITATION M Makefile M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/mvc/citation/citation-view.js M client/galaxy/scripts/mvc/library/library-folderlist-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/library/library-librarylist-view.js M client/galaxy/scripts/mvc/library/library-librarytoolbar-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/ui/ui-color-picker.js M client/galaxy/scripts/mvc/ui/ui-select-content.js M client/galaxy/scripts/mvc/user/user-preferences.js M client/galaxy/scripts/mvc/workflow/workflow-forms.js M client/galaxy/scripts/viz/phyloviz.js M client/galaxy/style/less/ui.less M config/galaxy.ini.sample M config/job_conf.xml.sample_advanced M config/plugins/interactive_environments/rstudio/config/allowed_images.yml.sample M config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample M config/plugins/interactive_environments/rstudio/static/js/rstudio.js M config/plugins/interactive_environments/rstudio/templates/rstudio.mako A doc/source/admin/special_topics/grafana.png M doc/source/admin/special_topics/index.rst A doc/source/admin/special_topics/performance_tracking.rst M lib/galaxy/config.py M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/conditional-requirements.txt M lib/galaxy/dependencies/dev-requirements.txt M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/managers/configuration.py M lib/galaxy/model/__init__.py M lib/galaxy/objectstore/azure_blob.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/model_operations.py M lib/galaxy/tools/data_manager/manager.py M lib/galaxy/tools/execute.py M lib/galaxy/tools/parameters/validation.py M lib/galaxy/web/base/controllers/admin.py M lib/galaxy/web/base/interactive_environments.py A lib/galaxy/web/framework/middleware/graphite.py M lib/galaxy/web/framework/middleware/remoteuser.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/web/proxy/js/package.json M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/reports/config.py M lib/galaxy/webapps/tool_shed/config.py M lib/tool_shed/galaxy_install/tools/data_manager.py M run_tests.sh M static/maps/mvc/citation/citation-view.js.map M static/maps/mvc/library/library-folderlist-view.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/maps/mvc/library/library-librarylist-view.js.map M static/maps/mvc/library/library-librarytoolbar-view.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/ui/ui-color-picker.js.map M static/maps/mvc/ui/ui-select-content.js.map M static/maps/mvc/user/user-preferences.js.map M static/maps/mvc/workflow/workflow-forms.js.map M static/maps/viz/phyloviz.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/citation/citation-view.js M static/scripts/mvc/library/library-folderlist-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/library/library-librarylist-view.js M static/scripts/mvc/library/library-librarytoolbar-view.js M static/scripts/mvc/tool/tool-form-base.js M static/scripts/mvc/tool/tool-form-composite.js M static/scripts/mvc/ui/ui-color-picker.js M static/scripts/mvc/ui/ui-select-content.js M static/scripts/mvc/user/user-preferences.js M static/scripts/mvc/workflow/workflow-forms.js M static/scripts/viz/phyloviz.js M static/style/blue/base.css M templates/admin/tool_shed_repository/select_tool_panel_section.mako M templates/user/index.mako M templates/webapps/galaxy/admin/center.mako M templates/webapps/galaxy/data_manager/index.mako M templates/webapps/galaxy/galaxy.masthead.mako M templates/webapps/tool_shed/base_panels.mako M test/api/test_jobs.py M test/api/test_workflows.py M test/galaxy_selenium/navigates_galaxy.py M test/qunit/tests/form_tests.js M test/qunit/tests/ui_tests.js M test/selenium_tests/framework.py M test/selenium_tests/test_workflow_run.py M tox.ini

Log Message: ----------- Merge pull request #8 from jmchilton/feature/pr_fs_access_job_version

Touch up config options.

Commit: b2871d15b7f0dab2291986173a7cd0825a26f6fe https://github.com/galaxyproject/galaxy/commit/b2871d15b7f0dab2291986173a7cd... Author: Pablo Moreno pablo.a.moreno@gmail.com Date: 2017-05-03 (Wed, 03 May 2017)

Changed paths: M config/job_conf.xml.sample_advanced

Log Message: ----------- Makes config path for k8s required in sample config file.

Commit: 8d09854c1d7e7e33c777897f11d771cb933db35b https://github.com/galaxyproject/galaxy/commit/8d09854c1d7e7e33c777897f11d77... Author: John Chilton jmchilton@gmail.com Date: 2017-05-04 (Thu, 04 May 2017)

Changed paths: M config/job_conf.xml.sample_advanced M lib/galaxy/jobs/runners/kubernetes.py

Log Message: ----------- Merge pull request #3972 from phnmnl/feature/pr_fs_access_job_version

Kubernetes runner: Non-privileged filesystem access, updated k8s Job version

Compare: https://github.com/galaxyproject/galaxy/compare/5077b7ce0e55...8d09854c1d7e