galaxy-commits August 2016

galaxy-commits@lists.galaxyproject.org

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160 discussions

[galaxyproject/galaxy] 4b2e0c: Parse internal parameters such as job resource sel...
by GitHub 18 Aug '16

18 Aug '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4b2e0c84e19001c8071b374a8e7daf609bb3aa88 https://github.com/galaxyproject/galaxy/commit/4b2e0c84e19001c8071b374a8e7d… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-09 (Tue, 09 Aug 2016) Changed paths: M lib/galaxy/datatypes/data.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Parse internal parameters such as job resource selections when data converter tools are executed implicitly Commit: 67bc8481dceb7062b90693fe31a94acefbdcda9f https://github.com/galaxyproject/galaxy/commit/67bc8481dceb7062b90693fe31a9… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-16 (Tue, 16 Aug 2016) Changed paths: M lib/galaxy/datatypes/data.py Log Message: ----------- Add comment for clarification Commit: dd5411339737302cea2240d9074796a7e0856179 https://github.com/galaxyproject/galaxy/commit/dd5411339737302cea2240d90747… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-08-18 (Thu, 18 Aug 2016) Changed paths: M lib/galaxy/datatypes/data.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Merge pull request #2761 from guerler/fix_implicit_converter Parse internal parameters such as job resource selections when data converter tools are executed implicitly Compare: https://github.com/galaxyproject/galaxy/compare/000e7ea7c9a8...dd5411339737

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[galaxyproject/galaxy] bf9a15: API, history contents: allow 'source' in payload
by GitHub 18 Aug '16

18 Aug '16

Branch: refs/heads/release_16.07 Home: https://github.com/galaxyproject/galaxy Commit: bf9a15389ef32de5ef09cc35876cc17154cb5a5d https://github.com/galaxyproject/galaxy/commit/bf9a15389ef32de5ef09cc35876c… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-08-17 (Wed, 17 Aug 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/history_contents.py 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 Log Message: ----------- API, history contents: allow 'source' in payload In create, checks both kwd and payload for 'source' parameter when creating a new hdca. This allows source to be passed in the body and not query string. This fixes the copy call in history-contents when copying an hdca by drag and drop in the multi history view. Commit: 6c2468832bdfbfa470596d2ae86f48dc54285139 https://github.com/galaxyproject/galaxy/commit/6c2468832bdfbfa470596d2ae86f… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-08-17 (Wed, 17 Aug 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/history_contents.py 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 Log Message: ----------- Merge pull request #2809 from carlfeberhard/fix.hdca-dnd [16.07] API, history contents: allow 'source' in payload Compare: https://github.com/galaxyproject/galaxy/compare/30d5b45d43c4...6c2468832bdf

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[galaxyproject/galaxy] c3d7ca: Revert str.split() syntax for Python 2 compatibili...
by GitHub 18 Aug '16

18 Aug '16

Branch: refs/heads/release_16.07 Home: https://github.com/galaxyproject/galaxy Commit: c3d7ca8eef014eb019493dbf06c250c0a586b97c https://github.com/galaxyproject/galaxy/commit/c3d7ca8eef014eb019493dbf06c2… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-08-17 (Wed, 17 Aug 2016) Changed paths: M lib/galaxy/jobs/runners/slurm.py Log Message: ----------- Revert str.split() syntax for Python 2 compatibility Commit: 30d5b45d43c483c12390900a43d13fc9cb6667d5 https://github.com/galaxyproject/galaxy/commit/30d5b45d43c483c12390900a43d1… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-08-17 (Wed, 17 Aug 2016) Changed paths: M lib/galaxy/jobs/runners/slurm.py Log Message: ----------- Merge pull request #2810 from natefoo/split-kwargs [16.07] Revert str.split() syntax for Python 2 compatibility Compare: https://github.com/galaxyproject/galaxy/compare/8d512c98e237...30d5b45d43c4

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[galaxyproject/galaxy]
by GitHub 17 Aug '16

17 Aug '16

Branch: refs/heads/master-toolshed Home: https://github.com/galaxyproject/galaxy

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[galaxyproject/usegalaxy-playbook] db2854: Separate Galaxy servers into web and job server gr...
by GitHub 17 Aug '16

17 Aug '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: db2854dbe969bd83119b035a3c78b148bb6f34c6 https://github.com/galaxyproject/usegalaxy-playbook/commit/db2854dbe969bd83… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-08-17 (Wed, 17 Aug 2016) Changed paths: M common/host_vars/galaxy-db-01.tacc.utexas.edu.yml M common_roles M galaxy.yml M galaxy_infrastructure.yml A production/group_vars/galaxyjobservers.yml M production/group_vars/galaxyservers.yml A production/group_vars/galaxywebservers.yml A production/host_vars/galaxy-web-03.tacc.utexas.edu.yml A production/host_vars/galaxy-web-04.tacc.utexas.edu.yml M production/inventory M roles/usegalaxy_admin/tasks/main.yml M roles/usegalaxy_privileged/tasks/main.yml M stage/group_vars/galaxyservers.yml M templates/galaxy/usegalaxy.org/config/job_conf.xml.j2 M templates/nginx/usegalaxy.j2 M templates/supervisor/galaxy.j2 A templates/supervisor/galaxy_handler.j2 Log Message: ----------- Separate Galaxy servers into web and job server groups, run jobs on galaxy-web-03 and galaxy-web-04.

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[galaxyproject/galaxy] 4ada33: prevent TS from creating sessions for repo status ...
by GitHub 17 Aug '16

17 Aug '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4ada33d06be9ab789a7aaee2d4366e25dbd98ce0 https://github.com/galaxyproject/galaxy/commit/4ada33d06be9ab789a7aaee2d436… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-08-04 (Thu, 04 Aug 2016) Changed paths: M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/buildapp.py M lib/galaxy/webapps/tool_shed/controllers/repository.py Log Message: ----------- prevent TS from creating sessions for repo status checks this had to be done: - enable Routes middleware - redirect in the middleware before the request reaches the app - properly forward the contents of the query string - move the controller method to the API namespace and properly decorate - provide the ability to not hexlify the response (so we can dump it in future Galaxy release) I hope that this work will allow easier transition from controllers to APIs and also smoother deprecation of API endpoints. Commit: c311c4a3c82d7d114075c400fe638bb0ab0a4a6e https://github.com/galaxyproject/galaxy/commit/c311c4a3c82d7d114075c400fe63… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-08-04 (Thu, 04 Aug 2016) Changed paths: M lib/galaxy/webapps/tool_shed/buildapp.py Log Message: ----------- reorder middleware imports, explicitly store and pass routes mapper Commit: 682a28de67c3f1ccd0900067e19299deac640cfe https://github.com/galaxyproject/galaxy/commit/682a28de67c3f1ccd0900067e192… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-08-04 (Thu, 04 Aug 2016) Changed paths: M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/buildapp.py Log Message: ----------- amke endpoint name more RESTful Commit: b41f500a9fb88c43dd8ed99178a101512db4d209 https://github.com/galaxyproject/galaxy/commit/b41f500a9fb88c43dd8ed99178a1… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-08-05 (Fri, 05 Aug 2016) Changed paths: M client/galaxy/style/less/base.less M static/style/blue/base.css Log Message: ----------- Merge branch 'dev' into sessionless_controller_using_redirect Commit: fb1703587b9170712aeafe09ab8068c7c981b47b https://github.com/galaxyproject/galaxy/commit/fb1703587b9170712aeafe09ab80… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-08-05 (Fri, 05 Aug 2016) Changed paths: M config/tool_shed.ini.sample M lib/galaxy/config.py M lib/galaxy/webapps/tool_shed/app.py M lib/galaxy/webapps/tool_shed/config.py Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into sessionless_controller_using_redirect Commit: 674f5989e4bf5abb1af8afe6477e6c2294ed7977 https://github.com/galaxyproject/galaxy/commit/674f5989e4bf5abb1af8afe6477e… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-08-05 (Fri, 05 Aug 2016) Changed paths: M lib/galaxy/config.py M lib/galaxy/webapps/tool_shed/app.py Log Message: ----------- make routes.middleware less chatty, and reorder import Commit: f957f80854411cbd29326805bf696338c0725ecb https://github.com/galaxyproject/galaxy/commit/f957f80854411cbd29326805bf69… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-08-05 (Fri, 05 Aug 2016) Changed paths: M lib/galaxy/webapps/tool_shed/buildapp.py Log Message: ----------- be python3 compatible, thanks EagleEyes Commit: 4d5851ae715e5f7bec6d5013f06001f527219f13 https://github.com/galaxyproject/galaxy/commit/4d5851ae715e5f7bec6d5013f060… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-08-08 (Mon, 08 Aug 2016) Changed paths: M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt M client/galaxy/scripts/layout/scratchbook.js M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/tool/tool-form.js M client/galaxy/scripts/mvc/ui/ui-buttons.js M config/job_conf.xml.sample_advanced M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/tools/deps/containers.py M lib/galaxy/tools/deps/docker_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/datatypes/custom_datatype_manager.py M lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/galaxy_install/installed_repository_manager.py M lib/tool_shed/galaxy_install/migrate/common.py M lib/tool_shed/galaxy_install/migrate/versions/0001_tools.py M lib/tool_shed/galaxy_install/migrate/versions/0002_tools.py M lib/tool_shed/galaxy_install/migrate/versions/0003_tools.py M lib/tool_shed/galaxy_install/migrate/versions/0004_tools.py M lib/tool_shed/galaxy_install/migrate/versions/0005_tools.py M lib/tool_shed/galaxy_install/migrate/versions/0006_tools.py M lib/tool_shed/galaxy_install/migrate/versions/0007_tools.py M lib/tool_shed/galaxy_install/migrate/versions/0008_tools.py M lib/tool_shed/galaxy_install/migrate/versions/0009_tools.py M lib/tool_shed/galaxy_install/migrate/versions/0010_tools.py M lib/tool_shed/galaxy_install/migrate/versions/0011_tools.py M lib/tool_shed/galaxy_install/migrate/versions/0012_tools.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/install_environment.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py M lib/tool_shed/galaxy_install/tool_migration_manager.py M lib/tool_shed/galaxy_install/tools/data_manager.py M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py M lib/tool_shed/galaxy_install/update_repository_manager.py M lib/tool_shed/grids/admin_grids.py M lib/tool_shed/grids/repository_grids.py M lib/tool_shed/grids/repository_review_grids.py M lib/tool_shed/managers/repositories.py M lib/tool_shed/metadata/metadata_generator.py M lib/tool_shed/metadata/repository_metadata_manager.py M lib/tool_shed/repository_types/registry.py M lib/tool_shed/tool_shed_registry.py M lib/tool_shed/tools/data_table_manager.py M lib/tool_shed/util/hg_util.py M lib/tool_shed/util/readme_util.py M lib/tool_shed/util/repository_content_util.py M lib/tool_shed/util/repository_util.py M lib/tool_shed/util/shed_util_common.py M lib/tool_shed/util/tool_util.py M lib/tool_shed/util/web_util.py M lib/tool_shed/util/workflow_util.py M lib/tool_shed/utility_containers/utility_container_manager.py M scripts/tool_shed/api/common.py M setup.cfg M static/maps/layout/scratchbook.js.map M static/maps/mvc/dataset/dataset-li.js.map M static/maps/mvc/tool/tool-form.js.map M static/maps/mvc/ui/ui-buttons.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/scratchbook.js M static/scripts/mvc/dataset/dataset-li.js M static/scripts/mvc/tool/tool-form.js M static/scripts/mvc/ui/ui-buttons.js R static/style/blue/tool_menu.css M templates/webapps/galaxy/admin/index.mako M templates/webapps/galaxy/workflow/editor.mako M templates/webapps/reports/index.mako M templates/webapps/tool_shed/admin/index.mako M templates/webapps/tool_shed/group/index.mako M templates/webapps/tool_shed/index.mako Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into sessionless_controller_using_redirect Commit: 62ca1312d6dbc56795f34f646ed59fb01955ddb3 https://github.com/galaxyproject/galaxy/commit/62ca1312d6dbc56795f34f646ed5… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-08-08 (Mon, 08 Aug 2016) Changed paths: M config/tool_shed.ini.sample M lib/galaxy/webapps/tool_shed/buildapp.py M lib/galaxy/webapps/tool_shed/config.py M lib/galaxy/webapps/tool_shed/controllers/hg.py R lib/galaxy/webapps/tool_shed/framework/middleware/hg.py M test/shed_functional/functional/test_0310_hg_api_features.py Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into sessionless_controller_using_redirect Conflicts: lib/galaxy/webapps/tool_shed/buildapp.py Commit: 123ceeb34ac1858fcc333d332bb2ae4e671d6c72 https://github.com/galaxyproject/galaxy/commit/123ceeb34ac1858fcc333d332bb2… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-08-15 (Mon, 15 Aug 2016) Changed paths: M .ci/first_startup.sh M Makefile 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/hdca-model.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/ui/ui-portlet.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/galaxy/style/less/ui.less M config/galaxy.ini.sample A doc/source/dev/build_a_job_runner.rst M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/neo4j.py M lib/galaxy/dependencies/conditional-requirements.txt M lib/galaxy/managers/datasets.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/deps/resolvers/galaxy_packages.py M lib/galaxy/tools/deps/resolvers/tool_shed_packages.py M lib/galaxy/tools/deps/views.py M lib/galaxy/tools/imp_exp/export_history.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/dataset_matcher.py M lib/galaxy/util/__init__.py M lib/galaxy/webapps/galaxy/api/datasets.py M lib/galaxy/webapps/galaxy/api/lda_datasets.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py M run.sh M scripts/common_startup.sh M static/maps/mvc/form/form-input.js.map M static/maps/mvc/form/form-parameters.js.map M static/maps/mvc/form/form-repeat.js.map M static/maps/mvc/form/form-section.js.map M static/maps/mvc/form/form-view.js.map M static/maps/mvc/history/hdca-model.js.map M static/maps/mvc/tool/tool-form-composite.js.map M static/maps/mvc/ui/ui-portlet.js.map M static/maps/mvc/ui/ui-select-default.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/form/form-input.js M static/scripts/mvc/form/form-parameters.js M static/scripts/mvc/form/form-repeat.js M static/scripts/mvc/form/form-section.js M static/scripts/mvc/form/form-view.js M static/scripts/mvc/history/hdca-model.js M static/scripts/mvc/tool/tool-form-composite.js M static/scripts/mvc/ui/ui-portlet.js M static/scripts/mvc/ui/ui-select-default.js M static/style/blue/base.css M test/qunit/test-data/fakeserver.js M test/qunit/tests/form_tests.js M test/unit/tools/test_tool_deps.py M tools/genomespace/genomespace_file_browser.py M tools/genomespace/genomespace_importer.py Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into sessionless_controller_using_redirect Commit: 85aec3bc119b1e8f450c3eff2da1414c53447cca https://github.com/galaxyproject/galaxy/commit/85aec3bc119b1e8f450c3eff2da1… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-08-15 (Mon, 15 Aug 2016) Changed paths: M .ci/flake8_lint_include_list.txt M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/style/less/library.less M lib/galaxy/app.py M lib/galaxy/config.py M lib/galaxy/datatypes/interval.py M lib/galaxy/queues.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/watcher.py A lib/galaxy/util/postfork.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/reports/buildapp.py M lib/galaxy/webapps/tool_shed/buildapp.py M lib/galaxy/webapps/tool_shed/controllers/hg.py M lib/galaxy/workflow/modules.py M lib/tool_shed/galaxy_install/update_repository_manager.py 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 M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tool/tool-form-composite.js M static/style/blue/base.css M static/style/blue/library.css M templates/webapps/galaxy/workflow/run.mako Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into sessionless_controller_using_redirect Commit: 0dd74d164fc32b186ccca334a0e97c8ae1fae6fa https://github.com/galaxyproject/galaxy/commit/0dd74d164fc32b186ccca334a0e9… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-08-16 (Tue, 16 Aug 2016) Changed paths: M lib/galaxy/webapps/tool_shed/buildapp.py Log Message: ----------- create own mapper for middleware redirects Commit: 3fd7ba3e8eb46caca843e85f9066cdf24f5d203d https://github.com/galaxyproject/galaxy/commit/3fd7ba3e8eb46caca843e85f9066… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-08-17 (Wed, 17 Aug 2016) Changed paths: M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/buildapp.py Log Message: ----------- fix pep8 Commit: 000e7ea7c9a8c7e069f3ca92c548e38110905003 https://github.com/galaxyproject/galaxy/commit/000e7ea7c9a8c7e069f3ca92c548… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-08-17 (Wed, 17 Aug 2016) Changed paths: M lib/galaxy/config.py M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/app.py M lib/galaxy/webapps/tool_shed/buildapp.py M lib/galaxy/webapps/tool_shed/controllers/repository.py Log Message: ----------- Merge pull request #2732 from martenson/sessionless_controller_using_redirect prevent TS from creating sessions for repo status checks Compare: https://github.com/galaxyproject/galaxy/compare/5cc3613ff555...000e7ea7c9a8

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[galaxyproject/infrastructure-playbook] 2b428e: Install slurm-drmaa on galaxy nodes. Also fix the ...
by GitHub 17 Aug '16

17 Aug '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 2b428e56a530a4c7065242aa3dff89c33ce87993 https://github.com/galaxyproject/infrastructure-playbook/commit/2b428e56a53… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-08-17 (Wed, 17 Aug 2016) Changed paths: M taccenv/group_vars/galaxyservers.yml Log Message: ----------- Install slurm-drmaa on galaxy nodes. Also fix the Docker yum repo url

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[galaxyproject/usegalaxy-playbook] f16a48: Fix reports (supervisor runs on 9001)
by GitHub 17 Aug '16

17 Aug '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: f16a4858e647e4040d45ff83afb681cd71e6320a https://github.com/galaxyproject/usegalaxy-playbook/commit/f16a4858e647e404… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-08-17 (Wed, 17 Aug 2016) Changed paths: M stage/inventory M templates/galaxy/common/config/reports.ini.j2 M templates/nginx/galaxy_test.j2 M templates/nginx/tacc_protected.j2 Log Message: ----------- Fix reports (supervisor runs on 9001)

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[galaxyproject/galaxy] dfccd9: Fix setting metadata in galaxy.json for working di...
by GitHub 17 Aug '16

17 Aug '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: dfccd902b00426c79670e77ef11696f381f5e10d https://github.com/galaxyproject/galaxy/commit/dfccd902b00426c79670e77ef116… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-08-04 (Thu, 04 Aug 2016) Changed paths: M lib/galaxy_ext/metadata/set_metadata.py Log Message: ----------- Fix setting metadata in galaxy.json for working directory isolation change. This has been broken since 16.04 I guess? Maybe retry internally means it hasn't been an issue? Commit: af6bd40a57608464e3e70226c46490681d213446 https://github.com/galaxyproject/galaxy/commit/af6bd40a57608464e3e70226c464… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-08-04 (Thu, 04 Aug 2016) Changed paths: M lib/galaxy/tools/parameters/output_collect.py Log Message: ----------- Fix setting dbkey in galaxy.json for discovered primary datasets. Based on the change - I guess this must have been broken a long time ago - so maybe it isn't used? A subsequent change will add a test though - so hopefully there will be no regressions of this again. Commit: e72201d2041a80db0042af9493b1f2f1512d68f7 https://github.com/galaxyproject/galaxy/commit/e72201d2041a80db0042af9493b1… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-08-04 (Thu, 04 Aug 2016) Changed paths: M lib/galaxy/jobs/__init__.py M test/base/interactor.py M test/functional/tools/samples_tool_conf.xml A test/functional/tools/tool_provided_metadata_1.xml Log Message: ----------- Improvements for metadata specification w/galaxy.json of explicit outputs. I call explicit outputs galaxy.json entries of type="dataset" (as opposed to type="new_primary_dataset" - which I call discovered datasets). Previously galaxy.json could set the name and extension of these datasets. I've added a test case to verify this and a small tweak to the tool test framework to allow easy testing of such metadata setting. In order to bring explicit output metadata setting closer to parity with discovered dataset metadata setting, I've added the ability to define 'dbkey' and 'info' entries in galaxy.json for these outputs. Commit: 1fab4dfaff3ebbb0f1c80c7b51f44125272b6cb9 https://github.com/galaxyproject/galaxy/commit/1fab4dfaff3ebbb0f1c80c7b51f4… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-08-04 (Thu, 04 Aug 2016) Changed paths: M test/base/interactor.py M test/functional/tools/tool_provided_metadata_1.xml Log Message: ----------- Add hack to test sleeping when verifying metadata. Seems like a race condition but I can't determine why there would be one here - this check should help determine if it is a race condition or something else. Commit: 76e84eb5e00e78e9e49667d39b2f3d91352f3d5a https://github.com/galaxyproject/galaxy/commit/76e84eb5e00e78e9e49667d39b2f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-08-04 (Thu, 04 Aug 2016) Changed paths: M test/functional/tools/samples_tool_conf.xml A test/functional/tools/tool_provided_metadata_2.xml Log Message: ----------- Add tool test for discovered dataset metadata from galaxy.json. Commit: 41701aa6fe696e2ef1b26dec261f416686d02e20 https://github.com/galaxyproject/galaxy/commit/41701aa6fe696e2ef1b26dec261f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-08-04 (Thu, 04 Aug 2016) Changed paths: M test/base/interactor.py Log Message: ----------- Improved error message when testing metadata in tool tests. Commit: 56bb42ad2536732c195c218c1b89cf174cd02b78 https://github.com/galaxyproject/galaxy/commit/56bb42ad2536732c195c218c1b89… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-08-04 (Thu, 04 Aug 2016) Changed paths: M lib/galaxy/tools/parser/xml.py M test/functional/tools/tool_provided_metadata_2.xml Log Message: ----------- Fix allow tool to just test discovered datasets. Previously some sort of test on the base file the primary datasets were keyed on was required. Commit: 9ae333987b2cd713526ae68800ade5e0a73b1e08 https://github.com/galaxyproject/galaxy/commit/9ae333987b2cd713526ae68800ad… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-08-04 (Thu, 04 Aug 2016) Changed paths: M test/base/interactor.py M test/functional/tools/samples_tool_conf.xml A test/functional/tools/tool_provided_metadata_3.xml Log Message: ----------- Test tool demo-ing discovered dataset datatype metadata w/galaxy.json. Also update the metadata test comparison to support non-textual values (e.g. floating point and integer metadata fields). Commit: 1e8dd73b6def69aa8533f087e22d99d3423f94b3 https://github.com/galaxyproject/galaxy/commit/1e8dd73b6def69aa8533f087e22d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-08-16 (Tue, 16 Aug 2016) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- Rework small for loop per @mvdbeek's suggestion... ... see https://github.com/galaxyproject/galaxy/pull/2697#discussion_r74939815 for context. Commit: 5cc3613ff55537df7dbcfe7d6ba7ef4a679be935 https://github.com/galaxyproject/galaxy/commit/5cc3613ff55537df7dbcfe7d6ba7… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-08-17 (Wed, 17 Aug 2016) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/tools/parser/xml.py M lib/galaxy_ext/metadata/set_metadata.py M test/base/interactor.py M test/functional/tools/samples_tool_conf.xml A test/functional/tools/tool_provided_metadata_1.xml A test/functional/tools/tool_provided_metadata_2.xml A test/functional/tools/tool_provided_metadata_3.xml Log Message: ----------- Merge pull request #2697 from jmchilton/metadata_fixing Fixes and improvements for galaxy.json. Compare: https://github.com/galaxyproject/galaxy/compare/0210fb31b676...5cc3613ff555

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[galaxyproject/galaxy] 510290: Add example of regressed 16.04 behavior related to...
by GitHub 17 Aug '16

17 Aug '16

Branch: refs/heads/release_16.04 Home: https://github.com/galaxyproject/galaxy Commit: 510290feea4bb328566770b636f9f093d00e93b0 https://github.com/galaxyproject/galaxy/commit/510290feea4bb328566770b636f9… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-08-16 (Tue, 16 Aug 2016) Changed paths: A test/functional/tools/dbkey_output_action.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Add example of regressed 16.04 behavior related to dbkey output actions. Commit: 88d02dba6e851f0f60758a575920f6e7b130e261 https://github.com/galaxyproject/galaxy/commit/88d02dba6e851f0f60758a575920… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-08-16 (Tue, 16 Aug 2016) Changed paths: M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Don't fill in a cheetah default if unavailable. ... in metadata hack from #961. Commit: 0110d5a05a4b1b357a3f321471fce1b2d4960e67 https://github.com/galaxyproject/galaxy/commit/0110d5a05a4b1b357a3f321471fc… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-08-16 (Tue, 16 Aug 2016) Changed paths: M test/functional/tools/dbkey_output_action.xml Log Message: ----------- Add a test case to dbkey_output_action.xml. Per @nsoranzo's template and suggestion. Commit: e06cf9a97802d4c6a2ab97d973a373675e68b751 https://github.com/galaxyproject/galaxy/commit/e06cf9a97802d4c6a2ab97d973a3… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-08-16 (Tue, 16 Aug 2016) Changed paths: M lib/galaxy/util/template.py Log Message: ----------- Add None check to fill_template... ... as requested by @nsoranzo. Commit: d1c58f7ab039cc457d7e3fc97857cd2c314c5e5c https://github.com/galaxyproject/galaxy/commit/d1c58f7ab039cc457d7e3fc97857… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-08-17 (Wed, 17 Aug 2016) Changed paths: M lib/galaxy/tools/actions/__init__.py M lib/galaxy/util/template.py A test/functional/tools/dbkey_output_action.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge pull request #2800 from jmchilton/dbkey_output_without_cond [16.04] Fix dbkey problem discovered by @hrhotz Compare: https://github.com/galaxyproject/galaxy/compare/752df7f82b12...d1c58f7ab039

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