November 2017 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/usegalaxy-playbook] a71ffe: Fix datatypes config path.
by GitHub 16 Nov '17

16 Nov '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: a71ffea273966efec7805f500beb3edc874d45d0 https://github.com/galaxyproject/usegalaxy-playbook/commit/a71ffea273966efe… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-11-16 (Thu, 16 Nov 2017) Changed paths: M env/main/templates/galaxy/config/job_conf.xml.j2 Log Message: ----------- Fix datatypes config path.

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[galaxyproject/infrastructure-playbook] c15b07: Set up additional mail forwards at TACC
by GitHub 16 Nov '17

16 Nov '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: c15b07641f91039d0acd69b379fff5cb9a0e1ac3 https://github.com/galaxyproject/infrastructure-playbook/commit/c15b07641f9… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-11-16 (Thu, 16 Nov 2017) Changed paths: M taccenv/playbook.yml Log Message: ----------- Set up additional mail forwards at TACC

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[galaxyproject/infrastructure-playbook] 189259: Fix grafana slurp database target for Main move
by GitHub 16 Nov '17

16 Nov '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 1892596434860fba38194bf5974640e6bb8164c5 https://github.com/galaxyproject/infrastructure-playbook/commit/18925964348… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-11-16 (Thu, 16 Nov 2017) Changed paths: M roles/stats/templates/galaxy_slurp.py.j2 Log Message: ----------- Fix grafana slurp database target for Main move

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[galaxyproject/usegalaxy-playbook] c8e661: Fix Jetstream datatypes config path.
by GitHub 16 Nov '17

16 Nov '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: c8e661e86541b0a9567359d85b5215c6afc59538 https://github.com/galaxyproject/usegalaxy-playbook/commit/c8e661e86541b0a9… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-11-16 (Thu, 16 Nov 2017) Changed paths: M env/main/host_vars/jetstream-iu0.galaxyproject.org.yml M env/main/host_vars/jetstream-tacc0.galaxyproject.org.yml M env/test/host_vars/jetstream-iu0.galaxyproject.org.yml M env/test/host_vars/jetstream-tacc0.galaxyproject.org.yml Log Message: ----------- Fix Jetstream datatypes config path.

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[galaxyproject/galaxy] 715760: fix few stray wiki links
by GitHub 16 Nov '17

16 Nov '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 7157600f85993eb8570079d7c7d5b82d0e2af3f6 https://github.com/galaxyproject/galaxy/commit/7157600f85993eb8570079d7c7d5… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-11-15 (Wed, 15 Nov 2017) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd M templates/user/register.mako M tools/data_source/microbial_import.xml Log Message: ----------- fix few stray wiki links Commit: 7745897e59114f750425cddd7d8d3c271bf6f802 https://github.com/galaxyproject/galaxy/commit/7745897e59114f750425cddd7d8d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-16 (Thu, 16 Nov 2017) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd M templates/user/register.mako M tools/data_source/microbial_import.xml Log Message: ----------- Merge pull request #5020 from martenson/wiki-cleanup fix few stray wiki links Compare: https://github.com/galaxyproject/galaxy/compare/5c28618a27d0...7745897e5911

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[galaxyproject/usegalaxy-playbook] 1a57b5: Changelog for manual fixes for Jetstream and Bridg...
by GitHub 15 Nov '17

15 Nov '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 1a57b5cc5a7846773ec795b0a9b668e0196118b5 https://github.com/galaxyproject/usegalaxy-playbook/commit/1a57b5cc5a784677… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-11-15 (Wed, 15 Nov 2017) Changed paths: M CHANGELOG.md Log Message: ----------- Changelog for manual fixes for Jetstream and Bridges Commit: 4622552c52d0cfd70afe5e072976b3f184fefd99 https://github.com/galaxyproject/usegalaxy-playbook/commit/4622552c52d0cfd7… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-11-15 (Wed, 15 Nov 2017) Changed paths: M env/main/files/galaxy/galaxy_version.yml M env/test/files/galaxy/galaxy_version.yml Log Message: ----------- Update Test and Main Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/889b5d5e53dc...…

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[galaxyproject/usegalaxy-playbook] 889b5d: Disable use of the xsede manager on Stampede becau...
by GitHub 15 Nov '17

15 Nov '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 889b5d5e53dc6d613c98c1b975b5c031be3e82ae https://github.com/galaxyproject/usegalaxy-playbook/commit/889b5d5e53dc6d61… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-11-15 (Wed, 15 Nov 2017) Changed paths: M env/main/host_vars/login5.stampede.tacc.utexas.edu.yml M env/test/host_vars/login5.stampede.tacc.utexas.edu.yml Log Message: ----------- Disable use of the xsede manager on Stampede because the stats collection script is asking for a sudo password.

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[galaxyproject/galaxy] d53903: parse_interpreter: log a warning only if interpret...
by GitHub 15 Nov '17

15 Nov '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d5390350b8cfbdb4910cf0e671dbffb66f27f9e4 https://github.com/galaxyproject/galaxy/commit/d5390350b8cfbdb4910cf0e671db… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-11-15 (Wed, 15 Nov 2017) Changed paths: M lib/galaxy/tools/parser/xml.py Log Message: ----------- parse_interpreter: log a warning only if interpreter is set Also return None instead of False if there is no `<command>`. Fix typo in warning. Commit: 5c28618a27d054c60285dc05064c03c3bb19ad14 https://github.com/galaxyproject/galaxy/commit/5c28618a27d054c60285dc05064c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-15 (Wed, 15 Nov 2017) Changed paths: M lib/galaxy/tools/parser/xml.py Log Message: ----------- Merge pull request #5015 from nsoranzo/fix_parse_interpreter parse_interpreter: log a warning only if interpreter is set Compare: https://github.com/galaxyproject/galaxy/compare/38c620c62bd7...5c28618a27d0

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[galaxyproject/galaxy] 08eb98: enhance hdca creation endpoint to accept lddas
by GitHub 15 Nov '17

15 Nov '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 08eb9859f25dff98edbf2fc4be95012219d389a5 https://github.com/galaxyproject/galaxy/commit/08eb9859f25dff98edbf2fc4be95… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-11-13 (Mon, 13 Nov 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/history_contents.py Log Message: ----------- enhance hdca creation endpoint to accept lddas by implementing automatic conversion of any such elements Commit: 5609bfc307cd9a6bdd86cd49128d3c4f8407613b https://github.com/galaxyproject/galaxy/commit/5609bfc307cd9a6bdd86cd49128d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-14 (Tue, 14 Nov 2017) Changed paths: M test/api/test_libraries.py M test/base/populators.py Log Message: ----------- More API library testing. Commit: 8a41921b49106276d1e8ed925464e734c07664d8 https://github.com/galaxyproject/galaxy/commit/8a41921b49106276d1e8ed925464… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-14 (Tue, 14 Nov 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/history_contents.py Log Message: ----------- Respect permissions when creating HDAs/HDCAs from LDDAs. Commit: 25e53e13453d594c56cf6f48474d74c7a9a09368 https://github.com/galaxyproject/galaxy/commit/25e53e13453d594c56cf6f48474d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-14 (Tue, 14 Nov 2017) Changed paths: M test/api/test_history_contents.py Log Message: ----------- API tests for creating HDCAs from LDDA elements. Commit: 47737659747955390292723d57381c2d3ca92f63 https://github.com/galaxyproject/galaxy/commit/47737659747955390292723d5738… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-14 (Tue, 14 Nov 2017) Changed paths: R .ci/flake8_lint_include_list.txt R .ci/flake8_wrapper_imports.sh M .ci/jenkins/selenium/run_tests.sh M .travis.yml M README.rst M client/galaxy/scripts/admin.toolshed.js M client/galaxy/scripts/apps/panels/admin-panel.js M client/galaxy/scripts/galaxy.interactive_environments.js M client/galaxy/scripts/galaxy.library.js M client/galaxy/scripts/galaxy.pages.js M client/galaxy/scripts/i18n.js M client/galaxy/scripts/layout/modal.js M client/galaxy/scripts/mvc/annotation.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/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/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/grid/grid-shared.js M client/galaxy/scripts/mvc/grid/grid-template.js M client/galaxy/scripts/mvc/grid/grid-view.js M client/galaxy/scripts/mvc/history/hda-li-edit.js M client/galaxy/scripts/mvc/history/hda-li.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 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test/unit/tools/test_history_imp_exp.py M test/unit/tools/test_parameter_parsing.py M test/unit/tools/test_parsing.py M test/unit/tools/test_select_parameters.py M test/unit/tools/test_tool_deps.py M test/unit/tools/test_tool_loader.py M test/unit/tools/test_toolbox.py M test/unit/tools/test_watcher.py M test/unit/tools_support.py M test/unit/visualizations/plugins/test_VisualizationPlugin.py M test/unit/visualizations/plugins/test_VisualizationsRegistry.py M test/unit/web/framework/test_webapp.py M test/unit/workflows/test_modules.py M test/unit/workflows/test_run_parameters.py M test/unit/workflows/test_workflow_progress.py M tools/filters/gff/gff_filter_by_attribute.py M tools/filters/gff/gff_filter_by_feature_count.py M tools/phenotype_association/senatag.py M tox.ini Log Message: ----------- Merge remote-tracking branch 'jmchilton/dev' into lib-to-colllection Commit: 87987b4c949b881ba59c17caa5fd8559c89eef6a https://github.com/galaxyproject/galaxy/commit/87987b4c949b881ba59c17caa5fd… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-11-15 (Wed, 15 Nov 2017) Changed paths: R .ci/flake8_lint_include_list.txt R .ci/flake8_wrapper_imports.sh M .ci/jenkins/selenium/run_tests.sh M .travis.yml M README.rst M client/galaxy/scripts/admin.toolshed.js M client/galaxy/scripts/apps/panels/admin-panel.js M client/galaxy/scripts/galaxy.interactive_environments.js M client/galaxy/scripts/galaxy.library.js M client/galaxy/scripts/galaxy.pages.js M client/galaxy/scripts/i18n.js M client/galaxy/scripts/layout/modal.js M client/galaxy/scripts/mvc/annotation.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 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static/scripts/viz/trackster.js M static/style/blue/trackster.css R templates/admin/library/grid.mako R templates/admin/library/new_library.mako M templates/admin/tool_shed_repository/repository_actions_menu.mako M templates/admin/tool_shed_repository/view_tool_metadata.mako M templates/show_params.mako M templates/webapps/galaxy/admin/center.mako R templates/webapps/galaxy/library/common/browse_library.mako R templates/webapps/galaxy/library/common/browse_library_opt.mako R templates/webapps/galaxy/library/common/common.mako R templates/webapps/galaxy/library/common/folder_info.mako R templates/webapps/galaxy/library/common/folder_permissions.mako R templates/webapps/galaxy/library/common/import_datasets_to_histories.mako R templates/webapps/galaxy/library/common/ldda_edit_info.mako R templates/webapps/galaxy/library/common/ldda_info.mako R templates/webapps/galaxy/library/common/ldda_permissions.mako R templates/webapps/galaxy/library/common/library_dataset_info.mako R 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test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py M test/unit/jobs/test_job_wrapper.py M test/unit/jobs/test_mapper.py M test/unit/jobs/test_runner_local.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/shed_unit/test_installed_repository_manager.py M test/unit/shed_unit/test_tool_panel_manager.py M test/unit/test_objectstore.py M test/unit/tools/test_actions.py M test/unit/tools/test_collect_primary_datasets.py M test/unit/tools/test_column_parameters.py M test/unit/tools/test_conda_resolution.py M test/unit/tools/test_data_parameters.py M test/unit/tools/test_dataset_matcher.py M test/unit/tools/test_evaluation.py M test/unit/tools/test_execution.py M test/unit/tools/test_history_imp_exp.py M test/unit/tools/test_parameter_parsing.py M test/unit/tools/test_parsing.py M test/unit/tools/test_select_parameters.py M test/unit/tools/test_tool_deps.py M test/unit/tools/test_tool_loader.py M test/unit/tools/test_toolbox.py M test/unit/tools/test_watcher.py M test/unit/tools_support.py M test/unit/visualizations/plugins/test_VisualizationPlugin.py M test/unit/visualizations/plugins/test_VisualizationsRegistry.py M test/unit/web/framework/test_webapp.py M test/unit/workflows/test_modules.py M test/unit/workflows/test_run_parameters.py M test/unit/workflows/test_workflow_progress.py M tools/filters/gff/gff_filter_by_attribute.py M tools/filters/gff/gff_filter_by_feature_count.py M tools/phenotype_association/senatag.py M tox.ini Log Message: ----------- Merge pull request #25 from jmchilton/lib-to-colllection Merge with dev and add more tests. Commit: abe1b240c33c0a2031a56fc52b8bcd5ec34ae27d https://github.com/galaxyproject/galaxy/commit/abe1b240c33c0a2031a56fc52b8b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-15 (Wed, 15 Nov 2017) Changed paths: M test/api/test_libraries.py Log Message: ----------- Fix broken library test I recently added. Commit: 38c620c62bd7f9cce5c3a792563d88ec5120e3e0 https://github.com/galaxyproject/galaxy/commit/38c620c62bd7f9cce5c3a792563d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-15 (Wed, 15 Nov 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/history_contents.py M test/api/test_history_contents.py M test/api/test_libraries.py M test/base/populators.py Log Message: ----------- Merge pull request #4998 from martenson/lib-to-colllection enhance hdca creation API endpoint to accept lddas Compare: https://github.com/galaxyproject/galaxy/compare/f44cbd5d8210...38c620c62bd7

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[galaxyproject/galaxy] ae48c9: Remove search templates (unused)
by GitHub 15 Nov '17

15 Nov '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ae48c9a3c1a4b50da6dadc1bb236456a22ed8472 https://github.com/galaxyproject/galaxy/commit/ae48c9a3c1a4b50da6dadc1bb236… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-11-15 (Wed, 15 Nov 2017) Changed paths: R templates/search/index.mako Log Message: ----------- Remove search templates (unused) Commit: f44cbd5d821096a667d6237f842e139c5d60fbc3 https://github.com/galaxyproject/galaxy/commit/f44cbd5d821096a667d6237f842e… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2017-11-15 (Wed, 15 Nov 2017) Changed paths: R templates/search/index.mako Log Message: ----------- Merge pull request #5014 from dannon/remove_search_templates Remove unused search template Compare: https://github.com/galaxyproject/galaxy/compare/7bede53beff3...f44cbd5d8210

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