- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 1be896: data_column to json config file
by GitHub 28 Mar '16

28 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 1be896fd157dffcd5c2f9b20dd0a5fc866faadbe https://github.com/galaxyproject/galaxy/commit/1be896fd157dffcd5c2f9b20dd0a… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M lib/galaxy/tools/parameters/wrapped_json.py Log Message: ----------- data_column to json config file Commit: 71d8b4a6c123f05aaedffd0e38db0d921b7a0410 https://github.com/galaxyproject/galaxy/commit/71d8b4a6c123f05aaedffd0e38db… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-28 (Mon, 28 Mar 2016) Changed paths: M lib/galaxy/tools/parameters/wrapped_json.py Log Message: ----------- Merge pull request #2026 from bgruening/param_configfile_data_column data_column to json config file Compare: https://github.com/galaxyproject/galaxy/compare/5a7ba04cd9f8...71d8b4a6c123

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[galaxyproject/galaxy] 962866: Remove install and test framework.
by GitHub 28 Mar '16

28 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 962866478a020b3fc794f76f89696ada60881d17 https://github.com/galaxyproject/galaxy/commit/962866478a020b3fc794f76f8969… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-25 (Fri, 25 Mar 2016) Changed paths: R test/install_and_test_tool_shed_repositories/__init__.py R test/install_and_test_tool_shed_repositories/base/__init__.py R test/install_and_test_tool_shed_repositories/base/test_db_util.py R test/install_and_test_tool_shed_repositories/base/twilltestcase.py R test/install_and_test_tool_shed_repositories/base/util.py R test/install_and_test_tool_shed_repositories/functional/__init__.py R test/install_and_test_tool_shed_repositories/functional/test_install_repositories.py R test/install_and_test_tool_shed_repositories/repositories_with_tools/__init__.py R test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py R test/install_and_test_tool_shed_repositories/tool_dependency_definitions/__init__.py R test/install_and_test_tool_shed_repositories/tool_dependency_definitions/functional_tests.py Log Message: ----------- Remove install and test framework. Commit: 5a7ba04cd9f85661a4681b00427b3c1aa815d988 https://github.com/galaxyproject/galaxy/commit/5a7ba04cd9f85661a4681b00427b… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2016-03-28 (Mon, 28 Mar 2016) Changed paths: R test/install_and_test_tool_shed_repositories/__init__.py R test/install_and_test_tool_shed_repositories/base/__init__.py R test/install_and_test_tool_shed_repositories/base/test_db_util.py R test/install_and_test_tool_shed_repositories/base/twilltestcase.py R test/install_and_test_tool_shed_repositories/base/util.py R test/install_and_test_tool_shed_repositories/functional/__init__.py R test/install_and_test_tool_shed_repositories/functional/test_install_repositories.py R test/install_and_test_tool_shed_repositories/repositories_with_tools/__init__.py R test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py R test/install_and_test_tool_shed_repositories/tool_dependency_definitions/__init__.py R test/install_and_test_tool_shed_repositories/tool_dependency_definitions/functional_tests.py Log Message: ----------- Merge pull request #2018 from jmchilton/remove_iat Remove install and test code. Compare: https://github.com/galaxyproject/galaxy/compare/62fae769345e...5a7ba04cd9f8

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[galaxyproject/usegalaxy-playbook] a4218f: Replaced GCC2016 abstracts due slide: March 25 is ...
by GitHub 28 Mar '16

28 Mar '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: a4218f633e911fc458dcdf30516b2820b4fbdd38 https://github.com/galaxyproject/usegalaxy-playbook/commit/a4218f633e911fc4… Author: tnabtaf <clements(a)galaxyproject.org> Date: 2016-03-28 (Mon, 28 Mar 2016) Changed paths: A files/galaxy/common/static/welcome_img/GCC2016OralAbstractsDueApril8.png M templates/galaxy/common/static/welcome.html.j2 Log Message: ----------- Replaced GCC2016 abstracts due slide: March 25 is now April 8

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[galaxyproject/galaxy] 207af3: Fix multiple flag for workflow dataset inputs
by GitHub 28 Mar '16

28 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 207af3d97565885491096488621c0f7bd664b8e4 https://github.com/galaxyproject/galaxy/commit/207af3d97565885491096488621c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-03-27 (Sun, 27 Mar 2016) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Fix multiple flag for workflow dataset inputs Commit: 62fae769345e75c3852fc89f867bbc36cdb3423e https://github.com/galaxyproject/galaxy/commit/62fae769345e75c3852fc89f867b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-28 (Mon, 28 Mar 2016) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Merge pull request #2021 from guerler/fix_collection_002 Fix multiple flag for workflow dataset inputs Compare: https://github.com/galaxyproject/galaxy/compare/18300c9dc66a...62fae769345e

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[galaxyproject/galaxy] ee0a65: fix duplication of select2 entries
by GitHub 28 Mar '16

28 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ee0a65bf13a1fff8084aa19fdfd4831b66dd096d https://github.com/galaxyproject/galaxy/commit/ee0a65bf13a1fff8084aa19fdfd4… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-28 (Mon, 28 Mar 2016) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M static/maps/mvc/library/library-foldertoolbar-view.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/library/library-foldertoolbar-view.js Log Message: ----------- fix duplication of select2 entries leverage caching Commit: 2c76ba7502c9fa99d2b02f44d79009b119a243f8 https://github.com/galaxyproject/galaxy/commit/2c76ba7502c9fa99d2b02f44d790… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-28 (Mon, 28 Mar 2016) Changed paths: 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: ----------- repack client Commit: 18300c9dc66af06fb24601a5f907be8e5ff18dcb https://github.com/galaxyproject/galaxy/commit/18300c9dc66af06fb24601a5f907… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-03-28 (Mon, 28 Mar 2016) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M static/maps/mvc/library/library-foldertoolbar-view.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/library/library-foldertoolbar-view.js Log Message: ----------- Merge pull request #2022 from martenson/fix-select-dup fix duplication of select2 entries Compare: https://github.com/galaxyproject/galaxy/compare/625d9e53c3c9...18300c9dc66a

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[galaxyproject/galaxy] f70df2: Upgrade content selector, add test cases
by GitHub 28 Mar '16

28 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f70df2206097ec99683e0433c597ad2b2ac2decf https://github.com/galaxyproject/galaxy/commit/f70df2206097ec99683e0433c597… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-03-27 (Sun, 27 Mar 2016) Changed paths: M client/galaxy/scripts/mvc/form/form-parameters.js R client/galaxy/scripts/mvc/form/form-select-content.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/utils/utils.js M client/galaxy/style/less/ui.less M static/maps/mvc/form/form-parameters.js.map M static/maps/mvc/form/form-select-content.js.map M static/maps/mvc/ui/ui-select-default.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/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/form/form-parameters.js M static/scripts/mvc/form/form-select-content.js M static/scripts/mvc/ui/ui-select-default.js M static/scripts/utils/utils.js M static/style/blue/base.css M test/qunit/test-app.js M test/qunit/tests/ui_tests.js Log Message: ----------- Upgrade content selector, add test cases Commit: d0f7ce260d42daf21a26a30dd0d5ae1d4cf01ebb https://github.com/galaxyproject/galaxy/commit/d0f7ce260d42daf21a26a30dd0d5… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-03-27 (Sun, 27 Mar 2016) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-content.js M client/galaxy/scripts/utils/utils.js R static/maps/mvc/form/form-select-content.js.map A static/maps/mvc/ui/ui-select-content.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 R static/scripts/mvc/form/form-select-content.js A static/scripts/mvc/ui/ui-select-content.js M static/scripts/utils/utils.js M test/qunit/tests/ui_tests.js Log Message: ----------- Add workflow content selectors and test cases Commit: 625d9e53c3c91ddde6c59b6a02e5163acbc5add3 https://github.com/galaxyproject/galaxy/commit/625d9e53c3c91ddde6c59b6a02e5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-28 (Mon, 28 Mar 2016) Changed paths: M client/galaxy/scripts/mvc/form/form-parameters.js R client/galaxy/scripts/mvc/form/form-select-content.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/utils/utils.js M client/galaxy/style/less/ui.less M static/maps/mvc/form/form-parameters.js.map R static/maps/mvc/form/form-select-content.js.map A static/maps/mvc/ui/ui-select-content.js.map M static/maps/mvc/ui/ui-select-default.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/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/form/form-parameters.js R static/scripts/mvc/form/form-select-content.js A static/scripts/mvc/ui/ui-select-content.js M static/scripts/mvc/ui/ui-select-default.js M static/scripts/utils/utils.js M static/style/blue/base.css M test/qunit/test-app.js M test/qunit/tests/ui_tests.js Log Message: ----------- Merge pull request #2011 from guerler/revise_content_select_000 Revise content selection, add test cases Compare: https://github.com/galaxyproject/galaxy/compare/5b16589f2901...625d9e53c3c9

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[galaxyproject/galaxy] a8c22e: Remove twill functional tests we don't actively ru...
by GitHub 26 Mar '16

26 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a8c22ee9dbc8eb0f59ea55748db7a9c5cae50bc0 https://github.com/galaxyproject/galaxy/commit/a8c22ee9dbc8eb0f59ea55748db7… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-25 (Fri, 25 Mar 2016) Changed paths: R test/functional/test_admin_features.py R test/functional/test_data_security.py R test/functional/test_dataset_features.py R test/functional/test_get_data.py R test/functional/test_library_features.py R test/functional/test_library_security.py R test/functional/test_metadata_editing.py R test/functional/test_sample_tracking.py R test/functional/test_tags.py R test/functional/test_ucsc_table_browser.py R test/functional/test_user_info.py Log Message: ----------- Remove twill functional tests we don't actively run. Commit: 5b16589f290139cba11b693452bae5570a60e47d https://github.com/galaxyproject/galaxy/commit/5b16589f290139cba11b693452ba… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-26 (Sat, 26 Mar 2016) Changed paths: R test/functional/test_admin_features.py R test/functional/test_data_security.py R test/functional/test_dataset_features.py R test/functional/test_get_data.py R test/functional/test_library_features.py R test/functional/test_library_security.py R test/functional/test_metadata_editing.py R test/functional/test_sample_tracking.py R test/functional/test_tags.py R test/functional/test_ucsc_table_browser.py R test/functional/test_user_info.py Log Message: ----------- Merge pull request #2019 from jmchilton/remove_twill_tests Remove twill functional tests we don't actively run. Compare: https://github.com/galaxyproject/galaxy/compare/c093c793b7ba...5b16589f2901

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[galaxyproject/galaxy] 85ef86: Improvements to workflow scaling performance testi...
by GitHub 26 Mar '16

26 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 85ef86ab2ee904c62d00f84e7220c661bd31e58c https://github.com/galaxyproject/galaxy/commit/85ef86ab2ee904c62d00f84e7220… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-21 (Mon, 21 Mar 2016) Changed paths: M lib/galaxy/workflow/scheduling_manager.py M scripts/summarize_timings.py A test/functional/tools/for_workflows/create_input_collection.xml A test/functional/tools/for_workflows/split.xml M test/functional/tools/samples_tool_conf.xml A test/manual/launch_and_run.sh A test/manual/workflow_job_conf.xml M test/manual/workflows_scaling.py Log Message: ----------- Improvements to workflow scaling performance testing scripts. - Implement a wrapper script for launching a docker-galaxy-stable setup a many ways for this task including: - Configure container's Galaxy with outer Galaxy's lib and test directory. - Collect log files. - Log a statement for interacting with the container easily while the test is running. - Disable unneeded services. - Implement a fan-in-fan-out style workflow for performance testing. - Add an option to test performance of scheduling workflows without actually running jobs. - Sample tool for creating large collections easily at beginning of tests (much faster than uploads). - Sample tool for splitting a file into a collection for fan in and out workflow test. - Assume Python 2.7 in scripts to simplify things. - Add documentation. Commit: da1f1bd8b2ae1ce7910b14c3dab0791dc0a67050 https://github.com/galaxyproject/galaxy/commit/da1f1bd8b2ae1ce7910b14c3dab0… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-21 (Mon, 21 Mar 2016) Changed paths: M test/functional/tools/for_workflows/create_input_collection.xml Log Message: ----------- Fixes to create_input_collection.xml based on comments from @nsoranzo. Commit: c093c793b7ba589c41e7df3041585922ddc840d8 https://github.com/galaxyproject/galaxy/commit/c093c793b7ba589c41e7df304158… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-25 (Fri, 25 Mar 2016) Changed paths: M lib/galaxy/workflow/scheduling_manager.py M scripts/summarize_timings.py A test/functional/tools/for_workflows/create_input_collection.xml A test/functional/tools/for_workflows/split.xml M test/functional/tools/samples_tool_conf.xml A test/manual/launch_and_run.sh A test/manual/workflow_job_conf.xml M test/manual/workflows_scaling.py Log Message: ----------- Merge pull request #1958 from jmchilton/workflow_scheduling_testing Improvements to workflow scaling performance testing scripts. Compare: https://github.com/galaxyproject/galaxy/compare/d9177a81e548...c093c793b7ba

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[galaxyproject/galaxy] 142383: Fix collection handling
by GitHub 25 Mar '16

25 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 1423836f1e3ef1032ce38128a5fd1191fb7d217a https://github.com/galaxyproject/galaxy/commit/1423836f1e3ef1032ce38128a5fd… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-03-25 (Fri, 25 Mar 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Fix collection handling Commit: d9177a81e5488f0248fba7a6e22e55885779f4a5 https://github.com/galaxyproject/galaxy/commit/d9177a81e5488f0248fba7a6e22e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-25 (Fri, 25 Mar 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Merge pull request #2015 from guerler/fix_collection_001 Fix collection handling Compare: https://github.com/galaxyproject/galaxy/compare/494b2f3e2726...d9177a81e548

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[galaxyproject/galaxy] 3240c2: Swap analyse to analyze to be consistent.
by GitHub 25 Mar '16

25 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 3240c20a4b5cd29a1f2e3764a8aa6cf84ca1e48d https://github.com/galaxyproject/galaxy/commit/3240c20a4b5cd29a1f2e3764a8aa… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-25 (Fri, 25 Mar 2016) Changed paths: M client/galaxy/scripts/mvc/library/library-dataset-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js 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/library/library-dataset-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- Swap analyse to analyze to be consistent. Commit: 494b2f3e272662d2f497ab9dd1a870f3f661554c https://github.com/galaxyproject/galaxy/commit/494b2f3e272662d2f497ab9dd1a8… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-25 (Fri, 25 Mar 2016) Changed paths: M client/galaxy/scripts/mvc/library/library-dataset-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js 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/library/library-dataset-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- Merge pull request #2020 from dannon/analyse Swap analyse to analyze to be consistent across the app. Compare: https://github.com/galaxyproject/galaxy/compare/b9ccf17376f6...494b2f3e2726

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