- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] f882cb: Pin flake8 and plugins in tox.ini
by GitHub 24 Jan '17

24 Jan '17

Branch: refs/heads/release_17.01 Home: https://github.com/galaxyproject/galaxy Commit: f882cb9b2ef45fd3b1dfb36d7bf1edb64b540e01 https://github.com/galaxyproject/galaxy/commit/f882cb9b2ef45fd3b1dfb36d7bf1… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-01-24 (Tue, 24 Jan 2017) Changed paths: M tox.ini Log Message: ----------- Pin flake8 and plugins in tox.ini For all tox environments used in .travis.yml except the ones allowed to fail. Commit: 191813ab80a237476012333a1cb96834ce933124 https://github.com/galaxyproject/galaxy/commit/191813ab80a237476012333a1cb9… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-01-24 (Tue, 24 Jan 2017) Changed paths: M tox.ini Log Message: ----------- Merge pull request #3476 from nsoranzo/release_17.01_pin_flake8 [17.01] Pin flake8 and plugins in tox.ini Compare: https://github.com/galaxyproject/galaxy/compare/dc49b1c220bb...191813ab80a2

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[galaxyproject/galaxy] 56c78e: Handle cases with missing parameter values
by GitHub 24 Jan '17

24 Jan '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 56c78eed802d1be39715965a67db6844308f9955 https://github.com/galaxyproject/galaxy/commit/56c78eed802d1be39715965a67db… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-11-16 (Wed, 16 Nov 2016) Changed paths: M lib/galaxy/tools/parameters/__init__.py Log Message: ----------- Handle cases with missing parameter values Commit: 065d9332fe3b09f00d2a515fc5714b3e98abbfe5 https://github.com/galaxyproject/galaxy/commit/065d9332fe3b09f00d2a515fc571… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-11-16 (Wed, 16 Nov 2016) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-view.js M client/galaxy/style/less/base.less M lib/galaxy/managers/workflows.py M lib/galaxy/workflow/modules.py M static/maps/mvc/library/library-dataset-view.js.map M static/maps/mvc/library/library-folderrow-view.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/maps/mvc/workflow/workflow-canvas.js.map M static/maps/mvc/workflow/workflow-manager.js.map M static/maps/mvc/workflow/workflow-node.js.map M static/maps/mvc/workflow/workflow-view-node.js.map M static/maps/mvc/workflow/workflow-view.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/library/library-dataset-view.js M static/scripts/mvc/library/library-folderrow-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/workflow/workflow-canvas.js M static/scripts/mvc/workflow/workflow-manager.js M static/scripts/mvc/workflow/workflow-view.js M static/style/blue/base.css Log Message: ----------- Start to revise handling of missing tools Commit: 41922b0618c945a4eab8136e27a40d6a62f94c21 https://github.com/galaxyproject/galaxy/commit/41922b0618c945a4eab8136e27a4… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-11-16 (Wed, 16 Nov 2016) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Raise exception if step type is invalid for now Commit: 5140b8bdc3f12fb17f5b0513eeb96610bac16f89 https://github.com/galaxyproject/galaxy/commit/5140b8bdc3f12fb17f5b0513eeb9… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-11-16 (Wed, 16 Nov 2016) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-view.js M static/maps/mvc/workflow/workflow-view.js.map M static/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Remove private function for node element view Commit: ffd44b86f5a06aab38bba46a9952ce150fa4c99e https://github.com/galaxyproject/galaxy/commit/ffd44b86f5a06aab38bba46a9952… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-11-16 (Wed, 16 Nov 2016) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Properly parse step error for missing tools Commit: adadf39b66d410ecf5b8d707b18abe36d5d457e8 https://github.com/galaxyproject/galaxy/commit/adadf39b66d410ecf5b8d707b18a… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-11-16 (Wed, 16 Nov 2016) Changed paths: M lib/galaxy/exceptions/__init__.py M lib/galaxy/exceptions/error_codes.json M lib/galaxy/managers/workflows.py M lib/galaxy/web/base/controller.py M lib/galaxy/workflow/modules.py Log Message: ----------- Add missing tool exception to shared exceptions, unify handling Commit: 7fe719cd414ca3aa194db3e74244e70cb2946bbf https://github.com/galaxyproject/galaxy/commit/7fe719cd414ca3aa194db3e74244… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-11-16 (Wed, 16 Nov 2016) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Avoid storing missing tool errors, resolves naming conflicts Commit: 3535326a46f9e7d53642b13bf404e50d5105ab66 https://github.com/galaxyproject/galaxy/commit/3535326a46f9e7d53642b13bf404… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-11-16 (Wed, 16 Nov 2016) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-canvas.js M client/galaxy/scripts/mvc/workflow/workflow-manager.js M client/galaxy/scripts/mvc/workflow/workflow-node.js M client/galaxy/scripts/mvc/workflow/workflow-view-node.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M lib/galaxy/managers/workflows.py M lib/galaxy/workflow/modules.py M static/maps/mvc/workflow/workflow-canvas.js.map M static/maps/mvc/workflow/workflow-manager.js.map M static/maps/mvc/workflow/workflow-node.js.map M static/maps/mvc/workflow/workflow-view-node.js.map M static/maps/mvc/workflow/workflow-view.js.map M static/scripts/mvc/workflow/workflow-canvas.js M static/scripts/mvc/workflow/workflow-manager.js M static/scripts/mvc/workflow/workflow-node.js M static/scripts/mvc/workflow/workflow-view-node.js M static/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Rename error identifier to indicate generic step related error Commit: 56bb347765231e4dcc1d7fa865d1a54a53921da5 https://github.com/galaxyproject/galaxy/commit/56bb347765231e4dcc1d7fa865d1… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-11-16 (Wed, 16 Nov 2016) Changed paths: M lib/galaxy/web/base/controller.py Log Message: ----------- This is not an upgrade message but an error which should be evaluated through step.get_errors Commit: 4b07c13e272ea5e452f7e4d8f76084b9d8a2ecd6 https://github.com/galaxyproject/galaxy/commit/4b07c13e272ea5e452f7e4d8f760… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-11-16 (Wed, 16 Nov 2016) Changed paths: M lib/galaxy/web/base/controller.py Log Message: ----------- Add comment Commit: 109abf0f178ecb9801ffa0c4afd87463e74b4015 https://github.com/galaxyproject/galaxy/commit/109abf0f178ecb9801ffa0c4afd8… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-11-16 (Wed, 16 Nov 2016) Changed paths: M lib/galaxy/managers/workflows.py M lib/galaxy/workflow/modules.py Log Message: ----------- Fix error message for updating workflow when tool is missing Commit: 20e380ea26b538dcf9c44882634b8f8e06d5167a https://github.com/galaxyproject/galaxy/commit/20e380ea26b538dcf9c44882634b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-11-16 (Wed, 16 Nov 2016) Changed paths: M lib/galaxy/managers/workflows.py M lib/galaxy/workflow/modules.py Log Message: ----------- Allow saving workflow without connections Commit: 2abac81f858cb8013f1e7f134901f884aa3acc1a https://github.com/galaxyproject/galaxy/commit/2abac81f858cb8013f1e7f134901… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-11-16 (Wed, 16 Nov 2016) Changed paths: M lib/galaxy/managers/workflows.py M lib/galaxy/workflow/modules.py Log Message: ----------- Prevent saving, connections not resolved for now Commit: dd40b1f64a08b2f9ce3d088eab6cad6374150974 https://github.com/galaxyproject/galaxy/commit/dd40b1f64a08b2f9ce3d088eab6c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-11-16 (Wed, 16 Nov 2016) Changed paths: M static/maps/mvc/workflow/workflow-canvas.js.map M static/maps/mvc/workflow/workflow-manager.js.map M static/scripts/mvc/workflow/workflow-canvas.js M static/scripts/mvc/workflow/workflow-manager.js Log Message: ----------- Repack scripts Commit: 0d6a7b66ff3babf7e6a2627a2631ea873ffed3b1 https://github.com/galaxyproject/galaxy/commit/0d6a7b66ff3babf7e6a2627a2631… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-11-16 (Wed, 16 Nov 2016) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Attempt to directly prevent saving workflow with missing nodes Commit: 2263caa44dc40e4ed30e1a67e21b35232576a631 https://github.com/galaxyproject/galaxy/commit/2263caa44dc40e4ed30e1a67e21b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-11-16 (Wed, 16 Nov 2016) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Validate cycles and step size before building model for workflow execution Commit: cdf31059a5202191e99e6fd10ac21ba088581c3c https://github.com/galaxyproject/galaxy/commit/cdf31059a5202191e99e6fd10ac2… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-11-16 (Wed, 16 Nov 2016) Changed paths: M lib/galaxy/workflow/steps.py M static/maps/mvc/workflow/workflow-view.js.map M static/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Always provide an order index, even for cyclic workflows use step index Commit: 3accc1e53ff09a295b54f5b17e68fef443a67f85 https://github.com/galaxyproject/galaxy/commit/3accc1e53ff09a295b54f5b17e68… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-11-16 (Wed, 16 Nov 2016) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-view.js M static/maps/mvc/workflow/workflow-view.js.map M static/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Only allow text editing if text field is available in regular step editor Commit: 1c9dd0dbe978f09d5fa0845065a7ecfaf953a03c https://github.com/galaxyproject/galaxy/commit/1c9dd0dbe978f09d5fa0845065a7… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-11-16 (Wed, 16 Nov 2016) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Avoid saving step parameters in temporary config object instead of regular state Commit: 6905f5bd413fd3612904ff0674140d4b9f5add92 https://github.com/galaxyproject/galaxy/commit/6905f5bd413fd3612904ff067414… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-12-01 (Thu, 01 Dec 2016) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-manager.js M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run.py M lib/galaxy/workflow/run_request.py M lib/galaxy/workflow/steps.py M static/maps/mvc/workflow/workflow-canvas.js.map M static/maps/mvc/workflow/workflow-manager.js.map M static/maps/mvc/workflow/workflow-node.js.map M static/maps/mvc/workflow/workflow-view-node.js.map M static/scripts/mvc/workflow/workflow-canvas.js M static/scripts/mvc/workflow/workflow-manager.js Log Message: ----------- Attempt to unify runtime state handling Commit: 7ebb6a36c9fad2d23c188c2fd173727bbe001d29 https://github.com/galaxyproject/galaxy/commit/7ebb6a36c9fad2d23c188c2fd173… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-12-01 (Thu, 01 Dec 2016) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Add abstract recover state function Commit: 0811c93fd839e4a31b37e4d1788526f163e41708 https://github.com/galaxyproject/galaxy/commit/0811c93fd839e4a31b37e4d17885… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-12-01 (Thu, 01 Dec 2016) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Align caller order, test unified runtime state handler Commit: 0d30b177a20745c3dc1e7f264eb36b47dd453f1b https://github.com/galaxyproject/galaxy/commit/0d30b177a20745c3dc1e7f264eb3… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-12-01 (Thu, 01 Dec 2016) Changed paths: M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/apps/tool-panel.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/page.js M 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test/unit/jobs/test_job_configuration.py M test/unit/jobs/test_job_output_checker.py M test/unit/jobs/test_job_wrapper.py M test/unit/jobs/test_mapper.py M test/unit/jobs/test_rule_helper.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_fabric_util.py M test/unit/shed_unit/test_td_common_util.py M test/unit/shed_unit/test_tool_panel_manager.py M test/unit/test_galaxy_transactions.py M test/unit/test_routes.py M test/unit/test_sockets.py M test/unit/tools/test_actions.py M test/unit/tools/test_citations.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_select_parameters.py M test/unit/tools/test_tool_external_files.py M test/unit/tools/test_toolbox.py M test/unit/tools/test_wrappers.py M test/unit/unittest_utils/galaxy_mock.py M test/unit/unittest_utils/tempfilecache.py M test/unit/unittest_utils/utility.py M test/unit/visualizations/plugins/test_VisualizationPlugin.py M test/unit/visualizations/plugins/test_VisualizationsRegistry.py M test/unit/web/base/test_HookPluginManager.py M test/unit/web/base/test_PageServingPluginManager.py M test/unit/web/base/test_PluginManager.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 test/unit/workflows/workflow_support.py M tools/data_source/fetch.py Log Message: ----------- Merge branch 'dev' into fix_workflow_issues Commit: a82565e5385ccacfeef5aa6dd4d61886e5826ab0 https://github.com/galaxyproject/galaxy/commit/a82565e5385ccacfeef5aa6dd4d6… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-12-02 (Fri, 02 Dec 2016) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Remove custom update_state caller Commit: 6fa53a4f062652d73d13d9562d43123fa83e4143 https://github.com/galaxyproject/galaxy/commit/6fa53a4f062652d73d13d9562d43… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-12-02 (Fri, 02 Dec 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/workflow/modules.py Log Message: ----------- Replace update with recover state Commit: e9b49f25919e7228d2d862bf9ba73b134a8600eb 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test/galaxy_selenium/has_driver.py A test/galaxy_selenium/navigates_galaxy.py A test/galaxy_selenium/navigation-data.yml A test/galaxy_selenium/sizzle.py A test/selenium_tests/__init__.py A test/selenium_tests/framework.py A test/selenium_tests/test_anon_history.py A test/selenium_tests/test_history_dataset_state.py A test/selenium_tests/test_history_options.py A test/selenium_tests/test_history_panel.py A test/selenium_tests/test_history_sharing.py A test/selenium_tests/test_login.py A test/selenium_tests/test_registration.py A test/selenium_tests/test_stock_tours.py A test/selenium_tests/test_uploads.py A test/selenium_tests/test_workflow_editor.py M test/unit/jobs/test_job_configuration.py Log Message: ----------- Merge branch 'dev' into fix_workflow_issues Commit: cfb3b40d6ae9e27162b7de71c0167af93199d7ea https://github.com/galaxyproject/galaxy/commit/cfb3b40d6ae9e27162b7de71c016… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-12-05 (Mon, 05 Dec 2016) Changed paths: M lib/galaxy/workflow/modules.py R templates/webapps/galaxy/workflow/editor_tool_form.mako Log Message: ----------- Remove workflow editor tool form mako Commit: f532fb2e8581c09dcd64daf87acd158938b35b27 https://github.com/galaxyproject/galaxy/commit/f532fb2e8581c09dcd64daf87acd… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-12-05 (Mon, 05 Dec 2016) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Fix decode runtime state signature Commit: 9c069a21f68a0ab7a4138ffc6277c4ad2f5aec63 https://github.com/galaxyproject/galaxy/commit/9c069a21f68a0ab7a4138ffc6277… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-12-05 (Mon, 05 Dec 2016) Changed paths: M lib/galaxy/exceptions/__init__.py M lib/galaxy/managers/workflows.py M test/unit/workflows/test_workflow_progress.py Log Message: ----------- Fix lint, unit tests Commit: d2665d88bf9cb60db773793f9f206b6ad4af1edc https://github.com/galaxyproject/galaxy/commit/d2665d88bf9cb60db773793f9f20… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-12-05 (Mon, 05 Dec 2016) Changed paths: M test/qunit/tests/workflow_editor_tests.js Log Message: ----------- Fix workflow qunit tests Commit: 61df5ac6f5269da4309b8b17767354b1704baa04 https://github.com/galaxyproject/galaxy/commit/61df5ac6f5269da4309b8b177673… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-12-05 (Mon, 05 Dec 2016) Changed paths: M test/unit/workflows/test_modules.py Log Message: ----------- Remove redundant and unused update state from test cases, replace with recover state Commit: 6be315ae8f1781eb6fdd9d7ae3ce3a5dc9763acb https://github.com/galaxyproject/galaxy/commit/6be315ae8f1781eb6fdd9d7ae3ce… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-12-06 (Tue, 06 Dec 2016) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Attempt to unify state handling for simple workflow modules Commit: 7a7b833c99d9b4ebc9efc9c8397896ddb16555aa 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lib/galaxy/tools/__init__.py M lib/galaxy/workflow/modules.py Log Message: ----------- Use shared from dict and workflow callers Commit: bae00397d80028c15327cf7ca2fed056927d4882 https://github.com/galaxyproject/galaxy/commit/bae00397d80028c15327cf7ca2fe… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-12-07 (Wed, 07 Dec 2016) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Remove redundant comment Commit: b393f007273274e0ce12efd204d2f59fa28bc34f https://github.com/galaxyproject/galaxy/commit/b393f007273274e0ce12efd204d2… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-12-07 (Wed, 07 Dec 2016) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Strip simple workflow form boilerplate class Commit: 7c479aa8b9f627273b84cb15cb288115d3b3df25 https://github.com/galaxyproject/galaxy/commit/7c479aa8b9f627273b84cb15cb28… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-12-07 (Wed, 07 Dec 2016) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Do not require any module inputs by default, remove unused subworkflow callers Commit: 15c1ecd26b7f1a10dd2f09b96303d5762773f8c3 https://github.com/galaxyproject/galaxy/commit/15c1ecd26b7f1a10dd2f09b96303… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-12-07 (Wed, 07 Dec 2016) Changed paths: M lib/galaxy/managers/workflows.py M lib/galaxy/workflow/modules.py Log Message: ----------- Fix lint, spacing Commit: 648d717298de9f5d12e612b1f769bd84e362aa88 https://github.com/galaxyproject/galaxy/commit/648d717298de9f5d12e612b1f769… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-12-08 (Thu, 08 Dec 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/workflow/modules.py M test/unit/workflows/test_modules.py Log Message: ----------- Improve state building resilience, fix test cases Commit: db3bb117dac67b8b47bda2fc08f5f26af50bc33f https://github.com/galaxyproject/galaxy/commit/db3bb117dac67b8b47bda2fc08f5… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-12-08 (Thu, 08 Dec 2016) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Resolve subworkflow data input names through connected data step states Commit: bd91f5aab9d9688af0c78d9b47859415a5c45244 https://github.com/galaxyproject/galaxy/commit/bd91f5aab9d9688af0c78d9b4785… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-12-08 (Thu, 08 Dec 2016) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Export with default labels Commit: c02c9e8dd590b0079267305ad8240144e06a2a24 https://github.com/galaxyproject/galaxy/commit/c02c9e8dd590b0079267305ad824… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-12-08 (Thu, 08 Dec 2016) Changed paths: M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run_request.py M test/api/test_workflow_extraction.py Log Message: ----------- Fix test cases, introduce temporary handling Commit: f745ee3558e0ca67d6d92ba1f19215a45fb7033b https://github.com/galaxyproject/galaxy/commit/f745ee3558e0ca67d6d92ba1f192… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-12-08 (Thu, 08 Dec 2016) Changed paths: M lib/galaxy/workflow/modules.py M test/api/test_workflows.py Log Message: ----------- Remove tool errors from export assertion test, use unified state for all modules Commit: 751f997491a183a28ee2c15ad637b219c04b25b6 https://github.com/galaxyproject/galaxy/commit/751f997491a183a28ee2c15ad637… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-12-08 (Thu, 08 Dec 2016) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Fix input parameter module types Commit: 38633fad618916d71b6439ef2484c9af9d3f399f https://github.com/galaxyproject/galaxy/commit/38633fad618916d71b6439ef2484… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-12-09 (Fri, 09 Dec 2016) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Basestring->string_types Commit: 34f5506080bc1c76df3e0267fa4aeeb32137f356 https://github.com/galaxyproject/galaxy/commit/34f5506080bc1c76df3e0267fa4a… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2016-12-09 (Fri, 09 Dec 2016) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Merge pull request #16 from dannon/py3_basestring Basestring->string_types Commit: f9abb47ebdb54fe0e01607fd076d52c229ff2ca9 https://github.com/galaxyproject/galaxy/commit/f9abb47ebdb54fe0e01607fd076d… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-12-11 (Sun, 11 Dec 2016) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/util/json.py Log Message: ----------- Use shared safe loads to load module states Commit: 9fc6162b749a4c0dd8c59da4ce0e199e64cfa0aa https://github.com/galaxyproject/galaxy/commit/9fc6162b749a4c0dd8c59da4ce0e… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-12-12 (Mon, 12 Dec 2016) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-view.js M lib/galaxy/workflow/modules.py M static/maps/mvc/workflow/workflow-view.js.map M static/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Parse dictionary, avoid unnecessary string conversion Commit: 026b43b92abe6b0c38de329526ebbeaf862b5674 https://github.com/galaxyproject/galaxy/commit/026b43b92abe6b0c38de329526eb… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-12-13 (Tue, 13 Dec 2016) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-view.js M lib/galaxy/workflow/modules.py M static/maps/mvc/workflow/workflow-view.js.map M static/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Use regular form build to build input module form Commit: c5f7416c7cde507f32e3ac2d6cd83fce94fcd05b https://github.com/galaxyproject/galaxy/commit/c5f7416c7cde507f32e3ac2d6cd8… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-12-14 (Wed, 14 Dec 2016) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-view.js M lib/galaxy/workflow/modules.py M static/maps/mvc/workflow/workflow-view.js.map M static/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Switch to regular form builder for non-tool modules, initial commit Commit: 8cc4e5910398d6dd3adfddabfe7822461b9ab4a5 https://github.com/galaxyproject/galaxy/commit/8cc4e5910398d6dd3adfddabfe78… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-12-14 (Wed, 14 Dec 2016) Changed paths: M lib/galaxy/workflow/modules.py R templates/webapps/galaxy/workflow/editor_generic_form.mako Log Message: ----------- Regular remove regular module form mako Commit: d41b1425e6695c70da052b4927b6990df9bcdd4b https://github.com/galaxyproject/galaxy/commit/d41b1425e6695c70da052b4927b6… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-12-14 (Wed, 14 Dec 2016) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-view.js M lib/galaxy/workflow/modules.py M static/maps/mvc/workflow/workflow-view.js.map M static/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Add basic selector for input dataset collection editor form input Commit: f9253351bfb90c51e0ba8ea4bd22e6da25d15d9b https://github.com/galaxyproject/galaxy/commit/f9253351bfb90c51e0ba8ea4bd22… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-12-14 (Wed, 14 Dec 2016) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Add value details to collection type selector Commit: ca14167cdf7fec0c3372e4a494282ecb58be0173 https://github.com/galaxyproject/galaxy/commit/ca14167cdf7fec0c3372e4a49428… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-12-19 (Mon, 19 Dec 2016) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-view.js M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M static/maps/mvc/workflow/workflow-view.js.map M static/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Move non-tool module handling to api, disable workflow parameter info panel for now Commit: 4476a2bfbf89e5abfe24ea9e63da7a3c6c404d09 https://github.com/galaxyproject/galaxy/commit/4476a2bfbf89e5abfe24ea9e63da… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-12-19 (Mon, 19 Dec 2016) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-manager.js M client/galaxy/scripts/mvc/workflow/workflow-node.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M lib/galaxy/managers/workflows.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M static/maps/mvc/workflow/workflow-manager.js.map M static/maps/mvc/workflow/workflow-node.js.map M static/maps/mvc/workflow/workflow-view.js.map M static/scripts/mvc/workflow/workflow-manager.js M static/scripts/mvc/workflow/workflow-node.js M static/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Indicate removal of form html building Commit: 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test/unit/jobs/test_mapper.py M test/unit/visualizations/plugins/test_VisualizationsRegistry.py M tools/filters/gff/gff_filter_by_attribute.py M tools/filters/gff/gff_filter_by_attribute.xml M tools/filters/gff/gff_filter_by_feature_count.py M tools/filters/gff/gff_filter_by_feature_count.xml Log Message: ----------- Merge branch 'dev' into fix_workflow_issues Commit: 5c49af7d0dddbb1e7cdb456535a57854e9460558 https://github.com/galaxyproject/galaxy/commit/5c49af7d0dddbb1e7cdb456535a5… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-12-21 (Wed, 21 Dec 2016) Changed paths: M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/workflow/workflow-node.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M lib/galaxy/tools/parameters/basic.py M lib/galaxy/workflow/modules.py M static/maps/mvc/form/form-parameters.js.map M static/maps/mvc/workflow/workflow-node.js.map M static/maps/mvc/workflow/workflow-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.map M static/scripts/mvc/form/form-parameters.js Log Message: ----------- Parse datalist handler for regular text input fields to front end Commit: da6406202e8848316cc19fbf095922b31c18eebd https://github.com/galaxyproject/galaxy/commit/da6406202e8848316cc19fbf0959… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-12-21 (Wed, 21 Dec 2016) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-manager.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M static/maps/mvc/workflow/workflow-manager.js.map M static/maps/mvc/workflow/workflow-view.js.map M static/scripts/mvc/workflow/workflow-manager.js M static/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Show workflow attributes instead of mock node content, remove special handling from show module form caller Commit: a8caede3f836fe1bc74b97dc2c5e50fd1ca95ea6 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scripts/functional_tests.py R scripts/run_selenium_tests.sh M static/maps/layout/menu.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/menu.js M templates/show_params.mako M test/base/driver_util.py R test/functional/workflow.py M test/galaxy_selenium/navigates_galaxy.py M test/integration/test_job_resubmission.py M test/selenium_tests/test_history_dataset_state.py M test/selenium_tests/test_history_sharing.py M test/selenium_tests/test_stock_tours.py A test/selenium_tests/test_tool_form.py Log Message: ----------- Merge branch 'dev' into fix_workflow_issues Commit: 9133618c041ba89e26d3661fb836e882c5b27e94 https://github.com/galaxyproject/galaxy/commit/9133618c041ba89e26d3661fb836… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-01-02 (Mon, 02 Jan 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-view.js M static/maps/mvc/workflow/workflow-view.js.map M static/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Fix workflow parameter panel in workflow editor Commit: d21c77c67b703a7c004ae14cac40c75dc31981de https://github.com/galaxyproject/galaxy/commit/d21c77c67b703a7c004ae14cac40… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-01-02 (Mon, 02 Jan 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-node.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M lib/galaxy/jobs/actions/post.py M static/maps/mvc/workflow/workflow-node.js.map M static/maps/mvc/workflow/workflow-view.js.map M static/scripts/mvc/workflow/workflow-node.js M static/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Parse job actions as dictionary Commit: c86ef0bbb54c19195cff8a46a752a07b246c040f https://github.com/galaxyproject/galaxy/commit/c86ef0bbb54c19195cff8a46a752… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-01-02 (Mon, 02 Jan 2017) Changed paths: M lib/galaxy/tools/parameters/grouping.py Log 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Date: 2017-01-03 (Tue, 03 Jan 2017) Changed paths: M lib/galaxy/jobs/actions/post.py Log Message: ----------- Remove unused import Commit: 24ad65e0ac533f279d3935949c324f61dd4647fc https://github.com/galaxyproject/galaxy/commit/24ad65e0ac533f279d3935949c32… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-01-03 (Tue, 03 Jan 2017) Changed paths: M test/api/test_workflow_extraction.py Log Message: ----------- Fix api test cases Commit: 10ac745c3ab78249f5c894c8ec1ce73af2d9fe0b https://github.com/galaxyproject/galaxy/commit/10ac745c3ab78249f5c894c8ec1c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-01-04 (Wed, 04 Jan 2017) Changed paths: M lib/tool_shed/util/workflow_util.py Log Message: ----------- Fix toolshed workflow utilities Commit: c8e1c8f53507a219a2f3475f271a202695237942 https://github.com/galaxyproject/galaxy/commit/c8e1c8f53507a219a2f3475f271a… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-01-04 (Wed, 04 Jan 2017) Changed paths: M 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client/galaxy/scripts/mvc/workflow/workflow-view.js M config/datatypes_conf.xml.sample M config/galaxy.ini.sample M config/job_conf.xml.sample_advanced M config/plugins/interactive_environments/jupyter/config/jupyter.xml M config/plugins/interactive_environments/rstudio/config/rstudio.xml M lib/galaxy/config.py M lib/galaxy/datatypes/constructive_solid_geometry.py M lib/galaxy/datatypes/images.py M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/actions/post.py M lib/galaxy/jobs/command_factory.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh M lib/galaxy/jobs/runners/util/job_script/__init__.py M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/tools/verify/asserts/text.py M lib/galaxy/web/base/controller.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/workflow/modules.py M run_tests.sh M static/maps/mvc/form/form-section.js.map M static/maps/mvc/tool/tool-form-composite.js.map A static/maps/mvc/workflow/workflow-icons.js.map M static/maps/mvc/workflow/workflow-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.map M static/scripts/mvc/form/form-section.js M static/scripts/mvc/tool/tool-form-composite.js A static/scripts/mvc/workflow/workflow-icons.js M static/scripts/mvc/workflow/workflow-view.js M templates/ind_share_base.mako R test/api/helpers.py M test/api/test_dataset_collections.py M test/api/test_datasets.py M test/api/test_histories.py M test/api/test_history_contents.py M test/api/test_history_contents_provenance.py M test/api/test_jobs.py M test/api/test_libraries.py M test/api/test_search.py M test/api/test_tools.py A test/api/test_visualizations.py R test/api/test_workflow_1.ga R test/api/test_workflow_2.ga R test/api/test_workflow_batch.ga M test/api/test_workflow_extraction.py R test/api/test_workflow_map_reduce_pause.ga R test/api/test_workflow_matching_lists.ga R test/api/test_workflow_missing_tool.ga R test/api/test_workflow_pause.ga R test/api/test_workflow_topoambigouity.ga R test/api/test_workflow_topoambigouity_auto_laidout.ga R test/api/test_workflow_validation_1.ga R test/api/test_workflow_with_runtime_input.ga M test/api/test_workflows.py R test/api/workflows_format_2/README.txt R test/api/workflows_format_2/__init__.py R test/api/workflows_format_2/converter.py R test/api/workflows_format_2/interface.py R test/api/workflows_format_2/main.py A test/base/data/test_workflow_1.ga A test/base/data/test_workflow_2.ga A test/base/data/test_workflow_batch.ga A test/base/data/test_workflow_map_reduce_pause.ga A test/base/data/test_workflow_matching_lists.ga A test/base/data/test_workflow_missing_tool.ga A test/base/data/test_workflow_pause.ga A test/base/data/test_workflow_topoambigouity.ga A test/base/data/test_workflow_topoambigouity_auto_laidout.ga A test/base/data/test_workflow_validation_1.ga A test/base/data/test_workflow_with_runtime_input.ga A test/base/populators.py A test/base/workflows_format_2/README.txt A test/base/workflows_format_2/__init__.py A test/base/workflows_format_2/converter.py A test/base/workflows_format_2/interface.py A test/base/workflows_format_2/main.py R test/casperjs/api-dataset-tests.js R test/casperjs/api-visualizations-tests.js M test/docker/base/Dockerfile M test/docker/base/run_test_wrapper.sh A test/functional/tools/for_workflows/mapper2.xml A test/functional/tools/python_environment_problem.py A test/functional/tools/python_environment_problem.xml M test/functional/tools/samples_tool_conf.xml M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/navigation-data.yml A test/integration/resubmission_default_job_conf.xml M test/integration/resubmission_runners.py M test/integration/test_job_resubmission.py M test/manual/workflows_scaling.py A test/selenium_tests/_workflow_fixtures.py M test/selenium_tests/framework.py M test/selenium_tests/test_history_dataset_state.py M test/selenium_tests/test_tool_form.py M test/selenium_tests/test_workflow_editor.py A test/selenium_tests/test_workflow_management.py A test/selenium_tests/test_workflow_run.py M test/unit/jobs/test_command_factory.py M test/unit/jobs/test_job_configuration.py M test/unit/tools_support.py M test/unit/workflows/workflow_support.py R tools/filters/gff/sort_gtf.py M tox.ini Log Message: ----------- Merge branch 'dev' into fix_workflow_issues Commit: 5f3ccc91e31b04e493fa6ff1ddfbe561904374f7 https://github.com/galaxyproject/galaxy/commit/5f3ccc91e31b04e493fa6ff1ddfb… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-01-08 (Sun, 08 Jan 2017) Changed paths: M lib/galaxy/managers/workflows.py M lib/galaxy/workflow/modules.py Log Message: ----------- Parse keywords in manager since not all modules require the optional exact_tools flag Commit: dc9c6032f25e9ec97f84e8b4e6e15d6a2e9d6f70 https://github.com/galaxyproject/galaxy/commit/dc9c6032f25e9ec97f84e8b4e6e1… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-01-08 (Sun, 08 Jan 2017) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Fix tool version matching Commit: 82aea503e11e1f5d010f4797d404f02275deb18f https://github.com/galaxyproject/galaxy/commit/82aea503e11e1f5d010f4797d404… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-09 (Mon, 09 Jan 2017) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Make important log message an info instead of a debug. Commit: 0f28f8549bc7dd375d4f5ffbf6d4e0f5b9fb122e https://github.com/galaxyproject/galaxy/commit/0f28f8549bc7dd375d4f5ffbf6d4… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-09 (Mon, 09 Jan 2017) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd A test/functional/tools/param_text_option.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Document using options within a text parameter. Commit: fb8a9628647eca0b4a35bc23f74f8b946bbbf716 https://github.com/galaxyproject/galaxy/commit/fb8a9628647eca0b4a35bc23f74f… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2017-01-09 (Mon, 09 Jan 2017) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/workflow/modules.py A test/functional/tools/param_text_option.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge pull request #17 from jmchilton/fix_workflow_issues_datalist Two small tweaks. Commit: 84d9e171bc9be48d237cc16e5d877de23e67a4d3 https://github.com/galaxyproject/galaxy/commit/84d9e171bc9be48d237cc16e5d87… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-01-14 (Sat, 14 Jan 2017) Changed paths: M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/workflow/workflow-canvas.js M client/galaxy/scripts/mvc/workflow/workflow-manager.js M client/galaxy/scripts/mvc/workflow/workflow-node.js M client/galaxy/scripts/mvc/workflow/workflow-view-node.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M client/galaxy/style/less/base.less M lib/galaxy/exceptions/__init__.py M lib/galaxy/exceptions/error_codes.json M lib/galaxy/jobs/actions/post.py M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/util/json.py M lib/galaxy/web/base/controller.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run.py M lib/galaxy/workflow/run_request.py M lib/galaxy/workflow/steps.py M lib/tool_shed/util/workflow_util.py M static/maps/mvc/form/form-parameters.js.map M static/maps/mvc/form/form-view.js.map M static/maps/mvc/library/library-dataset-view.js.map M static/maps/mvc/library/library-folderrow-view.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/maps/mvc/workflow/workflow-canvas.js.map M static/maps/mvc/workflow/workflow-manager.js.map M static/maps/mvc/workflow/workflow-node.js.map M static/maps/mvc/workflow/workflow-view-node.js.map M static/maps/mvc/workflow/workflow-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.map M static/scripts/mvc/form/form-parameters.js M static/scripts/mvc/form/form-view.js M static/scripts/mvc/library/library-dataset-view.js M static/scripts/mvc/library/library-folderrow-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/workflow/workflow-canvas.js M static/scripts/mvc/workflow/workflow-manager.js M static/scripts/mvc/workflow/workflow-node.js M static/scripts/mvc/workflow/workflow-view-node.js M static/scripts/mvc/workflow/workflow-view.js M static/style/blue/base.css R templates/webapps/galaxy/workflow/editor_generic_form.mako R templates/webapps/galaxy/workflow/editor_tool_form.mako M test/api/test_workflows.py A test/functional/tools/param_text_option.xml M test/functional/tools/samples_tool_conf.xml M test/qunit/tests/workflow_editor_tests.js M test/unit/workflows/test_modules.py M test/unit/workflows/test_workflow_progress.py Log Message: ----------- Merge branch 'fix_workflow_issues' of https://github.com/guerler/galaxy into fix_workflow_issues Commit: 0482416c7af9d62edecbb5cde4c88563385dd1bd https://github.com/galaxyproject/galaxy/commit/0482416c7af9d62edecbb5cde4c8… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-01-17 (Tue, 17 Jan 2017) Changed paths: M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/ui/ui-misc.js M lib/galaxy/tools/__init__.py M lib/galaxy/tools/data/__init__.py M lib/galaxy/tools/data_manager/manager.py M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/tools/deps/requirements.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/deps/resolvers/resolver_mixins.py M lib/galaxy/tools/deps/views.py M lib/galaxy/tools/errors.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/tools/imp_exp/export_history.py M lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/dynamic_options.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/tools/parameters/meta.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/tools/search/__init__.py M lib/galaxy/tools/util/galaxyops/__init__.py M lib/galaxy/tools/util/maf_utilities.py M lib/galaxy/tools/verify/asserts/__init__.py M lib/galaxy/tools/verify/test_data.py M lib/galaxy/tools/wrappers.py M lib/galaxy/webapps/galaxy/api/configuration.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/tool_shed/util/shed_util_common.py M static/maps/mvc/form/form-view.js.map M static/maps/mvc/ui/ui-misc.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/form/form-view.js M static/scripts/mvc/ui/ui-misc.js Log Message: ----------- Merge branch 'dev' into fix_workflow_issues Commit: 0b0419533a2b1247a426bdf51bbf23636fcfe43a https://github.com/galaxyproject/galaxy/commit/0b0419533a2b1247a426bdf51bbf… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-01-24 (Tue, 24 Jan 2017) Changed paths: M README.rst M client/galaxy/scripts/viz/trackster/tracks.js M config/galaxy.ini.sample A config/local_conda_mapping.yml.sample M doc/schema_template.md M lib/galaxy/config.py M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/runners/condor.py M lib/galaxy/model/orm/scripts.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/dependencies.py M lib/galaxy/tools/deps/requirements.py M lib/galaxy/tools/deps/resolvers/__init__.py M lib/galaxy/tools/deps/resolvers/brewed_tool_shed_packages.py M lib/galaxy/tools/deps/resolvers/conda.py A lib/galaxy/tools/deps/resolvers/default_conda_mapping.yml M lib/galaxy/tools/deps/resolvers/galaxy_packages.py M lib/galaxy/tools/deps/resolvers/homebrew.py M lib/galaxy/tools/deps/resolvers/modules.py M lib/galaxy/tools/deps/views.py M lib/galaxy/tools/errors.py M lib/galaxy/tools/linters/inputs.py M lib/galaxy/tools/search/__init__.py M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/util/object_wrapper.py A lib/galaxy/util/oset.py M lib/galaxy/util/properties.py M lib/galaxy/version.py M lib/galaxy/webapps/galaxy/api/configuration.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/util/shed_util_common.py M run.sh A scripts/manage_tool_dependencies.py M static/maps/viz/trackster/tracks.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/viz/trackster/tracks.js M test/docker/base/run_test_wrapper.sh M test/functional/tools/column_param.xml A test/functional/tools/explicit_conversion.xml M test/functional/tools/implicit_conversion.xml A test/functional/tools/legacy_r.xml M test/functional/tools/samples_tool_conf.xml M test/galaxy_selenium/navigates_galaxy.py M test/integration/test_resolvers.py M test/selenium_tests/test_history_dataset_state.py M test/selenium_tests/test_history_sharing.py M test/selenium_tests/test_tool_form.py M test/selenium_tests/test_workflow_editor.py M test/selenium_tests/test_workflow_management.py M test/unit/tools/test_tool_deps.py M tools/evolution/add_scores.xml M tools/extract/extract_genomic_dna.xml M tools/filters/pasteWrapper.xml M tools/maf/genebed_maf_to_fasta.xml M tools/maf/interval2maf.xml M tools/maf/interval2maf_pairwise.xml M tools/maf/interval_maf_to_merged_fasta.xml M tools/maf/macros.xml M tools/maf/maf_by_block_number.xml M tools/maf/maf_filter.xml M tools/maf/maf_limit_size.xml M tools/maf/maf_limit_to_species.xml M tools/maf/maf_reverse_complement.xml M tools/maf/maf_split_by_species.xml M tools/maf/maf_stats.xml M tools/maf/maf_thread_for_species.xml M tools/maf/maf_to_bed.xml M tools/maf/maf_to_fasta.xml M tools/maf/maf_to_interval.xml M tools/maf/vcf_to_maf_customtrack.xml M tools/metag_tools/shrimp_color_wrapper.xml M tools/metag_tools/shrimp_wrapper.xml M tools/next_gen_conversion/fastq_gen_conv.xml M tools/plotting/bar_chart.xml M tools/stats/aggregate_binned_scores_in_intervals.xml Log Message: ----------- Merge branch 'dev' into fix_workflow_issues Commit: 3c4413d31d991cf06b3217265e5f573c5fc26fc1 https://github.com/galaxyproject/galaxy/commit/3c4413d31d991cf06b3217265e5f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-24 (Tue, 24 Jan 2017) Changed paths: M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/workflow/workflow-canvas.js M client/galaxy/scripts/mvc/workflow/workflow-manager.js M client/galaxy/scripts/mvc/workflow/workflow-node.js M client/galaxy/scripts/mvc/workflow/workflow-view-node.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M client/galaxy/style/less/base.less M lib/galaxy/exceptions/__init__.py M lib/galaxy/exceptions/error_codes.json M lib/galaxy/jobs/actions/post.py M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/util/json.py M lib/galaxy/web/base/controller.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run.py M lib/galaxy/workflow/run_request.py M lib/galaxy/workflow/steps.py M lib/tool_shed/util/workflow_util.py M static/maps/mvc/form/form-parameters.js.map M static/maps/mvc/form/form-view.js.map M static/maps/mvc/library/library-dataset-view.js.map M static/maps/mvc/library/library-folderrow-view.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/maps/mvc/workflow/workflow-canvas.js.map M static/maps/mvc/workflow/workflow-manager.js.map M static/maps/mvc/workflow/workflow-node.js.map M static/maps/mvc/workflow/workflow-view-node.js.map M static/maps/mvc/workflow/workflow-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/bundled/login.bundled.js.map M static/scripts/mvc/form/form-parameters.js M static/scripts/mvc/form/form-view.js M static/scripts/mvc/library/library-dataset-view.js M static/scripts/mvc/library/library-folderrow-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/workflow/workflow-canvas.js M static/scripts/mvc/workflow/workflow-manager.js M static/scripts/mvc/workflow/workflow-node.js M static/scripts/mvc/workflow/workflow-view-node.js M static/scripts/mvc/workflow/workflow-view.js M static/style/blue/base.css R templates/webapps/galaxy/workflow/editor_generic_form.mako R templates/webapps/galaxy/workflow/editor_tool_form.mako M test/api/test_workflows.py A test/functional/tools/param_text_option.xml M test/functional/tools/samples_tool_conf.xml M test/qunit/tests/workflow_editor_tests.js M test/unit/workflows/test_modules.py M test/unit/workflows/test_workflow_progress.py Log Message: ----------- Merge pull request #3181 from guerler/fix_workflow_issues Normalizes the handling of steps and missing tools for the workflow editor Compare: https://github.com/galaxyproject/galaxy/compare/2ff068f133b0...3c4413d31d99

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[galaxyproject/galaxy] 84b574: Change link to appropriate test tool
by GitHub 24 Jan '17

24 Jan '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 84b5748b5396281cea8f606505d0b00dcb910a57 https://github.com/galaxyproject/galaxy/commit/84b5748b5396281cea8f606505d0… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-01-23 (Mon, 23 Jan 2017) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- Change link to appropriate test tool Commit: ff10ba6f83d41dd58cd02cf78c26b436c8999434 https://github.com/galaxyproject/galaxy/commit/ff10ba6f83d41dd58cd02cf78c26… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-01-23 (Mon, 23 Jan 2017) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- Add missing "remove_value" filter type and meta_ref filter attribute Fix links to tools. Commit: 03a807e374f8340c79e3e49ac52c686b3fc4b537 https://github.com/galaxyproject/galaxy/commit/03a807e374f8340c79e3e49ac52c… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-01-23 (Mon, 23 Jan 2017) Changed paths: M tools/evolution/add_scores.xml M tools/extract/extract_genomic_dna.xml M tools/filters/pasteWrapper.xml M tools/maf/genebed_maf_to_fasta.xml M tools/maf/interval2maf.xml M tools/maf/interval2maf_pairwise.xml M tools/maf/interval_maf_to_merged_fasta.xml M tools/maf/macros.xml M tools/maf/maf_by_block_number.xml M tools/maf/maf_filter.xml M tools/maf/maf_limit_size.xml M tools/maf/maf_limit_to_species.xml M tools/maf/maf_reverse_complement.xml M tools/maf/maf_split_by_species.xml M tools/maf/maf_stats.xml M tools/maf/maf_thread_for_species.xml M tools/maf/maf_to_bed.xml M tools/maf/maf_to_fasta.xml M tools/maf/maf_to_interval.xml M tools/maf/vcf_to_maf_customtrack.xml M tools/metag_tools/shrimp_color_wrapper.xml M tools/metag_tools/shrimp_wrapper.xml M tools/next_gen_conversion/fastq_gen_conv.xml M tools/stats/aggregate_binned_scores_in_intervals.xml Log Message: ----------- Lint some tools Commit: 2ff068f133b0cce1d7d1822758ef272eb2b027c9 https://github.com/galaxyproject/galaxy/commit/2ff068f133b0cce1d7d1822758ef… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-01-24 (Tue, 24 Jan 2017) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd M tools/evolution/add_scores.xml M tools/extract/extract_genomic_dna.xml M tools/filters/pasteWrapper.xml M tools/maf/genebed_maf_to_fasta.xml M tools/maf/interval2maf.xml M tools/maf/interval2maf_pairwise.xml M tools/maf/interval_maf_to_merged_fasta.xml M tools/maf/macros.xml M tools/maf/maf_by_block_number.xml M tools/maf/maf_filter.xml M tools/maf/maf_limit_size.xml M tools/maf/maf_limit_to_species.xml M tools/maf/maf_reverse_complement.xml M tools/maf/maf_split_by_species.xml M tools/maf/maf_stats.xml M tools/maf/maf_thread_for_species.xml M tools/maf/maf_to_bed.xml M tools/maf/maf_to_fasta.xml M tools/maf/maf_to_interval.xml M tools/maf/vcf_to_maf_customtrack.xml M tools/metag_tools/shrimp_color_wrapper.xml M tools/metag_tools/shrimp_wrapper.xml M tools/next_gen_conversion/fastq_gen_conv.xml M tools/stats/aggregate_binned_scores_in_intervals.xml Log Message: ----------- Merge pull request #3468 from nsoranzo/lint_tools Lint some tools Compare: https://github.com/galaxyproject/galaxy/compare/10eba9a9990e...2ff068f133b0

1 0

[galaxyproject/galaxy] 3f93b1: fix condor containers
by GitHub 24 Jan '17

24 Jan '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 3f93b19ff34bf51d81b353eb5e11e1748fa35df4 https://github.com/galaxyproject/galaxy/commit/3f93b19ff34bf51d81b353eb5e11… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2017-01-23 (Mon, 23 Jan 2017) Changed paths: M lib/galaxy/jobs/runners/condor.py Log Message: ----------- fix condor containers Commit: 915b653b91af25bf126125be875bd6ab2d9f320c https://github.com/galaxyproject/galaxy/commit/915b653b91af25bf126125be875b… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-01-23 (Mon, 23 Jan 2017) Changed paths: M lib/galaxy/jobs/runners/condor.py Log Message: ----------- Merge pull request #3463 from jmchilton/16.07_container_fix [16.07] fix condor containers Commit: 1c0c378debdee4aeb9699f11ad2b3314323888b6 https://github.com/galaxyproject/galaxy/commit/1c0c378debdee4aeb9699f11ad2b… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-01-23 (Mon, 23 Jan 2017) Changed paths: M lib/galaxy/jobs/runners/condor.py Log Message: ----------- Merge branch 'release_16.07' into release_16.10 Commit: ffa4af0a8e79acb673e90e543d67b7be0be3b631 https://github.com/galaxyproject/galaxy/commit/ffa4af0a8e79acb673e90e543d67… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-01-23 (Mon, 23 Jan 2017) Changed paths: M lib/galaxy/version.py Log Message: ----------- Merge pull request #3466 from jmchilton/version-17.01 [17.01] Update version to 17.01.rc1 Commit: c85b28c6d2c3e39801ea9138d84bfa2a0ded536c https://github.com/galaxyproject/galaxy/commit/c85b28c6d2c3e39801ea9138d84b… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-01-23 (Mon, 23 Jan 2017) Log Message: ----------- Merge branch 'release_16.10' into release_17.01 Commit: df8be3add7fc87fc5ad6e4e38217332a57d3915a https://github.com/galaxyproject/galaxy/commit/df8be3add7fc87fc5ad6e4e38217… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-23 (Mon, 23 Jan 2017) Changed paths: M lib/galaxy/tools/deps/__init__.py M test/integration/test_resolvers.py Log Message: ----------- Fix cached dependency manager. Broken with baf9b82847fc526af56ed8efa7aba4d31d62f400. Also fix test case that made me think it was okay in the first place. Commit: 28b7b1faff9420c0010c117b573917741b1974ef https://github.com/galaxyproject/galaxy/commit/28b7b1faff9420c0010c117b5739… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-23 (Mon, 23 Jan 2017) Changed paths: M lib/galaxy/dependencies/pinned-requirements.txt Log Message: ----------- Upgrade six to 1.10.0. This is required by the setuptools release released today. So if anything uses setuptools (e.g. it seems we get twill from PyPI instead of wheels.galaxyproject.org) it will fail because we have downgraded six it seems. Commit: 0bf7efb89a189e14e3b9d85ef2355a3821a498ce https://github.com/galaxyproject/galaxy/commit/0bf7efb89a189e14e3b9d85ef235… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-01-24 (Tue, 24 Jan 2017) Changed paths: M lib/galaxy/dependencies/pinned-requirements.txt Log Message: ----------- Merge pull request #3471 from jmchilton/17_01_six_upgrade [17.01] Upgrade six to 1.10.0. Commit: dc49b1c220bb96b1675ab50bdbccf7eca8d739bc https://github.com/galaxyproject/galaxy/commit/dc49b1c220bb96b1675ab50bdbcc… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-01-24 (Tue, 24 Jan 2017) Changed paths: M lib/galaxy/tools/deps/__init__.py M test/integration/test_resolvers.py Log Message: ----------- Merge pull request #3470 from jmchilton/cached_dependency_manager_fixes [17.01] Fix cached dependency manager. Commit: 10eba9a9990ec093fddb7adebcf0daf8893b374c https://github.com/galaxyproject/galaxy/commit/10eba9a9990ec093fddb7adebcf0… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-01-24 (Tue, 24 Jan 2017) Changed paths: M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/tools/deps/__init__.py M test/integration/test_resolvers.py Log Message: ----------- Merge branch 'release_17.01' into dev Compare: https://github.com/galaxyproject/galaxy/compare/0d05b3d089d1...10eba9a9990e

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[galaxyproject/galaxy] df8be3: Fix cached dependency manager.
by GitHub 24 Jan '17

24 Jan '17

Branch: refs/heads/release_17.01 Home: https://github.com/galaxyproject/galaxy Commit: df8be3add7fc87fc5ad6e4e38217332a57d3915a https://github.com/galaxyproject/galaxy/commit/df8be3add7fc87fc5ad6e4e38217… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-23 (Mon, 23 Jan 2017) Changed paths: M lib/galaxy/tools/deps/__init__.py M test/integration/test_resolvers.py Log Message: ----------- Fix cached dependency manager. Broken with baf9b82847fc526af56ed8efa7aba4d31d62f400. Also fix test case that made me think it was okay in the first place. Commit: dc49b1c220bb96b1675ab50bdbccf7eca8d739bc https://github.com/galaxyproject/galaxy/commit/dc49b1c220bb96b1675ab50bdbcc… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-01-24 (Tue, 24 Jan 2017) Changed paths: M lib/galaxy/tools/deps/__init__.py M test/integration/test_resolvers.py Log Message: ----------- Merge pull request #3470 from jmchilton/cached_dependency_manager_fixes [17.01] Fix cached dependency manager. Compare: https://github.com/galaxyproject/galaxy/compare/0bf7efb89a18...dc49b1c220bb

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[galaxyproject/galaxy] 28b7b1: Upgrade six to 1.10.0.
by GitHub 24 Jan '17

24 Jan '17

Branch: refs/heads/release_17.01 Home: https://github.com/galaxyproject/galaxy Commit: 28b7b1faff9420c0010c117b573917741b1974ef https://github.com/galaxyproject/galaxy/commit/28b7b1faff9420c0010c117b5739… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-23 (Mon, 23 Jan 2017) Changed paths: M lib/galaxy/dependencies/pinned-requirements.txt Log Message: ----------- Upgrade six to 1.10.0. This is required by the setuptools release released today. So if anything uses setuptools (e.g. it seems we get twill from PyPI instead of wheels.galaxyproject.org) it will fail because we have downgraded six it seems. Commit: 0bf7efb89a189e14e3b9d85ef2355a3821a498ce https://github.com/galaxyproject/galaxy/commit/0bf7efb89a189e14e3b9d85ef235… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-01-24 (Tue, 24 Jan 2017) Changed paths: M lib/galaxy/dependencies/pinned-requirements.txt Log Message: ----------- Merge pull request #3471 from jmchilton/17_01_six_upgrade [17.01] Upgrade six to 1.10.0. Compare: https://github.com/galaxyproject/galaxy/compare/c85b28c6d2c3...0bf7efb89a18

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[galaxyproject/usegalaxy-playbook] 84be4a: enable toolbox monitor, remove gff filters from te...
by GitHub 23 Jan '17

23 Jan '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 84be4aee0d3a9d88fb2fb6c2a92865bf67474ca3 https://github.com/galaxyproject/usegalaxy-playbook/commit/84be4aee0d3a9d88… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-12-05 (Mon, 05 Dec 2016) Changed paths: M files/galaxy/test.galaxyproject.org/config/tool_conf.xml M files/galaxy/usegalaxy.org/config/tool_conf.xml M files/galaxy/usegalaxy.org/var/integrated_tool_panel.xml Log Message: ----------- enable toolbox monitor, remove gff filters from test, update mutable Commit: 6bba141db14d14d8f802b7b034fcb1120cda3065 https://github.com/galaxyproject/usegalaxy-playbook/commit/6bba141db14d14d8… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-01-23 (Mon, 23 Jan 2017) Changed paths: A files/galaxy/common/static/welcome_img/GAMe2017RegisterNow.png A files/galaxy/common/static/welcome_img/ImmPortGalaxy.png A files/galaxy/common/static/welcome_img/PAG2017.png M files/galaxy/test.galaxyproject.org/var/integrated_tool_panel.xml M files/galaxy/test.galaxyproject.org/var/shed_tool_data_table_conf.xml M files/galaxy/usegalaxy.org/config/tool_conf.xml M files/galaxy/usegalaxy.org/var/integrated_tool_panel.xml M production/galaxy_version.yml M roles/usegalaxy_privileged/templates/archive_logs.sh.j2 M stage/galaxy_version.yml M templates/galaxy/common/static/welcome.html.j2 M templates/galaxy/test.galaxyproject.org/config/datatypes_conf.xml.j2 M templates/galaxy/test.galaxyproject.org/config/job_conf.xml.j2 M templates/galaxy/usegalaxy.org/config/datatypes_conf.xml.j2 M templates/galaxy/usegalaxy.org/config/job_conf.xml.j2 Log Message: ----------- Merge branch 'master' of https://github.com/galaxyproject/usegalaxy-playbook Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/37566d989afa...…

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[galaxyproject/galaxy] ea96b5: update badges
by GitHub 23 Jan '17

23 Jan '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ea96b5cdf0a7c191380e03209f646e3ad43e7ac3 https://github.com/galaxyproject/galaxy/commit/ea96b5cdf0a7c191380e03209f64… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-01-23 (Mon, 23 Jan 2017) Changed paths: M README.rst Log Message: ----------- update badges Commit: 1dc7df578a3cf9d7179002b8a2338669931bce47 https://github.com/galaxyproject/galaxy/commit/1dc7df578a3cf9d7179002b8a233… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-01-23 (Mon, 23 Jan 2017) Changed paths: M README.rst Log Message: ----------- fix badge style, flat is default Commit: 04458cef52a519872fd496f86b4289e6b5f9ec4e https://github.com/galaxyproject/galaxy/commit/04458cef52a519872fd496f86b42… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-01-23 (Mon, 23 Jan 2017) Changed paths: M README.rst Log Message: ----------- change badge docs color Commit: 0d05b3d089d1d80cf171b998a5f3cd282f030f5b https://github.com/galaxyproject/galaxy/commit/0d05b3d089d1d80cf171b998a5f3… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-01-23 (Mon, 23 Jan 2017) Changed paths: M README.rst Log Message: ----------- Merge pull request #3465 from martenson/gitter-button update readme badges Compare: https://github.com/galaxyproject/galaxy/compare/1ef900ab48ac...0d05b3d089d1

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[galaxyproject/galaxy] 3f93b1: fix condor containers
by GitHub 23 Jan '17

23 Jan '17

Branch: refs/heads/release_17.01 Home: https://github.com/galaxyproject/galaxy Commit: 3f93b19ff34bf51d81b353eb5e11e1748fa35df4 https://github.com/galaxyproject/galaxy/commit/3f93b19ff34bf51d81b353eb5e11… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2017-01-23 (Mon, 23 Jan 2017) Changed paths: M lib/galaxy/jobs/runners/condor.py Log Message: ----------- fix condor containers Commit: 915b653b91af25bf126125be875bd6ab2d9f320c https://github.com/galaxyproject/galaxy/commit/915b653b91af25bf126125be875b… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-01-23 (Mon, 23 Jan 2017) Changed paths: M lib/galaxy/jobs/runners/condor.py Log Message: ----------- Merge pull request #3463 from jmchilton/16.07_container_fix [16.07] fix condor containers Commit: 1c0c378debdee4aeb9699f11ad2b3314323888b6 https://github.com/galaxyproject/galaxy/commit/1c0c378debdee4aeb9699f11ad2b… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-01-23 (Mon, 23 Jan 2017) Changed paths: M lib/galaxy/jobs/runners/condor.py Log Message: ----------- Merge branch 'release_16.07' into release_16.10 Commit: c85b28c6d2c3e39801ea9138d84bfa2a0ded536c https://github.com/galaxyproject/galaxy/commit/c85b28c6d2c3e39801ea9138d84b… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-01-23 (Mon, 23 Jan 2017) Log Message: ----------- Merge branch 'release_16.10' into release_17.01 Compare: https://github.com/galaxyproject/galaxy/compare/ffa4af0a8e79...c85b28c6d2c3

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[galaxyproject/galaxy] ab8721: Update version to 17.01.rc1
by GitHub 23 Jan '17

23 Jan '17

Branch: refs/heads/release_17.01 Home: https://github.com/galaxyproject/galaxy Commit: ab87216d59178dee482adf4d065cc507d590f1f8 https://github.com/galaxyproject/galaxy/commit/ab87216d59178dee482adf4d065c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-23 (Mon, 23 Jan 2017) Changed paths: M lib/galaxy/version.py Log Message: ----------- Update version to 17.01.rc1 Commit: ffa4af0a8e79acb673e90e543d67b7be0be3b631 https://github.com/galaxyproject/galaxy/commit/ffa4af0a8e79acb673e90e543d67… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-01-23 (Mon, 23 Jan 2017) Changed paths: M lib/galaxy/version.py Log Message: ----------- Merge pull request #3466 from jmchilton/version-17.01 [17.01] Update version to 17.01.rc1 Compare: https://github.com/galaxyproject/galaxy/compare/d19f22e3fabf...ffa4af0a8e79

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[galaxyproject/galaxy] ab8721: Update version to 17.01.rc1
by GitHub 23 Jan '17

23 Jan '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ab87216d59178dee482adf4d065cc507d590f1f8 https://github.com/galaxyproject/galaxy/commit/ab87216d59178dee482adf4d065c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-23 (Mon, 23 Jan 2017) Changed paths: M lib/galaxy/version.py Log Message: ----------- Update version to 17.01.rc1 Commit: 68a033655f12cfa4c63073b60340a5d1e26d272e https://github.com/galaxyproject/galaxy/commit/68a033655f12cfa4c63073b60340… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-23 (Mon, 23 Jan 2017) Changed paths: M lib/galaxy/version.py Log Message: ----------- Update version to 17.05.dev Commit: d4f567201e9f084a851d07a393b2814793f51684 https://github.com/galaxyproject/galaxy/commit/d4f567201e9f084a851d07a393b2… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-23 (Mon, 23 Jan 2017) Log Message: ----------- Merge branch 'version-17.01' into version-17.05.dev Commit: 1ef900ab48acd9904ae16fa5f287c5167e217260 https://github.com/galaxyproject/galaxy/commit/1ef900ab48acd9904ae16fa5f287… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-01-23 (Mon, 23 Jan 2017) Changed paths: M lib/galaxy/version.py Log Message: ----------- Merge pull request #3467 from jmchilton/version-17.05.dev Version 17.05.dev Compare: https://github.com/galaxyproject/galaxy/compare/d19f22e3fabf...1ef900ab48ac

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[galaxyproject/galaxy] 3f93b1: fix condor containers
by GitHub 23 Jan '17

23 Jan '17

Branch: refs/heads/release_16.10 Home: https://github.com/galaxyproject/galaxy Commit: 3f93b19ff34bf51d81b353eb5e11e1748fa35df4 https://github.com/galaxyproject/galaxy/commit/3f93b19ff34bf51d81b353eb5e11… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2017-01-23 (Mon, 23 Jan 2017) Changed paths: M lib/galaxy/jobs/runners/condor.py Log Message: ----------- fix condor containers Commit: 915b653b91af25bf126125be875bd6ab2d9f320c https://github.com/galaxyproject/galaxy/commit/915b653b91af25bf126125be875b… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-01-23 (Mon, 23 Jan 2017) Changed paths: M lib/galaxy/jobs/runners/condor.py Log Message: ----------- Merge pull request #3463 from jmchilton/16.07_container_fix [16.07] fix condor containers Commit: 1c0c378debdee4aeb9699f11ad2b3314323888b6 https://github.com/galaxyproject/galaxy/commit/1c0c378debdee4aeb9699f11ad2b… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-01-23 (Mon, 23 Jan 2017) Changed paths: M lib/galaxy/jobs/runners/condor.py Log Message: ----------- Merge branch 'release_16.07' into release_16.10 Compare: https://github.com/galaxyproject/galaxy/compare/c9fdb6e3efd2...1c0c378debde

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[galaxyproject/galaxy]
by GitHub 23 Jan '17

23 Jan '17

Branch: refs/heads/release_17.01 Home: https://github.com/galaxyproject/galaxy

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[galaxyproject/galaxy] ce0780: Custom dbkey builds: additional variable escaping
by GitHub 23 Jan '17

23 Jan '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ce0780abef5fd1e832175975b6243525a6e4cbad https://github.com/galaxyproject/galaxy/commit/ce0780abef5fd1e832175975b624… Author: yhoogstrate <y.hoogstrate(a)gmail.com> Date: 2017-01-16 (Mon, 16 Jan 2017) Changed paths: M client/galaxy/scripts/viz/trackster/tracks.js M lib/galaxy/webapps/galaxy/controllers/user.py M static/maps/viz/trackster/tracks.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/viz/trackster/tracks.js Log Message: ----------- Custom dbkey builds: additional variable escaping Commit: 1b589f252ed12eefc48c37f018e04faf142e5898 https://github.com/galaxyproject/galaxy/commit/1b589f252ed12eefc48c37f018e0… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-23 (Mon, 23 Jan 2017) Changed paths: M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/ui/ui-misc.js M config/galaxy.ini.sample A config/local_conda_mapping.yml.sample M doc/schema_template.md M lib/galaxy/config.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/runners/condor.py M lib/galaxy/model/orm/scripts.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/data/__init__.py M lib/galaxy/tools/data_manager/manager.py M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/tools/deps/dependencies.py M lib/galaxy/tools/deps/requirements.py M lib/galaxy/tools/deps/resolvers/__init__.py M lib/galaxy/tools/deps/resolvers/brewed_tool_shed_packages.py M lib/galaxy/tools/deps/resolvers/conda.py A lib/galaxy/tools/deps/resolvers/default_conda_mapping.yml M lib/galaxy/tools/deps/resolvers/galaxy_packages.py M lib/galaxy/tools/deps/resolvers/homebrew.py M lib/galaxy/tools/deps/resolvers/modules.py M lib/galaxy/tools/deps/resolvers/resolver_mixins.py M lib/galaxy/tools/deps/views.py M lib/galaxy/tools/errors.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/tools/imp_exp/export_history.py M lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/dynamic_options.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/tools/parameters/meta.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/tools/search/__init__.py M lib/galaxy/tools/util/galaxyops/__init__.py M lib/galaxy/tools/util/maf_utilities.py M lib/galaxy/tools/verify/asserts/__init__.py M lib/galaxy/tools/verify/test_data.py M lib/galaxy/tools/wrappers.py M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/util/object_wrapper.py A lib/galaxy/util/oset.py M lib/galaxy/util/properties.py M lib/galaxy/webapps/galaxy/api/configuration.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/util/shed_util_common.py M run.sh A scripts/manage_tool_dependencies.py M static/maps/mvc/form/form-view.js.map M static/maps/mvc/ui/ui-misc.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/form/form-view.js M static/scripts/mvc/ui/ui-misc.js M test/docker/base/run_test_wrapper.sh M test/functional/tools/column_param.xml A test/functional/tools/explicit_conversion.xml M test/functional/tools/implicit_conversion.xml A test/functional/tools/legacy_r.xml M test/functional/tools/samples_tool_conf.xml M test/galaxy_selenium/navigates_galaxy.py M test/integration/test_resolvers.py M test/selenium_tests/test_history_dataset_state.py M test/selenium_tests/test_history_sharing.py M test/selenium_tests/test_tool_form.py M test/selenium_tests/test_workflow_editor.py M test/selenium_tests/test_workflow_management.py M test/unit/tools/test_tool_deps.py M tools/plotting/bar_chart.xml Log Message: ----------- Merge remote-tracking branch 'jmchilton/dev' into escape_vis Conflicts: static/scripts/bundled/libs.bundled.js.map Commit: d19f22e3fabfd7f22b6970fe857ed636462ca8e5 https://github.com/galaxyproject/galaxy/commit/d19f22e3fabfd7f22b6970fe857e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-23 (Mon, 23 Jan 2017) Changed paths: M client/galaxy/scripts/viz/trackster/tracks.js M lib/galaxy/webapps/galaxy/controllers/user.py M static/maps/viz/trackster/tracks.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/viz/trackster/tracks.js Log Message: ----------- Merge pull request #3448 from yhoogstrate/escape_vis Custom dbkey builds: additional variable escaping Compare: https://github.com/galaxyproject/galaxy/compare/8daa58adcc6c...d19f22e3fabf

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[galaxyproject/galaxy] 56ed9d: Fix linting of <conditional>s
by GitHub 23 Jan '17

23 Jan '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 56ed9db21d16e5c42e0d05c7102b681089ba2354 https://github.com/galaxyproject/galaxy/commit/56ed9db21d16e5c42e0d05c7102b… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-01-23 (Mon, 23 Jan 2017) Changed paths: M lib/galaxy/tools/linters/inputs.py Log Message: ----------- Fix linting of <conditional>s If the first param is boolean with truevalue="True" or falsavalue="False", or a select with an option having value "True" or "False", the linter was wrongly complaining with both: No <when /> block found for select option 'True' and: No <option /> block found for when block 'true' Commit: 8daa58adcc6c28004a2697407bce8f28d8bb5411 https://github.com/galaxyproject/galaxy/commit/8daa58adcc6c28004a2697407bce… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-23 (Mon, 23 Jan 2017) Changed paths: M lib/galaxy/tools/linters/inputs.py Log Message: ----------- Merge pull request #3464 from nsoranzo/conditional_linting Fix linting of <conditional>s Compare: https://github.com/galaxyproject/galaxy/compare/98ee91f46703...8daa58adcc6c

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[galaxyproject/galaxy] cd2cf4: Allow finer grain specification of requirements.
by GitHub 23 Jan '17

23 Jan '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: cd2cf494fe1ede4ae5b43417f0da21b2ca6473a0 https://github.com/galaxyproject/galaxy/commit/cd2cf494fe1ede4ae5b43417f0da… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-23 (Mon, 23 Jan 2017) Changed paths: M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/requirements.py M lib/galaxy/tools/deps/resolvers/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/xsd/galaxy.xsd A test/functional/tools/requirement_specification_1.xml A test/functional/tools/requirement_specification_2.xml Log Message: ----------- Allow finer grain specification of requirements. This adapts CWL-style ``SoftwareRequirement`` ``specs`` to solve #1927. Here I'm trying to implement the CWL specification in a way that helps enable the feasibility of Conda packaging in Galaxy. It is a delicate balancing act aimed to upset as many interested parties as I can. To understand the problem - consider the ``blast+`` requirement found in the Galaxy wrappers. It looks something like this: ``` <requirement type="package" version="2.2.31" name="blast+"> ``` Great, that works for Galaxy and Tool Shed packages. It doesn't work for bioconda at all. I think this problem is fairly uncommon - most packages have simple names shared across Debian, Brew, Conda, etc... - but it does happen in some cases that there are inconsistencies. Some people have taken to duplicating the requirement - this is bad and should not be done since they are mutually exclusive and Galaxy will attempt to resolve both. This introduces the following syntax for tools with profile >= 16.10: ``` <requirement type="package" version="2.2.31" name="blast+"> <specification uri="https://anaconda.org/bioconda/blast" /> <specification uri="https://packages.debian.org/sid/ncbi-blast+" version="2.2.31-3" /> </requirement> ``` This allows finer grain resolution of the requirement without sacrificing the abstract name at the top. It allows the name and the version to be adapted by resolvers as needed (hopefully rarely so). This syntax is the future facing one, but obviously this tool would not work on older Galaxy versions. To remedy this - an alternative syntax can be used for tools targetting Galaxy verions pre-16.10: ``` <requirement type="package" version="2.2" specification_uris="https://anaconda.org/bioconda/blast@2.2.31,https://packages.debian.org/jess…">blast+</requirement> ``` This syntax sucks - but it does give newer Galaxies the ability to resolve the specifications without breaking the more simple functionality for older Galaxies. For more information on the CWL side of this - checkout the discussion on https://github.com/common-workflow-language/cwltool/pull/214. The CWL specification information is defined at http://www.commonwl.org/v1.0/CommandLineTool.html#SoftwarePackage. Conflicts: lib/galaxy/tools/deps/__init__.py test/functional/tools/samples_tool_conf.xml Commit: 330d71d37ce7eaa60b5c8c20ae83aeb36fec4a6c https://github.com/galaxyproject/galaxy/commit/330d71d37ce7eaa60b5c8c20ae83… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-23 (Mon, 23 Jan 2017) Changed paths: M lib/galaxy/tools/deps/requirements.py M lib/galaxy/tools/xsd/galaxy.xsd R test/functional/tools/requirement_specification_1.xml R test/functional/tools/requirement_specification_2.xml Log Message: ----------- Remove tool XML modifications for requirement specifications. Per discussion on #3117 - some people were in favor of the idea but some were opposed. I think it is still important to implement this for CWL tools and useful from a library perspective. This just removes changes to Galaxy tool XML. Commit: baf9b82847fc526af56ed8efa7aba4d31d62f400 https://github.com/galaxyproject/galaxy/commit/baf9b82847fc526af56ed8efa7ab… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-23 (Mon, 23 Jan 2017) Changed paths: M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/resolvers/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- More modular config option handling for dependency resolvers. The handling of global configuration options for Conda specific options was hacky and a poor design. This is much more modular and allows the elegant cascading option sources for all resolvers. Commit: 49a11073a49242fbd86e3ec05fb5029194ec23fd https://github.com/galaxyproject/galaxy/commit/49a11073a49242fbd86e3ec05fb5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-23 (Mon, 23 Jan 2017) Changed paths: M lib/galaxy/tools/deps/resolvers/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Give resolver's with a resolve_all method an interface. This follows the existing pattern within the module. Commit: 8e20e71556cfc90da548243d390deb52d4e9110d https://github.com/galaxyproject/galaxy/commit/8e20e71556cfc90da548243d390d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-23 (Mon, 23 Jan 2017) Changed paths: M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/requirements.py M lib/galaxy/tools/deps/resolvers/__init__.py M lib/galaxy/tools/deps/resolvers/brewed_tool_shed_packages.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/deps/resolvers/galaxy_packages.py M lib/galaxy/tools/deps/resolvers/homebrew.py M lib/galaxy/tools/deps/resolvers/modules.py M test/unit/tools/test_tool_deps.py Log Message: ----------- Change interface of depependency resolver's resolve for consistency. If resolve_all takes in requirements, then so should resolve. Commit: 35b2b735ff7495576de88b7469c7118f65cb2838 https://github.com/galaxyproject/galaxy/commit/35b2b735ff7495576de88b7469c7… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-23 (Mon, 23 Jan 2017) Changed paths: M lib/galaxy/tools/deps/resolvers/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Modify specification interface with better name. Commit: 2fad74ddcf63c03fc2d7fd77fa3838de637a1bf4 https://github.com/galaxyproject/galaxy/commit/2fad74ddcf63c03fc2d7fd77fa38… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-23 (Mon, 23 Jan 2017) Changed paths: M lib/galaxy/tools/deps/resolvers/__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/modules.py M test/unit/tools/test_tool_deps.py Log Message: ----------- Implement dependency mapping for environment modules, galaxy packages, and Conda. Commit: 3d9cdeb70c0170b7795c35e458c878ebe19caf1a https://github.com/galaxyproject/galaxy/commit/3d9cdeb70c0170b7795c35e458c8… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-23 (Mon, 23 Jan 2017) Changed paths: M lib/galaxy/config.py M lib/galaxy/model/orm/scripts.py M lib/galaxy/util/properties.py M run.sh A scripts/manage_tool_dependencies.py Log Message: ----------- Outline infrastructure for managing Conda installations outside of Galaxy. - Construct a DependencyManager according to Galaxy's configuration before Galaxy starts to allow auto installation of Conda. - Add script for managing tool dependencies outside of a Galaxy environment. - Refactor to allow this to be done without duplicating logic related to defaults, configuration handling, etc.... Implements #3426. Commit: 312f941e46fdbbe6198b6b0e6a3f00867946a6bd https://github.com/galaxyproject/galaxy/commit/312f941e46fdbbe6198b6b0e6a3f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-23 (Mon, 23 Jan 2017) Changed paths: M config/galaxy.ini.sample M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Swap default for Conda "auto_init" to True. Everyone gets a Conda when Galaxy starts up. Commit: 0b7c6761c8dbb2baf7391dc4a08c4dbed2ccc7f2 https://github.com/galaxyproject/galaxy/commit/0b7c6761c8dbb2baf7391dc4a08c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-23 (Mon, 23 Jan 2017) Changed paths: M scripts/manage_tool_dependencies.py Log Message: ----------- Rework #3433 for changes in #3444. Commit: 9baf6d6d8d8d089a8d2c2687ef498a396006b920 https://github.com/galaxyproject/galaxy/commit/9baf6d6d8d8d089a8d2c2687ef49… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-23 (Mon, 23 Jan 2017) Changed paths: A config/local_conda_mapping.yml.sample M lib/galaxy/config.py A lib/galaxy/tools/deps/resolvers/default_conda_mapping.yml A test/functional/tools/legacy_r.xml M test/functional/tools/samples_tool_conf.xml M test/integration/test_resolvers.py Log Message: ----------- Samples and defaults for Conda mapping. - Map R to r-base and blast+ to blast for conda dependencies. - Add sample environment modules file showing off the new mapping feature. - Add integration test case to verify the default conda mapping (R -> r-base in particular). Commit: 3e3d41fb94c00a9c6b068626b6f541e714b2500e https://github.com/galaxyproject/galaxy/commit/3e3d41fb94c00a9c6b068626b6f5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-23 (Mon, 23 Jan 2017) Changed paths: M test/unit/tools/test_tool_deps.py Log Message: ----------- Fix unit test test_tool_deps to not auto-install Conda. This became the default behavior with conda_auto_init defaulting to True. Commit: 98ee91f467039f27f4e10d730f78057d1421e833 https://github.com/galaxyproject/galaxy/commit/98ee91f467039f27f4e10d730f78… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2017-01-23 (Mon, 23 Jan 2017) Changed paths: M config/galaxy.ini.sample A config/local_conda_mapping.yml.sample M lib/galaxy/config.py M lib/galaxy/model/orm/scripts.py M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/requirements.py M lib/galaxy/tools/deps/resolvers/__init__.py M lib/galaxy/tools/deps/resolvers/brewed_tool_shed_packages.py M lib/galaxy/tools/deps/resolvers/conda.py A lib/galaxy/tools/deps/resolvers/default_conda_mapping.yml M lib/galaxy/tools/deps/resolvers/galaxy_packages.py M lib/galaxy/tools/deps/resolvers/homebrew.py M lib/galaxy/tools/deps/resolvers/modules.py M lib/galaxy/util/properties.py M run.sh A scripts/manage_tool_dependencies.py A test/functional/tools/legacy_r.xml M test/functional/tools/samples_tool_conf.xml M test/integration/test_resolvers.py M test/unit/tools/test_tool_deps.py Log Message: ----------- Merge pull request #3444 from jmchilton/deps_framework_overhaul Implement Dependency Resolver Mapping Compare: https://github.com/galaxyproject/galaxy/compare/5bd8a0fa0232...98ee91f46703

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[galaxyproject/galaxy] 20632b: Adding fuzzy search to tool search
by GitHub 23 Jan '17

23 Jan '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 20632b2757f789bc751faa280fa34eebe78e41db https://github.com/galaxyproject/galaxy/commit/20632b2757f789bc751faa280fa3… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2016-12-21 (Wed, 21 Dec 2016) Changed paths: M lib/galaxy/tools/search/__init__.py M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Adding fuzzy search to tool search Commit: 659679005d0e0db7a9689cc738114742bf3140fc https://github.com/galaxyproject/galaxy/commit/659679005d0e0db7a9689cc73811… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-01-16 (Mon, 16 Jan 2017) Changed paths: M .ci/flake8_lint_include_list.txt M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js A client/galaxy/scripts/mvc/workflow/workflow-icons.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M config/datatypes_conf.xml.sample M config/galaxy.ini.sample M config/job_conf.xml.sample_advanced M config/plugins/interactive_environments/jupyter/config/jupyter.xml M config/plugins/interactive_environments/rstudio/config/rstudio.xml M config/plugins/tours/core.history.yaml M lib/galaxy/config.py M lib/galaxy/datatypes/constructive_solid_geometry.py M lib/galaxy/datatypes/images.py M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/actions/post.py M lib/galaxy/jobs/command_factory.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh M lib/galaxy/jobs/runners/util/job_script/__init__.py M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/container_resolvers/explicit.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/tools/verify/asserts/text.py M lib/galaxy/web/base/controller.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/workflow/modules.py M run_tests.sh M scripts/functional_tests.py R scripts/run_selenium_tests.sh M static/maps/layout/menu.js.map M static/maps/mvc/form/form-section.js.map M static/maps/mvc/tool/tool-form-composite.js.map A static/maps/mvc/workflow/workflow-icons.js.map M static/maps/mvc/workflow/workflow-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/layout/menu.js M static/scripts/mvc/form/form-section.js M static/scripts/mvc/tool/tool-form-composite.js A static/scripts/mvc/workflow/workflow-icons.js M static/scripts/mvc/workflow/workflow-view.js M templates/ind_share_base.mako M templates/show_params.mako R test/api/helpers.py M test/api/test_dataset_collections.py M test/api/test_datasets.py M test/api/test_histories.py M test/api/test_history_contents.py M test/api/test_history_contents_provenance.py M test/api/test_jobs.py M test/api/test_libraries.py M test/api/test_search.py M test/api/test_tools.py A test/api/test_visualizations.py R test/api/test_workflow_1.ga R test/api/test_workflow_2.ga R test/api/test_workflow_batch.ga M test/api/test_workflow_extraction.py R test/api/test_workflow_map_reduce_pause.ga R test/api/test_workflow_matching_lists.ga R test/api/test_workflow_missing_tool.ga R test/api/test_workflow_pause.ga R test/api/test_workflow_topoambigouity.ga R test/api/test_workflow_topoambigouity_auto_laidout.ga R test/api/test_workflow_validation_1.ga R test/api/test_workflow_with_runtime_input.ga M test/api/test_workflows.py R test/api/workflows_format_2/README.txt R test/api/workflows_format_2/__init__.py R test/api/workflows_format_2/converter.py R test/api/workflows_format_2/interface.py R test/api/workflows_format_2/main.py A test/base/data/test_workflow_1.ga A test/base/data/test_workflow_2.ga A test/base/data/test_workflow_batch.ga A test/base/data/test_workflow_map_reduce_pause.ga A test/base/data/test_workflow_matching_lists.ga A test/base/data/test_workflow_missing_tool.ga A test/base/data/test_workflow_pause.ga A test/base/data/test_workflow_topoambigouity.ga A test/base/data/test_workflow_topoambigouity_auto_laidout.ga A test/base/data/test_workflow_validation_1.ga A test/base/data/test_workflow_with_runtime_input.ga M test/base/driver_util.py A test/base/populators.py A test/base/workflows_format_2/README.txt A test/base/workflows_format_2/__init__.py A test/base/workflows_format_2/converter.py A test/base/workflows_format_2/interface.py A test/base/workflows_format_2/main.py R test/casperjs/api-dataset-tests.js R test/casperjs/api-visualizations-tests.js M test/docker/base/Dockerfile M test/docker/base/ansible_vars.yml M test/docker/base/run_test_wrapper.sh A test/functional/tools/for_workflows/mapper2.xml A test/functional/tools/python_environment_problem.py A test/functional/tools/python_environment_problem.xml M test/functional/tools/samples_tool_conf.xml R test/functional/workflow.py M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/navigation-data.yml A test/integration/resubmission_default_job_conf.xml M test/integration/resubmission_runners.py M test/integration/test_job_resubmission.py M test/manual/workflows_scaling.py A test/selenium_tests/_workflow_fixtures.py M test/selenium_tests/framework.py M test/selenium_tests/test_history_dataset_state.py M test/selenium_tests/test_stock_tours.py M test/selenium_tests/test_tool_form.py M test/selenium_tests/test_workflow_editor.py A test/selenium_tests/test_workflow_management.py A test/selenium_tests/test_workflow_run.py M test/unit/jobs/test_command_factory.py M test/unit/jobs/test_job_configuration.py M test/unit/tools_support.py M test/unit/workflows/workflow_support.py R tools/filters/gff/sort_gtf.py M tox.ini Log Message: ----------- Merging with dev Commit: ea0d50648c2c64abb7093fba47acec020919163f https://github.com/galaxyproject/galaxy/commit/ea0d50648c2c64abb7093fba47ac… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-01-16 (Mon, 16 Jan 2017) Changed paths: M .ci/jenkins/selenium/run_galaxy.bash M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/ui/ui-misc.js M config/datatypes_conf.xml.sample M config/plugins/interactive_environments/rstudio/templates/rstudio.mako M config/plugins/visualizations/charts/templates/charts.mako M config/plugins/visualizations/csg/templates/csg.mako M config/plugins/visualizations/graphviz/templates/graphviz.mako M config/plugins/visualizations/scatterplot/templates/scatterplot.mako M config/plugins/webhooks/demo/phdcomics/helper/__init__.py M config/plugins/webhooks/demo/phdcomics/static/script.js M doc/source/admin/webhooks.rst M doc/source/api/guidelines.rst M lib/galaxy/datatypes/binary.py A lib/galaxy/datatypes/converters/fastqbz2_to_fastq.xml A lib/galaxy/datatypes/converters/fastqcssangerbz2_to_fastqcssanger.xml A lib/galaxy/datatypes/converters/fastqcssangergz_to_fastqcssanger.xml A lib/galaxy/datatypes/converters/fastqgz_to_fastq.xml A lib/galaxy/datatypes/converters/fastqilluminabz2_to_fastqillumina.xml A lib/galaxy/datatypes/converters/fastqilluminagz_to_fastqillumina.xml A lib/galaxy/datatypes/converters/fastqsangerbz2_to_fastqsanger.xml A lib/galaxy/datatypes/converters/fastqsangergz_to_fastqsanger.xml A lib/galaxy/datatypes/converters/fastqsolexabz2_to_fastqsolexa.xml A lib/galaxy/datatypes/converters/fastqsolexagz_to_fastqsolexa.xml M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py A lib/galaxy/datatypes/test/diamond_db.dmnd M lib/galaxy/jobs/actions/post.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/requirements.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/deps/views.py M lib/galaxy/web/framework/middleware/remoteuser.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/util/shed_util_common.py M run_tests.sh A static/maps/libs/showdown.js.map M static/maps/mvc/form/form-view.js.map M static/maps/mvc/ui/ui-misc.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 A static/scripts/libs/showdown.js M static/scripts/mvc/form/form-view.js M static/scripts/mvc/ui/ui-misc.js M templates/ind_share_base.mako M templates/webapps/galaxy/history/share.mako A test-data/1.fastqsanger.bz2 A test-data/1.fastqsanger.gz M test/api/test_workflows.py M test/docker/README.md A test/functional/tools/compressed_bz2_fastq_conversion.xml A test/functional/tools/compressed_bz2_fastq_no_conversion.xml A test/functional/tools/compressed_gz_fastq_conversion.xml A test/functional/tools/compressed_gz_fastq_no_conversion.xml A test/functional/tools/implicit_conversion.xml A test/functional/tools/mulled_example_conflict.xml M test/functional/tools/sample_datatypes_conf.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merging with dev Commit: a4dec71b7ac0fedcd5f14179b7ace172d1466308 https://github.com/galaxyproject/galaxy/commit/a4dec71b7ac0fedcd5f14179b7ac… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-01-16 (Mon, 16 Jan 2017) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/tools/search/__init__.py M lib/galaxy/webapps/galaxy/api/tools.py Log Message: ----------- Adding Whoosh NgramFilter and making it configurable through config Commit: 28133bead15e955e70fcbec8e09d1de06598b345 https://github.com/galaxyproject/galaxy/commit/28133bead15e955e70fcbec8e09d… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-01-16 (Mon, 16 Jan 2017) Changed paths: M lib/galaxy/tools/search/__init__.py Log Message: ----------- Adding and removing blank lines Commit: 54b527b1fc35d6ea66215df04144491f42e558e4 https://github.com/galaxyproject/galaxy/commit/54b527b1fc35d6ea66215df04144… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-01-19 (Thu, 19 Jan 2017) Changed paths: M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt M lib/galaxy/jobs/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/data/__init__.py M lib/galaxy/tools/data_manager/manager.py M lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/tools/deps/resolvers/resolver_mixins.py M lib/galaxy/tools/errors.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/tools/imp_exp/export_history.py M lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/dynamic_options.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/tools/parameters/meta.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/tools/search/__init__.py M lib/galaxy/tools/util/galaxyops/__init__.py M lib/galaxy/tools/util/maf_utilities.py M lib/galaxy/tools/verify/asserts/__init__.py M lib/galaxy/tools/verify/test_data.py M lib/galaxy/tools/wrappers.py M lib/galaxy/webapps/galaxy/api/configuration.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/tool_shed/util/shed_util_common.py Log Message: ----------- Merging with dev Commit: 2573699c0ac1a12f808acb4006bc9e5f05f822a9 https://github.com/galaxyproject/galaxy/commit/2573699c0ac1a12f808acb4006bc… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-01-19 (Thu, 19 Jan 2017) Changed paths: M lib/galaxy/tools/search/__init__.py Log Message: ----------- Adding line breaks for import section Commit: 5bd8a0fa0232f5fa56cc4ace557d3b8f0d5cbdf0 https://github.com/galaxyproject/galaxy/commit/5bd8a0fa0232f5fa56cc4ace557d… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-01-23 (Mon, 23 Jan 2017) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/tools/search/__init__.py M lib/galaxy/webapps/galaxy/api/tools.py Log Message: ----------- Merge pull request #3356 from bgruening/fuzzysearch Fuzzy search for tools search Compare: https://github.com/galaxyproject/galaxy/compare/4eade311dbeb...5bd8a0fa0232

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[galaxyproject/galaxy] 3f93b1: fix condor containers
by GitHub 23 Jan '17

23 Jan '17

Branch: refs/heads/release_16.07 Home: https://github.com/galaxyproject/galaxy Commit: 3f93b19ff34bf51d81b353eb5e11e1748fa35df4 https://github.com/galaxyproject/galaxy/commit/3f93b19ff34bf51d81b353eb5e11… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2017-01-23 (Mon, 23 Jan 2017) Changed paths: M lib/galaxy/jobs/runners/condor.py Log Message: ----------- fix condor containers Commit: 915b653b91af25bf126125be875bd6ab2d9f320c https://github.com/galaxyproject/galaxy/commit/915b653b91af25bf126125be875b… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-01-23 (Mon, 23 Jan 2017) Changed paths: M lib/galaxy/jobs/runners/condor.py Log Message: ----------- Merge pull request #3463 from jmchilton/16.07_container_fix [16.07] fix condor containers Compare: https://github.com/galaxyproject/galaxy/compare/5b3debc51088...915b653b91af

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[galaxyproject/galaxy] 596d12: Implement ToolRequirements class
by GitHub 23 Jan '17

23 Jan '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 596d12da44908e158905d7c1bce30d9e3557b258 https://github.com/galaxyproject/galaxy/commit/596d12da44908e158905d7c1bce3… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-01-22 (Sun, 22 Jan 2017) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/dependencies.py M lib/galaxy/tools/deps/requirements.py M lib/galaxy/tools/deps/views.py A lib/galaxy/util/oset.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/util/shed_util_common.py M test/unit/tools/test_tool_deps.py Log Message: ----------- Implement ToolRequirements class This class holds indiviual ToolRequirement objects as an ordered set. This makes it easier to compare, intersect, and get unions of multiple ToolRequirements and to filter for resolvable or package type dependencies. This will be useful when installing tool dependencies in batch. Commit: 5ee7e2e3e26bdbdecec0b74ed4154734d9b56ae4 https://github.com/galaxyproject/galaxy/commit/5ee7e2e3e26bdbdecec0b74ed415… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-01-22 (Sun, 22 Jan 2017) Changed paths: M lib/galaxy/tools/deps/__init__.py Log Message: ----------- Log failed dep resolution just once Commit: 9c9b405b6f969421c2073a53dad117ffefed17c6 https://github.com/galaxyproject/galaxy/commit/9c9b405b6f969421c2073a53dad1… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-01-22 (Sun, 22 Jan 2017) Changed paths: M test/unit/tools/test_tool_deps.py Log Message: ----------- Add test for set on list of ToolRequirements Commit: 4eade311dbebdf90168821fafe3e4d09f4423565 https://github.com/galaxyproject/galaxy/commit/4eade311dbebdf90168821fafe3e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-23 (Mon, 23 Jan 2017) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/dependencies.py M lib/galaxy/tools/deps/requirements.py M lib/galaxy/tools/deps/views.py A lib/galaxy/util/oset.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/util/shed_util_common.py M test/unit/tools/test_tool_deps.py Log Message: ----------- Merge pull request #3461 from mvdbeek/ToolRequirements Implement ToolRequirements class Compare: https://github.com/galaxyproject/galaxy/compare/00d1e15f74be...4eade311dbeb

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[galaxyproject/galaxy] e5de94: fix condor containers
by GitHub 23 Jan '17

23 Jan '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: e5de94ceb9b6a8876a646d4cfc281d5c12f1125a https://github.com/galaxyproject/galaxy/commit/e5de94ceb9b6a8876a646d4cfc28… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2017-01-22 (Sun, 22 Jan 2017) Changed paths: M lib/galaxy/jobs/runners/condor.py Log Message: ----------- fix condor containers Commit: 00d1e15f74bec373934bceeb0d7ca73d8a93da78 https://github.com/galaxyproject/galaxy/commit/00d1e15f74bec373934bceeb0d7c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-23 (Mon, 23 Jan 2017) Changed paths: M lib/galaxy/jobs/runners/condor.py Log Message: ----------- Merge pull request #3462 from bgruening/fix_condor_containers fix condor containers Compare: https://github.com/galaxyproject/galaxy/compare/7700c3cf7f07...00d1e15f74be

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[galaxyproject/galaxy] 45bf7a: Make requirement tags in bar_chart.xml functional ...
by GitHub 22 Jan '17

22 Jan '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 45bf7ad8c4437edc95847de47e2f46a393fc1726 https://github.com/galaxyproject/galaxy/commit/45bf7ad8c4437edc95847de47e2f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-19 (Thu, 19 Jan 2017) Changed paths: M tools/plotting/bar_chart.xml Log Message: ----------- Make requirement tags in bar_chart.xml functional with default dependency resolver. I'm not sure if we need to update the version since previously these tags were purely for documentation and had no functional purpose. xref this comment https://github.com/galaxyproject/galaxy/pull/3444#issuecomment-273909855 from @bgruening Commit: 7700c3cf7f0789a4a921f32ff9b1e8037634d63e https://github.com/galaxyproject/galaxy/commit/7700c3cf7f0789a4a921f32ff9b1… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-01-22 (Sun, 22 Jan 2017) Changed paths: M tools/plotting/bar_chart.xml Log Message: ----------- Merge pull request #3454 from jmchilton/gnuplot_deps Make requirement tags in bar_chart.xml functional with default dependency resolvers. Compare: https://github.com/galaxyproject/galaxy/compare/d9f9a31c32b9...7700c3cf7f07

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[galaxyproject/galaxy] 5c4840: Various fixes for test image Docker user switching...
by GitHub 22 Jan '17

22 Jan '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 5c48402b0202e438d663c4dc151d835c7725a4f6 https://github.com/galaxyproject/galaxy/commit/5c48402b0202e438d663c4dc151d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-17 (Tue, 17 Jan 2017) Changed paths: M test/docker/base/run_test_wrapper.sh Log Message: ----------- Various fixes for test image Docker user switching. - Fix if testing as user with GID 109 (fixes #3425). - Fix if testing as a user with any UID or GID that already exists in the container. - More logging to indicate the "problems" being printed to standard output in these cases are not problems. - Fix sqlite being readonly in the container for the test user. Commit: d9f9a31c32b9d1a2121d5db6e2b8f81dbf12d7c8 https://github.com/galaxyproject/galaxy/commit/d9f9a31c32b9d1a2121d5db6e2b8… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-01-22 (Sun, 22 Jan 2017) Changed paths: M test/docker/base/run_test_wrapper.sh Log Message: ----------- Merge pull request #3443 from jmchilton/test_docker_fix Various fixes for test image Docker user switching. Compare: https://github.com/galaxyproject/galaxy/compare/3945f3b885a2...d9f9a31c32b9

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[galaxyproject/galaxy] f8552c: Document shared_inputs for parallelism tag in tool...
by GitHub 20 Jan '17

20 Jan '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f8552c19dc55ddeeeb7441190891f52cdd9d9ef3 https://github.com/galaxyproject/galaxy/commit/f8552c19dc55ddeeeb7441190891… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-20 (Fri, 20 Jan 2017) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- Document shared_inputs for parallelism tag in tool XSD. Commit: 22f4696f7d54a90a31f253d05a7ed1314db4b943 https://github.com/galaxyproject/galaxy/commit/22f4696f7d54a90a31f253d05a7e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-20 (Fri, 20 Jan 2017) Changed paths: A test/functional/tools/explicit_conversion.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Implement tool testing and documenting explicit conversion tags. Commit: 074e10ac00a7dde7c2fc5e76928392e073791b30 https://github.com/galaxyproject/galaxy/commit/074e10ac00a7dde7c2fc5e769283… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-20 (Fri, 20 Jan 2017) Changed paths: M doc/schema_template.md M lib/galaxy/tools/xsd/galaxy.xsd M test/functional/tools/explicit_conversion.xml M test/functional/tools/implicit_conversion.xml Log Message: ----------- Fix tool XSD to document <conversion> tag for data parameters. Rebased with English fixes and small tool cleanups thanks to @nsoranzo. Commit: dba4d95961a3ccadd4a0822f13f0f02730889a8a https://github.com/galaxyproject/galaxy/commit/dba4d95961a3ccadd4a0822f13f0… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-20 (Fri, 20 Jan 2017) Changed paths: M test/functional/tools/column_param.xml M test/functional/tools/explicit_conversion.xml M test/functional/tools/implicit_conversion.xml Log Message: ----------- Reduced usage of from_work_dir in test tools. Per recommendation of @bgruening. Commit: 3945f3b885a291c9b1a1ebf85a56137e2d1b22e2 https://github.com/galaxyproject/galaxy/commit/3945f3b885a291c9b1a1ebf85a56… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-01-20 (Fri, 20 Jan 2017) Changed paths: M doc/schema_template.md M lib/galaxy/tools/xsd/galaxy.xsd M test/functional/tools/column_param.xml A test/functional/tools/explicit_conversion.xml M test/functional/tools/implicit_conversion.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge pull request #3457 from jmchilton/xsd_fixes_2 Tool Documentation and Testing Improvements Compare: https://github.com/galaxyproject/galaxy/compare/d8f23b393527...3945f3b885a2

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[galaxyproject/galaxy] 1af158: Fix various transiently failing Selenium tests.
by GitHub 19 Jan '17

19 Jan '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 1af1583caa1b5c62c92573fe42693338ba457fcf https://github.com/galaxyproject/galaxy/commit/1af1583caa1b5c62c92573fe4269… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-19 (Thu, 19 Jan 2017) Changed paths: M test/galaxy_selenium/navigates_galaxy.py M test/selenium_tests/test_history_dataset_state.py M test/selenium_tests/test_tool_form.py Log Message: ----------- Fix various transiently failing Selenium tests. I'm pretty sure the problem is that I was waiting on conditions (e.g. datasets to become "ok") using the API and then assuming the state of the GUI elements was the same. Obviously though the GUI is polling the API and there is some lag there. This commit changes things to specifically wait on history panel GUI changes - obviously the better thing to wait on in a GUI test. Commit: d8f23b393527e2ea5b495cc850eeec25fdc64a8b https://github.com/galaxyproject/galaxy/commit/d8f23b393527e2ea5b495cc850ee… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-01-19 (Thu, 19 Jan 2017) Changed paths: M test/galaxy_selenium/navigates_galaxy.py M test/selenium_tests/test_history_dataset_state.py M test/selenium_tests/test_tool_form.py Log Message: ----------- Merge pull request #3450 from jmchilton/selenium_fixes_2 Fix various transiently failing Selenium tests. Compare: https://github.com/galaxyproject/galaxy/compare/60b57397e7f8...d8f23b393527

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[galaxyproject/galaxy] f50826: Do not wrap __class__ attribute of SafeStringWrapp...
by GitHub 19 Jan '17

19 Jan '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f5082604f7282587bb8385dbdb3bb91905bee87b https://github.com/galaxyproject/galaxy/commit/f5082604f7282587bb8385dbdb3b… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-01-19 (Thu, 19 Jan 2017) Changed paths: M lib/galaxy/util/object_wrapper.py Log Message: ----------- Do not wrap __class__ attribute of SafeStringWrapper Fix #3353 by not recursing on the parent classes, which may lead to an abstract class. Also fix a method name of "object" class. Commit: c9fdb6e3efd2721dc193ea5f1d5cfe6c014ad94e https://github.com/galaxyproject/galaxy/commit/c9fdb6e3efd2721dc193ea5f1d5c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-19 (Thu, 19 Jan 2017) Changed paths: M lib/galaxy/util/object_wrapper.py Log Message: ----------- Merge pull request #3449 from dannon/backport_mistargeted_3429 [16.10] Backport of 3429, safestringwrapper Commit: 60b57397e7f8227f0a5017141c81fdcc81d59ede https://github.com/galaxyproject/galaxy/commit/60b57397e7f8227f0a5017141c81… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-01-19 (Thu, 19 Jan 2017) Log Message: ----------- Merge branch 'release_16.10' into dev Compare: https://github.com/galaxyproject/galaxy/compare/b4475ba9df9b...60b57397e7f8

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