galaxy-commits August 2015

galaxy-commits@lists.galaxyproject.org

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124 discussions

[galaxyproject/galaxy] 4dd630: Fix version parsing in tool form
by GitHub 31 Aug '15

31 Aug '15

Branch: refs/heads/release_15.07 Home: https://github.com/galaxyproject/galaxy Commit: 4dd6304f055706e38176823a4166c6536618a042 https://github.com/galaxyproject/galaxy/commit/4dd6304f055706e38176823a4166… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-08-31 (Mon, 31 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/tools/tools-form.js M static/maps/mvc/tools/tools-form.js.map M static/scripts/mvc/tools/tools-form.js Log Message: ----------- Fix version parsing in tool form Commit: 3653bf5e37b13ea17cecd321fdbe9ce4fedcfbb8 https://github.com/galaxyproject/galaxy/commit/3653bf5e37b13ea17cecd321fdbe… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2015-08-31 (Mon, 31 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/tools/tools-form.js M static/maps/mvc/tools/tools-form.js.map M static/scripts/mvc/tools/tools-form.js Log Message: ----------- Merge pull request #677 from guerler/fix_version_002 [15.07] Fix version handling in tool form Compare: https://github.com/galaxyproject/galaxy/compare/525188d2a871...3653bf5e37b1

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[galaxyproject/infrastructure-playbook] 89b873: Update common_roles version
by GitHub 31 Aug '15

31 Aug '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 89b87312737d0756b16532c7cf140d8039b1747c https://github.com/galaxyproject/infrastructure-playbook/commit/89b87312737… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-08-31 (Mon, 31 Aug 2015) Changed paths: M common_roles Log Message: ----------- Update common_roles version Commit: 80a4025a60801b40dc46239ca16b39ec3cd756d0 https://github.com/galaxyproject/infrastructure-playbook/commit/80a4025a608… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-08-31 (Mon, 31 Aug 2015) Changed paths: A galaxyenv/host_vars/n2.galaxyproject.org.yml M galaxyenv/inventory M galaxyenv/secret_host_vars/default.yml A galaxyenv/secret_host_vars/n2.galaxyproject.org.yml M playbook.yml Log Message: ----------- Set up n2.galaxyproject.org for Jenkins. Compare: https://github.com/galaxyproject/infrastructure-playbook/compare/e997536619…

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[galaxyproject/galaxy] aa7968: Changed class naming to reflect use
by GitHub 31 Aug '15

31 Aug '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: aa7968aa9d13ab5de9fcebd427e5eca356cc1de4 https://github.com/galaxyproject/galaxy/commit/aa7968aa9d13ab5de9fcebd427e5… Author: Airistotal <danieltos.bouchard(a)gmail.com> Date: 2015-08-31 (Mon, 31 Aug 2015) Changed paths: M client/galaxy/style/less/reports.less M static/style/blue/base.css M static/style/blue/reports.css M templates/webapps/reports/job_info.mako M templates/webapps/reports/jobs_errors_per_tool.mako M templates/webapps/reports/jobs_per_month_all.mako M templates/webapps/reports/jobs_per_month_in_error.mako M templates/webapps/reports/jobs_per_tool.mako M templates/webapps/reports/jobs_per_user.mako M templates/webapps/reports/jobs_specified_month_all.mako M templates/webapps/reports/jobs_specified_month_in_error.mako M templates/webapps/reports/jobs_tool_per_month.mako M templates/webapps/reports/jobs_user_per_month.mako M templates/webapps/reports/registered_users.mako M templates/webapps/reports/registered_users_per_month.mako M templates/webapps/reports/registered_users_specified_date.mako M templates/webapps/reports/registered_users_specified_month.mako M templates/webapps/reports/requests_per_month_all.mako M templates/webapps/reports/requests_per_user.mako M templates/webapps/reports/requests_user_per_month.mako M templates/webapps/reports/run_stats.mako M templates/webapps/reports/system.mako M templates/webapps/reports/users_last_access_date.mako M templates/webapps/reports/users_user_disk_usage.mako M templates/webapps/reports/workflows_per_month_all.mako M templates/webapps/reports/workflows_per_user.mako M templates/webapps/reports/workflows_per_workflow.mako M templates/webapps/reports/workflows_user_per_month.mako Log Message: ----------- Changed class naming to reflect use Commit: 0a1617024c7923c12531fa9e18da3494833a6f1f https://github.com/galaxyproject/galaxy/commit/0a1617024c7923c12531fa9e18da… Author: Nitesh Turaga <nitesh.turaga(a)gmail.com> Date: 2015-08-31 (Mon, 31 Aug 2015) Changed paths: M client/galaxy/style/less/reports.less M static/style/blue/base.css M static/style/blue/reports.css M templates/webapps/reports/job_info.mako M templates/webapps/reports/jobs_errors_per_tool.mako M templates/webapps/reports/jobs_per_month_all.mako M templates/webapps/reports/jobs_per_month_in_error.mako M templates/webapps/reports/jobs_per_tool.mako M templates/webapps/reports/jobs_per_user.mako M templates/webapps/reports/jobs_specified_month_all.mako M templates/webapps/reports/jobs_specified_month_in_error.mako M templates/webapps/reports/jobs_tool_per_month.mako M templates/webapps/reports/jobs_user_per_month.mako M templates/webapps/reports/registered_users.mako M templates/webapps/reports/registered_users_per_month.mako M templates/webapps/reports/registered_users_specified_date.mako M templates/webapps/reports/registered_users_specified_month.mako M templates/webapps/reports/requests_per_month_all.mako M templates/webapps/reports/requests_per_user.mako M templates/webapps/reports/requests_user_per_month.mako M templates/webapps/reports/run_stats.mako M templates/webapps/reports/system.mako M templates/webapps/reports/users_last_access_date.mako M templates/webapps/reports/users_user_disk_usage.mako M templates/webapps/reports/workflows_per_month_all.mako M templates/webapps/reports/workflows_per_user.mako M templates/webapps/reports/workflows_per_workflow.mako M templates/webapps/reports/workflows_user_per_month.mako Log Message: ----------- Merge pull request #675 from Airistotal/dev Changed class naming to reflect use Compare: https://github.com/galaxyproject/galaxy/compare/f61f696724a0...0a1617024c79

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[galaxyproject/galaxy] 469d8b: Fixed change in class overlap
by GitHub 31 Aug '15

31 Aug '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 469d8b463e4711770925f4152c95769b7c1d04dc https://github.com/galaxyproject/galaxy/commit/469d8b463e4711770925f4152c95… Author: Airistotal <danieltos.bouchard(a)gmail.com> Date: 2015-08-28 (Fri, 28 Aug 2015) Changed paths: M client/galaxy/style/less/reports.less M static/style/blue/base.css M static/style/blue/reports.css M templates/webapps/reports/jobs_errors_per_tool.mako M templates/webapps/reports/jobs_per_month_all.mako M templates/webapps/reports/jobs_per_month_in_error.mako M templates/webapps/reports/jobs_per_tool.mako M templates/webapps/reports/jobs_per_user.mako M templates/webapps/reports/jobs_specified_month_all.mako M templates/webapps/reports/jobs_specified_month_in_error.mako M templates/webapps/reports/jobs_tool_per_month.mako M templates/webapps/reports/jobs_user_per_month.mako M templates/webapps/reports/registered_users.mako M templates/webapps/reports/registered_users_per_month.mako M templates/webapps/reports/registered_users_specified_date.mako M templates/webapps/reports/registered_users_specified_month.mako M templates/webapps/reports/requests_per_month_all.mako M templates/webapps/reports/requests_per_user.mako M templates/webapps/reports/requests_user_per_month.mako M templates/webapps/reports/workflows_per_month_all.mako M templates/webapps/reports/workflows_per_user.mako M templates/webapps/reports/workflows_per_workflow.mako M templates/webapps/reports/workflows_user_per_month.mako Log Message: ----------- Fixed change in class overlap Commit: ec8cba20398dcfe0fdd7a46ad93cf78fadc310ec https://github.com/galaxyproject/galaxy/commit/ec8cba20398dcfe0fdd7a46ad93c… Author: Airistotal <danieltos.bouchard(a)gmail.com> Date: 2015-08-28 (Fri, 28 Aug 2015) Changed paths: M .ci/flake8_blacklist.txt M .ci/flake8_wrapper.sh M client/galaxy/style/less/reports.less A doc/source/api/quickstart.rst M doc/source/api_doc.rst A doc/source/dev/faq.rst A doc/source/dev/index.rst M doc/source/index.rst M doc/source/ts_api_doc.rst M lib/galaxy/jobs/actions/post.py M lib/galaxy/managers/base.py M lib/galaxy/managers/datasets.py M lib/galaxy/managers/rbac_secured.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/data_manager/manager.py M lib/galaxy/util/xml_macros.py M lib/galaxy/web/framework/base.py M lib/galaxy/webapps/galaxy/api/lda_datasets.py M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/webapps/reports/buildapp.py M lib/galaxy/webapps/tool_shed/buildapp.py M lib/tool_shed/galaxy_install/repair_repository_manager.py M lib/tool_shed/metadata/metadata_generator.py M lib/tool_shed/util/shed_util_common.py M test/base/asserts/__init__.py M test/base/interactor.py M test/base/twilltestcase.py M test/casperjs/casperjs_runner.py M test/casperjs/server_env.py M test/install_and_test_tool_shed_repositories/base/twilltestcase.py M test/install_and_test_tool_shed_repositories/base/util.py M test/install_and_test_tool_shed_repositories/functional/test_install_repositories.py M test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py M test/install_and_test_tool_shed_repositories/tool_dependency_definitions/functional_tests.py M test/qunit/README.txt M test/qunit/package.json M test/unit/managers/test_DatasetManager.py M test/unit/tools/test_tool_loader.py Log Message: ----------- Merge branch 'dev' of https://github.com/galaxyproject/galaxy into dev Conflicts: client/galaxy/style/less/reports.less static/style/blue/base.css static/style/blue/reports.css Commit: f61f696724a0b264a8706d6bf682fa09c178bc5e https://github.com/galaxyproject/galaxy/commit/f61f696724a0b264a8706d6bf682… Author: Nitesh Turaga <nitesh.turaga(a)gmail.com> Date: 2015-08-31 (Mon, 31 Aug 2015) Changed paths: M client/galaxy/style/less/reports.less M static/style/blue/base.css M static/style/blue/reports.css M templates/webapps/reports/jobs_errors_per_tool.mako M templates/webapps/reports/jobs_per_month_all.mako M templates/webapps/reports/jobs_per_month_in_error.mako M templates/webapps/reports/jobs_per_tool.mako M templates/webapps/reports/jobs_per_user.mako M templates/webapps/reports/jobs_specified_month_all.mako M templates/webapps/reports/jobs_specified_month_in_error.mako M templates/webapps/reports/jobs_tool_per_month.mako M templates/webapps/reports/jobs_user_per_month.mako M templates/webapps/reports/registered_users.mako M templates/webapps/reports/registered_users_per_month.mako M templates/webapps/reports/registered_users_specified_date.mako M templates/webapps/reports/registered_users_specified_month.mako M templates/webapps/reports/requests_per_month_all.mako M templates/webapps/reports/requests_per_user.mako M templates/webapps/reports/requests_user_per_month.mako M templates/webapps/reports/workflows_per_month_all.mako M templates/webapps/reports/workflows_per_user.mako M templates/webapps/reports/workflows_per_workflow.mako M templates/webapps/reports/workflows_user_per_month.mako Log Message: ----------- Merge pull request #669 from Airistotal/dev Fix centering bug in firefox Compare: https://github.com/galaxyproject/galaxy/compare/d4af323d35e4...f61f696724a0

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[galaxyproject/galaxy] 8cd94b: When uploading tool_dependencies.xml to toolshed, ...
by GitHub 28 Aug '15

28 Aug '15

Branch: refs/heads/release_15.07 Home: https://github.com/galaxyproject/galaxy Commit: 8cd94be52d5030634e843a89d7025ecb6f18394b https://github.com/galaxyproject/galaxy/commit/8cd94be52d5030634e843a89d702… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-08-24 (Mon, 24 Aug 2015) Changed paths: M lib/tool_shed/dependencies/attribute_handlers.py M lib/tool_shed/dependencies/tool/tag_attribute_handler.py Log Message: ----------- When uploading tool_dependencies.xml to toolshed, do set toolshed repository attributes of package/repository tags that occur within actions that specify os or architecture. Commit: 525188d2a871fbb9b5e7438b18bb5412f62db975 https://github.com/galaxyproject/galaxy/commit/525188d2a871fbb9b5e7438b18bb… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2015-08-28 (Fri, 28 Aug 2015) Changed paths: M lib/tool_shed/dependencies/attribute_handlers.py M lib/tool_shed/dependencies/tool/tag_attribute_handler.py Log Message: ----------- Merge pull request #637 from blankenberg/recurse-toolshed-changeset-upload [release_15.07] Fix setting of toolshed repository attributes in special cases. Compare: https://github.com/galaxyproject/galaxy/compare/4fcdf9fda1d2...525188d2a871

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[galaxyproject/galaxy] 0fa73f: Don't overwrite $R_LIBS path during installation.
by GitHub 28 Aug '15

28 Aug '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 0fa73f2a81fed31fbfe778cf2197d46fa0d4f899 https://github.com/galaxyproject/galaxy/commit/0fa73f2a81fed31fbfe778cf2197… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2015-08-28 (Fri, 28 Aug 2015) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py Log Message: ----------- Don't overwrite $R_LIBS path during installation. Commit: d4af323d35e4a562c6f676ebf10e63253e4d53f8 https://github.com/galaxyproject/galaxy/commit/d4af323d35e4a562c6f676ebf10e… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2015-08-28 (Fri, 28 Aug 2015) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py Log Message: ----------- Merge pull request #671 from bgruening/extend_r_libs_path Don't overwrite $R_LIBS path during installation. Compare: https://github.com/galaxyproject/galaxy/compare/eae62ca2cb12...d4af323d35e4

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[galaxyproject/usegalaxy-playbook] fb77a4: update TTS
by GitHub 28 Aug '15

28 Aug '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: fb77a413a334a7974a582af4e13aa285469356b2 https://github.com/galaxyproject/usegalaxy-playbook/commit/fb77a413a334a797… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-08-28 (Fri, 28 Aug 2015) Changed paths: M stage/group_vars/toolshedservers.yml Log Message: ----------- update TTS

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[galaxyproject/galaxy] f28ddf: Use new path variable syntax available since Route...
by GitHub 28 Aug '15

28 Aug '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f28ddf779cc18ae87eff2c1d28c65622e367dbfb https://github.com/galaxyproject/galaxy/commit/f28ddf779cc18ae87eff2c1d28c6… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-08-28 (Fri, 28 Aug 2015) Changed paths: M lib/galaxy/web/framework/base.py M lib/galaxy/webapps/galaxy/api/lda_datasets.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/reports/buildapp.py M lib/galaxy/webapps/tool_shed/buildapp.py Log Message: ----------- Use new path variable syntax available since Routes 1.9 The old syntax is now documented only in the "Backward compatibility" section of Routes documentation. It is still supported, but may be removed in the future. Commit: eae62ca2cb122f5a0a674027fadc0a28d9dd179e https://github.com/galaxyproject/galaxy/commit/eae62ca2cb122f5a0a674027fadc… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-08-28 (Fri, 28 Aug 2015) Changed paths: M lib/galaxy/web/framework/base.py M lib/galaxy/webapps/galaxy/api/lda_datasets.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/reports/buildapp.py M lib/galaxy/webapps/tool_shed/buildapp.py Log Message: ----------- Merge pull request #665 from nsoranzo/dev Use new path variable syntax available since Routes 1.9 Compare: https://github.com/galaxyproject/galaxy/compare/bada494b85c9...eae62ca2cb12

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[galaxyproject/galaxy] 7ce4bd: Allow accessing repeat and conditional elements in...
by GitHub 27 Aug '15

27 Aug '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 7ce4bde8781645b09bb7ce54b9b7114c41ff9c36 https://github.com/galaxyproject/galaxy/commit/7ce4bde8781645b09bb7ce54b9b7… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-08-27 (Thu, 27 Aug 2015) Changed paths: M lib/galaxy/jobs/actions/post.py Log Message: ----------- Allow accessing repeat and conditional elements in PJA parameters. Use . instead of the | that would be the actual association name. Cannot use | because it is treated as a special character in this code. Parameters with . in the names break Galaxy in subtle ways anyway and so treating them as a special character here should not be a problem. Commit: bada494b85c93c5662275ab5652e29e7bfb9a0ac https://github.com/galaxyproject/galaxy/commit/bada494b85c93c5662275ab5652e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-27 (Thu, 27 Aug 2015) Changed paths: M lib/galaxy/jobs/actions/post.py Log Message: ----------- Merge pull request #662 from jmchilton/repeat_rename Allow accessing repeat and conditional elements in PJA parameters. Compare: https://github.com/galaxyproject/galaxy/compare/396bcc782082...bada494b85c9

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[galaxyproject/galaxy] e99353: fix TS API endpoint to correctly consume full relp...
by GitHub 27 Aug '15

27 Aug '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: e99353bd1cb83fc55ac4678c43bbf4ce8bcbed55 https://github.com/galaxyproject/galaxy/commit/e99353bd1cb83fc55ac4678c43bb… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-08-27 (Thu, 27 Aug 2015) Changed paths: M lib/galaxy/webapps/tool_shed/buildapp.py Log Message: ----------- fix TS API endpoint to correctly consume full relpath of the image Commit: 23a978709528d55ab02c4127e785df909adb47c4 https://github.com/galaxyproject/galaxy/commit/23a978709528d55ab02c4127e785… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-08-27 (Thu, 27 Aug 2015) Changed paths: M lib/tool_shed/util/shed_util_common.py Log Message: ----------- remove replaces for static prefix in image relpaths this is not a problem when in Tool Shed and it prevents people form using these paths ping @bgruening Commit: 183ddbed3e9d01f24d66fd0d49454ecdb9e95aa6 https://github.com/galaxyproject/galaxy/commit/183ddbed3e9d01f24d66fd0d4945… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-08-27 (Thu, 27 Aug 2015) Changed paths: M lib/tool_shed/util/shed_util_common.py Log Message: ----------- Eliminate ${static_path} from tool shed image links. I did not find a reason to use it. Commit: 396bcc782082e2965f67fc6ec87b02e79cf74859 https://github.com/galaxyproject/galaxy/commit/396bcc782082e2965f67fc6ec87b… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2015-08-27 (Thu, 27 Aug 2015) Changed paths: M lib/galaxy/webapps/tool_shed/buildapp.py M lib/tool_shed/util/shed_util_common.py Log Message: ----------- Merge pull request #660 from martenson/fix-tool-image-paths Fix tool image paths. Compare: https://github.com/galaxyproject/galaxy/compare/5d4d32a43221...396bcc782082

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galaxy-commits August 2015