- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 83bc5b: liftOver.loc was not accessible from local data
by GitHub 24 Aug '15

24 Aug '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 83bc5b74ff8c4d45ab4742af7a434c2f7d7869e6 https://github.com/galaxyproject/galaxy/commit/83bc5b74ff8c4d45ab4742af7a43… Author: youri <y.hoogstrate(a)erasmusmc.nl> Date: 2015-08-11 (Tue, 11 Aug 2015) Changed paths: M config/tool_data_table_conf.xml.sample M tools/extract/liftOver_wrapper.xml Log Message: ----------- liftOver.loc was not accessible from local data Commit: 6a38e0bda72ee44dc603b8f996a3c08427d579c1 https://github.com/galaxyproject/galaxy/commit/6a38e0bda72ee44dc603b8f996a3… Author: yhoogstrate <y.hoogstrate(a)erasmusmc.nl> Date: 2015-08-12 (Wed, 12 Aug 2015) Changed paths: M tools/extract/liftOver_wrapper.xml Log Message: ----------- Update liftOver_wrapper.xml version++ Commit: 2ae60fbd84d87931e26227c27db36aae9b1323b0 https://github.com/galaxyproject/galaxy/commit/2ae60fbd84d87931e26227c27db3… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-08-24 (Mon, 24 Aug 2015) Changed paths: M config/tool_data_table_conf.xml.sample M tools/extract/liftOver_wrapper.xml Log Message: ----------- Merge pull request #588 from yhoogstrate/liftOver liftOver.loc was not accessible in local data Compare: https://github.com/galaxyproject/galaxy/compare/57cea58942b7...2ae60fbd84d8

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[galaxyproject/galaxy] 98a3b4: add temporary $HOME directory during perl installa...
by GitHub 24 Aug '15

24 Aug '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 98a3b472654bdfa3f474c437877ec9924eddaf5f https://github.com/galaxyproject/galaxy/commit/98a3b472654bdfa3f474c437877e… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2015-08-22 (Sat, 22 Aug 2015) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py Log Message: ----------- add temporary $HOME directory during perl installations Commit: 6827aed9efb3b50f0b7f0d450b21d8d3c288543d https://github.com/galaxyproject/galaxy/commit/6827aed9efb3b50f0b7f0d450b21… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2015-08-22 (Sat, 22 Aug 2015) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py Log Message: ----------- Merge pull request #635 from bgruening/perl_env_15.05 [15.05] Add temporary $HOME directory during perl installations Commit: 6d3523e81f1e4a33cfb6c17458d6b8fd613c8ed2 https://github.com/galaxyproject/galaxy/commit/6d3523e81f1e4a33cfb6c17458d6… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-08-24 (Mon, 24 Aug 2015) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py Log Message: ----------- Merge branch 'release_15.05' into release_15.07 Commit: e36d5e4cdfba5adcf31701a97a99ebaae3763d12 https://github.com/galaxyproject/galaxy/commit/e36d5e4cdfba5adcf31701a97a99… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-08-24 (Mon, 24 Aug 2015) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py Log Message: ----------- Merge branch 'release_15.07' Commit: 57cea58942b7887b3e95e974fbcb3ebb54e05218 https://github.com/galaxyproject/galaxy/commit/57cea58942b7887b3e95e974fbcb… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-08-24 (Mon, 24 Aug 2015) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py Log Message: ----------- Merge branch 'master' into dev Compare: https://github.com/galaxyproject/galaxy/compare/51b3087c9c74...57cea58942b7

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[galaxyproject/galaxy] 98a3b4: add temporary $HOME directory during perl installa...
by GitHub 24 Aug '15

24 Aug '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/galaxy Commit: 98a3b472654bdfa3f474c437877ec9924eddaf5f https://github.com/galaxyproject/galaxy/commit/98a3b472654bdfa3f474c437877e… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2015-08-22 (Sat, 22 Aug 2015) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py Log Message: ----------- add temporary $HOME directory during perl installations Commit: 6827aed9efb3b50f0b7f0d450b21d8d3c288543d https://github.com/galaxyproject/galaxy/commit/6827aed9efb3b50f0b7f0d450b21… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2015-08-22 (Sat, 22 Aug 2015) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py Log Message: ----------- Merge pull request #635 from bgruening/perl_env_15.05 [15.05] Add temporary $HOME directory during perl installations Commit: 6d3523e81f1e4a33cfb6c17458d6b8fd613c8ed2 https://github.com/galaxyproject/galaxy/commit/6d3523e81f1e4a33cfb6c17458d6… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-08-24 (Mon, 24 Aug 2015) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py Log Message: ----------- Merge branch 'release_15.05' into release_15.07 Commit: e36d5e4cdfba5adcf31701a97a99ebaae3763d12 https://github.com/galaxyproject/galaxy/commit/e36d5e4cdfba5adcf31701a97a99… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-08-24 (Mon, 24 Aug 2015) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py Log Message: ----------- Merge branch 'release_15.07' Compare: https://github.com/galaxyproject/galaxy/compare/e51c6bba46c8...e36d5e4cdfba

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[galaxyproject/galaxy] 98a3b4: add temporary $HOME directory during perl installa...
by GitHub 24 Aug '15

24 Aug '15

Branch: refs/heads/release_15.07 Home: https://github.com/galaxyproject/galaxy Commit: 98a3b472654bdfa3f474c437877ec9924eddaf5f https://github.com/galaxyproject/galaxy/commit/98a3b472654bdfa3f474c437877e… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2015-08-22 (Sat, 22 Aug 2015) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py Log Message: ----------- add temporary $HOME directory during perl installations Commit: 6827aed9efb3b50f0b7f0d450b21d8d3c288543d https://github.com/galaxyproject/galaxy/commit/6827aed9efb3b50f0b7f0d450b21… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2015-08-22 (Sat, 22 Aug 2015) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py Log Message: ----------- Merge pull request #635 from bgruening/perl_env_15.05 [15.05] Add temporary $HOME directory during perl installations Commit: 6d3523e81f1e4a33cfb6c17458d6b8fd613c8ed2 https://github.com/galaxyproject/galaxy/commit/6d3523e81f1e4a33cfb6c17458d6… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-08-24 (Mon, 24 Aug 2015) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py Log Message: ----------- Merge branch 'release_15.05' into release_15.07 Compare: https://github.com/galaxyproject/galaxy/compare/60d3e71f0e10...6d3523e81f1e

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[galaxyproject/galaxy] 98a3b4: add temporary $HOME directory during perl installa...
by GitHub 22 Aug '15

22 Aug '15

Branch: refs/heads/release_15.05 Home: https://github.com/galaxyproject/galaxy Commit: 98a3b472654bdfa3f474c437877ec9924eddaf5f https://github.com/galaxyproject/galaxy/commit/98a3b472654bdfa3f474c437877e… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2015-08-22 (Sat, 22 Aug 2015) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py Log Message: ----------- add temporary $HOME directory during perl installations Commit: 6827aed9efb3b50f0b7f0d450b21d8d3c288543d https://github.com/galaxyproject/galaxy/commit/6827aed9efb3b50f0b7f0d450b21… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2015-08-22 (Sat, 22 Aug 2015) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py Log Message: ----------- Merge pull request #635 from bgruening/perl_env_15.05 [15.05] Add temporary $HOME directory during perl installations Compare: https://github.com/galaxyproject/galaxy/compare/5b604253364e...6827aed9efb3

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[galaxyproject/galaxy] 85c971: Remove existing wrong tool version associations in...
by GitHub 21 Aug '15

21 Aug '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 85c971287ba6b316a970053a2d76f8c49d82f16b https://github.com/galaxyproject/galaxy/commit/85c971287ba6b316a970053a2d76… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-08-21 (Fri, 21 Aug 2015) Changed paths: M lib/tool_shed/tools/tool_version_manager.py Log Message: ----------- Remove existing wrong tool version associations in ToolVersionManager.handle_tool_versions() . Fix #552. To fix a tool with a wrong lineage, click on "Set tool versions" on the "Repository Actions" menu. Commit: 360a6ad76d4325a634bbd13314351028f2965bff https://github.com/galaxyproject/galaxy/commit/360a6ad76d4325a634bbd1331435… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2015-08-21 (Fri, 21 Aug 2015) Changed paths: M lib/tool_shed/tools/tool_version_manager.py Log Message: ----------- Merge pull request #634 from nsoranzo/release_14.10 [14.10] Backport tool lineage fix. Commit: 46e67b5bfa041050f6fa5e99aee945953e1c5cc2 https://github.com/galaxyproject/galaxy/commit/46e67b5bfa041050f6fa5e99aee9… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-08-21 (Fri, 21 Aug 2015) Changed paths: M lib/tool_shed/tools/tool_version_manager.py Log Message: ----------- Merge branch 'release_14.10' into release_15.01 Commit: b23acda7d8657bb9ab66c4c3dbc37706ae6bc4bd https://github.com/galaxyproject/galaxy/commit/b23acda7d8657bb9ab66c4c3dbc3… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-08-21 (Fri, 21 Aug 2015) Changed paths: M lib/tool_shed/tools/tool_version_manager.py Log Message: ----------- Merge branch 'release_15.01' into release_15.03 Commit: 5b604253364eb29fecf94ed4cd4adca5e69bc060 https://github.com/galaxyproject/galaxy/commit/5b604253364eb29fecf94ed4cd4a… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-08-21 (Fri, 21 Aug 2015) Changed paths: M lib/tool_shed/tools/tool_version_manager.py Log Message: ----------- Merge branch 'release_15.03' into release_15.05 Commit: 60d3e71f0e10c3997a57a78268361ac9cbcd4560 https://github.com/galaxyproject/galaxy/commit/60d3e71f0e10c3997a57a7826836… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-08-21 (Fri, 21 Aug 2015) Changed paths: M lib/tool_shed/tools/tool_version_manager.py Log Message: ----------- Merge branch 'release_15.05' into release_15.07 Commit: e51c6bba46c83cdb8ecd1b42b34da8280ece180c https://github.com/galaxyproject/galaxy/commit/e51c6bba46c83cdb8ecd1b42b34d… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-08-21 (Fri, 21 Aug 2015) Changed paths: M lib/tool_shed/tools/tool_version_manager.py Log Message: ----------- Merge branch 'release_15.07' Commit: 51b3087c9c7474b0e93644f129a2ea3083e190bd https://github.com/galaxyproject/galaxy/commit/51b3087c9c7474b0e93644f129a2… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-08-21 (Fri, 21 Aug 2015) Log Message: ----------- Merge branch 'master' into dev Compare: https://github.com/galaxyproject/galaxy/compare/d375a8cc034a...51b3087c9c74

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[galaxyproject/galaxy] 85c971: Remove existing wrong tool version associations in...
by GitHub 21 Aug '15

21 Aug '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/galaxy Commit: 85c971287ba6b316a970053a2d76f8c49d82f16b https://github.com/galaxyproject/galaxy/commit/85c971287ba6b316a970053a2d76… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-08-21 (Fri, 21 Aug 2015) Changed paths: M lib/tool_shed/tools/tool_version_manager.py Log Message: ----------- Remove existing wrong tool version associations in ToolVersionManager.handle_tool_versions() . Fix #552. To fix a tool with a wrong lineage, click on "Set tool versions" on the "Repository Actions" menu. Commit: 360a6ad76d4325a634bbd13314351028f2965bff https://github.com/galaxyproject/galaxy/commit/360a6ad76d4325a634bbd1331435… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2015-08-21 (Fri, 21 Aug 2015) Changed paths: M lib/tool_shed/tools/tool_version_manager.py Log Message: ----------- Merge pull request #634 from nsoranzo/release_14.10 [14.10] Backport tool lineage fix. Commit: 46e67b5bfa041050f6fa5e99aee945953e1c5cc2 https://github.com/galaxyproject/galaxy/commit/46e67b5bfa041050f6fa5e99aee9… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-08-21 (Fri, 21 Aug 2015) Changed paths: M lib/tool_shed/tools/tool_version_manager.py Log Message: ----------- Merge branch 'release_14.10' into release_15.01 Commit: b23acda7d8657bb9ab66c4c3dbc37706ae6bc4bd https://github.com/galaxyproject/galaxy/commit/b23acda7d8657bb9ab66c4c3dbc3… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-08-21 (Fri, 21 Aug 2015) Changed paths: M lib/tool_shed/tools/tool_version_manager.py Log Message: ----------- Merge branch 'release_15.01' into release_15.03 Commit: 5b604253364eb29fecf94ed4cd4adca5e69bc060 https://github.com/galaxyproject/galaxy/commit/5b604253364eb29fecf94ed4cd4a… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-08-21 (Fri, 21 Aug 2015) Changed paths: M lib/tool_shed/tools/tool_version_manager.py Log Message: ----------- Merge branch 'release_15.03' into release_15.05 Commit: 60d3e71f0e10c3997a57a78268361ac9cbcd4560 https://github.com/galaxyproject/galaxy/commit/60d3e71f0e10c3997a57a7826836… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-08-21 (Fri, 21 Aug 2015) Changed paths: M lib/tool_shed/tools/tool_version_manager.py Log Message: ----------- Merge branch 'release_15.05' into release_15.07 Commit: e51c6bba46c83cdb8ecd1b42b34da8280ece180c https://github.com/galaxyproject/galaxy/commit/e51c6bba46c83cdb8ecd1b42b34d… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-08-21 (Fri, 21 Aug 2015) Changed paths: M lib/tool_shed/tools/tool_version_manager.py Log Message: ----------- Merge branch 'release_15.07' Compare: https://github.com/galaxyproject/galaxy/compare/d055102596d8...e51c6bba46c8

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[galaxyproject/galaxy] 85c971: Remove existing wrong tool version associations in...
by GitHub 21 Aug '15

21 Aug '15

Branch: refs/heads/release_15.07 Home: https://github.com/galaxyproject/galaxy Commit: 85c971287ba6b316a970053a2d76f8c49d82f16b https://github.com/galaxyproject/galaxy/commit/85c971287ba6b316a970053a2d76… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-08-21 (Fri, 21 Aug 2015) Changed paths: M lib/tool_shed/tools/tool_version_manager.py Log Message: ----------- Remove existing wrong tool version associations in ToolVersionManager.handle_tool_versions() . Fix #552. To fix a tool with a wrong lineage, click on "Set tool versions" on the "Repository Actions" menu. Commit: 360a6ad76d4325a634bbd13314351028f2965bff https://github.com/galaxyproject/galaxy/commit/360a6ad76d4325a634bbd1331435… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2015-08-21 (Fri, 21 Aug 2015) Changed paths: M lib/tool_shed/tools/tool_version_manager.py Log Message: ----------- Merge pull request #634 from nsoranzo/release_14.10 [14.10] Backport tool lineage fix. Commit: 46e67b5bfa041050f6fa5e99aee945953e1c5cc2 https://github.com/galaxyproject/galaxy/commit/46e67b5bfa041050f6fa5e99aee9… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-08-21 (Fri, 21 Aug 2015) Changed paths: M lib/tool_shed/tools/tool_version_manager.py Log Message: ----------- Merge branch 'release_14.10' into release_15.01 Commit: b23acda7d8657bb9ab66c4c3dbc37706ae6bc4bd https://github.com/galaxyproject/galaxy/commit/b23acda7d8657bb9ab66c4c3dbc3… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-08-21 (Fri, 21 Aug 2015) Changed paths: M lib/tool_shed/tools/tool_version_manager.py Log Message: ----------- Merge branch 'release_15.01' into release_15.03 Commit: 5b604253364eb29fecf94ed4cd4adca5e69bc060 https://github.com/galaxyproject/galaxy/commit/5b604253364eb29fecf94ed4cd4a… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-08-21 (Fri, 21 Aug 2015) Changed paths: M lib/tool_shed/tools/tool_version_manager.py Log Message: ----------- Merge branch 'release_15.03' into release_15.05 Commit: 60d3e71f0e10c3997a57a78268361ac9cbcd4560 https://github.com/galaxyproject/galaxy/commit/60d3e71f0e10c3997a57a7826836… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-08-21 (Fri, 21 Aug 2015) Changed paths: M lib/tool_shed/tools/tool_version_manager.py Log Message: ----------- Merge branch 'release_15.05' into release_15.07 Compare: https://github.com/galaxyproject/galaxy/compare/e8f90429e2ca...60d3e71f0e10

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[galaxyproject/galaxy] 85c971: Remove existing wrong tool version associations in...
by GitHub 21 Aug '15

21 Aug '15

Branch: refs/heads/release_15.05 Home: https://github.com/galaxyproject/galaxy Commit: 85c971287ba6b316a970053a2d76f8c49d82f16b https://github.com/galaxyproject/galaxy/commit/85c971287ba6b316a970053a2d76… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-08-21 (Fri, 21 Aug 2015) Changed paths: M lib/tool_shed/tools/tool_version_manager.py Log Message: ----------- Remove existing wrong tool version associations in ToolVersionManager.handle_tool_versions() . Fix #552. To fix a tool with a wrong lineage, click on "Set tool versions" on the "Repository Actions" menu. Commit: 360a6ad76d4325a634bbd13314351028f2965bff https://github.com/galaxyproject/galaxy/commit/360a6ad76d4325a634bbd1331435… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2015-08-21 (Fri, 21 Aug 2015) Changed paths: M lib/tool_shed/tools/tool_version_manager.py Log Message: ----------- Merge pull request #634 from nsoranzo/release_14.10 [14.10] Backport tool lineage fix. Commit: 46e67b5bfa041050f6fa5e99aee945953e1c5cc2 https://github.com/galaxyproject/galaxy/commit/46e67b5bfa041050f6fa5e99aee9… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-08-21 (Fri, 21 Aug 2015) Changed paths: M lib/tool_shed/tools/tool_version_manager.py Log Message: ----------- Merge branch 'release_14.10' into release_15.01 Commit: b23acda7d8657bb9ab66c4c3dbc37706ae6bc4bd https://github.com/galaxyproject/galaxy/commit/b23acda7d8657bb9ab66c4c3dbc3… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-08-21 (Fri, 21 Aug 2015) Changed paths: M lib/tool_shed/tools/tool_version_manager.py Log Message: ----------- Merge branch 'release_15.01' into release_15.03 Commit: 5b604253364eb29fecf94ed4cd4adca5e69bc060 https://github.com/galaxyproject/galaxy/commit/5b604253364eb29fecf94ed4cd4a… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-08-21 (Fri, 21 Aug 2015) Changed paths: M lib/tool_shed/tools/tool_version_manager.py Log Message: ----------- Merge branch 'release_15.03' into release_15.05 Compare: https://github.com/galaxyproject/galaxy/compare/c569f7856d41...5b604253364e

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[galaxyproject/galaxy] 85c971: Remove existing wrong tool version associations in...
by GitHub 21 Aug '15

21 Aug '15

Branch: refs/heads/release_15.03 Home: https://github.com/galaxyproject/galaxy Commit: 85c971287ba6b316a970053a2d76f8c49d82f16b https://github.com/galaxyproject/galaxy/commit/85c971287ba6b316a970053a2d76… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-08-21 (Fri, 21 Aug 2015) Changed paths: M lib/tool_shed/tools/tool_version_manager.py Log Message: ----------- Remove existing wrong tool version associations in ToolVersionManager.handle_tool_versions() . Fix #552. To fix a tool with a wrong lineage, click on "Set tool versions" on the "Repository Actions" menu. Commit: 360a6ad76d4325a634bbd13314351028f2965bff https://github.com/galaxyproject/galaxy/commit/360a6ad76d4325a634bbd1331435… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2015-08-21 (Fri, 21 Aug 2015) Changed paths: M lib/tool_shed/tools/tool_version_manager.py Log Message: ----------- Merge pull request #634 from nsoranzo/release_14.10 [14.10] Backport tool lineage fix. Commit: 46e67b5bfa041050f6fa5e99aee945953e1c5cc2 https://github.com/galaxyproject/galaxy/commit/46e67b5bfa041050f6fa5e99aee9… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-08-21 (Fri, 21 Aug 2015) Changed paths: M lib/tool_shed/tools/tool_version_manager.py Log Message: ----------- Merge branch 'release_14.10' into release_15.01 Commit: b23acda7d8657bb9ab66c4c3dbc37706ae6bc4bd https://github.com/galaxyproject/galaxy/commit/b23acda7d8657bb9ab66c4c3dbc3… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-08-21 (Fri, 21 Aug 2015) Changed paths: M lib/tool_shed/tools/tool_version_manager.py Log Message: ----------- Merge branch 'release_15.01' into release_15.03 Compare: https://github.com/galaxyproject/galaxy/compare/e06d6a1ccae7...b23acda7d865

1 0

[galaxyproject/galaxy] 85c971: Remove existing wrong tool version associations in...
by GitHub 21 Aug '15

21 Aug '15

Branch: refs/heads/release_15.01 Home: https://github.com/galaxyproject/galaxy Commit: 85c971287ba6b316a970053a2d76f8c49d82f16b https://github.com/galaxyproject/galaxy/commit/85c971287ba6b316a970053a2d76… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-08-21 (Fri, 21 Aug 2015) Changed paths: M lib/tool_shed/tools/tool_version_manager.py Log Message: ----------- Remove existing wrong tool version associations in ToolVersionManager.handle_tool_versions() . Fix #552. To fix a tool with a wrong lineage, click on "Set tool versions" on the "Repository Actions" menu. Commit: 360a6ad76d4325a634bbd13314351028f2965bff https://github.com/galaxyproject/galaxy/commit/360a6ad76d4325a634bbd1331435… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2015-08-21 (Fri, 21 Aug 2015) Changed paths: M lib/tool_shed/tools/tool_version_manager.py Log Message: ----------- Merge pull request #634 from nsoranzo/release_14.10 [14.10] Backport tool lineage fix. Commit: 46e67b5bfa041050f6fa5e99aee945953e1c5cc2 https://github.com/galaxyproject/galaxy/commit/46e67b5bfa041050f6fa5e99aee9… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-08-21 (Fri, 21 Aug 2015) Changed paths: M lib/tool_shed/tools/tool_version_manager.py Log Message: ----------- Merge branch 'release_14.10' into release_15.01 Compare: https://github.com/galaxyproject/galaxy/compare/4d2651a08540...46e67b5bfa04

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[galaxyproject/galaxy] 85c971: Remove existing wrong tool version associations in...
by GitHub 21 Aug '15

21 Aug '15

Branch: refs/heads/release_14.10 Home: https://github.com/galaxyproject/galaxy Commit: 85c971287ba6b316a970053a2d76f8c49d82f16b https://github.com/galaxyproject/galaxy/commit/85c971287ba6b316a970053a2d76… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-08-21 (Fri, 21 Aug 2015) Changed paths: M lib/tool_shed/tools/tool_version_manager.py Log Message: ----------- Remove existing wrong tool version associations in ToolVersionManager.handle_tool_versions() . Fix #552. To fix a tool with a wrong lineage, click on "Set tool versions" on the "Repository Actions" menu. Commit: 360a6ad76d4325a634bbd13314351028f2965bff https://github.com/galaxyproject/galaxy/commit/360a6ad76d4325a634bbd1331435… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2015-08-21 (Fri, 21 Aug 2015) Changed paths: M lib/tool_shed/tools/tool_version_manager.py Log Message: ----------- Merge pull request #634 from nsoranzo/release_14.10 [14.10] Backport tool lineage fix. Compare: https://github.com/galaxyproject/galaxy/compare/cbae8fab672e...360a6ad76d43

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[galaxyproject/galaxy] 682406: * Fix get_latest_installable_revision to use paths...
by GitHub 21 Aug '15

21 Aug '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 68240630668848b454aa51690ed1ac7bbfbc16e2 https://github.com/galaxyproject/galaxy/commit/68240630668848b454aa51690ed1… Author: chambm <matt.chambers42(a)gmail.com> Date: 2015-08-21 (Fri, 21 Aug 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/tool_shed/util/common_util.py Log Message: ----------- * Fix get_latest_installable_revision to use pathspec and params to work with recent changes to common_util.url_join * Fix common_util.url_join to handle a string as pathspec, instead of treating it as an a/r/r/a/y/ /o/f/ /c/h/a/r/a/c/t/e/r/s Commit: d375a8cc034acaea43e221cb60fe58ece5f5d4d6 https://github.com/galaxyproject/galaxy/commit/d375a8cc034acaea43e221cb60fe… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2015-08-21 (Fri, 21 Aug 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/tool_shed/util/common_util.py Log Message: ----------- Merge pull request #632 from chambm/bug/url_join-latest_revision-2 Cleaner commit history for #629 and array syntax for pathspec Compare: https://github.com/galaxyproject/galaxy/compare/eb59844dd2fa...d375a8cc034a

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[galaxyproject/galaxy] 093003: Fixed bug where max items per page was reset when ...
by GitHub 21 Aug '15

21 Aug '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 0930035a9f5629836702525822095daf598dce45 https://github.com/galaxyproject/galaxy/commit/0930035a9f562983670252582209… Author: Airistotal <danieltos.bouchard(a)gmail.com> Date: 2015-08-20 (Thu, 20 Aug 2015) Changed paths: M templates/spark_base.mako M templates/webapps/reports/jobs_errors_per_tool.mako M templates/webapps/reports/jobs_per_tool.mako M templates/webapps/reports/jobs_per_user.mako Log Message: ----------- Fixed bug where max items per page was reset when changing the amount of time sparklines spanned Commit: 673dd2b140791fade4c2943abc399d718b789950 https://github.com/galaxyproject/galaxy/commit/673dd2b140791fade4c2943abc39… Author: Airistotal <danieltos.bouchard(a)gmail.com> Date: 2015-08-20 (Thu, 20 Aug 2015) Changed paths: M client/galaxy/scripts/reports_webapp/run_stats.js M static/maps/reports_webapp/run_stats.js.map M static/scripts/reports_webapp/run_stats.js M templates/base.mako Log Message: ----------- Refactored where d3 is coming from Commit: 78251936e8df0256828f22130c42922190800ecc https://github.com/galaxyproject/galaxy/commit/78251936e8df0256828f22130c42… Author: Airistotal <danieltos.bouchard(a)gmail.com> Date: 2015-08-20 (Thu, 20 Aug 2015) Changed paths: M templates/base.mako M templates/webapps/reports/run_stats.mako Log Message: ----------- Moved d3 import to run_stats Commit: 963d3fe6591a19c3940daeb20c13a5c4566653ad https://github.com/galaxyproject/galaxy/commit/963d3fe6591a19c3940daeb20c13… Author: Airistotal <danieltos.bouchard(a)gmail.com> Date: 2015-08-21 (Fri, 21 Aug 2015) Changed paths: 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/run_stats.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 Log Message: ----------- Fixed bug where column sorting reset paging info Commit: 245a3ccd9ef5c37f45529c69f3802b7269025333 https://github.com/galaxyproject/galaxy/commit/245a3ccd9ef5c37f45529c69f380… Author: Airistotal <danieltos.bouchard(a)gmail.com> Date: 2015-08-21 (Fri, 21 Aug 2015) Changed paths: M templates/webapps/reports/run_stats.mako Log Message: ----------- Fixed error on homepage Commit: eb59844dd2fa28734fb0ce3a051d582e2eac723f https://github.com/galaxyproject/galaxy/commit/eb59844dd2fa28734fb0ce3a051d… Author: carlfeberhard <carlfeberhard(a)users.noreply.github.com> Date: 2015-08-21 (Fri, 21 Aug 2015) Changed paths: M client/galaxy/scripts/reports_webapp/run_stats.js M static/maps/reports_webapp/run_stats.js.map M static/scripts/reports_webapp/run_stats.js M templates/base.mako M templates/spark_base.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/run_stats.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 Log Message: ----------- Merge pull request #626 from Airistotal/dev Bug fix in Reports Compare: https://github.com/galaxyproject/galaxy/compare/950f471c2326...eb59844dd2fa

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[galaxyproject/usegalaxy-playbook] 84b736: hiding antons tools, they were adopted by devteam
by GitHub 21 Aug '15

21 Aug '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 84b736bf885b7df35aefd34625efb7a4c7ed6dd4 https://github.com/galaxyproject/usegalaxy-playbook/commit/84b736bf885b7df3… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-08-21 (Fri, 21 Aug 2015) Changed paths: M files/galaxy/usegalaxy.org/var/shed_tool_conf.xml Log Message: ----------- hiding antons tools, they were adopted by devteam

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[galaxyproject/galaxy] a3e511: Merge branch 'release_15.05'
by GitHub 21 Aug '15

21 Aug '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a3e511292afe6dcdbb3bf533ef6b6e2520c2c652 https://github.com/galaxyproject/galaxy/commit/a3e511292afe6dcdbb3bf533ef6b… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-08-12 (Wed, 12 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/form/form-select-content.js M lib/galaxy/auth/providers/ldap_ad.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/webapps/tool_shed/api/repositories.py M static/maps/mvc/form/form-select-content.js.map M static/scripts/mvc/form/form-select-content.js Log Message: ----------- Merge branch 'release_15.05' Commit: a8a1a150c6ec1a474753052b96b25aec8a22813e https://github.com/galaxyproject/galaxy/commit/a8a1a150c6ec1a474753052b96b2… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-08-12 (Wed, 12 Aug 2015) Changed paths: M lib/galaxy/version.py Log Message: ----------- Merge branch 'release_15.05' Commit: 130004feb10f1fe3a26908401146b8e47c1202ff https://github.com/galaxyproject/galaxy/commit/130004feb10f1fe3a26908401146… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-08-12 (Wed, 12 Aug 2015) Changed paths: M .ci/flake8_wrapper.sh M .ci/pep8_sources.txt M .gitignore M CONTRIBUTING.md A CONTRIBUTORS.md M LICENSE.txt M README.rst M client/GruntFile.js M client/README.md M client/bower.json R client/galaxy/scripts/galaxy.workflow_editor.canvas.js R client/galaxy/scripts/galaxy.workflows.js M client/galaxy/scripts/libs/d3.js M client/galaxy/scripts/libs/jquery/jquery.js M client/galaxy/scripts/libs/raven.js M client/galaxy/scripts/libs/require.js M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/dataset/dataset-choice.js M client/galaxy/scripts/mvc/form/form-data.js M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/form/form-section.js M 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client/toolshed/scripts/mvc/groups/group-list-view.js A client/toolshed/scripts/mvc/groups/group-listrow-view.js A client/toolshed/scripts/mvc/groups/group-model.js A client/toolshed/scripts/toolshed.groups.js M config/auth_conf.xml.sample M config/datatypes_conf.xml.sample M config/galaxy.ini.sample M config/job_conf.xml.sample_advanced M config/object_store_conf.xml.sample M config/plugins/interactive_environments/common/templates/ie.mako M config/plugins/interactive_environments/ipython/config/ipython.ini.sample M config/plugins/interactive_environments/ipython/config/ipython.xml M config/plugins/interactive_environments/ipython/templates/ipython.mako M config/plugins/interactive_environments/ipython/templates/notebook.ipynb A config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample A config/plugins/interactive_environments/rstudio/config/rstudio.xml A config/plugins/interactive_environments/rstudio/static/js/crypto/base64.js A config/plugins/interactive_environments/rstudio/static/js/crypto/jsbn.js A config/plugins/interactive_environments/rstudio/static/js/crypto/prng4.js A config/plugins/interactive_environments/rstudio/static/js/crypto/rng.js A config/plugins/interactive_environments/rstudio/static/js/crypto/rsa.js A config/plugins/interactive_environments/rstudio/static/js/crypto/rstudio.big.js A config/plugins/interactive_environments/rstudio/static/js/crypto/rstudio.min.js A config/plugins/interactive_environments/rstudio/static/js/crypto/rstudio/base64.js A config/plugins/interactive_environments/rstudio/static/js/crypto/rstudio/jsbn.js A config/plugins/interactive_environments/rstudio/static/js/crypto/rstudio/prng4.js A config/plugins/interactive_environments/rstudio/static/js/crypto/rstudio/rng.js A config/plugins/interactive_environments/rstudio/static/js/crypto/rstudio/rsa.js A config/plugins/interactive_environments/rstudio/static/js/crypto/wu/base64.js A 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config/plugins/visualizations/scatterplot/src/scatterplot-display.js M config/plugins/visualizations/scatterplot/static/scatterplot-edit.js M config/plugins/visualizations/sweepster/config/sweepster.xml M config/plugins/visualizations/trackster/config/trackster.xml M config/plugins/visualizations/visualization.dtd M config/tool_conf.xml.sample M config/tool_shed.ini.sample M cron/parse_builds.py M display_applications/ensembl/ensembl_bam.xml M display_applications/ensembl/ensembl_gff.xml M display_applications/ensembl/ensembl_interval_as_bed.xml M display_applications/gbrowse/gbrowse_gff.xml M display_applications/gbrowse/gbrowse_interval_as_bed.xml M display_applications/gbrowse/gbrowse_wig.xml M display_applications/igb/bam.xml M display_applications/igb/bb.xml M display_applications/igb/bed.xml M display_applications/igb/bedgraph.xml M display_applications/igb/bigwig.xml M display_applications/igb/gtf.xml M display_applications/igb/wig.xml M display_applications/igv/bam.xml M display_applications/igv/gff.xml A display_applications/igv/interval_as_bed.xml M display_applications/igv/vcf.xml M display_applications/rviewer/bed.xml M display_applications/rviewer/vcf.xml A doc/source/api_doc.rst M doc/source/conf.py M doc/source/index.rst R doc/source/lib/fpconst.rst M doc/source/lib/galaxy.actions.rst A doc/source/lib/galaxy.auth.providers.rst A doc/source/lib/galaxy.auth.rst A doc/source/lib/galaxy.dataset_collections.rst A doc/source/lib/galaxy.dataset_collections.types.rst M doc/source/lib/galaxy.datatypes.converters.rst A doc/source/lib/galaxy.datatypes.dataproviders.rst M doc/source/lib/galaxy.datatypes.display_applications.rst M doc/source/lib/galaxy.datatypes.rst M doc/source/lib/galaxy.datatypes.util.rst M doc/source/lib/galaxy.eggs.rst M doc/source/lib/galaxy.exceptions.rst M doc/source/lib/galaxy.external_services.result_handlers.rst M doc/source/lib/galaxy.external_services.rst M doc/source/lib/galaxy.forms.rst M doc/source/lib/galaxy.jobs.actions.rst 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test/functional/tool-data/fasta_indexes.loc M test/functional/tool-data/sample_tool_data_tables.xml M test/functional/tools/code_file.py A test/functional/tools/dbkey_filter_input.xml A test/functional/tools/dbkey_filter_multi_input.xml A test/functional/tools/environment_variables.xml A test/functional/tools/library_data.xml A test/functional/tools/metadata_bcf.xml A test/functional/tools/output_collection_filter.xml M test/functional/tools/sample_datatypes_conf.xml M test/functional/tools/samples_tool_conf.xml M test/install_and_test_tool_shed_repositories/base/util.py M test/qunit/test-common.js M test/qunit/tests/workflow_editor_tests.js M test/unit/jobs/test_job_configuration.py M test/unit/jobs/test_job_wrapper.py M test/unit/jobs/test_runner_local.py M test/unit/tool_shed_unit_tests/test_td_common_util.py M test/unit/tools/test_evaluation.py M test/unit/tools/test_parameter_parsing.py M test/unit/tools/test_tool_dependency_description.py M test/unit/tools/test_tool_deps.py M test/unit/tools/test_tool_loader.py M test/unit/unittest_utils/galaxy_mock.py A test/unit/visualizations/plugins/__init__.py A test/unit/visualizations/plugins/test_VisualizationPlugin.py A test/unit/visualizations/plugins/test_VisualizationsRegistry.py R test/unit/visualizations/test_VisualizationsRegistry.py M tools/data_source/bed_convert.xml M tools/data_source/genbank.xml M tools/data_source/import.xml M tools/data_source/microbial_import.xml M tools/data_source/ucsc_tablebrowser_archaea.xml M tools/data_source/ucsc_tablebrowser_test.xml M tools/data_source/upload.py M tools/data_source/upload.xml M tools/evolution/codingSnps.xml M tools/evolution/codingSnps_filter.py M tools/extract/liftOver_wrapper.xml M tools/filters/axt_to_lav.xml M tools/filters/axt_to_lav_code.py M tools/filters/catWrapper.xml M tools/filters/changeCase.xml M tools/filters/condense_characters.xml M tools/filters/cutWrapper.xml M tools/filters/gff/extract_GFF_Features.xml M tools/filters/gff/gff_filter_by_attribute.xml M tools/filters/gff/gff_filter_by_feature_count.xml M tools/filters/gff/gtf_filter_by_attribute_values_list.xml M tools/filters/headWrapper.xml M tools/filters/joiner2.xml M tools/filters/lav_to_bed.py M tools/filters/lav_to_bed.xml M tools/filters/lav_to_bed_code.py M tools/filters/pasteWrapper.xml M tools/filters/remove_beginning.xml M tools/filters/tailWrapper.xml M tools/filters/ucsc_gene_table_to_intervals.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/maf_by_block_number.xml M tools/maf/maf_filter.py M tools/maf/maf_filter.xml M tools/maf/maf_limit_size.xml M tools/maf/maf_reverse_complement.py 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_to_fasta.xml M tools/plotting/bar_chart.xml M tools/plotting/boxplot.xml M tools/solid_tools/maq_cs_wrapper_code.py M tools/stats/filtering.xml M tools/stats/grouping.py M tools/stats/gsummary.py M tools/stats/gsummary.xml M tools/stats/gsummary.xml.groups M tools/visualization/LAJ.xml M tools/visualization/LAJ_code.py Log Message: ----------- Merge branch 'release_15.07' Commit: 737248d41d4e1d682361b85d48ea65574367e59d https://github.com/galaxyproject/galaxy/commit/737248d41d4e1d682361b85d48ea… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-20 (Thu, 20 Aug 2015) Changed paths: M lib/galaxy/workflow/render.py Log Message: ----------- Fix for valid height/width definitions in workflow rendering code. Commit: b8fd98979c775daf46a768572fb30f4467fd7458 https://github.com/galaxyproject/galaxy/commit/b8fd98979c775daf46a768572fb3… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-20 (Thu, 20 Aug 2015) Changed paths: M lib/galaxy/workflow/render.py Log Message: ----------- Fix the second (and final) issue preventing workflow rendering from generating valid SVGs -- incorrect usage of arrow_end; this is intended to be a unique identifier for the element and not a boolean. This wasn't preventing render (on firefox or chrome) like the previous issue, but it would cause warnings. Commit: 083789526105abda87a701835b8ff44e0ec89405 https://github.com/galaxyproject/galaxy/commit/083789526105abda87a701835b8f… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2015-08-21 (Fri, 21 Aug 2015) Changed paths: M lib/galaxy/workflow/render.py Log Message: ----------- Merge pull request #625 from dannon/release_15.07 [release_15.07] Fix for valid height/width definitions in workflow rendering code, and fix identifiers. Commit: b29e81014979d2e72d704a22560a278cfec42927 https://github.com/galaxyproject/galaxy/commit/b29e81014979d2e72d704a22560a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-21 (Fri, 21 Aug 2015) Changed paths: M lib/galaxy/workflow/render.py Log Message: ----------- Fix for valid height/width definitions in workflow rendering code. Commit: 4d2651a085405f2b4ba37f26fa917f9524584b1a https://github.com/galaxyproject/galaxy/commit/4d2651a085405f2b4ba37f26fa91… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-21 (Fri, 21 Aug 2015) Changed paths: M lib/galaxy/workflow/render.py Log Message: ----------- Fix the second (and final) issue preventing workflow rendering from generating valid SVGs -- incorrect usage of arrow_end; this is intended to be a unique identifier for the element and not a boolean. This wasn't preventing render (on firefox or chrome) like the previous issue, but it would cause warnings. Commit: e06d6a1ccae792abb45ff96d63bf8ab51e685231 https://github.com/galaxyproject/galaxy/commit/e06d6a1ccae792abb45ff96d63bf… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-21 (Fri, 21 Aug 2015) Changed paths: M lib/galaxy/workflow/render.py Log Message: ----------- Merge branch 'release_15.01' into release_15.03 Commit: c569f7856d41fe9b51808302569283c800a4eb93 https://github.com/galaxyproject/galaxy/commit/c569f7856d41fe9b518083025692… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-21 (Fri, 21 Aug 2015) Changed paths: M lib/galaxy/workflow/render.py Log Message: ----------- Merge branch 'release_15.03' into release_15.05 Commit: e8f90429e2ca3efc6dbb9f02b1d5fbe8afc446a5 https://github.com/galaxyproject/galaxy/commit/e8f90429e2ca3efc6dbb9f02b1d5… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-21 (Fri, 21 Aug 2015) Log Message: ----------- Merge branch 'release_15.05' into release_15.07 Commit: d055102596d85b5a3d6da90e8397016f6daf2271 https://github.com/galaxyproject/galaxy/commit/d055102596d85b5a3d6da90e8397… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-21 (Fri, 21 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M lib/galaxy/model/__init__.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/workflow/render.py M lib/tool_shed/metadata/repository_metadata_manager.py M scripts/cleanup_datasets/cleanup_datasets.py M static/maps/mvc/workflow/workflow-terminals.js.map M static/scripts/mvc/workflow/workflow-terminals.js M test/unit/test_galaxy_mapping.py Log Message: ----------- Merge branch 'release_15.07' Commit: 950f471c2326cc8d90c7efe372c063f47ed7f3e4 https://github.com/galaxyproject/galaxy/commit/950f471c2326cc8d90c7efe372c0… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-21 (Fri, 21 Aug 2015) Changed paths: M lib/galaxy/workflow/render.py Log Message: ----------- Merge branch 'master' into dev Compare: https://github.com/galaxyproject/galaxy/compare/795e30171149...950f471c2326

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[galaxyproject/galaxy] 6dc5f0: Merge branch 'security-20150812-xss' into release_...
by GitHub 21 Aug '15

21 Aug '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/galaxy Commit: 6dc5f022c73d5bde3b4ef1abe31a8d3b37ade9c3 https://github.com/galaxyproject/galaxy/commit/6dc5f022c73d5bde3b4ef1abe31a… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-08-12 (Wed, 12 Aug 2015) Changed paths: M lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- Merge branch 'security-20150812-xss' into release_15.01 Commit: 096a1686badda620acb507deaf9382ccee37086a https://github.com/galaxyproject/galaxy/commit/096a1686badda620acb507deaf93… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-08-12 (Wed, 12 Aug 2015) Changed paths: M lib/galaxy/webapps/tool_shed/api/repositories.py Log Message: ----------- Merge branch 'security-20150812-shed' into release_15.01 Commit: 8b2387a1c1772b07473170df23bf5eea2aed0e54 https://github.com/galaxyproject/galaxy/commit/8b2387a1c1772b07473170df23bf… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-08-13 (Thu, 13 Aug 2015) Changed paths: M lib/tool_shed/metadata/repository_metadata_manager.py Log Message: ----------- fix regenerating repo metadata when coming from batch interface it used to create only single instalable revision (the latest) Commit: 98ec06c7d6e4d23c1e2d35fa2d04511bae8ab90c https://github.com/galaxyproject/galaxy/commit/98ec06c7d6e4d23c1e2d35fa2d04… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-08-13 (Thu, 13 Aug 2015) Changed paths: M lib/tool_shed/metadata/repository_metadata_manager.py Log Message: ----------- Merge pull request #600 from martenson/ts-metadata-batch-reset [release_15.07] fix regenerating repo metadata when coming from batch interface Commit: c938e66e98512d85120c1c06d485a13000ff82c1 https://github.com/galaxyproject/galaxy/commit/c938e66e98512d85120c1c06d485… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-08-13 (Thu, 13 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M static/maps/mvc/workflow/workflow-terminals.js.map M static/scripts/mvc/workflow/workflow-terminals.js Log Message: ----------- Fix output collection terminal base class Commit: 79dbff19674dbe667887b92d070165ade85ae834 https://github.com/galaxyproject/galaxy/commit/79dbff19674dbe667887b92d0701… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-13 (Thu, 13 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M static/maps/mvc/workflow/workflow-terminals.js.map M static/scripts/mvc/workflow/workflow-terminals.js Log Message: ----------- Merge pull request #602 from guerler/fix_collections_000 [15.07] Fix output collection terminal base class Commit: 238d908ccecd6411a3a72f7396933b3771f7e5aa https://github.com/galaxyproject/galaxy/commit/238d908ccecd6411a3a72f739693… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-08-19 (Wed, 19 Aug 2015) Changed paths: M lib/galaxy/model/__init__.py M scripts/cleanup_datasets/cleanup_datasets.py Log Message: ----------- Fix purging datasets whose total_size is None. Fix the error: Removing disk, file /opt/galaxy/database/files/000/dataset_192.dat Error attempting to purge data file: /opt/galaxy/database/files/000/dataset_192.dat error: unsupported operand type(s) for -=: 'Decimal' and 'NoneType' when running: python scripts/cleanup_datasets/cleanup_datasets.py config/galaxy.ini -d 10 -3 -r Commit: a1bff672f39da8610543ba572c322d53eda88b4f https://github.com/galaxyproject/galaxy/commit/a1bff672f39da8610543ba572c32… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-08-19 (Wed, 19 Aug 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/tools.py Log Message: ----------- Fix bug in tool reloading API where ID not passed Commit: 71f28c99e539acf828a03e8288e1de4af40a887e https://github.com/galaxyproject/galaxy/commit/71f28c99e539acf828a03e8288e1… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-19 (Wed, 19 Aug 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/tools.py Log Message: ----------- Merge pull request #622 from erasche/tool-reloading-fix [15.01] Tool reloading fix Commit: 01278aa956f5791badaa6e475d94f679adab10b1 https://github.com/galaxyproject/galaxy/commit/01278aa956f5791badaa6e475d94… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-19 (Wed, 19 Aug 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/tools.py Log Message: ----------- Merge branch 'release_15.01' into release_15.03 Commit: 483ea9e735bf7de22f7ce7abb6105c9b929ea928 https://github.com/galaxyproject/galaxy/commit/483ea9e735bf7de22f7ce7abb610… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-19 (Wed, 19 Aug 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/tools.py Log Message: ----------- Merge branch 'release_15.03' into release_15.05 Commit: b4df5e944bddcbd03699a4b3b395044cc3c4886c https://github.com/galaxyproject/galaxy/commit/b4df5e944bddcbd03699a4b3b395… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-19 (Wed, 19 Aug 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/tools.py Log Message: ----------- Resolve merge conflict merging forward 15.05-15.07 Commit: a9827fae31d8826bf2426c5285fe789dfe61295d https://github.com/galaxyproject/galaxy/commit/a9827fae31d8826bf2426c5285fe… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-08-20 (Thu, 20 Aug 2015) Changed paths: M test/unit/test_galaxy_mapping.py Log Message: ----------- Fix failing tests for 238d908ccecd6411a3a72f7396933b3771f7e5aa. Commit: baf8fe6759fe283516c5242d42ab8274b5a3baf0 https://github.com/galaxyproject/galaxy/commit/baf8fe6759fe283516c5242d42ab… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2015-08-20 (Thu, 20 Aug 2015) Changed paths: M test/unit/test_galaxy_mapping.py Log Message: ----------- Merge pull request #1 from jmchilton/release_fix Fix failing tests for 238d908ccecd6411a3a72f7396933b3771f7e5aa. Commit: 14a8ee95f3dd8a671ee9a1edac8fc3cd686a4395 https://github.com/galaxyproject/galaxy/commit/14a8ee95f3dd8a671ee9a1edac8f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-20 (Thu, 20 Aug 2015) Changed paths: M lib/galaxy/model/__init__.py M scripts/cleanup_datasets/cleanup_datasets.py M test/unit/test_galaxy_mapping.py Log Message: ----------- Merge pull request #616 from nsoranzo/release_15.05 [15.05] Fix purging datasets whose total_size is None. Commit: a34f13a9f6eb216665ea97e1314f7b76c74c5778 https://github.com/galaxyproject/galaxy/commit/a34f13a9f6eb216665ea97e1314f… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-08-20 (Thu, 20 Aug 2015) Changed paths: M lib/galaxy/model/__init__.py M scripts/cleanup_datasets/cleanup_datasets.py M test/unit/test_galaxy_mapping.py Log Message: ----------- Merge branch 'release_15.05' into release_15.07 Commit: 737248d41d4e1d682361b85d48ea65574367e59d https://github.com/galaxyproject/galaxy/commit/737248d41d4e1d682361b85d48ea… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-20 (Thu, 20 Aug 2015) Changed paths: M lib/galaxy/workflow/render.py Log Message: ----------- Fix for valid height/width definitions in workflow rendering code. Commit: b8fd98979c775daf46a768572fb30f4467fd7458 https://github.com/galaxyproject/galaxy/commit/b8fd98979c775daf46a768572fb3… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-20 (Thu, 20 Aug 2015) Changed paths: M lib/galaxy/workflow/render.py Log Message: ----------- Fix the second (and final) issue preventing workflow rendering from generating valid SVGs -- incorrect usage of arrow_end; this is intended to be a unique identifier for the element and not a boolean. This wasn't preventing render (on firefox or chrome) like the previous issue, but it would cause warnings. Commit: 083789526105abda87a701835b8ff44e0ec89405 https://github.com/galaxyproject/galaxy/commit/083789526105abda87a701835b8f… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2015-08-21 (Fri, 21 Aug 2015) Changed paths: M lib/galaxy/workflow/render.py Log Message: ----------- Merge pull request #625 from dannon/release_15.07 [release_15.07] Fix for valid height/width definitions in workflow rendering code, and fix identifiers. Commit: b29e81014979d2e72d704a22560a278cfec42927 https://github.com/galaxyproject/galaxy/commit/b29e81014979d2e72d704a22560a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-21 (Fri, 21 Aug 2015) Changed paths: M lib/galaxy/workflow/render.py Log Message: ----------- Fix for valid height/width definitions in workflow rendering code. Commit: 4d2651a085405f2b4ba37f26fa917f9524584b1a https://github.com/galaxyproject/galaxy/commit/4d2651a085405f2b4ba37f26fa91… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-21 (Fri, 21 Aug 2015) Changed paths: M lib/galaxy/workflow/render.py Log Message: ----------- Fix the second (and final) issue preventing workflow rendering from generating valid SVGs -- incorrect usage of arrow_end; this is intended to be a unique identifier for the element and not a boolean. This wasn't preventing render (on firefox or chrome) like the previous issue, but it would cause warnings. Commit: e06d6a1ccae792abb45ff96d63bf8ab51e685231 https://github.com/galaxyproject/galaxy/commit/e06d6a1ccae792abb45ff96d63bf… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-21 (Fri, 21 Aug 2015) Changed paths: M lib/galaxy/workflow/render.py Log Message: ----------- Merge branch 'release_15.01' into release_15.03 Commit: c569f7856d41fe9b51808302569283c800a4eb93 https://github.com/galaxyproject/galaxy/commit/c569f7856d41fe9b518083025692… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-21 (Fri, 21 Aug 2015) Changed paths: M lib/galaxy/workflow/render.py Log Message: ----------- Merge branch 'release_15.03' into release_15.05 Commit: e8f90429e2ca3efc6dbb9f02b1d5fbe8afc446a5 https://github.com/galaxyproject/galaxy/commit/e8f90429e2ca3efc6dbb9f02b1d5… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-21 (Fri, 21 Aug 2015) Log Message: ----------- Merge branch 'release_15.05' into release_15.07 Commit: d055102596d85b5a3d6da90e8397016f6daf2271 https://github.com/galaxyproject/galaxy/commit/d055102596d85b5a3d6da90e8397… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-21 (Fri, 21 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M lib/galaxy/model/__init__.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/workflow/render.py M lib/tool_shed/metadata/repository_metadata_manager.py M scripts/cleanup_datasets/cleanup_datasets.py M static/maps/mvc/workflow/workflow-terminals.js.map M static/scripts/mvc/workflow/workflow-terminals.js M test/unit/test_galaxy_mapping.py Log Message: ----------- Merge branch 'release_15.07' Compare: https://github.com/galaxyproject/galaxy/compare/130004feb10f...d055102596d8

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[galaxyproject/galaxy] b29e81: Fix for valid height/width definitions in workflow...
by GitHub 21 Aug '15

21 Aug '15

Branch: refs/heads/release_15.07 Home: https://github.com/galaxyproject/galaxy Commit: b29e81014979d2e72d704a22560a278cfec42927 https://github.com/galaxyproject/galaxy/commit/b29e81014979d2e72d704a22560a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-21 (Fri, 21 Aug 2015) Changed paths: M lib/galaxy/workflow/render.py Log Message: ----------- Fix for valid height/width definitions in workflow rendering code. Commit: 4d2651a085405f2b4ba37f26fa917f9524584b1a https://github.com/galaxyproject/galaxy/commit/4d2651a085405f2b4ba37f26fa91… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-21 (Fri, 21 Aug 2015) Changed paths: M lib/galaxy/workflow/render.py Log Message: ----------- Fix the second (and final) issue preventing workflow rendering from generating valid SVGs -- incorrect usage of arrow_end; this is intended to be a unique identifier for the element and not a boolean. This wasn't preventing render (on firefox or chrome) like the previous issue, but it would cause warnings. Commit: e06d6a1ccae792abb45ff96d63bf8ab51e685231 https://github.com/galaxyproject/galaxy/commit/e06d6a1ccae792abb45ff96d63bf… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-21 (Fri, 21 Aug 2015) Changed paths: M lib/galaxy/workflow/render.py Log Message: ----------- Merge branch 'release_15.01' into release_15.03 Commit: c569f7856d41fe9b51808302569283c800a4eb93 https://github.com/galaxyproject/galaxy/commit/c569f7856d41fe9b518083025692… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-21 (Fri, 21 Aug 2015) Changed paths: M lib/galaxy/workflow/render.py Log Message: ----------- Merge branch 'release_15.03' into release_15.05 Commit: e8f90429e2ca3efc6dbb9f02b1d5fbe8afc446a5 https://github.com/galaxyproject/galaxy/commit/e8f90429e2ca3efc6dbb9f02b1d5… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-21 (Fri, 21 Aug 2015) Log Message: ----------- Merge branch 'release_15.05' into release_15.07 Compare: https://github.com/galaxyproject/galaxy/compare/083789526105...e8f90429e2ca

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[galaxyproject/galaxy] b29e81: Fix for valid height/width definitions in workflow...
by GitHub 21 Aug '15

21 Aug '15

Branch: refs/heads/release_15.05 Home: https://github.com/galaxyproject/galaxy Commit: b29e81014979d2e72d704a22560a278cfec42927 https://github.com/galaxyproject/galaxy/commit/b29e81014979d2e72d704a22560a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-21 (Fri, 21 Aug 2015) Changed paths: M lib/galaxy/workflow/render.py Log Message: ----------- Fix for valid height/width definitions in workflow rendering code. Commit: 4d2651a085405f2b4ba37f26fa917f9524584b1a https://github.com/galaxyproject/galaxy/commit/4d2651a085405f2b4ba37f26fa91… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-21 (Fri, 21 Aug 2015) Changed paths: M lib/galaxy/workflow/render.py Log Message: ----------- Fix the second (and final) issue preventing workflow rendering from generating valid SVGs -- incorrect usage of arrow_end; this is intended to be a unique identifier for the element and not a boolean. This wasn't preventing render (on firefox or chrome) like the previous issue, but it would cause warnings. Commit: e06d6a1ccae792abb45ff96d63bf8ab51e685231 https://github.com/galaxyproject/galaxy/commit/e06d6a1ccae792abb45ff96d63bf… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-21 (Fri, 21 Aug 2015) Changed paths: M lib/galaxy/workflow/render.py Log Message: ----------- Merge branch 'release_15.01' into release_15.03 Commit: c569f7856d41fe9b51808302569283c800a4eb93 https://github.com/galaxyproject/galaxy/commit/c569f7856d41fe9b518083025692… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-21 (Fri, 21 Aug 2015) Changed paths: M lib/galaxy/workflow/render.py Log Message: ----------- Merge branch 'release_15.03' into release_15.05 Compare: https://github.com/galaxyproject/galaxy/compare/14a8ee95f3dd...c569f7856d41

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[galaxyproject/galaxy] b29e81: Fix for valid height/width definitions in workflow...
by GitHub 21 Aug '15

21 Aug '15

Branch: refs/heads/release_15.03 Home: https://github.com/galaxyproject/galaxy Commit: b29e81014979d2e72d704a22560a278cfec42927 https://github.com/galaxyproject/galaxy/commit/b29e81014979d2e72d704a22560a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-21 (Fri, 21 Aug 2015) Changed paths: M lib/galaxy/workflow/render.py Log Message: ----------- Fix for valid height/width definitions in workflow rendering code. Commit: 4d2651a085405f2b4ba37f26fa917f9524584b1a https://github.com/galaxyproject/galaxy/commit/4d2651a085405f2b4ba37f26fa91… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-21 (Fri, 21 Aug 2015) Changed paths: M lib/galaxy/workflow/render.py Log Message: ----------- Fix the second (and final) issue preventing workflow rendering from generating valid SVGs -- incorrect usage of arrow_end; this is intended to be a unique identifier for the element and not a boolean. This wasn't preventing render (on firefox or chrome) like the previous issue, but it would cause warnings. Commit: e06d6a1ccae792abb45ff96d63bf8ab51e685231 https://github.com/galaxyproject/galaxy/commit/e06d6a1ccae792abb45ff96d63bf… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-21 (Fri, 21 Aug 2015) Changed paths: M lib/galaxy/workflow/render.py Log Message: ----------- Merge branch 'release_15.01' into release_15.03 Compare: https://github.com/galaxyproject/galaxy/compare/01278aa956f5...e06d6a1ccae7

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[galaxyproject/galaxy] b29e81: Fix for valid height/width definitions in workflow...
by GitHub 21 Aug '15

21 Aug '15

Branch: refs/heads/release_15.01 Home: https://github.com/galaxyproject/galaxy Commit: b29e81014979d2e72d704a22560a278cfec42927 https://github.com/galaxyproject/galaxy/commit/b29e81014979d2e72d704a22560a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-21 (Fri, 21 Aug 2015) Changed paths: M lib/galaxy/workflow/render.py Log Message: ----------- Fix for valid height/width definitions in workflow rendering code. Commit: 4d2651a085405f2b4ba37f26fa917f9524584b1a https://github.com/galaxyproject/galaxy/commit/4d2651a085405f2b4ba37f26fa91… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-21 (Fri, 21 Aug 2015) Changed paths: M lib/galaxy/workflow/render.py Log Message: ----------- Fix the second (and final) issue preventing workflow rendering from generating valid SVGs -- incorrect usage of arrow_end; this is intended to be a unique identifier for the element and not a boolean. This wasn't preventing render (on firefox or chrome) like the previous issue, but it would cause warnings. Compare: https://github.com/galaxyproject/galaxy/compare/71f28c99e539...4d2651a08540

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[galaxyproject/galaxy] 737248: Fix for valid height/width definitions in workflow...
by GitHub 21 Aug '15

21 Aug '15

Branch: refs/heads/release_15.07 Home: https://github.com/galaxyproject/galaxy Commit: 737248d41d4e1d682361b85d48ea65574367e59d https://github.com/galaxyproject/galaxy/commit/737248d41d4e1d682361b85d48ea… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-20 (Thu, 20 Aug 2015) Changed paths: M lib/galaxy/workflow/render.py Log Message: ----------- Fix for valid height/width definitions in workflow rendering code. Commit: b8fd98979c775daf46a768572fb30f4467fd7458 https://github.com/galaxyproject/galaxy/commit/b8fd98979c775daf46a768572fb3… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-20 (Thu, 20 Aug 2015) Changed paths: M lib/galaxy/workflow/render.py Log Message: ----------- Fix the second (and final) issue preventing workflow rendering from generating valid SVGs -- incorrect usage of arrow_end; this is intended to be a unique identifier for the element and not a boolean. This wasn't preventing render (on firefox or chrome) like the previous issue, but it would cause warnings. Commit: 083789526105abda87a701835b8ff44e0ec89405 https://github.com/galaxyproject/galaxy/commit/083789526105abda87a701835b8f… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2015-08-21 (Fri, 21 Aug 2015) Changed paths: M lib/galaxy/workflow/render.py Log Message: ----------- Merge pull request #625 from dannon/release_15.07 [release_15.07] Fix for valid height/width definitions in workflow rendering code, and fix identifiers. Compare: https://github.com/galaxyproject/galaxy/compare/a34f13a9f6eb...083789526105

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[galaxyproject/galaxy] 9fb615: Change FTP icon to open folder icon
by GitHub 20 Aug '15

20 Aug '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 9fb615f83a15ae31cbc4376733831604d0d4d04b https://github.com/galaxyproject/galaxy/commit/9fb615f83a15ae31cbc437673383… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-08-20 (Thu, 20 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/upload/composite/composite-row.js M client/galaxy/scripts/mvc/upload/default/default-row.js M client/galaxy/scripts/mvc/upload/default/default-view.js M static/maps/mvc/upload/composite/composite-row.js.map M static/maps/mvc/upload/default/default-row.js.map M static/maps/mvc/upload/default/default-view.js.map M static/scripts/mvc/upload/composite/composite-row.js M static/scripts/mvc/upload/default/default-row.js M static/scripts/mvc/upload/default/default-view.js Log Message: ----------- Change FTP icon to open folder icon Commit: 94dfbaa10a783a98e7488e0aa28e7551497657db https://github.com/galaxyproject/galaxy/commit/94dfbaa10a783a98e7488e0aa28e… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-08-20 (Thu, 20 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/upload/composite/composite-row.js M client/galaxy/scripts/mvc/upload/default/default-row.js M client/galaxy/scripts/mvc/upload/default/default-view.js M static/maps/mvc/upload/composite/composite-row.js.map M static/maps/mvc/upload/default/default-row.js.map M static/maps/mvc/upload/default/default-view.js.map M static/scripts/mvc/upload/composite/composite-row.js M static/scripts/mvc/upload/default/default-row.js M static/scripts/mvc/upload/default/default-view.js Log Message: ----------- Change pencil icon to edit icon Commit: 8be164f92c6896f2d9d0297d96c8073bd2612ec6 https://github.com/galaxyproject/galaxy/commit/8be164f92c6896f2d9d0297d96c8… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-08-20 (Thu, 20 Aug 2015) Changed paths: M test/qunit/tests/upload_dialog_tests.js Log Message: ----------- Fix tests Commit: 795e30171149e65d14e1031b2f4d652da8f5f25c https://github.com/galaxyproject/galaxy/commit/795e30171149e65d14e1031b2f4d… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-08-20 (Thu, 20 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/upload/composite/composite-row.js M client/galaxy/scripts/mvc/upload/default/default-row.js M client/galaxy/scripts/mvc/upload/default/default-view.js M static/maps/mvc/upload/composite/composite-row.js.map M static/maps/mvc/upload/default/default-row.js.map M static/maps/mvc/upload/default/default-view.js.map M static/scripts/mvc/upload/composite/composite-row.js M static/scripts/mvc/upload/default/default-row.js M static/scripts/mvc/upload/default/default-view.js M test/qunit/tests/upload_dialog_tests.js Log Message: ----------- Merge pull request #628 from guerler/upload_002 Change uploader icons Compare: https://github.com/galaxyproject/galaxy/compare/6ead1de53c17...795e30171149

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[galaxyproject/galaxy] aceb82: Remove fastx_clipper_sequences.txt, moved to tools...
by GitHub 20 Aug '15

20 Aug '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: aceb82247003c71565d57794d5572858d21a7712 https://github.com/galaxyproject/galaxy/commit/aceb82247003c71565d57794d557… Author: Lance Parsons <lparsons(a)genomics.princeton.edu> Date: 2015-08-18 (Tue, 18 Aug 2015) Changed paths: R tool-data/fastx_clipper_sequences.txt Log Message: ----------- Remove fastx_clipper_sequences.txt, moved to toolshed Commit: 6ead1de53c17cb0e3e1465f2076b3c43ea81cbc4 https://github.com/galaxyproject/galaxy/commit/6ead1de53c17cb0e3e1465f2076b… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-08-20 (Thu, 20 Aug 2015) Changed paths: R tool-data/fastx_clipper_sequences.txt Log Message: ----------- Merge pull request #611 from lparsons/fastx_clipper_sequences Remove fastx_clipper_sequences.txt, moved to toolshed Compare: https://github.com/galaxyproject/galaxy/compare/0f883ef776bd...6ead1de53c17

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[galaxyproject/galaxy] 238d90: Fix purging datasets whose total_size is None.
by GitHub 20 Aug '15

20 Aug '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 238d908ccecd6411a3a72f7396933b3771f7e5aa https://github.com/galaxyproject/galaxy/commit/238d908ccecd6411a3a72f739693… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-08-19 (Wed, 19 Aug 2015) Changed paths: M lib/galaxy/model/__init__.py M scripts/cleanup_datasets/cleanup_datasets.py Log Message: ----------- Fix purging datasets whose total_size is None. Fix the error: Removing disk, file /opt/galaxy/database/files/000/dataset_192.dat Error attempting to purge data file: /opt/galaxy/database/files/000/dataset_192.dat error: unsupported operand type(s) for -=: 'Decimal' and 'NoneType' when running: python scripts/cleanup_datasets/cleanup_datasets.py config/galaxy.ini -d 10 -3 -r Commit: a9827fae31d8826bf2426c5285fe789dfe61295d https://github.com/galaxyproject/galaxy/commit/a9827fae31d8826bf2426c5285fe… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-08-20 (Thu, 20 Aug 2015) Changed paths: M test/unit/test_galaxy_mapping.py Log Message: ----------- Fix failing tests for 238d908ccecd6411a3a72f7396933b3771f7e5aa. Commit: baf8fe6759fe283516c5242d42ab8274b5a3baf0 https://github.com/galaxyproject/galaxy/commit/baf8fe6759fe283516c5242d42ab… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2015-08-20 (Thu, 20 Aug 2015) Changed paths: M test/unit/test_galaxy_mapping.py Log Message: ----------- Merge pull request #1 from jmchilton/release_fix Fix failing tests for 238d908ccecd6411a3a72f7396933b3771f7e5aa. Commit: 14a8ee95f3dd8a671ee9a1edac8fc3cd686a4395 https://github.com/galaxyproject/galaxy/commit/14a8ee95f3dd8a671ee9a1edac8f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-20 (Thu, 20 Aug 2015) Changed paths: M lib/galaxy/model/__init__.py M scripts/cleanup_datasets/cleanup_datasets.py M test/unit/test_galaxy_mapping.py Log Message: ----------- Merge pull request #616 from nsoranzo/release_15.05 [15.05] Fix purging datasets whose total_size is None. Commit: a34f13a9f6eb216665ea97e1314f7b76c74c5778 https://github.com/galaxyproject/galaxy/commit/a34f13a9f6eb216665ea97e1314f… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-08-20 (Thu, 20 Aug 2015) Changed paths: M lib/galaxy/model/__init__.py M scripts/cleanup_datasets/cleanup_datasets.py M test/unit/test_galaxy_mapping.py Log Message: ----------- Merge branch 'release_15.05' into release_15.07 Commit: 0f883ef776bd71348b82be29221abbbc1751d45f https://github.com/galaxyproject/galaxy/commit/0f883ef776bd71348b82be29221a… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-08-20 (Thu, 20 Aug 2015) Changed paths: M lib/galaxy/model/__init__.py M scripts/cleanup_datasets/cleanup_datasets.py M test/unit/test_galaxy_mapping.py Log Message: ----------- Merge branch 'release_15.07' into dev Conflicts: lib/galaxy/model/__init__.py Compare: https://github.com/galaxyproject/galaxy/compare/c429777c9368...0f883ef776bd

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