galaxy-commits August 2015

galaxy-commits@lists.galaxyproject.org

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[galaxyproject/galaxy] fc82f7: Fix objectstore inheritance, pop some basic config...
by GitHub 25 Aug '15

25 Aug '15

Branch: refs/heads/release_15.07 Home: https://github.com/galaxyproject/galaxy Commit: fc82f779521a1b7afcb2495d6748f78e8ee36a1a https://github.com/galaxyproject/galaxy/commit/fc82f779521a1b7afcb2495d6748… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-24 (Mon, 24 Aug 2015) Changed paths: M lib/galaxy/objectstore/__init__.py M lib/galaxy/objectstore/s3.py Log Message: ----------- Fix objectstore inheritance, pop some basic configuration up to the main ObjectStore class. Commit: 2a7896782d6d4b6407f64bca447087883952119b https://github.com/galaxyproject/galaxy/commit/2a7896782d6d4b6407f64bca4470… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-08-25 (Tue, 25 Aug 2015) Changed paths: M lib/galaxy/objectstore/__init__.py M lib/galaxy/objectstore/s3.py Log Message: ----------- Merge pull request #639 from dannon/objectstore_fix_inheritance [release_15.07] Fix objectstore inheritance, pop some basic configuration up to the m… Compare: https://github.com/galaxyproject/galaxy/compare/6d3523e81f1e...2a7896782d6d

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[galaxyproject/usegalaxy-playbook] 7a8c35: update mutable confs
by GitHub 24 Aug '15

24 Aug '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 7a8c3597eaf87ee1b0bcd1ce4f27ed19ca8fd852 https://github.com/galaxyproject/usegalaxy-playbook/commit/7a8c3597eaf87ee1… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-08-24 (Mon, 24 Aug 2015) Changed paths: M files/galaxy/test.galaxyproject.org/var/integrated_tool_panel.xml M files/galaxy/test.galaxyproject.org/var/shed_tool_conf.xml Log Message: ----------- update mutable confs

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[galaxyproject/usegalaxy-playbook] 0fda9b: A preliminary tool list for Test
by GitHub 24 Aug '15

24 Aug '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 0fda9b7ef500d6fc51971954c5118b14dac32e3a https://github.com/galaxyproject/usegalaxy-playbook/commit/0fda9b7ef500d6fc… Author: Enis Afgan <afgane(a)gmail.com> Date: 2015-08-24 (Mon, 24 Aug 2015) Changed paths: M files/galaxy/test.galaxyproject.org/tool_list.yaml Log Message: ----------- A preliminary tool list for Test

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[galaxyproject/usegalaxy-playbook] ea34fa: update test
by GitHub 24 Aug '15

24 Aug '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: ea34fae405168670195fdfd1c94288972dde4bc3 https://github.com/galaxyproject/usegalaxy-playbook/commit/ea34fae405168670… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-08-24 (Mon, 24 Aug 2015) Changed paths: M stage/group_vars/all.yml Log Message: ----------- update test

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[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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galaxy-commits August 2015