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galaxy-commits
August 2015
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September 2023
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----- 2022 -----
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----- 2021 -----
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----- 2020 -----
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----- 2019 -----
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----- 2018 -----
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----- 2017 -----
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----- 2013 -----
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----- 2012 -----
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----- 2011 -----
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----- 2010 -----
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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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