October 2015 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] efecf4: Change user preference datatype to text instead of...
by GitHub 29 Oct '15

29 Oct '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: efecf4e459f8bc16f3f8f51f7c55ca6e945c2a61 https://github.com/galaxyproject/galaxy/commit/efecf4e459f8bc16f3f8f51f7c55… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-10-14 (Wed, 14 Oct 2015) Changed paths: A lib/galaxy/model/migrate/versions/0130_change_pref_datatype.py Log Message: ----------- Change user preference datatype to text instead of an arbitrarily limited varchar Commit: 303ee4153775e2de2109ceccd6b2dd6181de099b https://github.com/galaxyproject/galaxy/commit/303ee4153775e2de2109ceccd6b2… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-10-14 (Wed, 14 Oct 2015) Changed paths: M lib/galaxy/model/mapping.py Log Message: ----------- Forgot the other commit. Commit: fb754751d99ec2d8db87a51d53b1375bef42135c https://github.com/galaxyproject/galaxy/commit/fb754751d99ec2d8db87a51d53b1… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-10-14 (Wed, 14 Oct 2015) Changed paths: M lib/galaxy/model/mapping.py Log Message: ----------- Use the more abstract Text type, corresponding to what was used in the migration script. Commit: c8c2f96b041a0083a3f817e7cf716946df9ef98f https://github.com/galaxyproject/galaxy/commit/c8c2f96b041a0083a3f817e7cf71… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-10-29 (Thu, 29 Oct 2015) Changed paths: M lib/galaxy/model/mapping.py A lib/galaxy/model/migrate/versions/0130_change_pref_datatype.py Log Message: ----------- Merge pull request #916 from dannon/pref_bump Change user preference datatype to text Compare: https://github.com/galaxyproject/galaxy/compare/3cf8fcc216f5...c8c2f96b041a

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[galaxyproject/usegalaxy-playbook] 3d85c7: Update galaxyprojectdotorg.galaxy role to 0.6.1
by GitHub 28 Oct '15

28 Oct '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 3d85c7126b951850e321d150d9379c2f8d06e429 https://github.com/galaxyproject/usegalaxy-playbook/commit/3d85c7126b951850… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-10-28 (Wed, 28 Oct 2015) Changed paths: M roles/galaxyprojectdotorg.galaxy/meta/.galaxy_install_info M roles/galaxyprojectdotorg.galaxy/tasks/dependencies.yml Log Message: ----------- Update galaxyprojectdotorg.galaxy role to 0.6.1

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[galaxyproject/ansible-galaxy]
by GitHub 28 Oct '15

28 Oct '15

Branch: refs/tags/0.6.1 Home: https://github.com/galaxyproject/ansible-galaxy

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[galaxyproject/ansible-galaxy] 2f4cbc: virtualenv_command is still required if `virtualen...
by GitHub 28 Oct '15

28 Oct '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/ansible-galaxy Commit: 2f4cbc0969fcb875727a510dd819c03bada3903e https://github.com/galaxyproject/ansible-galaxy/commit/2f4cbc0969fcb875727a… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-10-28 (Wed, 28 Oct 2015) Changed paths: M tasks/dependencies.yml Log Message: ----------- virtualenv_command is still required if `virtualenv` isn't on $PATH, even if the venv already exists.

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[galaxyproject/usegalaxy-playbook] 499aa7: Mutable configs on Test
by GitHub 28 Oct '15

28 Oct '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 499aa77b352f08148d5c01b86bd24168c318b61c https://github.com/galaxyproject/usegalaxy-playbook/commit/499aa77b352f0814… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-10-28 (Wed, 28 Oct 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 M files/galaxy/test.galaxyproject.org/var/shed_tool_data_table_conf.xml Log Message: ----------- Mutable configs on Test Commit: cf2e3d17533ed5127b5d0552930e495eb143de74 https://github.com/galaxyproject/usegalaxy-playbook/commit/cf2e3d17533ed512… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-10-28 (Wed, 28 Oct 2015) Changed paths: M stage/group_vars/all.yml M stage/group_vars/galaxyservers.yml Log Message: ----------- Update Test Commit: fbf7179def5e363a5a0011475873688b01ecf68d https://github.com/galaxyproject/usegalaxy-playbook/commit/fbf7179def5e363a… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-10-28 (Wed, 28 Oct 2015) Changed paths: M templates/supervisor/galaxy.conf.j2 Log Message: ----------- Update supervisor Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/b84b446a6cf3...…

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[galaxyproject/galaxy] b7c8a6: Rename lib/galaxy/main.py to scripts/galaxy-main s...
by GitHub 28 Oct '15

28 Oct '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b7c8a6d334461b0d61928e03bd112ee9344e8f2d https://github.com/galaxyproject/galaxy/commit/b7c8a6d334461b0d61928e03bd11… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-10-27 (Tue, 27 Oct 2015) Changed paths: M lib/galaxy/main.py A scripts/galaxy-main Log Message: ----------- Rename lib/galaxy/main.py to scripts/galaxy-main since that makes more sense and doesn't result in lib/galaxy/ being added to sys.path. Create a symlink at lib/galaxy/main.py for backward compatibility. Commit: 7010e38b6ff76014ae66ea62a7763942dacbfcd2 https://github.com/galaxyproject/galaxy/commit/7010e38b6ff76014ae66ea62a776… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-10-27 (Tue, 27 Oct 2015) Changed paths: M client/galaxy/scripts/galaxy.library.js M lib/galaxy/managers/configuration.py M scripts/binary_compatibility.py M static/maps/galaxy.library.js.map M static/scripts/galaxy.library.js Log Message: ----------- Merge branch 'dev' of https://github.com/galaxyproject/galaxy into smash_eggs Commit: 3cf8fcc216f552a8dca542bc9ea3ada02c42e78c https://github.com/galaxyproject/galaxy/commit/3cf8fcc216f552a8dca542bc9ea3… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2015-10-28 (Wed, 28 Oct 2015) Changed paths: M lib/galaxy/main.py A scripts/galaxy-main Log Message: ----------- Merge pull request #994 from natefoo/smash_eggs Rename lib/galaxy/main.py to scripts/galaxy-main Compare: https://github.com/galaxyproject/galaxy/compare/f7d8bf7dbcf4...3cf8fcc216f5

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[galaxyproject/galaxy] 091128: UI, list of pairs collection creator: create regex...
by GitHub 28 Oct '15

28 Oct '15

Branch: refs/heads/release_15.10 Home: https://github.com/galaxyproject/galaxy Commit: 0911287df7a5d7e810d83bbcd1e4cb1f849314d7 https://github.com/galaxyproject/galaxy/commit/0911287df7a5d7e810d83bbcd1e4… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-10-14 (Wed, 14 Oct 2015) Changed paths: M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M static/maps/mvc/collection/list-of-pairs-collection-creator.js.map M static/scripts/mvc/collection/list-of-pairs-collection-creator.js Log Message: ----------- UI, list of pairs collection creator: create regexp from filters for name creation Commit: 3b133d0d9206f6162494b3f5aa4c04581368480e https://github.com/galaxyproject/galaxy/commit/3b133d0d9206f6162494b3f5aa4c… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-10-28 (Wed, 28 Oct 2015) Changed paths: M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M static/maps/mvc/collection/list-of-pairs-collection-creator.js.map M static/scripts/mvc/collection/list-of-pairs-collection-creator.js Log Message: ----------- Merge pull request #917 from carlfeberhard/release_15.10 [15.10] UI, list of pairs collection creator: create regexp from filters for … Compare: https://github.com/galaxyproject/galaxy/compare/7bcbf140936b...3b133d0d9206

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[galaxyproject/galaxy] de2bde: Fix a regression introduced during egg smashing th...
by GitHub 28 Oct '15

28 Oct '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: de2bde9f69bd225f94af97b45b5682235b2ba86b https://github.com/galaxyproject/galaxy/commit/de2bde9f69bd225f94af97b45b56… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-10-27 (Tue, 27 Oct 2015) Changed paths: M lib/galaxy/jobs/runners/drmaa.py Log Message: ----------- Fix a regression introduced during egg smashing that broke the drmaa_library_path param to the drmaa runner (importing drmaa needs to be delayed until runner initialization so that the param to modify $DRMAA_LIBRARY_PATH can be evaluated). Commit: 04f5b3087a3f1a5ba78e0a7c9313b3c2c82e8b87 https://github.com/galaxyproject/galaxy/commit/04f5b3087a3f1a5ba78e0a7c9313… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-10-27 (Tue, 27 Oct 2015) Changed paths: M client/galaxy/scripts/galaxy.library.js M lib/galaxy/managers/configuration.py M scripts/binary_compatibility.py M static/maps/galaxy.library.js.map M static/scripts/galaxy.library.js Log Message: ----------- Merge branch 'dev' of https://github.com/galaxyproject/galaxy into smash-eggs-bugfix2 Commit: 04a32c7864bdeb078916b90a0b70cb059cc6ab1b https://github.com/galaxyproject/galaxy/commit/04a32c7864bdeb078916b90a0b70… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-10-28 (Wed, 28 Oct 2015) Changed paths: M lib/galaxy/jobs/runners/drmaa.py Log Message: ----------- Add a comment explaining the strange import behavior in drmaa to guard against future regression Commit: f7d8bf7dbcf49c17273084c425e0a31e0ae3f7d8 https://github.com/galaxyproject/galaxy/commit/f7d8bf7dbcf49c17273084c425e0… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-10-28 (Wed, 28 Oct 2015) Changed paths: M lib/galaxy/jobs/runners/drmaa.py Log Message: ----------- Merge pull request #996 from natefoo/smash-eggs-bugfix2 Fix a regression introduced during egg smashing that broke the drmaa_library_path param Compare: https://github.com/galaxyproject/galaxy/compare/70bd41546151...f7d8bf7dbcf4

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[galaxyproject/galaxy] c70c1a: Fix deferred dom removal
by GitHub 28 Oct '15

28 Oct '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c70c1aabd872c1aaec3742188b74ba5c972c3c4a https://github.com/galaxyproject/galaxy/commit/c70c1aabd872c1aaec3742188b74… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-10-27 (Tue, 27 Oct 2015) Changed paths: M client/galaxy/scripts/mvc/app/app-analysis.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/tools.js M client/galaxy/scripts/mvc/tools/tools-form-base.js M client/galaxy/scripts/utils/deferred.js M static/maps/mvc/app/app-analysis.js.map M static/maps/mvc/dataset/dataset-li-edit.js.map M static/maps/mvc/tools.js.map M static/maps/mvc/tools/tools-form-base.js.map M static/maps/utils/deferred.js.map M static/scripts/mvc/app/app-analysis.js M static/scripts/mvc/dataset/dataset-li-edit.js M static/scripts/mvc/tools.js M static/scripts/mvc/tools/tools-form-base.js M static/scripts/utils/deferred.js Log Message: ----------- Fix deferred dom removal Remove empty line Fix comments Fix log location Fix comments Commit: 70bd41546151e2ee0a464b8bafb6b6da1767080d https://github.com/galaxyproject/galaxy/commit/70bd41546151e2ee0a464b8bafb6… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-10-28 (Wed, 28 Oct 2015) Changed paths: M client/galaxy/scripts/mvc/app/app-analysis.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/tools.js M client/galaxy/scripts/mvc/tools/tools-form-base.js M client/galaxy/scripts/utils/deferred.js M static/maps/mvc/app/app-analysis.js.map M static/maps/mvc/dataset/dataset-li-edit.js.map M static/maps/mvc/tools.js.map M static/maps/mvc/tools/tools-form-base.js.map M static/maps/utils/deferred.js.map M static/scripts/mvc/app/app-analysis.js M static/scripts/mvc/dataset/dataset-li-edit.js M static/scripts/mvc/tools.js M static/scripts/mvc/tools/tools-form-base.js M static/scripts/utils/deferred.js Log Message: ----------- Merge pull request #997 from guerler/performance_001 Fix deferred dom removal Compare: https://github.com/galaxyproject/galaxy/compare/3529ef6b6e96...70bd41546151

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[galaxyproject/usegalaxy-playbook] b84b44: Update Main
by GitHub 28 Oct '15

28 Oct '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: b84b446a6cf3e285c7d4a352ef66e1609d4a4cbc https://github.com/galaxyproject/usegalaxy-playbook/commit/b84b446a6cf3e285… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-10-28 (Wed, 28 Oct 2015) Changed paths: M production/group_vars/all.yml Log Message: ----------- Update Main

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