- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] c938e6: Fix output collection terminal base class
by GitHub 13 Aug '15

13 Aug '15

Branch: refs/heads/release_15.07 Home: https://github.com/galaxyproject/galaxy 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 Compare: https://github.com/galaxyproject/galaxy/compare/98ec06c7d6e4...79dbff19674d

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[galaxyproject/usegalaxy-playbook] 5db56b: update tts
by GitHub 13 Aug '15

13 Aug '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 5db56b63bbf67e4625fd8b85d52a95f56bb23967 https://github.com/galaxyproject/usegalaxy-playbook/commit/5db56b63bbf67e46… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-08-13 (Thu, 13 Aug 2015) Changed paths: M stage/group_vars/toolshedservers.yml Log Message: ----------- update tts

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[galaxyproject/galaxy] 8b2387: fix regenerating repo metadata when coming from ba...
by GitHub 13 Aug '15

13 Aug '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy 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: cafe872bfb20633de770be9b2a8c6111eed75023 https://github.com/galaxyproject/galaxy/commit/cafe872bfb20633de770be9b2a8c… 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: ----------- Merge branch 'release_15.07' into dev Compare: https://github.com/galaxyproject/galaxy/compare/635ef189df60...cafe872bfb20

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[galaxyproject/usegalaxy-playbook] f1a579: Change from ssh to https for submodule
by GitHub 13 Aug '15

13 Aug '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: f1a579d197ea764eb580d00f60674148eae61c51 https://github.com/galaxyproject/usegalaxy-playbook/commit/f1a579d197ea764e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-08-13 (Thu, 13 Aug 2015) Changed paths: M .gitmodules Log Message: ----------- Change from ssh to https for submodule

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[galaxyproject/galaxy] 303597: Remove old cloudlaunch in favor of https://github....
by GitHub 13 Aug '15

13 Aug '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 303597e48a8503aac09c33910aa5482a374f06a1 https://github.com/galaxyproject/galaxy/commit/303597e48a8503aac09c33910aa5… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-12 (Wed, 12 Aug 2015) Changed paths: M client/galaxy/scripts/galaxy.menu.js M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/managers/configuration.py R lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py M static/maps/galaxy.menu.js.map M static/scripts/galaxy.menu.js R templates/webapps/galaxy/cloud/index.mako Log Message: ----------- Remove old cloudlaunch in favor of https://github.com/galaxyproject/cloudlaunch, at launch.usegalaxy.org Commit: 635ef189df60e9a1ce6e0e8c177fdc3b136da9a1 https://github.com/galaxyproject/galaxy/commit/635ef189df60e9a1ce6e0e8c177f… Author: Nitesh Turaga <nitesh.turaga(a)gmail.com> Date: 2015-08-13 (Thu, 13 Aug 2015) Changed paths: M client/galaxy/scripts/galaxy.menu.js M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/managers/configuration.py R lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py M static/maps/galaxy.menu.js.map M static/scripts/galaxy.menu.js R templates/webapps/galaxy/cloud/index.mako Log Message: ----------- Merge pull request #597 from dannon/no_more_cloudlaunch Remove old cloudlaunch in favor of … Compare: https://github.com/galaxyproject/galaxy/compare/369760aabe27...635ef189df60

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[galaxyproject/galaxy] 8b2387: fix regenerating repo metadata when coming from ba...
by GitHub 13 Aug '15

13 Aug '15

Branch: refs/heads/release_15.07 Home: https://github.com/galaxyproject/galaxy 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 Compare: https://github.com/galaxyproject/galaxy/compare/b3da771a637a...98ec06c7d6e4

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[galaxyproject/usegalaxy-playbook] b6501c: Install package_bcftools_1_2 using the new tool ro...
by GitHub 13 Aug '15

13 Aug '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: b6501c58a3a33f0b990dd3b3d98e2583e104aad8 https://github.com/galaxyproject/usegalaxy-playbook/commit/b6501c58a3a33f0b… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-08-13 (Thu, 13 Aug 2015) Changed paths: M files/galaxy/test.galaxyproject.org/tool_list.yaml M files/galaxy/usegalaxy.org/tool_list.yaml M production/secret_vars/galaxyservers.yml M stage/secret_vars/galaxyservers.yml Log Message: ----------- Install package_bcftools_1_2 using the new tool role

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[galaxyproject/usegalaxy-playbook] 112b97: Fix README formatting
by GitHub 13 Aug '15

13 Aug '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 112b97d3b97d965c9488eb9025e3be0df17fbd83 https://github.com/galaxyproject/usegalaxy-playbook/commit/112b97d3b97d965c… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-08-13 (Thu, 13 Aug 2015) Changed paths: M README.md Log Message: ----------- Fix README formatting

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[galaxyproject/usegalaxy-playbook] deeb1b: Add Tools role for installing tools. See the readm...
by GitHub 13 Aug '15

13 Aug '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: deeb1b74939fb05e5475a3cb9f27d2784ac5fb42 https://github.com/galaxyproject/usegalaxy-playbook/commit/deeb1b74939fb05e… Author: Enis Afgan <afgane(a)gmail.com> Date: 2015-08-05 (Wed, 05 Aug 2015) Changed paths: M README.md A files/galaxy/test.galaxyproject.org/tool_list.yaml A files/galaxy/usegalaxy.org/tool_list.yaml M production/group_vars/galaxyservers.yml M production/secret_vars/galaxyservers.yml A roles/galaxyprojectdotorg.tools/LICENSE A roles/galaxyprojectdotorg.tools/README.md A roles/galaxyprojectdotorg.tools/defaults/main.yml A roles/galaxyprojectdotorg.tools/files/README.md A roles/galaxyprojectdotorg.tools/files/dbkeys_list.yaml.sample A roles/galaxyprojectdotorg.tools/files/install_tool_shed_tools.py A roles/galaxyprojectdotorg.tools/files/tool_list.yaml A roles/galaxyprojectdotorg.tools/files/tool_list.yaml.sample A roles/galaxyprojectdotorg.tools/meta/.galaxy_install_info A roles/galaxyprojectdotorg.tools/meta/main.yml A roles/galaxyprojectdotorg.tools/tasks/main.yml A roles/galaxyprojectdotorg.tools/tasks/tools.yml M stage/group_vars/galaxyservers.yml M stage/secret_vars/galaxyservers.yml A tools.yml Log Message: ----------- Add Tools role for installing tools. See the readme for usage details. What's still missing is the exact toolset for the appropriate server (see files/galaxy/test.galaxyproject.org/tool_list.yaml and files/galaxy/usegalaxy.org/tool_list.yaml) and the admin user's API key for each of the servers in the vault. Commit: 584f62e1420aa9577fbf81ef1f003d11bd4e9ce4 https://github.com/galaxyproject/usegalaxy-playbook/commit/584f62e1420aa957… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-08-13 (Thu, 13 Aug 2015) Changed paths: M README.md A files/galaxy/test.galaxyproject.org/tool_list.yaml A files/galaxy/usegalaxy.org/tool_list.yaml M production/group_vars/galaxyservers.yml M production/secret_vars/galaxyservers.yml A roles/galaxyprojectdotorg.tools/LICENSE A roles/galaxyprojectdotorg.tools/README.md A roles/galaxyprojectdotorg.tools/defaults/main.yml A roles/galaxyprojectdotorg.tools/files/README.md A roles/galaxyprojectdotorg.tools/files/dbkeys_list.yaml.sample A roles/galaxyprojectdotorg.tools/files/install_tool_shed_tools.py A roles/galaxyprojectdotorg.tools/files/tool_list.yaml A roles/galaxyprojectdotorg.tools/files/tool_list.yaml.sample A roles/galaxyprojectdotorg.tools/meta/.galaxy_install_info A roles/galaxyprojectdotorg.tools/meta/main.yml A roles/galaxyprojectdotorg.tools/tasks/main.yml A roles/galaxyprojectdotorg.tools/tasks/tools.yml M stage/group_vars/galaxyservers.yml M stage/secret_vars/galaxyservers.yml A tools.yml Log Message: ----------- Merge pull request #9 from afgane/master Add Tools role for installing tools. See the readme for usage details… Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/5b7016088ab5...…

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[galaxyproject/galaxy] e3f225: This commit implements #382 in response to the lac...
by GitHub 13 Aug '15

13 Aug '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: e3f2255a09ac4a4827aa9a38908ac21285f7c482 https://github.com/galaxyproject/galaxy/commit/e3f2255a09ac4a4827aa9a38908a… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-08-05 (Wed, 05 Aug 2015) Changed paths: M CONTRIBUTING.md M doc/source/project/organization.rst Log Message: ----------- This commit implements #382 in response to the lack of explicit language on how reversions are to be handled. This is in response to the events transpiring in #433 and #449. Additionally this PR corrects the misspelling of the pluralization of the word veto. This is a direct follow up, per procedures with a single squashed commit, of #450. Commit: 369760aabe2747d64411c7c2dc61c701a9064c3d https://github.com/galaxyproject/galaxy/commit/369760aabe2747d64411c7c2dc61… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2015-08-13 (Thu, 13 Aug 2015) Changed paths: M CONTRIBUTING.md M doc/source/project/organization.rst Log Message: ----------- Merge pull request #556 from erasche/contributing-wip-revert-v3 [PROCEDURES] Explicit language on reversions and WIP v3 Compare: https://github.com/galaxyproject/galaxy/compare/6925bbd85cf7...369760aabe27

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