- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] f3c593: fix column order in Custom Builds
by GitHub 16 Sep '17

16 Sep '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f3c593fc59f0c1a43ddc992feed582cc7668caee https://github.com/galaxyproject/galaxy/commit/f3c593fc59f0c1a43ddc992feed5… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2017-09-16 (Sat, 16 Sep 2017) Changed paths: M client/galaxy/scripts/mvc/user/user-custom-builds.js M static/maps/mvc/user/user-custom-builds.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/user/user-custom-builds.js Log Message: ----------- fix column order in Custom Builds Commit: 8f337f692f2aa2a5aef766bc525929c51cad7324 https://github.com/galaxyproject/galaxy/commit/8f337f692f2aa2a5aef766bc5259… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-09-17 (Sun, 17 Sep 2017) Changed paths: M client/galaxy/scripts/mvc/user/user-custom-builds.js M static/maps/mvc/user/user-custom-builds.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/user/user-custom-builds.js Log Message: ----------- Merge pull request #4634 from anatskiy/custom_builds_fix Fix data order in Custom Builds Compare: https://github.com/galaxyproject/galaxy/compare/13881bd264eb...8f337f692f2a

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[galaxyproject/galaxy] 2c77d3: Write out registry once per job
by GitHub 16 Sep '17

16 Sep '17

Branch: refs/heads/release_17.05 Home: https://github.com/galaxyproject/galaxy Commit: 2c77d386def0dc21b8aa40d5d7cf5f8934c16a74 https://github.com/galaxyproject/galaxy/commit/2c77d386def0dc21b8aa40d5d7cf… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-09-15 (Fri, 15 Sep 2017) Changed paths: M lib/galaxy/datatypes/registry.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/command_factory.py M lib/galaxy/tools/evaluation.py Log Message: ----------- Write out registry once per job Commit: e03ee53f3c398fe429ba1fe8693782a06b20cd73 https://github.com/galaxyproject/galaxy/commit/e03ee53f3c398fe429ba1fe86937… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-09-16 (Sat, 16 Sep 2017) Changed paths: M lib/galaxy/app.py M lib/galaxy/datatypes/registry.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/tools/actions/metadata.py Log Message: ----------- Remove references to integrated_datatypes_config Commit: 03d9a9c6fba0e26fae080a7ebb65fd6f0676477e https://github.com/galaxyproject/galaxy/commit/03d9a9c6fba0e26fae080a7ebb65… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-09-16 (Sat, 16 Sep 2017) Changed paths: M lib/galaxy/app.py M lib/galaxy/datatypes/registry.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/command_factory.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/tools/actions/metadata.py M lib/galaxy/tools/evaluation.py Log Message: ----------- Merge pull request #4633 from mvdbeek/backport_registry_to_working_dir [17.05] Backport #4600: Write datatypes registry xml to working directory Compare: https://github.com/galaxyproject/galaxy/compare/97e8e3618531...03d9a9c6fba0

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[galaxyproject/galaxy] ac0844: Swap sanitize whitelist form to use a post.
by GitHub 16 Sep '17

16 Sep '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ac084495978a8e5b607d90cf45dfb36c853aaf79 https://github.com/galaxyproject/galaxy/commit/ac084495978a8e5b607d90cf45df… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-09-15 (Fri, 15 Sep 2017) Changed paths: M templates/webapps/galaxy/admin/sanitize_whitelist.mako Log Message: ----------- Swap sanitize whitelist form to use a post. Commit: 13881bd264eb647bff4019ebbbf52aabf134f92b https://github.com/galaxyproject/galaxy/commit/13881bd264eb647bff4019ebbbf5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-16 (Sat, 16 Sep 2017) Changed paths: M templates/webapps/galaxy/admin/sanitize_whitelist.mako Log Message: ----------- Merge pull request #4625 from dannon/sanitize_whitelist_post Swap sanitize whitelist form to use a post. Compare: https://github.com/galaxyproject/galaxy/compare/4c9cc67a8f10...13881bd264eb

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[galaxyproject/galaxy] 289799: Refactored a dataset variable to hda
by GitHub 16 Sep '17

16 Sep '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 2897992ab56b69164a916ec400a2ed92b9c72d20 https://github.com/galaxyproject/galaxy/commit/2897992ab56b69164a916ec400a2… Author: Vahid <VJalili(a)users.noreply.github.com> Date: 2017-09-15 (Fri, 15 Sep 2017) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- Refactored a dataset variable to hda Commit: 4c9cc67a8f107887f341b1e386b2ac994acc2ba5 https://github.com/galaxyproject/galaxy/commit/4c9cc67a8f107887f341b1e386b2… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-16 (Sat, 16 Sep 2017) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- Merge pull request #4630 from VJalili/patch-4 Refactored a dataset variable to hda Compare: https://github.com/galaxyproject/galaxy/compare/6dbd47e66197...4c9cc67a8f10

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[galaxyproject/galaxy] 432d7f: Restore correct metadata path in setup_external_me...
by GitHub 16 Sep '17

16 Sep '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 432d7f44053a7c7d1fde1504e3f382edf2a539ec https://github.com/galaxyproject/galaxy/commit/432d7f44053a7c7d1fde1504e3f3… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-09-16 (Sat, 16 Sep 2017) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- Restore correct metadata path in setup_external_metdata This is a change I shouldn't have touched in https://github.com/galaxyproject/galaxy/pull/4600 Commit: 6dbd47e661971969c734a46938a06c42b85eea8f https://github.com/galaxyproject/galaxy/commit/6dbd47e661971969c734a46938a0… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-16 (Sat, 16 Sep 2017) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- Merge pull request #4632 from mvdbeek/fix_unintended_change [BUG] Restore tool provided metadata path in setup_external_metdata Compare: https://github.com/galaxyproject/galaxy/compare/22b0542d0bb7...6dbd47e66197

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[galaxyproject/galaxy] 0624a0: remove macos testing
by GitHub 16 Sep '17

16 Sep '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 0624a043a73f1a16fc36621b1c61a5cf52c67ba4 https://github.com/galaxyproject/galaxy/commit/0624a043a73f1a16fc36621b1c61… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-09-15 (Fri, 15 Sep 2017) Changed paths: M .travis.yml Log Message: ----------- remove macos testing Commit: 22b0542d0bb7a2f88b1503b53a8950d236be0f25 https://github.com/galaxyproject/galaxy/commit/22b0542d0bb7a2f88b1503b53a89… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-16 (Sat, 16 Sep 2017) Changed paths: M .travis.yml Log Message: ----------- Merge pull request #4631 from martenson/disable-macos-travis disable MacOS CI on travis Compare: https://github.com/galaxyproject/galaxy/compare/153dfaa68080...22b0542d0bb7

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[galaxyproject/galaxy] 7d2cd2: replace colon and comma in role names since they a...
by GitHub 15 Sep '17

15 Sep '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 7d2cd2272299b94b01c8d22c0c1f7f5cbfb2b91a https://github.com/galaxyproject/galaxy/commit/7d2cd2272299b94b01c8d22c0c1f… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-09-15 (Fri, 15 Sep 2017) Changed paths: M client/galaxy/scripts/mvc/library/library-dataset-view.js M static/maps/mvc/library/library-dataset-view.js.map M static/scripts/mvc/library/library-dataset-view.js Log Message: ----------- replace colon and comma in role names since they are also separators Commit: 3b4bd3bb6fa922c9e2156fe87660de409acf3367 https://github.com/galaxyproject/galaxy/commit/3b4bd3bb6fa922c9e2156fe87660… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-09-15 (Fri, 15 Sep 2017) Changed paths: M static/maps/mvc/library/library-dataset-view.js.map M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/library/library-dataset-view.js Log Message: ----------- make client Commit: 153dfaa68080481607a90731c5a0825754cf713d https://github.com/galaxyproject/galaxy/commit/153dfaa68080481607a90731c5a0… Author: Eric Rasche <hxr(a)hx42.org> Date: 2017-09-16 (Sat, 16 Sep 2017) Changed paths: M client/galaxy/scripts/mvc/library/library-dataset-view.js M static/maps/mvc/library/library-dataset-view.js.map M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/library/library-dataset-view.js Log Message: ----------- Merge pull request #4621 from martenson/library-sharing-roles replace separators in library sharing role names Compare: https://github.com/galaxyproject/galaxy/compare/ea7b27443715...153dfaa68080

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[galaxyproject/galaxy] 860f0a: Some function description updates
by GitHub 15 Sep '17

15 Sep '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 860f0ab6ba6c45c98b5c9f3f002096cc9ef0c7b6 https://github.com/galaxyproject/galaxy/commit/860f0ab6ba6c45c98b5c9f3f0020… Author: Vahid <VJalili(a)users.noreply.github.com> Date: 2017-09-15 (Fri, 15 Sep 2017) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Some function description updates Commit: e3e26ae202369876eb1523562b2582f2a15495cb https://github.com/galaxyproject/galaxy/commit/e3e26ae202369876eb1523562b25… Author: Vahid <VJalili(a)users.noreply.github.com> Date: 2017-09-15 (Fri, 15 Sep 2017) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Updated a comment Commit: 3cca06a153253f65f752d1f80aae2fd2e3cf221e https://github.com/galaxyproject/galaxy/commit/3cca06a153253f65f752d1f80aae… Author: Vahid <VJalili(a)users.noreply.github.com> Date: 2017-09-15 (Fri, 15 Sep 2017) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- updated a comment. Commit: 604fdde4248dc2d7f261e63449ab5530463058a3 https://github.com/galaxyproject/galaxy/commit/604fdde4248dc2d7f261e63449ab… Author: Vahid <VJalili(a)users.noreply.github.com> Date: 2017-09-15 (Fri, 15 Sep 2017) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- typo Commit: ea7b27443715730597e273b315dce875910738ce https://github.com/galaxyproject/galaxy/commit/ea7b27443715730597e273b315dc… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-09-15 (Fri, 15 Sep 2017) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/model/__init__.py Log Message: ----------- Merge pull request #4629 from VJalili/patch-3 Updated function description and fix some typos Compare: https://github.com/galaxyproject/galaxy/compare/fe88dab79b0b...ea7b27443715

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[galaxyproject/galaxy] 69af37: Typo fix
by GitHub 15 Sep '17

15 Sep '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 69af37f653569117371413bfadd06e5428486526 https://github.com/galaxyproject/galaxy/commit/69af37f653569117371413bfadd0… Author: Vahid <VJalili(a)users.noreply.github.com> Date: 2017-09-15 (Fri, 15 Sep 2017) Changed paths: M lib/galaxy/objectstore/__init__.py Log Message: ----------- Typo fix Commit: fe88dab79b0b47245c079ebc372563392c917f30 https://github.com/galaxyproject/galaxy/commit/fe88dab79b0b47245c079ebc3725… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-09-15 (Fri, 15 Sep 2017) Changed paths: M lib/galaxy/objectstore/__init__.py Log Message: ----------- Merge pull request #4628 from VJalili/patch-3 Typo fix Compare: https://github.com/galaxyproject/galaxy/compare/540322e38856...fe88dab79b0b

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[galaxyproject/galaxy] 1c1ca9: Fix loose->lose in help text for library dataset v...
by GitHub 15 Sep '17

15 Sep '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 1c1ca9bd91298e2265cb4a9e6982f18c3e4ae39d https://github.com/galaxyproject/galaxy/commit/1c1ca9bd91298e2265cb4a9e6982… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-09-15 (Fri, 15 Sep 2017) Changed paths: M client/galaxy/scripts/mvc/library/library-dataset-view.js M static/maps/mvc/library/library-dataset-view.js.map M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/library/library-dataset-view.js Log Message: ----------- Fix loose->lose in help text for library dataset view. Commit: d5aba7da15f5a05821e7659828bd701fd438769e https://github.com/galaxyproject/galaxy/commit/d5aba7da15f5a05821e7659828bd… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-09-15 (Fri, 15 Sep 2017) Changed paths: M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/parser/yaml.py M lib/galaxy/tools/util/maf_utilities.py Log Message: ----------- Three more looses. Commit: 7831b9889897e1d51ba2004cc8fcc5df079c0594 https://github.com/galaxyproject/galaxy/commit/7831b9889897e1d51ba2004cc8fc… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-09-15 (Fri, 15 Sep 2017) Changed paths: M client/galaxy/scripts/mvc/library/library-dataset-view.js M static/maps/mvc/library/library-dataset-view.js.map M static/scripts/mvc/library/library-dataset-view.js Log Message: ----------- Occurred, spelling. Commit: 0ea6272f5d35a769bc63a4706c503793fa903fe2 https://github.com/galaxyproject/galaxy/commit/0ea6272f5d35a769bc63a4706c50… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-09-15 (Fri, 15 Sep 2017) Changed paths: M client/galaxy/scripts/mvc/library/library-folder-view.js M client/galaxy/scripts/mvc/library/library-folderlist-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/library/library-library-view.js M client/galaxy/scripts/mvc/library/library-librarylist-view.js M client/toolshed/scripts/mvc/groups/group-detail-view.js M client/toolshed/scripts/mvc/groups/group-list-view.js M static/maps/mvc/library/library-folder-view.js.map M static/maps/mvc/library/library-folderlist-view.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/maps/mvc/library/library-library-view.js.map M static/maps/mvc/library/library-librarylist-view.js.map M static/scripts/mvc/library/library-folder-view.js M static/scripts/mvc/library/library-folderlist-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/library/library-library-view.js M static/scripts/mvc/library/library-librarylist-view.js M static/toolshed/scripts/mvc/groups/group-detail-view.js M static/toolshed/scripts/mvc/groups/group-list-view.js Log Message: ----------- More spelling. Commit: 540322e38856cc86a4a3d91aa3ac670418378d90 https://github.com/galaxyproject/galaxy/commit/540322e38856cc86a4a3d91aa3ac… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-09-15 (Fri, 15 Sep 2017) Changed paths: M client/galaxy/scripts/mvc/library/library-dataset-view.js M client/galaxy/scripts/mvc/library/library-folder-view.js M client/galaxy/scripts/mvc/library/library-folderlist-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/library/library-library-view.js M client/galaxy/scripts/mvc/library/library-librarylist-view.js M client/toolshed/scripts/mvc/groups/group-detail-view.js M client/toolshed/scripts/mvc/groups/group-list-view.js M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/parser/yaml.py M lib/galaxy/tools/util/maf_utilities.py M static/maps/mvc/library/library-dataset-view.js.map M static/maps/mvc/library/library-folder-view.js.map M static/maps/mvc/library/library-folderlist-view.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/maps/mvc/library/library-library-view.js.map M static/maps/mvc/library/library-librarylist-view.js.map M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/library/library-dataset-view.js M static/scripts/mvc/library/library-folder-view.js M static/scripts/mvc/library/library-folderlist-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/library/library-library-view.js M static/scripts/mvc/library/library-librarylist-view.js M static/toolshed/scripts/mvc/groups/group-detail-view.js M static/toolshed/scripts/mvc/groups/group-list-view.js Log Message: ----------- Merge pull request #4626 from dannon/loose_use Misc. spelling/grammatical error fixes. Compare: https://github.com/galaxyproject/galaxy/compare/64af1bd9e962...540322e38856

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