April 2017 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 334f4d: Remove old, unused search controller. This would ...
by GitHub 06 Apr '17

06 Apr '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 334f4d7a19882ad97aec75f50b61fda5eb807974 https://github.com/galaxyproject/galaxy/commit/334f4d7a19882ad97aec75f50b61… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-04-06 (Thu, 06 Apr 2017) Changed paths: M lib/galaxy/webapps/galaxy/buildapp.py R lib/galaxy/webapps/galaxy/controllers/search.py Log Message: ----------- Remove old, unused search controller. This would be implemented as a clientside route if we ever pursued development. Commit: 69ff6ab906d94fdb4da3bd0b858fce2de3b349fa https://github.com/galaxyproject/galaxy/commit/69ff6ab906d94fdb4da3bd0b858f… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-04-06 (Thu, 06 Apr 2017) Changed paths: M lib/galaxy/webapps/galaxy/buildapp.py R lib/galaxy/webapps/galaxy/controllers/search.py Log Message: ----------- Merge pull request #3894 from dannon/search_controller_removal Remove old, unused search controller. Compare: https://github.com/galaxyproject/galaxy/compare/dc80d8c7dcb1...69ff6ab906d9

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[galaxyproject/galaxy] eb0ff2: Update to a new Docker test image to fix dependenc...
by GitHub 06 Apr '17

06 Apr '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: eb0ff254a59196499e7c714b4fc8d744ef463df9 https://github.com/galaxyproject/galaxy/commit/eb0ff254a59196499e7c714b4fc8… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-04-06 (Thu, 06 Apr 2017) Changed paths: M run_tests.sh Log Message: ----------- Update to a new Docker test image to fix dependency bugs. Hopefully this will fix tests for #3179. Commit: dc80d8c7dcb194300b622d8cfc9fd2dd5d11a811 https://github.com/galaxyproject/galaxy/commit/dc80d8c7dcb194300b622d8cfc9f… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-04-06 (Thu, 06 Apr 2017) Changed paths: M run_tests.sh Log Message: ----------- Merge pull request #3890 from jmchilton/fix_docker_testing Update to a new Docker test image to fix dependency bugs. Compare: https://github.com/galaxyproject/galaxy/compare/d19be8bf46c4...dc80d8c7dcb1

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[galaxyproject/galaxy] 232e80: Python3: Use shlex_quote() from six.moves instead ...
by GitHub 06 Apr '17

06 Apr '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 232e8096925dd7739b98120c172b5cb092192f3e https://github.com/galaxyproject/galaxy/commit/232e8096925dd7739b98120c172b… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-04-06 (Thu, 06 Apr 2017) Changed paths: M lib/galaxy/tools/wrappers.py Log Message: ----------- Python3: Use shlex_quote() from six.moves instead of pipes.quote() Commit: d19be8bf46c41d12e0a4d6c34454cc150cc06378 https://github.com/galaxyproject/galaxy/commit/d19be8bf46c41d12e0a4d6c34454… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-04-06 (Thu, 06 Apr 2017) Changed paths: M lib/galaxy/tools/wrappers.py Log Message: ----------- Merge pull request #3891 from nsoranzo/python3 Python3: Use shlex_quote() from six.moves instead of pipes.quote() Compare: https://github.com/galaxyproject/galaxy/compare/af37dd55de28...d19be8bf46c4

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[galaxyproject/galaxy]
by GitHub 06 Apr '17

06 Apr '17

Branch: refs/heads/revert-3871-history_drag_drop Home: https://github.com/galaxyproject/galaxy

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[galaxyproject/galaxy] d19a15: Allow nest param in the dynamic_tool rule -> argum...
by GitHub 06 Apr '17

06 Apr '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d19a158e10ada652fb1bf1549dac4f1f3446aa5a https://github.com/galaxyproject/galaxy/commit/d19a158e10ada652fb1bf1549dac… Author: lecorguille <lecorguille(a)users.noreply.github.com> Date: 2017-02-23 (Thu, 23 Feb 2017) Changed paths: M lib/galaxy/jobs/dynamic_tool_destination.py Log Message: ----------- Allow nest param in the dynamic_tool rule -> argument Commit: 73921a21e9164bad342269ed3fe3c347d42a5c8d https://github.com/galaxyproject/galaxy/commit/73921a21e9164bad342269ed3fe3… Author: lecorguille <lecorguille(a)users.noreply.github.com> Date: 2017-02-28 (Tue, 28 Feb 2017) Changed paths: M lib/galaxy/jobs/dynamic_tool_destination.py Log Message: ----------- change the tool_destinations.yml the argument rules syntax Commit: 705eb17b02b748ce76b5644386c793a610d9ab90 https://github.com/galaxyproject/galaxy/commit/705eb17b02b748ce76b5644386c7… Author: lecorguille <lecorguille(a)users.noreply.github.com> Date: 2017-02-28 (Tue, 28 Feb 2017) Changed paths: M lib/galaxy/jobs/dynamic_tool_destination.py Log Message: ----------- fix python syntax Commit: d624b04f25510475bd1cb48fbcbdca471bc1a5d7 https://github.com/galaxyproject/galaxy/commit/d624b04f25510475bd1cb48fbcbd… Author: lecorguille <lecorguille(a)users.noreply.github.com> Date: 2017-02-28 (Tue, 28 Feb 2017) Changed paths: M config/tool_destinations.yml.sample Log Message: ----------- update the documentation Commit: af37dd55de283602338f07452c92224eb0490fa6 https://github.com/galaxyproject/galaxy/commit/af37dd55de283602338f07452c92… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-04-06 (Thu, 06 Apr 2017) Changed paths: M config/tool_destinations.yml.sample M lib/galaxy/jobs/dynamic_tool_destination.py Log Message: ----------- Merge pull request #3657 from lecorguille/dynamic_tool_nest_param Allow nest param in the dynamic_tool rule -> argument Compare: https://github.com/galaxyproject/galaxy/compare/bcd24e845477...af37dd55de28

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[galaxyproject/galaxy] 74f97a: Fix for dropping into run workflow iframe
by GitHub 06 Apr '17

06 Apr '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 74f97a8942cd13572293ff79aec600fcdab4ed88 https://github.com/galaxyproject/galaxy/commit/74f97a8942cd13572293ff79aec6… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-04-05 (Wed, 05 Apr 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-content.js M static/maps/mvc/ui/ui-select-content.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/ui/ui-select-content.js Log Message: ----------- Fix for dropping into run workflow iframe Commit: 7304d5bdc4997da727747f86cf7049bb2452050a https://github.com/galaxyproject/galaxy/commit/7304d5bdc4997da727747f86cf70… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-04-05 (Wed, 05 Apr 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/ui/ui-misc.js M client/galaxy/scripts/mvc/ui/ui-select-content.js M client/galaxy/scripts/mvc/ui/ui-table.js A client/galaxy/scripts/mvc/user/user-custom-builds.js M client/galaxy/scripts/mvc/user/user-preferences.js M client/galaxy/style/less/ui.less M lib/galaxy/web/framework/base.py M lib/galaxy/webapps/galaxy/api/histories.py M lib/galaxy/webapps/galaxy/api/users.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/user.py A static/GruntFile.js A static/GruntFile.js.map M static/maps/layout/menu.js.map M static/maps/mvc/form/form-parameters.js.map M static/maps/mvc/ui/ui-misc.js.map M static/maps/mvc/ui/ui-select-content.js.map M static/maps/mvc/ui/ui-table.js.map A static/maps/mvc/user/user-custom-builds.js.map M static/maps/mvc/user/user-preferences.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/layout/menu.js M static/scripts/mvc/form/form-parameters.js M static/scripts/mvc/ui/ui-misc.js M static/scripts/mvc/ui/ui-select-content.js M static/scripts/mvc/ui/ui-table.js A static/scripts/mvc/user/user-custom-builds.js M static/scripts/mvc/user/user-preferences.js M static/style/blue/base.css R templates/user/dbkeys.mako Log Message: ----------- Merge branch 'dev' into history_drag_drop_000 Commit: ba91462362c59a1a0dbbfdc80920642de10dbd20 https://github.com/galaxyproject/galaxy/commit/ba91462362c59a1a0dbbfdc80920… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-04-05 (Wed, 05 Apr 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-content.js M static/maps/mvc/ui/ui-select-content.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/ui/ui-select-content.js Log Message: ----------- Add delay attribute to time success/error highlighting Commit: 37b6d907cbc338793f950d33904421faf376f2c3 https://github.com/galaxyproject/galaxy/commit/37b6d907cbc338793f950d339044… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-04-05 (Wed, 05 Apr 2017) Changed paths: M client/galaxy/style/less/ui.less M static/style/blue/base.css Log Message: ----------- Remove unused cursor style Commit: 6f95ba9c2c7637fef29d639b19cde81cc3f0ec74 https://github.com/galaxyproject/galaxy/commit/6f95ba9c2c7637fef29d639b19cd… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-04-05 (Wed, 05 Apr 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/histories.py Log Message: ----------- Merge branch 'dev' into history_drag_drop_000 Commit: d2205c4167aa543be633721b6650098bca6835b4 https://github.com/galaxyproject/galaxy/commit/d2205c4167aa543be633721b6650… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-04-05 (Wed, 05 Apr 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/users.py Log Message: ----------- Merge branch 'dev' into history_drag_drop_000 Commit: 6a625b2c6116992bd475cffe4f11a8ced41110fe https://github.com/galaxyproject/galaxy/commit/6a625b2c6116992bd475cffe4f11… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-04-05 (Wed, 05 Apr 2017) Changed paths: M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Merge branch 'dev' into history_drag_drop_000 Commit: bcd24e845477d72761072baf014119b3dda2372d https://github.com/galaxyproject/galaxy/commit/bcd24e845477d72761072baf0141… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-04-06 (Thu, 06 Apr 2017) Changed paths: M client/galaxy/scripts/mvc/history/history-view-edit.js M client/galaxy/scripts/mvc/ui/ui-select-content.js M client/galaxy/style/less/ui.less M static/maps/mvc/history/history-view-edit.js.map M static/maps/mvc/ui/ui-select-content.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/history/history-view-edit.js M static/scripts/mvc/ui/ui-select-content.js M static/style/blue/base.css Log Message: ----------- Merge pull request #3886 from guerler/history_drag_drop_000 History drag-and-drop feature with iframe support for run workflow form Compare: https://github.com/galaxyproject/galaxy/compare/5055172e64bb...bcd24e845477

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[galaxyproject/galaxy] 72a3fe: Unused glob in buildapp
by GitHub 05 Apr '17

05 Apr '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 72a3fea37f3cb622f0b509a72921ad11ecabf99f https://github.com/galaxyproject/galaxy/commit/72a3fea37f3cb622f0b509a72921… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-04-05 (Wed, 05 Apr 2017) Changed paths: M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Unused glob in buildapp Commit: 5055172e64bb48ec0eb6d3e4b4ec6461cbc19162 https://github.com/galaxyproject/galaxy/commit/5055172e64bb48ec0eb6d3e4b4ec… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2017-04-05 (Wed, 05 Apr 2017) Changed paths: M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Merge pull request #3889 from dannon/unused_glob Unused glob in buildapp Compare: https://github.com/galaxyproject/galaxy/compare/c6ce56dd0a2d...5055172e64bb

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[galaxyproject/galaxy] d9bb8a: Remove unused model import from users api
by GitHub 05 Apr '17

05 Apr '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d9bb8a7d300c723a172ecc288e332c2a2763f872 https://github.com/galaxyproject/galaxy/commit/d9bb8a7d300c723a172ecc288e33… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-04-05 (Wed, 05 Apr 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/users.py Log Message: ----------- Remove unused model import from users api Commit: c6ce56dd0a2ddb7b5e4760b3bab7be80ef367ba3 https://github.com/galaxyproject/galaxy/commit/c6ce56dd0a2ddb7b5e4760b3bab7… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-04-05 (Wed, 05 Apr 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/users.py Log Message: ----------- Merge pull request #3888 from guerler/remove_unused_model Remove unused model import from users api Compare: https://github.com/galaxyproject/galaxy/compare/c9863b251ee8...c6ce56dd0a2d

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[galaxyproject/galaxy] d9d4ce: Looks like this was always using trans.hsitory ins...
by GitHub 05 Apr '17

05 Apr '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d9d4ce0ad349d506eb8e902f079453dd4cf9ba16 https://github.com/galaxyproject/galaxy/commit/d9d4ce0ad349d506eb8e902f0794… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-04-05 (Wed, 05 Apr 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/histories.py Log Message: ----------- Looks like this was always using trans.hsitory instead of the id that was passed to the endpoint. Commit: c9863b251ee831f0a7f97935f86e3d46f692ae9f https://github.com/galaxyproject/galaxy/commit/c9863b251ee831f0a7f97935f86e… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2017-04-05 (Wed, 05 Apr 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/histories.py Log Message: ----------- Merge pull request #3887 from dannon/fix_broken_jenkins Fix new history endpoint providing custom builds metadata Compare: https://github.com/galaxyproject/galaxy/compare/d607c7e0b134...c9863b251ee8

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[galaxyproject/galaxy] d32317: Add build endpoints to user api
by GitHub 05 Apr '17

05 Apr '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d32317438c407799c2b33364af6e553fa03fbdfa https://github.com/galaxyproject/galaxy/commit/d32317438c407799c2b33364af6e… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-03-15 (Wed, 15 Mar 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/users.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Add build endpoints to user api Commit: 814d58f9810283c1e851b6c6ec062ab3cb0784bf https://github.com/galaxyproject/galaxy/commit/814d58f9810283c1e851b6c6ec06… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-03-15 (Wed, 15 Mar 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/users.py Log Message: ----------- Remove empty lines, reduce comments Commit: c12c2d1dff45afe1a62321f45a26e2de2d696a99 https://github.com/galaxyproject/galaxy/commit/c12c2d1dff45afe1a62321f45a26… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-03-15 (Wed, 15 Mar 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/users.py Log Message: ----------- Add potential len files to response for now, might move to client-side further down the road Commit: 72fb0d6f043e5085323059f80a39a9c2fab43b88 https://github.com/galaxyproject/galaxy/commit/72fb0d6f043e5085323059f80a39… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-03-15 (Wed, 15 Mar 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/users.py Log Message: ----------- Fix error handling for build deletion Commit: 32a8633f4e0b4fc06ba3b61027ae3127cd0c7ece https://github.com/galaxyproject/galaxy/commit/32a8633f4e0b4fc06ba3b61027ae… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-03-15 (Wed, 15 Mar 2017) Changed paths: M client/galaxy/scripts/mvc/user/user-preferences.js M lib/galaxy/webapps/galaxy/api/users.py M lib/galaxy/webapps/galaxy/buildapp.py M static/maps/mvc/user/user-preferences.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/user/user-preferences.js Log Message: ----------- Add link to user preference page, return exception if chrom count failed Commit: 2153ef5b76a1958c0067abb6c5492d1df6767c3c https://github.com/galaxyproject/galaxy/commit/2153ef5b76a1958c0067abb6c549… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-03-15 (Wed, 15 Mar 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js M lib/galaxy/webapps/galaxy/buildapp.py 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 Log Message: ----------- Add route for custom builds Commit: d42848ec9b73a89e1cbe20a3250481bd1b41a93a https://github.com/galaxyproject/galaxy/commit/d42848ec9b73a89e1cbe20a32504… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-03-15 (Wed, 15 Mar 2017) Changed paths: A client/galaxy/scripts/mvc/user/user-custom-builds.js M lib/galaxy/webapps/galaxy/api/users.py M lib/galaxy/webapps/galaxy/buildapp.py A static/maps/mvc/user/user-custom-builds.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 A static/scripts/mvc/user/user-custom-builds.js Log Message: ----------- Add client view for custom builds, add api endpoint for builds metadata Commit: 0b26d561aabdb5af6e21e8d845f15325e18d8751 https://github.com/galaxyproject/galaxy/commit/0b26d561aabdb5af6e21e8d845f1… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-03-15 (Wed, 15 Mar 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-table.js M client/galaxy/scripts/mvc/user/user-custom-builds.js M static/maps/mvc/ui/ui-table.js.map M static/maps/mvc/user/user-custom-builds.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/ui/ui-table.js Log Message: ----------- Align style of table view component to other ui views Commit: 689560d7db23240df193fc913d8165643eea8cac https://github.com/galaxyproject/galaxy/commit/689560d7db23240df193fc913d81… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-03-15 (Wed, 15 Mar 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-table.js M client/galaxy/scripts/mvc/user/user-custom-builds.js M lib/galaxy/webapps/galaxy/api/users.py M lib/galaxy/webapps/galaxy/buildapp.py M static/maps/mvc/user/user-custom-builds.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/user/user-custom-builds.js Log Message: ----------- Implement and connect client add request with endpoint Commit: 06f61927b5f9f6d35c7c0bdebdd330bae56f6710 https://github.com/galaxyproject/galaxy/commit/06f61927b5f9f6d35c7c0bdebdd3… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-03-15 (Wed, 15 Mar 2017) Changed paths: M client/galaxy/scripts/mvc/user/user-custom-builds.js M lib/galaxy/webapps/galaxy/api/users.py M lib/galaxy/webapps/galaxy/buildapp.py M static/maps/mvc/user/user-custom-builds.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/user/user-custom-builds.js Log Message: ----------- Fix delete request, fix error triggered by attempting invalid conversions Commit: 8b5e27aaeae1ac9b35b0959f2cccaa6988d69163 https://github.com/galaxyproject/galaxy/commit/8b5e27aaeae1ac9b35b0959f2ccc… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-03-15 (Wed, 15 Mar 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/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/user/user-custom-builds.js Log Message: ----------- Add name validator Commit: d2692dc77bdd4db48cbcc77d9cd776e0cd7e8bab https://github.com/galaxyproject/galaxy/commit/d2692dc77bdd4db48cbcc77d9cd7… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-03-15 (Wed, 15 Mar 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-table.js M client/galaxy/scripts/mvc/user/user-custom-builds.js M lib/galaxy/webapps/galaxy/api/users.py M static/maps/mvc/ui/ui-table.js.map M static/maps/mvc/user/user-custom-builds.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/ui/ui-table.js M static/scripts/mvc/user/user-custom-builds.js Log Message: ----------- Sort custom builds in table Commit: b1b87358e7fdb991cf1ef1b90aabfc8d182304b1 https://github.com/galaxyproject/galaxy/commit/b1b87358e7fdb991cf1ef1b90aab… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-03-15 (Wed, 15 Mar 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/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/user/user-custom-builds.js Log Message: ----------- Reset form after submission, highlight missing/failed chrom count Commit: 200b3837c7956e4ee5b19b01eb67e62375e58e97 https://github.com/galaxyproject/galaxy/commit/200b3837c7956e4ee5b19b01eb67… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-03-15 (Wed, 15 Mar 2017) Changed paths: M client/galaxy/scripts/mvc/user/user-preferences.js M static/maps/mvc/user/user-preferences.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/user/user-preferences.js Log Message: ----------- Remove debug statements for user preferences Commit: 15273ad1489c9cdc216126ff36c2ec2d912e4165 https://github.com/galaxyproject/galaxy/commit/15273ad1489c9cdc216126ff36c2… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-03-16 (Thu, 16 Mar 2017) Changed paths: M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/ui/ui-misc.js M client/galaxy/scripts/mvc/user/user-custom-builds.js M lib/galaxy/webapps/galaxy/api/users.py M static/maps/mvc/form/form-parameters.js.map M static/maps/mvc/ui/ui-misc.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/form/form-parameters.js M static/scripts/mvc/ui/ui-misc.js M static/scripts/mvc/user/user-custom-builds.js Log Message: ----------- Add uploader element Commit: bb5b8cf525562e1a930ad03a4071dffd341865e5 https://github.com/galaxyproject/galaxy/commit/bb5b8cf525562e1a930ad03a4071… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-03-16 (Thu, 16 Mar 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-misc.js M static/maps/mvc/ui/ui-misc.js.map M static/scripts/mvc/ui/ui-misc.js Log Message: ----------- Declare submit caller for upload element Commit: 474b0c1d2ceade095fd995d19ba30334be612458 https://github.com/galaxyproject/galaxy/commit/474b0c1d2ceade095fd995d19ba3… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-03-16 (Thu, 16 Mar 2017) Changed paths: M client/galaxy/scripts/mvc/user/user-custom-builds.js M lib/galaxy/webapps/galaxy/api/users.py M lib/galaxy/webapps/galaxy/controllers/user.py M static/maps/mvc/user/user-custom-builds.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/user/user-custom-builds.js Log Message: ----------- Sort models in table, fix message parameter, properly return models with count attribute Commit: 39c9f79970579556eac63c12d40174ee95e2c337 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static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/user/user-custom-builds.js Log Message: ----------- Fix success message Commit: f5844252ae9feee554342e69562c3ae65985bb82 https://github.com/galaxyproject/galaxy/commit/f5844252ae9feee554342e69562c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-03-17 (Fri, 17 Mar 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/users.py Log Message: ----------- Attempt to determine line count upon file upload to allow early validation Commit: aea96855bb5da18623c51ab6e6885f5c9acaf19e https://github.com/galaxyproject/galaxy/commit/aea96855bb5da18623c51ab6e688… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-03-17 (Fri, 17 Mar 2017) Changed paths: M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/ui/ui-misc.js M client/galaxy/scripts/mvc/user/user-custom-builds.js M static/maps/mvc/form/form-parameters.js.map M static/maps/mvc/ui/ui-misc.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/form/form-parameters.js M static/scripts/mvc/ui/ui-misc.js M static/scripts/mvc/user/user-custom-builds.js Log Message: ----------- Merge branch 'add_uploader' into remove_custom_builds_mako Commit: e78e1607db1eacc175c8f731cdb879fe3e293476 https://github.com/galaxyproject/galaxy/commit/e78e1607db1eacc175c8f731cdb8… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-03-17 (Fri, 17 Mar 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-misc.js M static/maps/mvc/ui/ui-misc.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/ui/ui-misc.js Log Message: ----------- Upload and preview file using HTML5, client-side file reader Commit: b557e31a4c29fcab875837c1ccc3c9cd9f37f6ba 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static/maps/mvc/user/user-custom-builds.js.map M static/scripts/mvc/user/user-custom-builds.js Log Message: ----------- Set default to fasta selection Commit: 95b6f033a447d25b5826a4e368caf2fc15201d10 https://github.com/galaxyproject/galaxy/commit/95b6f033a447d25b5826a4e368ca… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-03-17 (Fri, 17 Mar 2017) Changed paths: M client/galaxy/scripts/mvc/user/user-custom-builds.js M lib/galaxy/webapps/galaxy/api/users.py M static/maps/mvc/user/user-custom-builds.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/user/user-custom-builds.js Log Message: ----------- Display installed builds as searchable list Commit: 6b2a4ebd3653f25ef01e109ac7bdad601d6959a5 https://github.com/galaxyproject/galaxy/commit/6b2a4ebd3653f25ef01e109ac7bd… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-03-17 (Fri, 17 Mar 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/users.py Log Message: ----------- Len-file hdas not needed in metadata Commit: 39c1b1b24998d9ce77d660ad5dee525f71156720 https://github.com/galaxyproject/galaxy/commit/39c1b1b24998d9ce77d660ad5dee… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-03-17 (Fri, 17 Mar 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/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/user/user-custom-builds.js Log Message: ----------- Render len type help section Commit: 76bcf23b434984cd45002192a72bb90d3c06ade5 https://github.com/galaxyproject/galaxy/commit/76bcf23b434984cd45002192a72b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-03-17 (Fri, 17 Mar 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/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/user/user-custom-builds.js Log Message: ----------- Add help section content Commit: ad73c7d39d93683aba1b065b6660c4b5a98554bf https://github.com/galaxyproject/galaxy/commit/ad73c7d39d93683aba1b065b6660… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-03-17 (Fri, 17 Mar 2017) Changed paths: R templates/user/dbkeys.mako Log Message: ----------- Remove mako Commit: 5ee585c681326072c489f26d2d2b084a6995a349 https://github.com/galaxyproject/galaxy/commit/5ee585c681326072c489f26d2d2b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-03-17 (Fri, 17 Mar 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/user.py Log Message: ----------- Remove controller endpoint Commit: ff5166c2930f54a05601ab9a934319689df9c3f8 https://github.com/galaxyproject/galaxy/commit/ff5166c2930f54a05601ab9a9343… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-03-17 (Fri, 17 Mar 2017) Changed paths: M client/galaxy/scripts/layout/menu.js M lib/galaxy/webapps/galaxy/controllers/user.py M static/maps/layout/menu.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/menu.js Log Message: ----------- Redirect masthead link to new custom builds ui Commit: a89a4f726ba60110810c99b372a53b48e9152c4e https://github.com/galaxyproject/galaxy/commit/a89a4f726ba60110810c99b372a5… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-03-17 (Fri, 17 Mar 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/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/user/user-custom-builds.js Log Message: ----------- Revise style Commit: 72c96bd5c6c6c3c1dea3a662dd2fa2d802822401 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static/scripts/mvc/collection/base-creator.js M static/scripts/mvc/collection/list-collection-creator.js M static/scripts/mvc/collection/list-of-pairs-collection-creator.js M static/scripts/mvc/library/library-foldertoolbar-view.js M test/api/test_libraries.py M test/docker/base/run_test_wrapper.sh Log Message: ----------- Merge branch 'dev' into remove_custom_builds_mako Commit: 2872a31881f2f404b2962464ffb734065e96d1b3 https://github.com/galaxyproject/galaxy/commit/2872a31881f2f404b2962464ffb7… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-03-21 (Tue, 21 Mar 2017) Changed paths: M client/galaxy/scripts/mvc/user/user-custom-builds.js M client/galaxy/style/less/ui.less M static/maps/mvc/user/user-custom-builds.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/user/user-custom-builds.js M static/style/blue/base.css Log Message: ----------- Move styles out of code 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afbb3b5a1e26a0a3e9698cec71ed5d733189d451 https://github.com/galaxyproject/galaxy/commit/afbb3b5a1e26a0a3e9698cec71ed… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-03-22 (Wed, 22 Mar 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/users.py Log Message: ----------- Add additional error message for fasta conversions Commit: 368b276ded599e7f0c206b852cdd901199b16b7e https://github.com/galaxyproject/galaxy/commit/368b276ded599e7f0c206b852cdd… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-03-22 (Wed, 22 Mar 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/users.py Log Message: ----------- Parse correct dataset id Commit: 50283125ea37f313afdfd0d69b92a0380fc77e17 https://github.com/galaxyproject/galaxy/commit/50283125ea37f313afdfd0d69b92… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-03-22 (Wed, 22 Mar 2017) Changed paths: M client/galaxy/scripts/mvc/collection/list-collection-creator.js M 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templates/admin/tool_shed_repository/select_tool_panel_section.mako M test/shed_functional/functional/test_1150_datatype_converters.py Log Message: ----------- Merge branch 'dev' into remove_custom_builds_mako Commit: 76bd515879d4353bff066d0b2526d68d86cdff56 https://github.com/galaxyproject/galaxy/commit/76bd515879d4353bff066d0b2526… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-03-22 (Wed, 22 Mar 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/users.py M lib/galaxy/webapps/galaxy/controllers/user.py Log Message: ----------- Fix lint Commit: b0325cef02f995a589dc14425d1ae73d7ef4cfee https://github.com/galaxyproject/galaxy/commit/b0325cef02f995a589dc14425d1a… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-03-22 (Wed, 22 Mar 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/users.py Log Message: ----------- Post determine fasta results Commit: 3b7d44e6f7b773218fad0820464efa4610130938 https://github.com/galaxyproject/galaxy/commit/3b7d44e6f7b773218fad0820464e… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-03-23 (Thu, 23 Mar 2017) Changed paths: M client/galaxy/style/less/ui.less M static/style/blue/base.css Log Message: ----------- Fix message margin in left column Commit: 4a0f00fc1e3f383450968a9732edb479378f82ac https://github.com/galaxyproject/galaxy/commit/4a0f00fc1e3f383450968a9732ed… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-03-23 (Thu, 23 Mar 2017) Changed paths: M client/galaxy/scripts/mvc/user/user-custom-builds.js M lib/galaxy/webapps/galaxy/api/users.py M static/maps/mvc/user/user-custom-builds.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/user/user-custom-builds.js Log Message: ----------- Trigger jobs when custom build has been added, check for linecount file on reload Commit: 95be12787ace869bf01f6c30e4b62ba7a4739c96 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config/plugins/interactive_environments/ethercalc/templates/ethercalc.mako R config/plugins/visualizations/charts/static/repository/build/cytoscape_basic.js R config/plugins/visualizations/charts/static/repository/build/cytoscape_basic.js.map A config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js A config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js.map M config/plugins/visualizations/charts/static/repository/build/registry.js M config/plugins/visualizations/charts/static/repository/build/registry.js.map M config/plugins/visualizations/charts/static/repository/build/registry.tmp.js M config/plugins/visualizations/charts/static/repository/registry.json A config/plugins/visualizations/charts/static/repository/utilities/sifjson.js M config/plugins/visualizations/charts/static/repository/utilities/utils.js R config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/basic/config.js R 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lib/galaxy/managers/collections.py M lib/galaxy/managers/collections_util.py M lib/galaxy/managers/datasets.py M lib/galaxy/managers/workflows.py M lib/galaxy/queue_worker.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/cache.py M lib/galaxy/tools/toolbox/watcher.py M static/maps/mvc/collection/base-creator.js.map M static/maps/mvc/collection/list-collection-creator.js.map M static/maps/mvc/collection/list-of-pairs-collection-creator.js.map M static/maps/mvc/collection/pair-collection-creator.js.map M static/maps/mvc/history/history-contents.js.map M static/maps/mvc/history/history-view-edit.js.map M static/maps/mvc/tool/tools.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/collection/base-creator.js M static/scripts/mvc/collection/list-collection-creator.js M static/scripts/mvc/collection/list-of-pairs-collection-creator.js M static/scripts/mvc/collection/pair-collection-creator.js M static/scripts/mvc/history/history-contents.js M static/scripts/mvc/history/history-view-edit.js M static/scripts/mvc/tool/tools.js M static/style/blue/base.css M test/api/test_history_contents.py M test/api/test_jobs.py M test/api/test_tools.py M test/base/api_asserts.py M test/base/driver_util.py M test/base/populators.py M test/functional/tools/create_10.xml A test/functional/tools/create_2.xml M test/functional/tools/samples_tool_conf.xml M test/galaxy_selenium/has_driver.py M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/sizzle.py M test/qunit/test-data/paired-collection-creator.data.js M test/selenium_tests/test_collection_builders.py M test/selenium_tests/test_tool_form.py M test/selenium_tests/test_uploads.py M test/unit/tools/test_toolbox.py M test/unit/tools/test_watcher.py Log Message: ----------- Merge branch 'dev' into 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client/galaxy/scripts/mvc/upload/collection/collection-view.js M client/galaxy/scripts/mvc/upload/upload-view.js M client/galaxy/style/less/upload.less M lib/galaxy/tools/parameters/basic.py M static/maps/mvc/collection/base-creator.js.map M static/maps/mvc/collection/list-collection-creator.js.map M static/maps/mvc/collection/list-of-pairs-collection-creator.js.map M static/maps/mvc/collection/pair-collection-creator.js.map M static/maps/mvc/history/history-view-edit.js.map A static/maps/mvc/upload/collection/collection-row.js.map A static/maps/mvc/upload/collection/collection-view.js.map M static/maps/mvc/upload/upload-view.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 M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/collection/base-creator.js M static/scripts/mvc/collection/list-collection-creator.js M static/scripts/mvc/collection/list-of-pairs-collection-creator.js M static/scripts/mvc/collection/pair-collection-creator.js M static/scripts/mvc/history/history-view-edit.js A static/scripts/mvc/upload/collection/collection-row.js A static/scripts/mvc/upload/collection/collection-view.js M static/scripts/mvc/upload/upload-view.js M static/style/blue/base.css M test/galaxy_selenium/navigates_galaxy.py M test/selenium_tests/test_collection_builders.py M test/selenium_tests/test_uploads.py M test/shed_functional/functional/test_1090_repository_dependency_handling.py Log Message: ----------- Merge branch 'dev' into remove_custom_builds_mako Commit: 405dbd3b7f3022332fb6c660f88e67361fbb5429 https://github.com/galaxyproject/galaxy/commit/405dbd3b7f3022332fb6c660f88e… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-04-04 (Tue, 04 Apr 2017) Changed paths: M client/galaxy/scripts/mvc/user/user-custom-builds.js M lib/galaxy/webapps/galaxy/api/histories.py M lib/galaxy/webapps/galaxy/api/users.py M lib/galaxy/webapps/galaxy/buildapp.py M static/maps/mvc/user/user-custom-builds.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/user/user-custom-builds.js Log Message: ----------- Move custom build metadata endpoint to histories Commit: a16c5320fd647b45dbad197714fc52d2a5254548 https://github.com/galaxyproject/galaxy/commit/a16c5320fd647b45dbad197714fc… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-04-04 (Tue, 04 Apr 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js M lib/galaxy/webapps/galaxy/api/histories.py M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Wait for history panel, workaround until overall ui has been visited Commit: 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M static/maps/mvc/user/user-preferences.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/layout/menu.js M static/scripts/mvc/form/form-parameters.js M static/scripts/mvc/ui/ui-misc.js M static/scripts/mvc/ui/ui-table.js A static/scripts/mvc/user/user-custom-builds.js M static/scripts/mvc/user/user-preferences.js M static/style/blue/base.css R templates/user/dbkeys.mako Log Message: ----------- Merge remote-tracking branch 'guerler/remove_custom_builds_mako' into dev Compare: https://github.com/galaxyproject/galaxy/compare/8bbd423909d7...d607c7e0b134

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