March 2018 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] ee924e: fix the inconsistency between two fixes
by GitHub 13 Mar '18

13 Mar '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ee924ec173edf4bd7a02b9c1d9b366ff607c1176 https://github.com/galaxyproject/galaxy/commit/ee924ec173edf4bd7a02b9c1d9b3… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-03-13 (Tue, 13 Mar 2018) Changed paths: M lib/galaxy/managers/libraries.py Log Message: ----------- fix the inconsistency between two fixes Commit: 4558ad64f0bcd54b99bac0e3f3db12c192b8a3aa https://github.com/galaxyproject/galaxy/commit/4558ad64f0bcd54b99bac0e3f3db… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-13 (Tue, 13 Mar 2018) Changed paths: M lib/galaxy/managers/libraries.py Log Message: ----------- Merge pull request #5683 from martenson/fix-2-fixes fix the inconsistency between two library fixes Compare: https://github.com/galaxyproject/galaxy/compare/76b305b72a67...4558ad64f0bc

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[galaxyproject/galaxy]
by GitHub 13 Mar '18

13 Mar '18

Branch: refs/tags/v18.01 Home: https://github.com/galaxyproject/galaxy

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[galaxyproject/galaxy] cf4936: Minor cleanup in galaxy.tools.actions
by GitHub 13 Mar '18

13 Mar '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: cf4936b3d480011a4638a393776dd5ec94f11ae4 https://github.com/galaxyproject/galaxy/commit/cf4936b3d480011a4638a393776d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-12 (Mon, 12 Mar 2018) Changed paths: M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Minor cleanup in galaxy.tools.actions Commit: 513b6a5d65676a2f03d6c4580d16e053d8fe6aaf https://github.com/galaxyproject/galaxy/commit/513b6a5d65676a2f03d6c4580d16… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-12 (Mon, 12 Mar 2018) Changed paths: M lib/galaxy/workflow/run_request.py Log Message: ----------- Fix a few mutable default params in workflow/run_request. Commit: 332d79eb72c4bae90c911707d4db9285556c59b1 https://github.com/galaxyproject/galaxy/commit/332d79eb72c4bae90c911707d4db… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-12 (Mon, 12 Mar 2018) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Fix 'uknown' typo in model exceptions Commit: 04404f915c70b90a9d4a56dbeb030748163dce16 https://github.com/galaxyproject/galaxy/commit/04404f915c70b90a9d4a56dbeb03… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-12 (Mon, 12 Mar 2018) Changed paths: M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Support re-execution of immediate PJAs when requing jobs Commit: b685b53d13b9fa91c4abcb631fc3cd5c68d5d9c4 https://github.com/galaxyproject/galaxy/commit/b685b53d13b9fa91c4abcb631fc3… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-12 (Mon, 12 Mar 2018) Changed paths: M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Ship context along with PJA execution when remapping workflow immediate actions Commit: 6a7fb23f11e26b3761cb71128a4c5e0ac605d818 https://github.com/galaxyproject/galaxy/commit/6a7fb23f11e26b3761cb71128a4c… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-13 (Tue, 13 Mar 2018) Changed paths: M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Instead of denoting unused var from items(), just use values() Commit: f1dd060d73ccb369aafb1a56e902e4d4faf6dd64 https://github.com/galaxyproject/galaxy/commit/f1dd060d73ccb369aafb1a56e902… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-03-13 (Tue, 13 Mar 2018) Changed paths: M test/api/test_workflows.py Log Message: ----------- Test rename PJA when resuming a failed job Commit: 8dfc1523d31e56a3e632e0d490d08c15722764d5 https://github.com/galaxyproject/galaxy/commit/8dfc1523d31e56a3e632e0d490d0… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-13 (Tue, 13 Mar 2018) Changed paths: M test/api/test_workflows.py Log Message: ----------- Merge pull request #26 from mvdbeek/workflow-resume-pjas Test rename PJA when resuming a failed job Commit: 040bf5ba77562cc20b822b2068860c2bf6c0399e https://github.com/galaxyproject/galaxy/commit/040bf5ba77562cc20b822b206886… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-03-13 (Tue, 13 Mar 2018) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/workflow/run_request.py M test/api/test_workflows.py Log Message: ----------- Merge pull request #5678 from dannon/workflow-resume-pjas [18.01] Support re-execution of immediate PJAs when re-queing jobs Commit: 31cb24e4229767425a72d6981bcb359b15792254 https://github.com/galaxyproject/galaxy/commit/31cb24e4229767425a72d6981bcb… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-03-13 (Tue, 13 Mar 2018) Changed paths: M static/maps/mvc/form/form-parameters.js.map M static/maps/mvc/grid/grid-shared.js.map M static/maps/mvc/grid/grid-template.js.map M static/maps/mvc/grid/grid-view.js.map M static/maps/mvc/history/hdca-li-edit.js.map M static/maps/mvc/history/history-list.js.map M static/maps/mvc/history/history-view-edit.js.map M static/maps/mvc/list/list-view.js.map M static/maps/mvc/tool/tool-genomespace.js.map M static/maps/mvc/ui/ui-select-genomespace.js.map M static/maps/mvc/workflow/workflow.js.map M static/maps/onload.js.map M static/maps/ui/loading-indicator.js.map M static/maps/utils/config.js.map M static/maps/viz/trackster.js.map M static/maps/viz/trackster/filters.js.map M static/maps/viz/trackster/painters.js.map M static/maps/viz/trackster/slotting.js.map M static/maps/viz/trackster/tracks.js.map M static/maps/viz/visualization.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/extended.bundled.js M static/scripts/bundled/extended.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/form/form-parameters.js M static/scripts/mvc/grid/grid-shared.js M static/scripts/mvc/grid/grid-template.js M static/scripts/mvc/grid/grid-view.js M static/scripts/mvc/history/hdca-li-edit.js M static/scripts/mvc/history/history-list.js M static/scripts/mvc/history/history-view-edit.js M static/scripts/mvc/list/list-view.js M static/scripts/mvc/tool/tool-genomespace.js M static/scripts/mvc/ui/ui-select-genomespace.js M static/scripts/mvc/workflow/workflow.js M static/scripts/onload.js M static/scripts/ui/loading-indicator.js M static/scripts/utils/config.js M static/scripts/viz/trackster.js M static/scripts/viz/trackster/filters.js M static/scripts/viz/trackster/painters.js M static/scripts/viz/trackster/slotting.js M static/scripts/viz/trackster/tracks.js M static/scripts/viz/visualization.js M static/style/blue/base.css Log Message: ----------- add built client with maps for 18.01 tagging Commit: 0182d8d0bec3cf78401434e5c07b012eabcda7e3 https://github.com/galaxyproject/galaxy/commit/0182d8d0bec3cf78401434e5c07b… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-03-13 (Tue, 13 Mar 2018) Changed paths: M lib/galaxy/version.py Log Message: ----------- Update version to 18.01 Commit: 93f778498ac7ec1fb50461147b7173c0301ba91a https://github.com/galaxyproject/galaxy/commit/93f778498ac7ec1fb50461147b71… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-03-13 (Tue, 13 Mar 2018) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/workflow/run_request.py M test/api/test_workflows.py Log Message: ----------- Merge branch 'release_18.01' into dev Commit: 76b305b72a676dbac7b041af225f1884040c4788 https://github.com/galaxyproject/galaxy/commit/76b305b72a676dbac7b041af225f… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-03-13 (Tue, 13 Mar 2018) Changed paths: M lib/galaxy/managers/libraries.py Log Message: ----------- Merge branch 'dev' of github.com:galaxyproject/galaxy into dev Compare: https://github.com/galaxyproject/galaxy/compare/7ad5dbab4f0d...76b305b72a67

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[galaxyproject/galaxy] 0182d8: Update version to 18.01
by GitHub 13 Mar '18

13 Mar '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: 0182d8d0bec3cf78401434e5c07b012eabcda7e3 https://github.com/galaxyproject/galaxy/commit/0182d8d0bec3cf78401434e5c07b… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-03-13 (Tue, 13 Mar 2018) Changed paths: M lib/galaxy/version.py Log Message: ----------- Update version to 18.01

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[galaxyproject/galaxy] 252118: use a set instead of list
by GitHub 13 Mar '18

13 Mar '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 2521181f5a6d65cfbcee0ed6e876b17cf1e82c9c https://github.com/galaxyproject/galaxy/commit/2521181f5a6d65cfbcee0ed6e876… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-03-13 (Tue, 13 Mar 2018) Changed paths: M lib/galaxy/managers/libraries.py Log Message: ----------- use a set instead of list could be faster per mvdbeek Commit: f8088792e46f1652b4810161357f251340732d97 https://github.com/galaxyproject/galaxy/commit/f8088792e46f1652b4810161357f… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2018-03-13 (Tue, 13 Mar 2018) Changed paths: M lib/galaxy/managers/libraries.py Log Message: ----------- Simplify empty set creation Commit: 7ad5dbab4f0df50937feb5c0d1859d8ec86c0735 https://github.com/galaxyproject/galaxy/commit/7ad5dbab4f0df50937feb5c0d185… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-13 (Tue, 13 Mar 2018) Changed paths: M lib/galaxy/managers/libraries.py Log Message: ----------- Merge pull request #5681 from martenson/set-from-list library manager - use a set instead of list Compare: https://github.com/galaxyproject/galaxy/compare/ccc5cfc95846...7ad5dbab4f0d

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[galaxyproject/galaxy] 31cb24: add built client with maps for 18.01 tagging
by GitHub 13 Mar '18

13 Mar '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: 31cb24e4229767425a72d6981bcb359b15792254 https://github.com/galaxyproject/galaxy/commit/31cb24e4229767425a72d6981bcb… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-03-13 (Tue, 13 Mar 2018) Changed paths: M static/maps/mvc/form/form-parameters.js.map M static/maps/mvc/grid/grid-shared.js.map M static/maps/mvc/grid/grid-template.js.map M static/maps/mvc/grid/grid-view.js.map M static/maps/mvc/history/hdca-li-edit.js.map M static/maps/mvc/history/history-list.js.map M static/maps/mvc/history/history-view-edit.js.map M static/maps/mvc/list/list-view.js.map M static/maps/mvc/tool/tool-genomespace.js.map M static/maps/mvc/ui/ui-select-genomespace.js.map M static/maps/mvc/workflow/workflow.js.map M static/maps/onload.js.map M static/maps/ui/loading-indicator.js.map M static/maps/utils/config.js.map M static/maps/viz/trackster.js.map M static/maps/viz/trackster/filters.js.map M static/maps/viz/trackster/painters.js.map M static/maps/viz/trackster/slotting.js.map M static/maps/viz/trackster/tracks.js.map M static/maps/viz/visualization.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/extended.bundled.js M static/scripts/bundled/extended.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/form/form-parameters.js M static/scripts/mvc/grid/grid-shared.js M static/scripts/mvc/grid/grid-template.js M static/scripts/mvc/grid/grid-view.js M static/scripts/mvc/history/hdca-li-edit.js M static/scripts/mvc/history/history-list.js M static/scripts/mvc/history/history-view-edit.js M static/scripts/mvc/list/list-view.js M static/scripts/mvc/tool/tool-genomespace.js M static/scripts/mvc/ui/ui-select-genomespace.js M static/scripts/mvc/workflow/workflow.js M static/scripts/onload.js M static/scripts/ui/loading-indicator.js M static/scripts/utils/config.js M static/scripts/viz/trackster.js M static/scripts/viz/trackster/filters.js M static/scripts/viz/trackster/painters.js M static/scripts/viz/trackster/slotting.js M static/scripts/viz/trackster/tracks.js M static/scripts/viz/visualization.js M static/style/blue/base.css Log Message: ----------- add built client with maps for 18.01 tagging

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[galaxyproject/galaxy] cf4936: Minor cleanup in galaxy.tools.actions
by GitHub 13 Mar '18

13 Mar '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: cf4936b3d480011a4638a393776dd5ec94f11ae4 https://github.com/galaxyproject/galaxy/commit/cf4936b3d480011a4638a393776d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-12 (Mon, 12 Mar 2018) Changed paths: M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Minor cleanup in galaxy.tools.actions Commit: 513b6a5d65676a2f03d6c4580d16e053d8fe6aaf https://github.com/galaxyproject/galaxy/commit/513b6a5d65676a2f03d6c4580d16… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-12 (Mon, 12 Mar 2018) Changed paths: M lib/galaxy/workflow/run_request.py Log Message: ----------- Fix a few mutable default params in workflow/run_request. Commit: 332d79eb72c4bae90c911707d4db9285556c59b1 https://github.com/galaxyproject/galaxy/commit/332d79eb72c4bae90c911707d4db… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-12 (Mon, 12 Mar 2018) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Fix 'uknown' typo in model exceptions Commit: 04404f915c70b90a9d4a56dbeb030748163dce16 https://github.com/galaxyproject/galaxy/commit/04404f915c70b90a9d4a56dbeb03… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-12 (Mon, 12 Mar 2018) Changed paths: M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Support re-execution of immediate PJAs when requing jobs Commit: b685b53d13b9fa91c4abcb631fc3cd5c68d5d9c4 https://github.com/galaxyproject/galaxy/commit/b685b53d13b9fa91c4abcb631fc3… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-12 (Mon, 12 Mar 2018) Changed paths: M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Ship context along with PJA execution when remapping workflow immediate actions Commit: 6a7fb23f11e26b3761cb71128a4c5e0ac605d818 https://github.com/galaxyproject/galaxy/commit/6a7fb23f11e26b3761cb71128a4c… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-13 (Tue, 13 Mar 2018) Changed paths: M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Instead of denoting unused var from items(), just use values() Commit: f1dd060d73ccb369aafb1a56e902e4d4faf6dd64 https://github.com/galaxyproject/galaxy/commit/f1dd060d73ccb369aafb1a56e902… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-03-13 (Tue, 13 Mar 2018) Changed paths: M test/api/test_workflows.py Log Message: ----------- Test rename PJA when resuming a failed job Commit: 8dfc1523d31e56a3e632e0d490d08c15722764d5 https://github.com/galaxyproject/galaxy/commit/8dfc1523d31e56a3e632e0d490d0… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-13 (Tue, 13 Mar 2018) Changed paths: M test/api/test_workflows.py Log Message: ----------- Merge pull request #26 from mvdbeek/workflow-resume-pjas Test rename PJA when resuming a failed job Commit: 040bf5ba77562cc20b822b2068860c2bf6c0399e https://github.com/galaxyproject/galaxy/commit/040bf5ba77562cc20b822b206886… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-03-13 (Tue, 13 Mar 2018) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/workflow/run_request.py M test/api/test_workflows.py Log Message: ----------- Merge pull request #5678 from dannon/workflow-resume-pjas [18.01] Support re-execution of immediate PJAs when re-queing jobs Compare: https://github.com/galaxyproject/galaxy/compare/5cf3d44a6ad5...040bf5ba7756

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[galaxyproject/galaxy] cb5e81: replace incorrect list add syntax
by GitHub 13 Mar '18

13 Mar '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: cb5e81b6a1209ef89dd7edc9bdd870c8953a96a5 https://github.com/galaxyproject/galaxy/commit/cb5e81b6a1209ef89dd7edc9bdd8… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-03-12 (Mon, 12 Mar 2018) Changed paths: M lib/galaxy/managers/libraries.py Log Message: ----------- replace incorrect list add syntax Commit: 6b9afb6b360108b194c03ca262a20013b444ece9 https://github.com/galaxyproject/galaxy/commit/6b9afb6b360108b194c03ca262a2… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-03-12 (Mon, 12 Mar 2018) Changed paths: M lib/galaxy/managers/libraries.py Log Message: ----------- rmeove overly zealous syntax fix thanks to dannon Commit: 5cf3d44a6ad5f53c3f263ac2a28484686e44ea6a https://github.com/galaxyproject/galaxy/commit/5cf3d44a6ad5f53c3f263ac2a284… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-13 (Tue, 13 Mar 2018) Changed paths: M lib/galaxy/managers/libraries.py Log Message: ----------- Merge pull request #5676 from martenson/fix-library-add [18.01] replace incorrect list add syntax Commit: ccc5cfc95846e75fe6b4d48b0e4e1a5886ae9d53 https://github.com/galaxyproject/galaxy/commit/ccc5cfc95846e75fe6b4d48b0e4e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-13 (Tue, 13 Mar 2018) Changed paths: M lib/galaxy/managers/libraries.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_18.01' into dev Compare: https://github.com/galaxyproject/galaxy/compare/1cc5f3fe1a06...ccc5cfc95846

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[galaxyproject/galaxy] cb5e81: replace incorrect list add syntax
by GitHub 13 Mar '18

13 Mar '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: cb5e81b6a1209ef89dd7edc9bdd870c8953a96a5 https://github.com/galaxyproject/galaxy/commit/cb5e81b6a1209ef89dd7edc9bdd8… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-03-12 (Mon, 12 Mar 2018) Changed paths: M lib/galaxy/managers/libraries.py Log Message: ----------- replace incorrect list add syntax Commit: 6b9afb6b360108b194c03ca262a20013b444ece9 https://github.com/galaxyproject/galaxy/commit/6b9afb6b360108b194c03ca262a2… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-03-12 (Mon, 12 Mar 2018) Changed paths: M lib/galaxy/managers/libraries.py Log Message: ----------- rmeove overly zealous syntax fix thanks to dannon Commit: 5cf3d44a6ad5f53c3f263ac2a28484686e44ea6a https://github.com/galaxyproject/galaxy/commit/5cf3d44a6ad5f53c3f263ac2a284… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-13 (Tue, 13 Mar 2018) Changed paths: M lib/galaxy/managers/libraries.py Log Message: ----------- Merge pull request #5676 from martenson/fix-library-add [18.01] replace incorrect list add syntax Compare: https://github.com/galaxyproject/galaxy/compare/1a5f6a349909...5cf3d44a6ad5

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[galaxyproject/galaxy] 1dfaa4: Rebuild client only if there are changes
by GitHub 13 Mar '18

13 Mar '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 1dfaa476c0198f9be9a20c239fcd4c63e9b3966a https://github.com/galaxyproject/galaxy/commit/1dfaa476c0198f9be9a20c239fcd… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-03-13 (Tue, 13 Mar 2018) Changed paths: M scripts/common_startup.sh Log Message: ----------- Rebuild client only if there are changes in the client/ directory since the last build. Commit: 1cc5f3fe1a0635a68135d5591e18b33b0950504e https://github.com/galaxyproject/galaxy/commit/1cc5f3fe1a0635a68135d5591e18… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-13 (Tue, 13 Mar 2018) Changed paths: M scripts/common_startup.sh Log Message: ----------- Merge pull request #5679 from nsoranzo/git_diff_client Rebuild client only if there are changes Compare: https://github.com/galaxyproject/galaxy/compare/4fc638070845...1cc5f3fe1a06

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