galaxy-commits February 2018

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[galaxyproject/galaxy] c00e77: Fix lack of feedback when slow grids are loading d...
by GitHub 27 Feb '18

27 Feb '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: c00e772159f6a121bc4f7759fa57f48e79c48f32 https://github.com/galaxyproject/galaxy/commit/c00e772159f6a121bc4f7759fa57… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-02-21 (Wed, 21 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/grid/grid-shared.js M client/galaxy/scripts/mvc/grid/grid-view.js M client/galaxy/scripts/mvc/history/history-list.js M client/galaxy/scripts/mvc/list/list-view.js M client/galaxy/scripts/mvc/workflow/workflow.js M client/galaxy/scripts/ui/loading-indicator.js Log Message: ----------- Fix lack of feedback when slow grids are loading data from the server. Fixes #5473 (after numerous other backend optimizations also). Commit: d8585f6a6f87735d072635495bd49047da746624 https://github.com/galaxyproject/galaxy/commit/d8585f6a6f87735d072635495bd4… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-02-27 (Tue, 27 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/grid/grid-shared.js M client/galaxy/scripts/mvc/grid/grid-view.js M client/galaxy/scripts/mvc/history/history-list.js M client/galaxy/scripts/mvc/list/list-view.js M client/galaxy/scripts/mvc/workflow/workflow.js M client/galaxy/scripts/ui/loading-indicator.js Log Message: ----------- Merge pull request #5582 from jmchilton/indicators [18.01] Fix lack of feedback when slow grids are loading data from the server. Compare: https://github.com/galaxyproject/galaxy/compare/c8407786f25c...d8585f6a6f87

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[galaxyproject/usegalaxy-playbook] dd4b14: Main mutable configs
by GitHub 27 Feb '18

27 Feb '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: dd4b1410d020827dde11de761d7c7ad575f4ba1e https://github.com/galaxyproject/usegalaxy-playbook/commit/dd4b1410d020827d… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-02-26 (Mon, 26 Feb 2018) Changed paths: M env/main/files/galaxy/var/integrated_tool_panel.xml M env/main/files/galaxy/var/shed_tool_conf.xml Log Message: ----------- Main mutable configs

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[galaxyproject/usegalaxy-playbook] 9de278: Test mutable configs
by GitHub 27 Feb '18

27 Feb '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 9de278cf3019b47e753bd6e5dfa660c8b67997d7 https://github.com/galaxyproject/usegalaxy-playbook/commit/9de278cf3019b47e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-02-26 (Mon, 26 Feb 2018) Changed paths: M env/test/files/galaxy/var/integrated_tool_panel.xml M env/test/files/galaxy/var/shed_tool_conf.xml Log Message: ----------- Test mutable configs

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[galaxyproject/usegalaxy-playbook] 0088bb: Mutable configs for new tool installs
by GitHub 27 Feb '18

27 Feb '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 0088bb471eedd62aade63ebe54bfd958e67887c4 https://github.com/galaxyproject/usegalaxy-playbook/commit/0088bb471eedd62a… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-02-26 (Mon, 26 Feb 2018) Changed paths: M env/main/files/galaxy/var/integrated_tool_panel.xml M env/main/files/galaxy/var/shed_tool_conf.xml M env/main/files/galaxy/var/shed_tool_data_table_conf.xml M env/test/files/galaxy/var/integrated_tool_panel.xml M env/test/files/galaxy/var/shed_tool_conf.xml M env/test/files/galaxy/var/shed_tool_data_table_conf.xml Log Message: ----------- Mutable configs for new tool installs

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[galaxyproject/usegalaxy-playbook] 95baed: Updated lastz.
by GitHub 27 Feb '18

27 Feb '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 95baede7590b49cc84b4ce2d105b924091e56bc2 https://github.com/galaxyproject/usegalaxy-playbook/commit/95baede7590b49cc… Author: Dave B <dave(a)bx.psu.edu> Date: 2018-02-26 (Mon, 26 Feb 2018) Changed paths: M env/main/files/galaxy/var/integrated_tool_panel.xml M env/main/files/galaxy/var/shed_tool_conf.xml M env/main/files/galaxy/var/shed_tool_data_table_conf.xml Log Message: ----------- Updated lastz.

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[galaxyproject/usegalaxy-playbook] a3feca: update MTS
by GitHub 27 Feb '18

27 Feb '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: a3feca909a532438a65302bb71c927bc44188393 https://github.com/galaxyproject/usegalaxy-playbook/commit/a3feca909a532438… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-02-26 (Mon, 26 Feb 2018) Changed paths: M env/toolshed/group_vars/toolshedservers/vars.yml Log Message: ----------- update MTS

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[galaxyproject/usegalaxy-playbook] c72e72: update tts
by GitHub 27 Feb '18

27 Feb '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: c72e7203b1cbb8419957e56c4bf0f67abbd772f0 https://github.com/galaxyproject/usegalaxy-playbook/commit/c72e7203b1cbb841… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-02-26 (Mon, 26 Feb 2018) Changed paths: M env/testtoolshed/group_vars/toolshedservers/vars.yml Log Message: ----------- update tts Commit: f2054837373e14d18ad4dcf0399ea085bc19c68d https://github.com/galaxyproject/usegalaxy-playbook/commit/f2054837373e14d1… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-02-26 (Mon, 26 Feb 2018) Changed paths: M env/common/templates/nginx/toolshed.j2 Log Message: ----------- Merge branch 'master' of https://github.com/galaxyproject/usegalaxy-playbook Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/c3fd2231c3a6...…

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[galaxyproject/usegalaxy-playbook] c3fd22: Remove packed static route from TTS nginx
by GitHub 27 Feb '18

27 Feb '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: c3fd2231c3a6d4bb14457ab057716a928f2aec55 https://github.com/galaxyproject/usegalaxy-playbook/commit/c3fd2231c3a6d4bb… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-02-26 (Mon, 26 Feb 2018) Changed paths: M env/common/templates/nginx/toolshed.j2 Log Message: ----------- Remove packed static route from TTS nginx

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[galaxyproject/usegalaxy-playbook] b985a8: Updated Hisat2
by GitHub 27 Feb '18

27 Feb '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: b985a826e22147b34abfa805611364a1760daa85 https://github.com/galaxyproject/usegalaxy-playbook/commit/b985a826e22147b3… Author: Dave B <dave(a)bx.psu.edu> Date: 2018-02-26 (Mon, 26 Feb 2018) Changed paths: M env/main/files/galaxy/var/integrated_tool_panel.xml M env/main/files/galaxy/var/shed_tool_conf.xml M env/main/files/galaxy/var/shed_tool_data_table_conf.xml Log Message: ----------- Updated Hisat2

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[galaxyproject/galaxy] d9d8f5: Eliminate precreated datasets concept in upload AP...
by GitHub 27 Feb '18

27 Feb '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d9d8f5d327827758d8d1cbe19b7cee84acc66071 https://github.com/galaxyproject/galaxy/commit/d9d8f5d327827758d8d1cbe19b7c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-02-26 (Mon, 26 Feb 2018) Changed paths: M lib/galaxy/actions/library.py M lib/galaxy/tools/actions/upload.py M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/tools/parameters/grouping.py M tools/data_source/upload.xml Log Message: ----------- Eliminate precreated datasets concept in upload API. Was used by the async controller in the past I think (https://github.com/galaxyproject/galaxy/blob/v13.01/lib/galaxy/webapps/gala…), but doesn't seem to be used now. Commit: 73a0d72e0c98dfdcfdb60e228f757b4ea3967be1 https://github.com/galaxyproject/galaxy/commit/73a0d72e0c98dfdcfdb60e228f75… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2018-02-26 (Mon, 26 Feb 2018) Changed paths: M lib/galaxy/actions/library.py M lib/galaxy/tools/actions/upload.py M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/tools/parameters/grouping.py M tools/data_source/upload.xml Log Message: ----------- Merge pull request #5604 from jmchilton/persist_uploads_remove Eliminate precreated datasets concept in upload API. Compare: https://github.com/galaxyproject/galaxy/compare/2af4091e42b6...73a0d72e0c98

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galaxy-commits February 2018