- galaxy-commits - lists.galaxyproject.org

[galaxyproject/usegalaxy-playbook] cdec49: Fix more missed section IDs
by Nate Coraor 08 Feb '19

08 Feb '19

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: cdec49e30402d91c06c3bdb3991db2e7de22527e https://github.com/galaxyproject/usegalaxy-playbook/commit/cdec49e30402d91c… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2019-02-08 (Fri, 08 Feb 2019) Changed paths: M env/main/files/galaxy/var/migrated_tools_conf.xml M env/main/files/galaxy/var/shed_tool_conf.xml Log Message: ----------- Fix more missed section IDs

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[galaxyproject/usegalaxy-playbook] cf14ca: Rearrange Main tool panel
by Nate Coraor 08 Feb '19

08 Feb '19

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: cf14ca73a0b601da6948c20cc244ac3ab04b7e3f https://github.com/galaxyproject/usegalaxy-playbook/commit/cf14ca73a0b601da… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2019-02-08 (Fri, 08 Feb 2019) Changed paths: M env/main/files/galaxy/config/tool_conf.xml M env/main/files/galaxy/var/integrated_tool_panel.xml M env/main/files/galaxy/var/migrated_tools_conf.xml M env/main/files/galaxy/var/shed_tool_conf.xml Log Message: ----------- Rearrange Main tool panel

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[galaxyproject/usegalaxy-playbook] 5ef886: Add Jeremy to reserved
by Nate Coraor 08 Feb '19

08 Feb '19

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 5ef88653b16b7673e764d3aafa124c40cab457a0 https://github.com/galaxyproject/usegalaxy-playbook/commit/5ef88653b16b7673… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2019-02-08 (Fri, 08 Feb 2019) Changed paths: M env/common/files/galaxy/dynamic_rules/multi_dynamic_walltime.py M env/common/files/galaxy/dynamic_rules/reserved.py Log Message: ----------- Add Jeremy to reserved

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[galaxyproject/galaxy] a5fa1b: remove underline from history datasets
by Dannon 08 Feb '19

08 Feb '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a5fa1b829a599bf33a5dd188d6417751f854d314 https://github.com/galaxyproject/galaxy/commit/a5fa1b829a599bf33a5dd188d641… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2019-01-17 (Thu, 17 Jan 2019) Changed paths: M client/galaxy/style/scss/list-item.scss Log Message: ----------- remove underline from history datasets Commit: d0d64bf1d9491d74b73ca656ce9f5e1ed25a414e https://github.com/galaxyproject/galaxy/commit/d0d64bf1d9491d74b73ca656ce9f… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2019-02-06 (Wed, 06 Feb 2019) Changed paths: M client/galaxy/style/scss/list-item.scss Log Message: ----------- add underline on hover to history items Commit: b6a97619b457fb841a1910ef41d3f7db4b36e2c0 https://github.com/galaxyproject/galaxy/commit/b6a97619b457fb841a1910ef41d3… Author: Dannon <dannon.baker(a)gmail.com> Date: 2019-02-08 (Fri, 08 Feb 2019) Changed paths: M client/galaxy/style/scss/list-item.scss Log Message: ----------- Merge pull request #7235 from martenson/remove-underline remove underline from history datasets Compare: https://github.com/galaxyproject/galaxy/compare/09bca89259ca...b6a97619b457

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[galaxyproject/galaxy] 97d20b: Remove overlapping tooltip from dropdown button in...
by Martin Cech 08 Feb '19

08 Feb '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 97d20b4db7872394c9c103441d27fed8709b2574 https://github.com/galaxyproject/galaxy/commit/97d20b4db7872394c9c103441d27… Author: guerler <aysam.guerler(a)gmail.com> Date: 2019-02-07 (Thu, 07 Feb 2019) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- Remove overlapping tooltip from dropdown button in library toolbar Commit: 09bca89259ca2b31af030b416dfbc2a560dda0ff https://github.com/galaxyproject/galaxy/commit/09bca89259ca2b31af030b416dfb… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2019-02-08 (Fri, 08 Feb 2019) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- Merge pull request #7321 from guerler/fix_tooltip_library Remove overlapping tooltip from dropdown button in library toolbar Compare: https://github.com/galaxyproject/galaxy/compare/edbab28e01b8...09bca89259ca

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[galaxyproject/galaxy] 1d19fd: Add note about HTTP Range also to Apache docs
by Dannon 08 Feb '19

08 Feb '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 1d19fd535ab39a89f7a957e28116c8f83fdcc241 https://github.com/galaxyproject/galaxy/commit/1d19fd535ab39a89f7a957e28116… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2019-02-08 (Fri, 08 Feb 2019) Changed paths: M doc/source/admin/apache.md M doc/source/admin/nginx.md Log Message: ----------- Add note about HTTP Range also to Apache docs Commit: edbab28e01b82055dfe763c9c78d2dc25c1c86f8 https://github.com/galaxyproject/galaxy/commit/edbab28e01b82055dfe763c9c78d… Author: Dannon <dannon.baker(a)gmail.com> Date: 2019-02-07 (Thu, 07 Feb 2019) Changed paths: M doc/source/admin/apache.md M doc/source/admin/nginx.md Log Message: ----------- Merge pull request #7334 from nsoranzo/followup_on_7323 Add note about HTTP Range also to Apache docs Compare: https://github.com/galaxyproject/galaxy/compare/a1f188b79545...edbab28e01b8

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[galaxyproject/galaxy] 0a7583: More contrast
by Nate Coraor 08 Feb '19

08 Feb '19

Branch: refs/heads/release_19.01 Home: https://github.com/galaxyproject/galaxy Commit: 0a7583b6de024d02b7063fa3f59c7febe63df5f5 https://github.com/galaxyproject/galaxy/commit/0a7583b6de024d02b7063fa3f59c… Author: Helena Rasche <hxr(a)hx42.org> Date: 2019-02-06 (Wed, 06 Feb 2019) Changed paths: M client/galaxy/style/scss/base.scss M client/galaxy/style/scss/theme/blue.scss Log Message: ----------- More contrast Commit: 87c82595771438b0e8244b32885430e4fe1bab6e https://github.com/galaxyproject/galaxy/commit/87c82595771438b0e8244b328854… Author: Helena Rasche <hxr(a)hx42.org> Date: 2019-02-06 (Wed, 06 Feb 2019) Changed paths: M client/galaxy/style/scss/base.scss Log Message: ----------- Add box-shadow Commit: 12fde52494541d73da42a41d026c8a0217d7533c https://github.com/galaxyproject/galaxy/commit/12fde52494541d73da42a41d026c… Author: Helena Rasche <hxr(a)hx42.org> Date: 2019-02-06 (Wed, 06 Feb 2019) Changed paths: M client/galaxy/style/scss/theme/blue.scss Log Message: ----------- remove inaccurate comment Commit: 23d4af5dafbb768ba61c6cf8849cd17087f31520 https://github.com/galaxyproject/galaxy/commit/23d4af5dafbb768ba61c6cf8849c… Author: Helena Rasche <hxr(a)hx42.org> Date: 2019-02-06 (Wed, 06 Feb 2019) Changed paths: M client/galaxy/style/scss/base.scss Log Message: ----------- Revert "Add box-shadow" This reverts commit 87c82595771438b0e8244b32885430e4fe1bab6e. Commit: f0026962219ebad2177f57ebee5ae9b837882e60 https://github.com/galaxyproject/galaxy/commit/f0026962219ebad2177f57ebee5a… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2019-02-07 (Thu, 07 Feb 2019) Changed paths: M client/galaxy/style/scss/base.scss M client/galaxy/style/scss/theme/blue.scss Log Message: ----------- Merge pull request #7309 from erasche/more-contrast [19.01] More contrast in CSS Compare: https://github.com/galaxyproject/galaxy/compare/8f7263a1dcce...f0026962219e

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[galaxyproject/galaxy] 041152: Add note about Range support
by Dannon 07 Feb '19

07 Feb '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 041152bd146e3c3fa0a1904a513b0ddab681eedd https://github.com/galaxyproject/galaxy/commit/041152bd146e3c3fa0a1904a513b… Author: pvanheus <pvh(a)sanbi.ac.za> Date: 2019-02-07 (Thu, 07 Feb 2019) Changed paths: M doc/source/admin/nginx.md Log Message: ----------- Add note about Range support Add note explaining that nginx sendfile support is required for Range (and thus IGV/JBrowse) to work. Commit: a1f188b79545debd3828469a7f0f9b8a8b5535b2 https://github.com/galaxyproject/galaxy/commit/a1f188b79545debd3828469a7f0f… Author: Dannon <dannon.baker(a)gmail.com> Date: 2019-02-07 (Thu, 07 Feb 2019) Changed paths: M doc/source/admin/nginx.md Log Message: ----------- Merge pull request #7323 from pvanheus/patch-12 Add note about Range support Compare: https://github.com/galaxyproject/galaxy/compare/e0cfaa452e2c...a1f188b79545

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[galaxyproject/galaxy] 68a66f: update h5py dependency
by John Chilton 07 Feb '19

07 Feb '19

Branch: refs/heads/release_19.01 Home: https://github.com/galaxyproject/galaxy Commit: 68a66f462e007fdbcf8e966fc5cc1a7ea06a8527 https://github.com/galaxyproject/galaxy/commit/68a66f462e007fdbcf8e966fc5cc… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2019-02-05 (Tue, 05 Feb 2019) Changed paths: M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt Log Message: ----------- update h5py dependency Commit: d79514b823371c36c12dcbb6aef25a4490cd50ca https://github.com/galaxyproject/galaxy/commit/d79514b823371c36c12dcbb6aef2… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2019-02-05 (Tue, 05 Feb 2019) Changed paths: M lib/galaxy/tools/verify/asserts/__init__.py Log Message: ----------- allow assertions on binary inputs Commit: e37036af04ac34dd7c865f5f11ccaa0ee4e17e9a https://github.com/galaxyproject/galaxy/commit/e37036af04ac34dd7c865f5f11cc… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2019-02-05 (Tue, 05 Feb 2019) Changed paths: A lib/galaxy/tools/verify/asserts/hdf5.py Log Message: ----------- add hdf5 assert tests Commit: db2987b2b21fefad9feb2af0bd4f93b7d490361f https://github.com/galaxyproject/galaxy/commit/db2987b2b21fefad9feb2af0bd4f… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2019-02-05 (Tue, 05 Feb 2019) Changed paths: A test/functional/tools/validation_hdf5.xml Log Message: ----------- add test tool for new assertions Commit: d4420b75662b7667d430f78be67b09e69037a77b https://github.com/galaxyproject/galaxy/commit/d4420b75662b7667d430f78be67b… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2019-02-05 (Tue, 05 Feb 2019) Changed paths: M test/functional/tools/samples_tool_conf.xml Log Message: ----------- register new test tool Commit: a00fd508b758fc73aeb537ca98156fff1c7ac14d https://github.com/galaxyproject/galaxy/commit/a00fd508b758fc73aeb537ca9815… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2019-02-05 (Tue, 05 Feb 2019) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- adopt XSD for new syntax Commit: cb13e56e6bd00a932e9594241fe043f845d4f815 https://github.com/galaxyproject/galaxy/commit/cb13e56e6bd00a932e9594241fe0… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2019-02-05 (Tue, 05 Feb 2019) Changed paths: A test-data/matrix.cool Log Message: ----------- add test-data for new hdf5 based tool test Commit: e9f40f2f95a611f0fab6d81bb225cf409b86f353 https://github.com/galaxyproject/galaxy/commit/e9f40f2f95a611f0fab6d81bb225… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2019-02-05 (Tue, 05 Feb 2019) Changed paths: M lib/galaxy/tools/verify/asserts/hdf5.py Log Message: ----------- fix pep8 Commit: 2a97f726cc86d44610738d04755622e8e4b8342a https://github.com/galaxyproject/galaxy/commit/2a97f726cc86d44610738d047556… Author: John Chilton <jmchilton(a)gmail.com> Date: 2019-02-05 (Tue, 05 Feb 2019) Changed paths: M lib/galaxy/tools/verify/asserts/hdf5.py M lib/galaxy/tools/xsd/galaxy.xsd M test/functional/tools/validation_hdf5.xml Log Message: ----------- Tweaks to hdf5 testing. - This is in galaxy-lib so h5py import should probably be conditional. - Namespace very generic test functions a bit by adding h5 into the names. - Stricter validation of XSD (the other assertions don't have this but that is problematic on their part), I'm not sure if the docs will render unevenly now though - we may want to revisit that and do this for all the assertions. Commit: 3d4ff4fc372bc6b44b384af944b548915427fda4 https://github.com/galaxyproject/galaxy/commit/3d4ff4fc372bc6b44b384af944b5… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2019-02-05 (Tue, 05 Feb 2019) Changed paths: M lib/galaxy/tools/verify/asserts/hdf5.py M lib/galaxy/tools/xsd/galaxy.xsd M test/functional/tools/validation_hdf5.xml Log Message: ----------- Merge pull request #41 from jmchilton/hdf5_tests Tweaks to hdf5 testing. Commit: d36cf51f6b63407fd96e49918fe6092d993275a9 https://github.com/galaxyproject/galaxy/commit/d36cf51f6b63407fd96e49918fe6… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2019-02-06 (Wed, 06 Feb 2019) Changed paths: M lib/galaxy/tools/verify/asserts/hdf5.py M lib/galaxy/tools/xsd/galaxy.xsd M test/functional/tools/validation_hdf5.xml Log Message: ----------- change "name" to "key" Commit: 8f7263a1dcce4a2d3e5c251e4253dece2998e61d https://github.com/galaxyproject/galaxy/commit/8f7263a1dcce4a2d3e5c251e4253… Author: John Chilton <jmchilton(a)gmail.com> Date: 2019-02-07 (Thu, 07 Feb 2019) Changed paths: M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt M lib/galaxy/tools/verify/asserts/__init__.py A lib/galaxy/tools/verify/asserts/hdf5.py M lib/galaxy/tools/xsd/galaxy.xsd A test-data/matrix.cool M test/functional/tools/samples_tool_conf.xml A test/functional/tools/validation_hdf5.xml Log Message: ----------- Merge pull request #7301 from bgruening/hdf5_tests Add new test syntax specific for HDF5 files Compare: https://github.com/galaxyproject/galaxy/compare/e3f1234b2c13...8f7263a1dcce

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[galaxyproject/galaxy] ab8ab1: Trim whitespace.
by Nicola Soranzo 07 Feb '19

07 Feb '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ab8ab10be77e243025fefb185dce6945914ed7a2 https://github.com/galaxyproject/galaxy/commit/ab8ab10be77e243025fefb185dce… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2019-02-07 (Thu, 07 Feb 2019) Changed paths: M client/galaxy/scripts/layout/menu.js Log Message: ----------- Trim whitespace. Commit: 321caf78e4fac8859d2a0b308cff25763d7ba1ef https://github.com/galaxyproject/galaxy/commit/321caf78e4fac8859d2a0b308cff… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2019-02-07 (Thu, 07 Feb 2019) Changed paths: M client/galaxy/scripts/ui/popupmenu.js Log Message: ----------- Fix popupmenu creation. Commit: 69a6d1aabaf242b0748a3205695364c9740a7cda https://github.com/galaxyproject/galaxy/commit/69a6d1aabaf242b0748a32056953… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2019-02-07 (Thu, 07 Feb 2019) Changed paths: M client/galaxy/scripts/mvc/upload/collection/collection-view.js M client/galaxy/scripts/mvc/upload/composite/composite-row.js M client/galaxy/scripts/mvc/upload/composite/composite-view.js Log Message: ----------- Client format. Commit: e0cfaa452e2cfb06b6560e6285ca499b0eabda57 https://github.com/galaxyproject/galaxy/commit/e0cfaa452e2cfb06b6560e6285ca… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2019-02-07 (Thu, 07 Feb 2019) Changed paths: M client/galaxy/scripts/ui/popupmenu.js Log Message: ----------- Merge pull request #7318 from dannon/fix_popupmenu_creation Fix popupmenu creation Compare: https://github.com/galaxyproject/galaxy/compare/d19c30cc0a41...e0cfaa452e2c

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