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

[galaxyproject/usegalaxy-playbook] 9a4760: Update uniprot to 0.2, update sra_tools to 2.9.1, ...
by GitHub 07 Dec '18

07 Dec '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 9a476008536d522bc34e82816ae82292682797d5 https://github.com/galaxyproject/usegalaxy-playbook/commit/9a476008536d522b… Author: Dave B <dave(a)bx.psu.edu> Date: 2018-12-07 (Fri, 07 Dec 2018) Changed paths: 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 M env/test/files/galaxy/var/integrated_tool_panel.xml M env/test/files/galaxy/var/shed_tool_conf.xml Log Message: ----------- Update uniprot to 0.2, update sra_tools to 2.9.1, install annotateMyIDs 3.5.0, hide CTD and DGI **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 4c2f95: Fix hashing, AND was not the right operation
by GitHub 07 Dec '18

07 Dec '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4c2f95b1f469d9789e65c4c9be97c4e137014ece https://github.com/galaxyproject/galaxy/commit/4c2f95b1f469d9789e65c4c9be97… Author: Helena Rasche <hxr(a)hx42.org> Date: 2018-12-07 (Fri, 07 Dec 2018) Changed paths: M client/galaxy/scripts/utils/utils.js Log Message: ----------- Fix hashing, AND was not the right operation Commit: bddfe3889031a31ad3efd1dadd8482a6301a9ad9 https://github.com/galaxyproject/galaxy/commit/bddfe3889031a31ad3efd1dadd84… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-12-07 (Fri, 07 Dec 2018) Changed paths: M client/galaxy/scripts/utils/utils.js Log Message: ----------- Merge pull request #7081 from erasche/fix-hash Fix hashing, AND was not the right operation Compare: https://github.com/galaxyproject/galaxy/compare/b453f531e51c...bddfe3889031 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 35fd29: Fix Error display
by GitHub 06 Dec '18

06 Dec '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 35fd29062587002f70f660e4a7675bd23545fc85 https://github.com/galaxyproject/galaxy/commit/35fd29062587002f70f660e4a767… Author: jvanbraekel <29703119+jvanbraekel(a)users.noreply.github.com> Date: 2018-12-06 (Thu, 06 Dec 2018) Changed paths: M templates/admin/tool_shed_repository/manage_repository.mako Log Message: ----------- Fix Error display The template display was broken in case of error. 'in_error_state is never defined it should be 'repository.in_error_state' instead. This was leading to some wrong field type display and not displaying the details about the error. Commit: b453f531e51c6fc91d44d777de486b31c82cf726 https://github.com/galaxyproject/galaxy/commit/b453f531e51c6fc91d44d777de48… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-12-06 (Thu, 06 Dec 2018) Changed paths: M templates/admin/tool_shed_repository/manage_repository.mako Log Message: ----------- Merge pull request #7080 from jvanbraekel/patch-1 Fix toolshed repository error display Compare: https://github.com/galaxyproject/galaxy/compare/16f3be66be84...b453f531e51c **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] be4369: Avoid using make for autobuild; reducing necessary...
by GitHub 06 Dec '18

06 Dec '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: be43693ef05dfae85872412f198d87a31424f486 https://github.com/galaxyproject/galaxy/commit/be43693ef05dfae85872412f198d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-11-29 (Thu, 29 Nov 2018) Changed paths: M scripts/common_startup.sh Log Message: ----------- Avoid using make for autobuild; reducing necessary dependencies out of the box. Commit: 77aec5a79dc18e224ca6246659f68a49864a46cf https://github.com/galaxyproject/galaxy/commit/77aec5a79dc18e224ca6246659f6… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-11-29 (Thu, 29 Nov 2018) Changed paths: M scripts/common_startup.sh Log Message: ----------- Standardize on spaces in common_startup.sh (tabs were mixed in here) Commit: fa408f485048ee8c7afeb96ac6c9da8dea4661f3 https://github.com/galaxyproject/galaxy/commit/fa408f485048ee8c7afeb96ac6c9… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-11-29 (Thu, 29 Nov 2018) Changed paths: M scripts/common_startup.sh Log Message: ----------- exit with error code (and appropriate message) on either build failure Commit: 66fae561b29507a69f5c32690be4791f86f5cdd7 https://github.com/galaxyproject/galaxy/commit/66fae561b29507a69f5c32690be4… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-12-02 (Sun, 02 Dec 2018) Changed paths: M scripts/common_startup.sh Log Message: ----------- Don't use pushd/popd Commit: 57459954de189cb1fd9b6ab8654c8f4700241ea2 https://github.com/galaxyproject/galaxy/commit/57459954de189cb1fd9b6ab8654c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-12-05 (Wed, 05 Dec 2018) Changed paths: M scripts/common_startup.sh Log Message: ----------- Merge pull request #7060 from dannon/no-make-for-autobuild [18.09] Eliminate dependency on make for automatic client build Commit: 16f3be66be84ac9827f4c0fa213d9ead9ba30bd2 https://github.com/galaxyproject/galaxy/commit/16f3be66be84ac9827f4c0fa213d… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-12-06 (Thu, 06 Dec 2018) Changed paths: M scripts/common_startup.sh Log Message: ----------- Merge branch 'release_18.09' into dev Compare: https://github.com/galaxyproject/galaxy/compare/4bf27f464216...16f3be66be84 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] f5301c: Dependencies fixes, follow up on #7070
by GitHub 06 Dec '18

06 Dec '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f5301c264592f5a6d3f7747b1f930f82384c9495 https://github.com/galaxyproject/galaxy/commit/f5301c264592f5a6d3f7747b1f93… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-12-05 (Wed, 05 Dec 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/default/Pipfile M lib/galaxy/dependencies/pipfiles/default/pinned-dev-requirements.txt M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt Log Message: ----------- Dependencies fixes, follow up on #7070 Commit: 7eb436cebc39363330e9b0503c36b00cb763dbc5 https://github.com/galaxyproject/galaxy/commit/7eb436cebc39363330e9b0503c36… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-12-05 (Wed, 05 Dec 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/default/pinned-dev-requirements.txt M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt M lib/galaxy/dependencies/pipfiles/update.sh Log Message: ----------- Update all dependencies with `make update-dependencies` using pipenv 2018.11.26 . Also remove oscillating `python_version < '3.0'` environment marker for `azure-storage-nspkg` package. Commit: 4bf27f4642163be0c3b0b7399453833ba1013a8c https://github.com/galaxyproject/galaxy/commit/4bf27f4642163be0c3b0b7399453… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-12-06 (Thu, 06 Dec 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/default/Pipfile M lib/galaxy/dependencies/pipfiles/default/pinned-dev-requirements.txt M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt M lib/galaxy/dependencies/pipfiles/update.sh Log Message: ----------- Merge pull request #7079 from nsoranzo/follow-up_on_7070 Follow-up on #7070 Compare: https://github.com/galaxyproject/galaxy/compare/c4dbf8615e98...4bf27f464216 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] be4369: Avoid using make for autobuild; reducing necessary...
by GitHub 05 Dec '18

05 Dec '18

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy Commit: be43693ef05dfae85872412f198d87a31424f486 https://github.com/galaxyproject/galaxy/commit/be43693ef05dfae85872412f198d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-11-29 (Thu, 29 Nov 2018) Changed paths: M scripts/common_startup.sh Log Message: ----------- Avoid using make for autobuild; reducing necessary dependencies out of the box. Commit: 77aec5a79dc18e224ca6246659f68a49864a46cf https://github.com/galaxyproject/galaxy/commit/77aec5a79dc18e224ca6246659f6… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-11-29 (Thu, 29 Nov 2018) Changed paths: M scripts/common_startup.sh Log Message: ----------- Standardize on spaces in common_startup.sh (tabs were mixed in here) Commit: fa408f485048ee8c7afeb96ac6c9da8dea4661f3 https://github.com/galaxyproject/galaxy/commit/fa408f485048ee8c7afeb96ac6c9… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-11-29 (Thu, 29 Nov 2018) Changed paths: M scripts/common_startup.sh Log Message: ----------- exit with error code (and appropriate message) on either build failure Commit: 66fae561b29507a69f5c32690be4791f86f5cdd7 https://github.com/galaxyproject/galaxy/commit/66fae561b29507a69f5c32690be4… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-12-02 (Sun, 02 Dec 2018) Changed paths: M scripts/common_startup.sh Log Message: ----------- Don't use pushd/popd Commit: 57459954de189cb1fd9b6ab8654c8f4700241ea2 https://github.com/galaxyproject/galaxy/commit/57459954de189cb1fd9b6ab8654c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-12-05 (Wed, 05 Dec 2018) Changed paths: M scripts/common_startup.sh Log Message: ----------- Merge pull request #7060 from dannon/no-make-for-autobuild [18.09] Eliminate dependency on make for automatic client build Compare: https://github.com/galaxyproject/galaxy/compare/46ad1992bdbf...57459954de18 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] eeffb2: Implement colourful tags
by GitHub 05 Dec '18

05 Dec '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: eeffb26423a2b6380087c01af5d3390c2fd9b0df https://github.com/galaxyproject/galaxy/commit/eeffb26423a2b6380087c01af5d3… Author: Helena Rasche <hxr(a)hx42.org> Date: 2018-12-04 (Tue, 04 Dec 2018) Changed paths: M client/galaxy/scripts/mvc/history/history-item-li.js Log Message: ----------- Implement colourful tags Commit: e6c4292fd5a3182f01f16dfd445359f5dcb87e0c https://github.com/galaxyproject/galaxy/commit/e6c4292fd5a3182f01f16dfd4453… Author: Helena Rasche <hxr(a)hx42.org> Date: 2018-12-04 (Tue, 04 Dec 2018) Changed paths: M client/galaxy/scripts/mvc/history/history-item-li.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/galaxy/scripts/utils/utils.js Log Message: ----------- Move to correct location Commit: 5865fe3513232fe893dd2a638a54218599be11a9 https://github.com/galaxyproject/galaxy/commit/5865fe3513232fe893dd2a638a54… Author: Helena Rasche <hxr(a)hx42.org> Date: 2018-12-04 (Tue, 04 Dec 2018) Changed paths: M client/galaxy/scripts/mvc/history/history-item-li.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/galaxy/scripts/utils/utils.js Log Message: ----------- Add colorFg function Commit: 12576ef49477f51137cf0f223600a00c2c7b90e3 https://github.com/galaxyproject/galaxy/commit/12576ef49477f51137cf0f223600… Author: Helena Rasche <hxr(a)hx42.org> Date: 2018-12-04 (Tue, 04 Dec 2018) Changed paths: M client/galaxy/scripts/mvc/history/history-item-li.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/galaxy/scripts/utils/utils.js Log Message: ----------- Replace with style function Commit: 0e7f2b3595a4235b1672205bd13b73153014f139 https://github.com/galaxyproject/galaxy/commit/0e7f2b3595a4235b1672205bd13b… Author: Helena Rasche <hxr(a)hx42.org> Date: 2018-12-04 (Tue, 04 Dec 2018) Changed paths: M client/galaxy/scripts/utils/utils.js Log Message: ----------- revert to grey border Commit: ad9787ef7050e3747b1b862ba857b1a2557174a0 https://github.com/galaxyproject/galaxy/commit/ad9787ef7050e3747b1b862ba857… Author: Helena Rasche <hxr(a)hx42.org> Date: 2018-12-05 (Wed, 05 Dec 2018) Changed paths: M client/galaxy/scripts/utils/utils.js Log Message: ----------- cleanup/docs Commit: c4dbf8615e98ae8778715e1169b537c8148af3b0 https://github.com/galaxyproject/galaxy/commit/c4dbf8615e98ae8778715e1169b5… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-12-05 (Wed, 05 Dec 2018) Changed paths: M client/galaxy/scripts/mvc/history/history-item-li.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/galaxy/scripts/utils/utils.js Log Message: ----------- Merge pull request #7072 from erasche/colour-tags Make tags more colourful Compare: https://github.com/galaxyproject/galaxy/compare/199cca9417d4...c4dbf8615e98 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 3931b8: improved parsing of sizes (bytes)
by GitHub 05 Dec '18

05 Dec '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 3931b8ec355df64e780f640d39ac0928d7c8afde https://github.com/galaxyproject/galaxy/commit/3931b8ec355df64e780f640d39ac… Author: M Bernt <m.bernt(a)ufz.de> Date: 2018-12-04 (Tue, 04 Dec 2018) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- improved parsing of sizes (bytes) before floats like without byte extension were not recognized (eg 1.0) Commit: 27cc49d3f785c643b4dcdbf0da09d1bf63ee44f9 https://github.com/galaxyproject/galaxy/commit/27cc49d3f785c643b4dcdbf0da09… Author: M Bernt <m.bernt(a)ufz.de> Date: 2018-12-04 (Tue, 04 Dec 2018) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- size_to_bytes: use only regex, remove assert, add exceptions Commit: c90d71dd44794f8499813804290d08d3fdae6a6f https://github.com/galaxyproject/galaxy/commit/c90d71dd44794f8499813804290d… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2018-12-04 (Tue, 04 Dec 2018) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- Raise ValueError, fix spacing Commit: df51c468898e6bbc236e5a30a2758de4d06c9642 https://github.com/galaxyproject/galaxy/commit/df51c468898e6bbc236e5a30a275… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2018-12-04 (Tue, 04 Dec 2018) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- Add missing empty line Commit: 26a6b1c83381d1c75131f330d8b8f4c23680f1dd https://github.com/galaxyproject/galaxy/commit/26a6b1c83381d1c75131f330d8b8… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2018-12-04 (Tue, 04 Dec 2018) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- Stricter regexp Commit: 199cca9417d484b8c4998f66beb4892de69accf3 https://github.com/galaxyproject/galaxy/commit/199cca9417d484b8c4998f66beb4… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2018-12-05 (Wed, 05 Dec 2018) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- Merge pull request #7067 from bernt-matthias/topic/size-parse Improved parsing of sizes (bytes) Compare: https://github.com/galaxyproject/galaxy/compare/ee8880657865...199cca9417d4 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/usegalaxy-playbook] c13eca: remove biostar config from Main
by GitHub 04 Dec '18

04 Dec '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: c13eca7a954958839de6c7ae96eea3705a031801 https://github.com/galaxyproject/usegalaxy-playbook/commit/c13eca7a95495883… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-12-04 (Tue, 04 Dec 2018) Changed paths: M env/main/group_vars/galaxyservers/vars.yml Log Message: ----------- remove biostar config from Main **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] cf25f7: Fix nesting of repeats and error when repeat is pr...
by GitHub 04 Dec '18

04 Dec '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: cf25f7dcec6f7f7b13aac93a18ced291d5e74444 https://github.com/galaxyproject/galaxy/commit/cf25f7dcec6f7f7b13aac93a18ce… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-12-04 (Tue, 04 Dec 2018) Changed paths: M lib/galaxy/tools/parameters/meta.py Log Message: ----------- Fix nesting of repeats and error when repeat is provided literally. This fixex #7048, where in addition to repeat values ('repeat_0|param: some_value') there are also values for the repeat param itself ('repeat': []). Commit: 3a93fd4f2321bf141b2ccf34ea80c42ee517b33d https://github.com/galaxyproject/galaxy/commit/3a93fd4f2321bf141b2ccf34ea80… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-12-04 (Tue, 04 Dec 2018) Changed paths: M test/unit/tools/test_parameter_parsing.py Log Message: ----------- Add test for proper nesting in process_keys and a unit test for https://github.com/galaxyproject/galaxy/issues/7048 Commit: 46ad1992bdbf478495b14780e96e251d00ceb700 https://github.com/galaxyproject/galaxy/commit/46ad1992bdbf478495b14780e96e… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-12-04 (Tue, 04 Dec 2018) Changed paths: M lib/galaxy/tools/parameters/meta.py M test/unit/tools/test_parameter_parsing.py Log Message: ----------- Merge pull request #7071 from mvdbeek/fix_process_key [18.09] Fix process key Commit: ee88806578655fff9d32e72e90468e0ca87c877b https://github.com/galaxyproject/galaxy/commit/ee88806578655fff9d32e72e9046… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-12-04 (Tue, 04 Dec 2018) Changed paths: M lib/galaxy/tools/parameters/meta.py M test/unit/tools/test_parameter_parsing.py Log Message: ----------- Merge branch 'release_18.09' into dev Compare: https://github.com/galaxyproject/galaxy/compare/aaa8d1a61cb5...ee8880657865 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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