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

[galaxyproject/galaxy] 0a3682: Revert "Fix links in rule builder to not interfere...
by GitHub 24 Apr '18

24 Apr '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 0a3682804f9acf39cff12826eea04905a211e45d https://github.com/galaxyproject/galaxy/commit/0a3682804f9acf39cff12826eea0… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-04-24 (Tue, 24 Apr 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue Log Message: ----------- Revert "Fix links in rule builder to not interfere with the library router." This reverts commit d4a890f2fc46c4dd82a77e3a5772546d88a6b95d. Commit: 4f4cb148b748aa5ca3b1f27d978565728f7df7d8 https://github.com/galaxyproject/galaxy/commit/4f4cb148b748aa5ca3b1f27d9785… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-04-24 (Tue, 24 Apr 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue Log Message: ----------- better fix for href containing hashes removing href messes with styles and also with bs4 (e.g. active highlighting of dropdowns was broken) Commit: f3455f5276d1abd44ac4e68b9a9e62059640a19f https://github.com/galaxyproject/galaxy/commit/f3455f5276d1abd44ac4e68b9a9e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-04-24 (Tue, 24 Apr 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue Log Message: ----------- Merge pull request #5968 from martenson/ux-builder rule builder - better fix for inactive links Compare: https://github.com/galaxyproject/galaxy/compare/393f436ce594...f3455f5276d1

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[galaxyproject/galaxy] a5c75d: Correct access for FTP files in composite datatype
by GitHub 24 Apr '18

24 Apr '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: a5c75d2f954f697497747412fd2a998fa61019b0 https://github.com/galaxyproject/galaxy/commit/a5c75d2f954f697497747412fd2a… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2018-04-20 (Fri, 20 Apr 2018) Changed paths: M lib/galaxy/tools/parameters/grouping.py Log Message: ----------- Correct access for FTP files in composite datatype Commit: 88bf6bbdaa2d15355192eb3c9087151f7712209d https://github.com/galaxyproject/galaxy/commit/88bf6bbdaa2d15355192eb3c9087… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-04-24 (Tue, 24 Apr 2018) Changed paths: M lib/galaxy/tools/parameters/grouping.py Log Message: ----------- Merge pull request #5943 from erasche/fix-ftp-composite-upload [18.01] Correct access for FTP files in composite datatype Compare: https://github.com/galaxyproject/galaxy/compare/9f8021f1b4ec...88bf6bbdaa2d

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[galaxyproject/galaxy] ab92eb: Allow using the rule based collection builders rig...
by GitHub 24 Apr '18

24 Apr '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ab92eb6691903e35b75c16bee8f77e0b40db8085 https://github.com/galaxyproject/galaxy/commit/ab92eb6691903e35b75c16bee8f7… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-04-23 (Mon, 23 Apr 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- Allow using the rule based collection builders right from libraries. Commit: 7fd12ec7b83ee303aedb9d77b31d479000b7b5f3 https://github.com/galaxyproject/galaxy/commit/7fd12ec7b83ee303aedb9d77b31d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-04-23 (Mon, 23 Apr 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue M client/package.json M client/webpack.config.js Log Message: ----------- Rev handsontable client dep - fixes global style contamination of that component. Commit: d4a890f2fc46c4dd82a77e3a5772546d88a6b95d https://github.com/galaxyproject/galaxy/commit/d4a890f2fc46c4dd82a77e3a5772… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-04-23 (Mon, 23 Apr 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue Log Message: ----------- Fix links in rule builder to not interfere with the library router. Commit: 1209f35a1a6b5647a58b5c5f5c93d73388db8d64 https://github.com/galaxyproject/galaxy/commit/1209f35a1a6b5647a58b5c5f5c93… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-04-23 (Mon, 23 Apr 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue Log Message: ----------- Pleasant error handling if duplicate identifiers encountered. - Print a pretty error for this scenerio. - Improve the error state of the widget to add a cancel and "okay" button - the cancel button dimisses the widget and the okay button gives the reseracher a chance to return to the rules and try again. Commit: f042f51b366e4c6c82643f30b0fd7bc5fde7950a https://github.com/galaxyproject/galaxy/commit/f042f51b366e4c6c82643f30b0fd… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-04-23 (Mon, 23 Apr 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue Log Message: ----------- Style improvements for error messages in RuleBuilder. Commit: 393f436ce5946440df2e0b6de04ebc6558a57b3f https://github.com/galaxyproject/galaxy/commit/393f436ce5946440df2e0b6de04e… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-04-24 (Tue, 24 Apr 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/package.json M client/webpack.config.js Log Message: ----------- Merge pull request #5929 from jmchilton/library_2_rules Allow using the rule based collection builders right from libraries. Compare: https://github.com/galaxyproject/galaxy/compare/581e949dff5a...393f436ce594

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[galaxyproject/galaxy] 8d052b: bootstrap4 regression fix - extra large rule build...
by GitHub 24 Apr '18

24 Apr '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 8d052bad353959bf2465bac5322b5a939f3f5b68 https://github.com/galaxyproject/galaxy/commit/8d052bad353959bf2465bac5322b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-04-24 (Tue, 24 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/ui/ui-modal.js Log Message: ----------- bootstrap4 regression fix - extra large rule builder modal. Make the rule builder expand to larger screens more aggressively again, the BS4 branch capped the width at like 900px - make this much larger. Fixes https://github.com/galaxyproject/galaxy/projects/10#card-8949949. Commit: 581e949dff5ae99195960af48ba7aad0edbec3c4 https://github.com/galaxyproject/galaxy/commit/581e949dff5ae99195960af48ba7… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-04-24 (Tue, 24 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/ui/ui-modal.js Log Message: ----------- Merge pull request #5965 from jmchilton/modal_width_fix bootstrap4 regression fix - extra large rule builder modal. Compare: https://github.com/galaxyproject/galaxy/compare/0f88e4e9ebe4...581e949dff5a

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[galaxyproject/galaxy] a77ea2: Fix history list shared error
by GitHub 23 Apr '18

23 Apr '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a77ea2751e2659797421ab49d03d5dc9d11f67eb https://github.com/galaxyproject/galaxy/commit/a77ea2751e2659797421ab49d03d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-04-23 (Mon, 23 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/history/history-list.js Log Message: ----------- Fix history list shared error Commit: 8de398c7e440d979f036a15cfa46f0570a617893 https://github.com/galaxyproject/galaxy/commit/8de398c7e440d979f036a15cfa46… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-04-23 (Mon, 23 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/history/history-list.js Log Message: ----------- Refactoring while bugfixing in history-list Commit: 0f88e4e9ebe4b4724f4c6ecc3c7ecd5d0fce7cc6 https://github.com/galaxyproject/galaxy/commit/0f88e4e9ebe4b4724f4c6ecc3c7e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-04-23 (Mon, 23 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/history/history-list.js Log Message: ----------- Merge pull request #5962 from dannon/fix_shared_history_list_bug Fix shared history list bug Compare: https://github.com/galaxyproject/galaxy/compare/63a3cfad3065...0f88e4e9ebe4

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[galaxyproject/galaxy] 36a182: Resort to os.path.exists() also for paths not endi...
by GitHub 23 Apr '18

23 Apr '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 36a182a6c8b6e49bfb90bb452e443ccd746758bb https://github.com/galaxyproject/galaxy/commit/36a182a6c8b6e49bfb90bb452e44… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-04-21 (Sat, 21 Apr 2018) Changed paths: M lib/galaxy/tools/data/__init__.py Log Message: ----------- Resort to os.path.exists() also for paths not ending in .loc Fix installation of gatk2 iuc's repo, which otherwise does not add the data tables to `config/shed_tool_data_table_conf.xml` . Introduced in commit 43c9c287a9a3520d77cc9235dfbfa6ac6cf33227 . Commit: d80e60ce74aabe64e131d560085af099d52b81cf https://github.com/galaxyproject/galaxy/commit/d80e60ce74aabe64e131d560085a… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-04-23 (Mon, 23 Apr 2018) Changed paths: M lib/galaxy/tools/data/__init__.py Log Message: ----------- Merge pull request #5947 from nsoranzo/release_17.05_fix_gatk2_install [17.05] Resort to os.path.exists() also for paths not ending in .loc Commit: 8e6cdd73aa4d77ad022c97544b5da060e036065e https://github.com/galaxyproject/galaxy/commit/8e6cdd73aa4d77ad022c97544b5d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-04-23 (Mon, 23 Apr 2018) Changed paths: M lib/galaxy/tools/data/__init__.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_17.05' into release_17.09 Commit: 9f8021f1b4ecc0e072f6b0b89a457a09feea0ab1 https://github.com/galaxyproject/galaxy/commit/9f8021f1b4ecc0e072f6b0b89a45… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-04-23 (Mon, 23 Apr 2018) Changed paths: M lib/galaxy/tools/data/__init__.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_17.09' into release_18.01 Commit: 63a3cfad30656b7fa8516e9c386f144f0f3b1fe3 https://github.com/galaxyproject/galaxy/commit/63a3cfad30656b7fa8516e9c386f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-04-23 (Mon, 23 Apr 2018) Changed paths: M lib/galaxy/tools/data/__init__.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_18.01' into dev Compare: https://github.com/galaxyproject/galaxy/compare/9e3cc281564a...63a3cfad3065

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[galaxyproject/galaxy] 36a182: Resort to os.path.exists() also for paths not endi...
by GitHub 23 Apr '18

23 Apr '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: 36a182a6c8b6e49bfb90bb452e443ccd746758bb https://github.com/galaxyproject/galaxy/commit/36a182a6c8b6e49bfb90bb452e44… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-04-21 (Sat, 21 Apr 2018) Changed paths: M lib/galaxy/tools/data/__init__.py Log Message: ----------- Resort to os.path.exists() also for paths not ending in .loc Fix installation of gatk2 iuc's repo, which otherwise does not add the data tables to `config/shed_tool_data_table_conf.xml` . Introduced in commit 43c9c287a9a3520d77cc9235dfbfa6ac6cf33227 . Commit: d80e60ce74aabe64e131d560085af099d52b81cf https://github.com/galaxyproject/galaxy/commit/d80e60ce74aabe64e131d560085a… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-04-23 (Mon, 23 Apr 2018) Changed paths: M lib/galaxy/tools/data/__init__.py Log Message: ----------- Merge pull request #5947 from nsoranzo/release_17.05_fix_gatk2_install [17.05] Resort to os.path.exists() also for paths not ending in .loc Commit: 8e6cdd73aa4d77ad022c97544b5da060e036065e https://github.com/galaxyproject/galaxy/commit/8e6cdd73aa4d77ad022c97544b5d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-04-23 (Mon, 23 Apr 2018) Changed paths: M lib/galaxy/tools/data/__init__.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_17.05' into release_17.09 Commit: 9f8021f1b4ecc0e072f6b0b89a457a09feea0ab1 https://github.com/galaxyproject/galaxy/commit/9f8021f1b4ecc0e072f6b0b89a45… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-04-23 (Mon, 23 Apr 2018) Changed paths: M lib/galaxy/tools/data/__init__.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_17.09' into release_18.01 Compare: https://github.com/galaxyproject/galaxy/compare/2d772d74b940...9f8021f1b4ec

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[galaxyproject/galaxy] 36a182: Resort to os.path.exists() also for paths not endi...
by GitHub 23 Apr '18

23 Apr '18

Branch: refs/heads/release_17.09 Home: https://github.com/galaxyproject/galaxy Commit: 36a182a6c8b6e49bfb90bb452e443ccd746758bb https://github.com/galaxyproject/galaxy/commit/36a182a6c8b6e49bfb90bb452e44… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-04-21 (Sat, 21 Apr 2018) Changed paths: M lib/galaxy/tools/data/__init__.py Log Message: ----------- Resort to os.path.exists() also for paths not ending in .loc Fix installation of gatk2 iuc's repo, which otherwise does not add the data tables to `config/shed_tool_data_table_conf.xml` . Introduced in commit 43c9c287a9a3520d77cc9235dfbfa6ac6cf33227 . Commit: d80e60ce74aabe64e131d560085af099d52b81cf https://github.com/galaxyproject/galaxy/commit/d80e60ce74aabe64e131d560085a… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-04-23 (Mon, 23 Apr 2018) Changed paths: M lib/galaxy/tools/data/__init__.py Log Message: ----------- Merge pull request #5947 from nsoranzo/release_17.05_fix_gatk2_install [17.05] Resort to os.path.exists() also for paths not ending in .loc Commit: 8e6cdd73aa4d77ad022c97544b5da060e036065e https://github.com/galaxyproject/galaxy/commit/8e6cdd73aa4d77ad022c97544b5d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-04-23 (Mon, 23 Apr 2018) Changed paths: M lib/galaxy/tools/data/__init__.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_17.05' into release_17.09 Compare: https://github.com/galaxyproject/galaxy/compare/beb28d4aff2a...8e6cdd73aa4d

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[galaxyproject/galaxy] 36a182: Resort to os.path.exists() also for paths not endi...
by GitHub 23 Apr '18

23 Apr '18

Branch: refs/heads/release_17.05 Home: https://github.com/galaxyproject/galaxy Commit: 36a182a6c8b6e49bfb90bb452e443ccd746758bb https://github.com/galaxyproject/galaxy/commit/36a182a6c8b6e49bfb90bb452e44… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-04-21 (Sat, 21 Apr 2018) Changed paths: M lib/galaxy/tools/data/__init__.py Log Message: ----------- Resort to os.path.exists() also for paths not ending in .loc Fix installation of gatk2 iuc's repo, which otherwise does not add the data tables to `config/shed_tool_data_table_conf.xml` . Introduced in commit 43c9c287a9a3520d77cc9235dfbfa6ac6cf33227 . Commit: d80e60ce74aabe64e131d560085af099d52b81cf https://github.com/galaxyproject/galaxy/commit/d80e60ce74aabe64e131d560085a… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-04-23 (Mon, 23 Apr 2018) Changed paths: M lib/galaxy/tools/data/__init__.py Log Message: ----------- Merge pull request #5947 from nsoranzo/release_17.05_fix_gatk2_install [17.05] Resort to os.path.exists() also for paths not ending in .loc Compare: https://github.com/galaxyproject/galaxy/compare/34421966d41a...d80e60ce74aa

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[galaxyproject/infrastructure-playbook] b2fb46: Fix stats/upgrade stats components
by GitHub 23 Apr '18

23 Apr '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: b2fb46db5f10c868a15cff8676e503f5bde1570a https://github.com/galaxyproject/infrastructure-playbook/commit/b2fb46db5f1… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-23 (Mon, 23 Apr 2018) Changed paths: R env/tacc/group_vars/stats/vars.yml R env/tacc/group_vars/stats/vault.yml R env/tacc/group_vars/statsservers.yml A env/tacc/group_vars/statsservers/vars.yml A env/tacc/group_vars/statsservers/vault.yml M roles/stats/defaults/main.yml M roles/stats/tasks/main.yml Log Message: ----------- Fix stats/upgrade stats components Commit: 73dc2d961db7f2ee524f41582e14c4f7fddd7b6d https://github.com/galaxyproject/infrastructure-playbook/commit/73dc2d961db… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-23 (Mon, 23 Apr 2018) Changed paths: M env/tacc/group_vars/all.yml M env/tacc/group_vars/galaxyservers.yml M env/tacc/group_vars/statsservers/vars.yml M env/tacc/playbook.yml A env/tacc/telegraf.yml M env/tacc/templates/supervisor/stats.j2 A roles/dj-wasabi.telegraf/.gitignore A roles/dj-wasabi.telegraf/.travis.yml A roles/dj-wasabi.telegraf/CHANGELOG.md A roles/dj-wasabi.telegraf/README.md A roles/dj-wasabi.telegraf/defaults/main.yml A roles/dj-wasabi.telegraf/handlers/main.yml A roles/dj-wasabi.telegraf/meta/.galaxy_install_info A roles/dj-wasabi.telegraf/meta/main.yml A roles/dj-wasabi.telegraf/molecule/default/Dockerfile.j2 A roles/dj-wasabi.telegraf/molecule/default/INSTALL.rst A roles/dj-wasabi.telegraf/molecule/default/create.yml A roles/dj-wasabi.telegraf/molecule/default/destroy.yml A roles/dj-wasabi.telegraf/molecule/default/molecule.yml A roles/dj-wasabi.telegraf/molecule/default/playbook.yml A roles/dj-wasabi.telegraf/molecule/default/tests/test_default.py A roles/dj-wasabi.telegraf/molecule/default/tests/test_default.pyc A roles/dj-wasabi.telegraf/molecule/default/yaml-lint.yml A roles/dj-wasabi.telegraf/tasks/Debian.yml A roles/dj-wasabi.telegraf/tasks/RedHat.yml A roles/dj-wasabi.telegraf/tasks/main.yml A roles/dj-wasabi.telegraf/templates/etc-opt-telegraf-telegraf.conf.j2 A roles/dj-wasabi.telegraf/templates/telegraf-extra-plugin.conf.j2 A roles/dj-wasabi.telegraf/templates/telegraf.conf.j2 M roles/sentry/tasks/main.yml M roles/stats/tasks/main.yml R roles/stats/templates/telegraf.conf.j2 Log Message: ----------- Run telegraf on everything, and have Galaxy log to a telegraf+statsd running host-local so these stats can be separated Compare: https://github.com/galaxyproject/infrastructure-playbook/compare/dd951a455b…

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