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

[galaxyproject/galaxy] 96dcf5: Fix quota styling for new anchor/link.
by GitHub 04 May '18

04 May '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: 96dcf54c438809c988eb063cf079bc7dbf4a5fe0 https://github.com/galaxyproject/galaxy/commit/96dcf54c438809c988eb063cf079… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-04 (Fri, 04 May 2018) Changed paths: M client/galaxy/style/scss/base.scss M static/style/blue/base.css Log Message: ----------- Fix quota styling for new anchor/link. Commit: 6bb5fa02fc20fdfbb69085a5a0bfe57dfc7ef93a https://github.com/galaxyproject/galaxy/commit/6bb5fa02fc20fdfbb69085a5a0bf… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-04 (Fri, 04 May 2018) Changed paths: M client/galaxy/scripts/mvc/user/user-quotameter.js M client/galaxy/style/scss/base.scss M static/style/blue/base.css Log Message: ----------- Use standard styling for quotameter; this fixes danger/warning/success indicators and visibility. Commit: 89c12d6da2c797dbe2803768ad27657ac9a8e999 https://github.com/galaxyproject/galaxy/commit/89c12d6da2c797dbe2803768ad27… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-04 (Fri, 04 May 2018) Changed paths: M client/galaxy/style/scss/base.scss M static/style/blue/base.css Log Message: ----------- More standard quota-meter-text color Commit: b7c8fbe7c20c8c02cef182d7843a21d15346c1f1 https://github.com/galaxyproject/galaxy/commit/b7c8fbe7c20c8c02cef182d7843a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-04 (Fri, 04 May 2018) Changed paths: M client/galaxy/style/scss/galaxy_bootstrap/variables.scss M static/style/blue/base.css Log Message: ----------- Tinker with brand-succcess, address the brightness concern (which makes many locations look better, at least to me) Commit: 23b0169a17f3a4b1b705ee0dc0afe613e1cc29cd https://github.com/galaxyproject/galaxy/commit/23b0169a17f3a4b1b705ee0dc0af… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-04 (Fri, 04 May 2018) Changed paths: M client/galaxy/style/scss/base.scss M static/style/blue/base.css Log Message: ----------- Fix non-capped usage display as well. Commit: 7c44139dc82e6cf1486b23593c811e0f653af932 https://github.com/galaxyproject/galaxy/commit/7c44139dc82e6cf1486b23593c81… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-05-04 (Fri, 04 May 2018) Changed paths: M client/galaxy/scripts/mvc/user/user-quotameter.js M client/galaxy/style/scss/base.scss M client/galaxy/style/scss/galaxy_bootstrap/variables.scss M static/style/blue/base.css Log Message: ----------- Merge pull request #6062 from dannon/fix_quotameter_styling Fix quotameter styling Compare: https://github.com/galaxyproject/galaxy/compare/2a9e44e7a217...7c44139dc82e **NOTE:** This service 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] d729c3: Rules - bug fix for apply_rules tool on nested col...
by GitHub 04 May '18

04 May '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: d729c31ffd6e7198e5970eaeda2bcf3a65c20ba6 https://github.com/galaxyproject/galaxy/commit/d729c31ffd6e7198e5970eaeda2b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-05-04 (Fri, 04 May 2018) Changed paths: M lib/galaxy/managers/collections.py Log Message: ----------- Rules - bug fix for apply_rules tool on nested collections. Commit: 2a9e44e7a217f0ec3d48dd10811b23bd8da86c44 https://github.com/galaxyproject/galaxy/commit/2a9e44e7a217f0ec3d48dd10811b… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-05-04 (Fri, 04 May 2018) Changed paths: M lib/galaxy/managers/collections.py Log Message: ----------- Merge pull request #6065 from jmchilton/rule_fixes_4 [18.05] Rules - bug fix for apply_rules tool on nested collections. Compare: https://github.com/galaxyproject/galaxy/compare/011e76a72647...2a9e44e7a217 **NOTE:** This service 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] f371d3: RuleBuilder - Fix paired identifier casting issue.
by GitHub 04 May '18

04 May '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: f371d3f7094086ae183b3abc9cb3dc38ff361886 https://github.com/galaxyproject/galaxy/commit/f371d3f7094086ae183b3abc9cb3… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-05-03 (Thu, 03 May 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue Log Message: ----------- RuleBuilder - Fix paired identifier casting issue. Commit: 3b5d8ae99c5d6d8f040d6554320bb50e41fa58a4 https://github.com/galaxyproject/galaxy/commit/3b5d8ae99c5d6d8f040d6554320b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-05-03 (Thu, 03 May 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue Log Message: ----------- RuleBuilder - Fix x in column definition screen to eliminate correct def. Commit: 011e76a72647a48a3415a36bd19c17e2688175df https://github.com/galaxyproject/galaxy/commit/011e76a72647a48a3415a36bd19c… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-05-04 (Fri, 04 May 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue Log Message: ----------- Merge pull request #6056 from jmchilton/rule_Builder_fixes_2 [18.05] Yet more rule builder fixes. Compare: https://github.com/galaxyproject/galaxy/compare/1b41cbba59bb...011e76a72647 **NOTE:** This service 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] 8bee7b: Improve error message for mismatched data inputs
by GitHub 04 May '18

04 May '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: 8bee7b80cbe7c898da0c9968d1aae291da807b6d https://github.com/galaxyproject/galaxy/commit/8bee7b80cbe7c898da0c9968d1aa… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-05-04 (Fri, 04 May 2018) Changed paths: M lib/galaxy/util/permutations.py Log Message: ----------- Improve error message for mismatched data inputs Commit: f7354c0eb3e2198ba3536d22b4a6fad27822650e https://github.com/galaxyproject/galaxy/commit/f7354c0eb3e2198ba3536d22b4a6… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-05-04 (Fri, 04 May 2018) Changed paths: M lib/galaxy/util/permutations.py Log Message: ----------- Merge pull request #6060 from mvdbeek/improve_error_message_unmatched_collections [18.01] Improve error message for mismatched data inputs Compare: https://github.com/galaxyproject/galaxy/compare/545b7a4fe2be...f7354c0eb3e2 **NOTE:** This service 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] 5bd2cb: Alter `extra_data` column on an oidc-related table...
by GitHub 04 May '18

04 May '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: 5bd2cbd80b35cc5ddddce808f17c13ce1381bc36 https://github.com/galaxyproject/galaxy/commit/5bd2cbd80b35cc5ddddce808f17c… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-05-03 (Thu, 03 May 2018) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py M lib/galaxy/model/migrate/versions/0141_add_oidc_tables.py Log Message: ----------- Alter `extra_data` column on an oidc-related table from TXT to JSON. Commit: 1b41cbba59bb09bdac305ff9de8d64dc4f873ee9 https://github.com/galaxyproject/galaxy/commit/1b41cbba59bb09bdac305ff9de8d… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-05-04 (Fri, 04 May 2018) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py M lib/galaxy/model/migrate/versions/0141_add_oidc_tables.py Log Message: ----------- Merge pull request #6057 from VJalili/alter_extra_data [18.05] Alter the type of extra_data column of OIDC table. Compare: https://github.com/galaxyproject/galaxy/compare/3292445872d9...1b41cbba59bb **NOTE:** This service 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] 624e90: [18.01] More tool state performance fixes.
by GitHub 04 May '18

04 May '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: 624e9028cc3b359dc3b546f735ab62ec00439f97 https://github.com/galaxyproject/galaxy/commit/624e9028cc3b359dc3b546f735ab… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-05-02 (Wed, 02 May 2018) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/dataset_matcher.py Log Message: ----------- [18.01] More tool state performance fixes. Fix performance problems that can be encountered when matching collection inputs. It would use the old style matching to find an initial value to plug into the tool state - if there were no collections that matched or there were some big collections toward the top of the history that did not match this could completely undo performance fixes in 5997. More Pythonic input type conditional logic. Commit: 545b7a4fe2bee6c967f0b4dcf850df842491e6bc https://github.com/galaxyproject/galaxy/commit/545b7a4fe2bee6c967f0b4dcf850… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2018-05-04 (Fri, 04 May 2018) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/dataset_matcher.py Log Message: ----------- Merge pull request #6046 from jmchilton/tool_state_part_2 [18.01] More tool state performance fixes. Compare: https://github.com/galaxyproject/galaxy/compare/b35340c77f26...545b7a4fe2be **NOTE:** This service 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/infrastructure-playbook] 34cb08: disable influxdb max-row-limit
by GitHub 03 May '18

03 May '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 34cb08186081111e9672fff41ea29e727dc3c27c https://github.com/galaxyproject/infrastructure-playbook/commit/34cb0818608… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-05-03 (Thu, 03 May 2018) Changed paths: M roles/stats/templates/influxdb.conf.j2 Log Message: ----------- disable influxdb max-row-limit to prevent data being cut off from display maybe we will need a limit eventually, but 10k seems too low Commit: 6ab46e62ce743debc531bd3aa4789e87bb0f2877 https://github.com/galaxyproject/infrastructure-playbook/commit/6ab46e62ce7… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-05-03 (Thu, 03 May 2018) Changed paths: M roles/stats/templates/influxdb.conf.j2 Log Message: ----------- Merge pull request #23 from galaxyproject/martenson-patch-3 disable influxdb max-row-limit Compare: https://github.com/galaxyproject/infrastructure-playbook/compare/1daa68776b… **NOTE:** This service 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] dd3826: update Test
by GitHub 03 May '18

03 May '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: dd3826dc5bfd20e1c1fc094b84adbec6240c59f6 https://github.com/galaxyproject/usegalaxy-playbook/commit/dd3826dc5bfd20e1… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-05-03 (Thu, 03 May 2018) Changed paths: M env/test/files/galaxy/galaxy_version.yml Log Message: ----------- update Test Commit: 55bc28e603e61b5217f41316228e67ef03b2f74b https://github.com/galaxyproject/usegalaxy-playbook/commit/55bc28e603e61b52… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-05-03 (Thu, 03 May 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: ----------- Merge branch 'master' of https://github.com/galaxyproject/usegalaxy-playbook Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/7ceff21faf47...… **NOTE:** This service 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/infrastructure-playbook] 34cb08: disable influxdb max-row-limit
by GitHub 03 May '18

03 May '18

Branch: refs/heads/martenson-patch-3 Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 34cb08186081111e9672fff41ea29e727dc3c27c https://github.com/galaxyproject/infrastructure-playbook/commit/34cb0818608… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-05-03 (Thu, 03 May 2018) Changed paths: M roles/stats/templates/influxdb.conf.j2 Log Message: ----------- disable influxdb max-row-limit to prevent data being cut off from display maybe we will need a limit eventually, but 10k seems too low **NOTE:** This service 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] 7ceff2: Uninstalled versions of snpeff and snpsift that we...
by GitHub 03 May '18

03 May '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 7ceff21faf4737faa78265bac4f4561434dc42eb https://github.com/galaxyproject/usegalaxy-playbook/commit/7ceff21faf4737fa… Author: Dave B <dave(a)bx.psu.edu> Date: 2018-05-03 (Thu, 03 May 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: ----------- Uninstalled versions of snpeff and snpsift that were incorrectly loading in center pane **NOTE:** This service 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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