- galaxy-commits - lists.galaxyproject.org

[galaxyproject/usegalaxy-playbook] b9fdc1: Install cutadapt version 1.16
by GitHub 10 Sep '18

10 Sep '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: b9fdc182abaef5430a5b50b0efc107614f33705e https://github.com/galaxyproject/usegalaxy-playbook/commit/b9fdc182abaef543… Author: Dave B <dave(a)bx.psu.edu> Date: 2018-09-10 (Mon, 10 Sep 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: ----------- Install cutadapt version 1.16 **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] 8695a0: Keep newly broken tool in toolbox
by GitHub 10 Sep '18

10 Sep '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 8695a0d9bc4481ebf49ec9fc13db1c066243b12c https://github.com/galaxyproject/galaxy/commit/8695a0d9bc4481ebf49ec9fc13db… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-08 (Sat, 08 Sep 2018) Changed paths: M lib/galaxy/tools/cache.py M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Keep newly broken tool in toolbox That's handy when developing tools and you messed up something so bad the tool isn't valid anymore. We retrieve the non-broken previous version from the tool cache. Commit: 947389887b011fc277ac776b3f6c21c3dd6df96d https://github.com/galaxyproject/galaxy/commit/947389887b011fc277ac776b3f6c… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-08 (Sat, 08 Sep 2018) Changed paths: M test/unit/tools/test_toolbox.py Log Message: ----------- Add unit test that exercises reloading for broken tools Commit: dc49c3ea0ebd64ac2d1b51a67e7c18df06255804 https://github.com/galaxyproject/galaxy/commit/dc49c3ea0ebd64ac2d1b51a67e7c… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-08 (Sat, 08 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js M lib/galaxy/tools/__init__.py M lib/galaxy/tools/toolbox/base.py M test/unit/tools/test_toolbox.py Log Message: ----------- Provide visual feedback if tool is broken Commit: d42fb41cb0599488b17008849b79dc064f7e54f9 https://github.com/galaxyproject/galaxy/commit/d42fb41cb0599488b17008849b79… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-09-10 (Mon, 10 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js M lib/galaxy/tools/__init__.py M lib/galaxy/tools/cache.py M lib/galaxy/tools/toolbox/base.py M test/unit/tools/test_toolbox.py Log Message: ----------- Merge pull request #6681 from mvdbeek/continue_reloading_if_tool_is_broken Keep newly broken tool in toolbox Compare: https://github.com/galaxyproject/galaxy/compare/64bb339a31e8...d42fb41cb059 **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] 8b8806: update Test, remove gccbosc slide
by GitHub 10 Sep '18

10 Sep '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 8b88069457747738c9f06f1865ec2a4096902061 https://github.com/galaxyproject/usegalaxy-playbook/commit/8b88069457747738… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-09-10 (Mon, 10 Sep 2018) Changed paths: M env/common/templates/galaxy/static/welcome.html.j2 M env/test/files/galaxy/galaxy_version.yml Log Message: ----------- update Test, remove gccbosc slide **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] e0d120: document the sniff_compressed_dynamic_datatypes_de...
by GitHub 07 Sep '18

07 Sep '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: e0d1208834deb7762564d5ae1cdc84da682dde5f https://github.com/galaxyproject/galaxy/commit/e0d1208834deb7762564d5ae1cdc… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-08-28 (Tue, 28 Aug 2018) Changed paths: M config/galaxy.yml.sample M doc/source/admin/galaxy_options.rst M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- document the sniff_compressed_dynamic_datatypes_default config and include in sample Commit: b34414adc8a5afad30d4822dfbc794cfc3bad9ff https://github.com/galaxyproject/galaxy/commit/b34414adc8a5afad30d4822dfbc7… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-08-28 (Tue, 28 Aug 2018) Changed paths: M config/galaxy.yml.sample M doc/source/admin/galaxy_options.rst M lib/galaxy/config.py M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- switch the default to sniff compressed datatypes Commit: 0acdc8a1a3eecae23b1dfe0876cf15d0ab41aa05 https://github.com/galaxyproject/galaxy/commit/0acdc8a1a3eecae23b1dfe0876cf… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-08-29 (Wed, 29 Aug 2018) Changed paths: M test/api/test_tools_upload.py Log Message: ----------- adjust test definitions for compressed handling so it tests the new defaults Commit: 7c339c9bffb58a71053e8d6dd20122498061f7ec https://github.com/galaxyproject/galaxy/commit/7c339c9bffb58a71053e8d6dd201… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-29 (Wed, 29 Aug 2018) Changed paths: M test/api/test_tools_upload.py Log Message: ----------- Use uses_test_history for selected upload tests Commit: d437875513c4d88f5096952a63eca62a96ed68bb https://github.com/galaxyproject/galaxy/commit/d437875513c4d88f5096952a63ec… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-08-29 (Wed, 29 Aug 2018) Changed paths: M test/api/test_tools_upload.py Log Message: ----------- Merge pull request #29 from mvdbeek/martenson-rename-and-document-config-value Use uses_test_history for selected upload tests Commit: e1b32368028cf9360ecef6400c6ce26f1bb0adc8 https://github.com/galaxyproject/galaxy/commit/e1b32368028cf9360ecef6400c6c… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-08-30 (Thu, 30 Aug 2018) Changed paths: M test/api/test_tools_upload.py Log Message: ----------- fix tests for the bed.gz dtaatype compressed beds are not part of the datatypes_conf.xml.sample Commit: 4a21ac30ea51aba6df2d98076a67caaa2e3feed0 https://github.com/galaxyproject/galaxy/commit/4a21ac30ea51aba6df2d98076a67… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-08-30 (Thu, 30 Aug 2018) Changed paths: M test/api/test_tools_upload.py Log Message: ----------- Merge branch 'rename-and-document-config-value' of github.com:martenson/galaxy into rename-and-document-config-value Commit: 9b5724d62d614d8f1e721f169ed76d0c5c6a789c https://github.com/galaxyproject/galaxy/commit/9b5724d62d614d8f1e721f169ed7… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-08-30 (Thu, 30 Aug 2018) Changed paths: M test/api/test_tools_upload.py Log Message: ----------- add back the unstable flags for bed.gz datasets I expect the datatypes_conf.xml bed compress default will change in near future Commit: 64bb339a31e8e2559bbb4ba81e8f27f65d1fe412 https://github.com/galaxyproject/galaxy/commit/64bb339a31e8e2559bbb4ba81e8f… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2018-09-08 (Sat, 08 Sep 2018) Changed paths: M config/galaxy.yml.sample M doc/source/admin/galaxy_options.rst M lib/galaxy/config.py M lib/galaxy/webapps/galaxy/config_schema.yml M test/api/test_tools_upload.py Log Message: ----------- Merge pull request #6641 from martenson/rename-and-document-config-value document config for sniffing compressed files, enable by default Compare: https://github.com/galaxyproject/galaxy/compare/f5194910f724...64bb339a31e8 **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] d6f017: Escape parenthesis in output names
by GitHub 07 Sep '18

07 Sep '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d6f01741a111180f5a4f3a4af56d017250dca124 https://github.com/galaxyproject/galaxy/commit/d6f01741a111180f5a4f3a4af56d… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-07 (Fri, 07 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-manager.js Log Message: ----------- Escape parenthesis in output names Otherwise this leads to: ``` webpack-internal:///0:1468 Uncaught Error: Syntax error, unrecognized expression: .callout.with (parenthesis) at Function.Sizzle.error (webpack-internal:///0:1468) at Sizzle.tokenize (webpack-internal:///0:2125) at Function.Sizzle (webpack-internal:///0:838) at Function.jQuery.find (webpack-internal:///453:290) at jQuery.fn.init.find (webpack-internal:///0:2792) at jQuery.fn.init.jQuery.fn.find (webpack-internal:///453:677) at child.eval (webpack-internal:///760:322) at Function.each (webpack-internal:///0:371) at Object.eval (webpack-internal:///760:319) at Function.each (webpack-internal:///0:371) ``` Commit: f5194910f724554df3b2ac17ff489c0c986cc1ac https://github.com/galaxyproject/galaxy/commit/f5194910f724554df3b2ac17ff48… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-09-07 (Fri, 07 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-manager.js Log Message: ----------- Merge pull request #6680 from mvdbeek/subworkflow_escape_names Fix wf-editor when loading subworkflow with parenthesis in label Compare: https://github.com/galaxyproject/galaxy/compare/95462754c09f...f5194910f724 **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] e110c8: Use the error severity to send fewer messages to l...
by GitHub 07 Sep '18

07 Sep '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: e110c831b2694088b19cfb35a8ca9d876431b381 https://github.com/galaxyproject/usegalaxy-playbook/commit/e110c831b2694088… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-09-07 (Fri, 07 Sep 2018) Changed paths: M env/test/templates/nginx/galaxy_test.j2 Log Message: ----------- Use the error severity to send fewer messages to logflux Commit: 8bb9241f6b6de6a2f1bedad5bece5521203abb2b https://github.com/galaxyproject/usegalaxy-playbook/commit/8bb9241f6b6de6a2… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-09-07 (Fri, 07 Sep 2018) Changed paths: A env/common/templates/nginx/default.j2 M env/test/group_vars/webservers/vars.yml A env/test/templates/nginx/default.j2 Log Message: ----------- Default nginx server for Galaxy servers w/ the status module enabled. Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/828cac65b3e7...… **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/infrastructure-playbook] d45011: Configure telegraf on Galaxy servers to log nginx.
by GitHub 07 Sep '18

07 Sep '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: d45011459599ad8d6985b8d891113ae6463f73a7 https://github.com/galaxyproject/infrastructure-playbook/commit/d4501145959… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-09-07 (Fri, 07 Sep 2018) Changed paths: M env/tacc/group_vars/galaxyservers.yml Log Message: ----------- Configure telegraf on Galaxy servers to log nginx. **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] 384a16: Allow schema to validate
by GitHub 07 Sep '18

07 Sep '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: 384a165aab2d579ee4c2dceba61f21c42c8c2dc4 https://github.com/galaxyproject/galaxy/commit/384a165aab2d579ee4c2dceba61f… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2018-04-19 (Thu, 19 Apr 2018) Changed paths: M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- Allow schema to validate Commit: 0b95898ccf68b8497dff9f322b44abc5668dfce6 https://github.com/galaxyproject/galaxy/commit/0b95898ccf68b8497dff9f322b44… Author: E Rasche <hxr(a)hx42.org> Date: 2018-05-01 (Tue, 01 May 2018) Changed paths: M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- Document pbkdf2 Commit: 3efda23b4fe84f1a61d83aba07186e46c81990ce https://github.com/galaxyproject/galaxy/commit/3efda23b4fe84f1a61d83aba0718… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-09-07 (Fri, 07 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- Restore logging block in galaxy config schema. Commit: 7d7a875af398c440040e78dcc2516aae1c6eb041 https://github.com/galaxyproject/galaxy/commit/7d7a875af398c440040e78dcc251… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-09-07 (Fri, 07 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- Merge pull request #5919 from erasche/fix-config-validate [18.01] Allow schema to validate Compare: https://github.com/galaxyproject/galaxy/compare/6d9df51f36e2...7d7a875af398 **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] 828cac: Set data type for logflux
by GitHub 07 Sep '18

07 Sep '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 828cac65b3e7d6ec6960cc2c649e940da4841383 https://github.com/galaxyproject/usegalaxy-playbook/commit/828cac65b3e7d6ec… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-09-07 (Fri, 07 Sep 2018) Changed paths: M env/test/group_vars/logfluxservers.yml Log Message: ----------- Set data type for logflux **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] ee0c83: Serialize select field options
by GitHub 07 Sep '18

07 Sep '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ee0c8327e4b2f848c9f9d3c0003cc49781c149f4 https://github.com/galaxyproject/galaxy/commit/ee0c8327e4b2f848c9f9d3c0003c… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-07 (Fri, 07 Sep 2018) Changed paths: M lib/galaxy/web/form_builder.py Log Message: ----------- Serialize select field options This fixes the empty select list in the beta install interface. Commit: 95462754c09facf8ae767b88767003b2d00c1da1 https://github.com/galaxyproject/galaxy/commit/95462754c09facf8ae767b887670… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-09-07 (Fri, 07 Sep 2018) Changed paths: M lib/galaxy/web/form_builder.py Log Message: ----------- Merge pull request #6677 from mvdbeek/fix_shed_tool_conf_selection Serialize select field options, fixes beta install Compare: https://github.com/galaxyproject/galaxy/compare/ba22818ff45e...95462754c09f **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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