galaxy-commits January 2018

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[galaxyproject/galaxy] 747309: Fix tool-shed-config-validate
by GitHub 25 Jan '18

25 Jan '18

Branch: refs/heads/release_17.09 Home: https://github.com/galaxyproject/galaxy Commit: 747309b2786da3e18cdd962d977b2ee72afdb5dc https://github.com/galaxyproject/galaxy/commit/747309b2786da3e18cdd962d977b… Author: ValentinChCloud <chavaldranis(a)gmail.com> Date: 2018-01-19 (Fri, 19 Jan 2018) Changed paths: M lib/galaxy/webapps/config_manage.py Log Message: ----------- Fix tool-shed-config-validate Commit: 73418ab7875e7e5fb2669a13fc0d55a40b7180a3 https://github.com/galaxyproject/galaxy/commit/73418ab7875e7e5fb2669a13fc0d… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-01-25 (Thu, 25 Jan 2018) Changed paths: M lib/galaxy/webapps/config_manage.py Log Message: ----------- Merge pull request #5343 from ValentinChCloud/fixes [17.09] Fix tool-shed-config-validate Compare: https://github.com/galaxyproject/galaxy/compare/7996a4c0c73e...73418ab7875e

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[galaxyproject/galaxy] e821d4: Try next dep. resolver if building env failed
by GitHub 25 Jan '18

25 Jan '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: e821d469e60959614147bde59163d75681bae266 https://github.com/galaxyproject/galaxy/commit/e821d469e60959614147bde59163… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-01-25 (Thu, 25 Jan 2018) Changed paths: M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/views.py Log Message: ----------- Try next dep. resolver if building env failed Otherwise an exception ("Conda dependency seemingly installed but failed to build job environment." comes to mind) would entirely stop the job submission. Ping @bgruening. Commit: c0cf41a15ccf7f9060c4dd891ff4b16814f7ecbc https://github.com/galaxyproject/galaxy/commit/c0cf41a15ccf7f9060c4dd891ff4… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-01-25 (Thu, 25 Jan 2018) Changed paths: M lib/galaxy/tools/deps/__init__.py Log Message: ----------- Avoid duplicate dependency installation The previous commit changed the resolver logic to try all resolvers, so that when building an environment fails, the next resolver can be tried. Since dependency resolution and installation are coupled it would be possible to install dependencies multiple times for different resolvers (e.g for Conda and Conda versionless). To avoid this we stop installation once a set of dependencies has been resolved. Commit: b24217c25b3d7b0ad50b33723515f763a48b99fb https://github.com/galaxyproject/galaxy/commit/b24217c25b3d7b0ad50b33723515… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-01-25 (Thu, 25 Jan 2018) Changed paths: M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/views.py Log Message: ----------- Merge pull request #5036 from mvdbeek/resolver_improvements Try next dep. resolver if building env failed Compare: https://github.com/galaxyproject/galaxy/compare/e79048be5a4f...b24217c25b3d

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[galaxyproject/galaxy] 545a92: Constrain workflow tool panel entries to those not...
by GitHub 25 Jan '18

25 Jan '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 545a920790f70322c7ed7e67688d121c1b6eab45 https://github.com/galaxyproject/galaxy/commit/545a920790f70322c7ed7e67688d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-01-23 (Tue, 23 Jan 2018) Changed paths: M lib/galaxy/model/mapping.py Log Message: ----------- Constrain workflow tool panel entries to those not deleted. Commit: a31ff8a73f769544df1927b0b5ec016ec74e79fb https://github.com/galaxyproject/galaxy/commit/a31ff8a73f769544df1927b0b5ec… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-01-23 (Tue, 23 Jan 2018) Changed paths: M lib/galaxy/model/mapping.py Log Message: ----------- Mutable default arg fix in mapping init Commit: e79048be5a4fc82979137ab9c845ddcf1dd5b93d https://github.com/galaxyproject/galaxy/commit/e79048be5a4fc82979137ab9c845… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-01-25 (Thu, 25 Jan 2018) Changed paths: M lib/galaxy/model/mapping.py Log Message: ----------- Merge pull request #5368 from dannon/workflow-tool-menu Workflow tool menu fix for deleted workflows Compare: https://github.com/galaxyproject/galaxy/compare/e11048881cb6...e79048be5a4f

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[galaxyproject/galaxy] 3aacf9: Make TabularToolDataTable._deduplicate_data() fast...
by GitHub 25 Jan '18

25 Jan '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 3aacf9442aff4ddfec6363018a7220034548a48e https://github.com/galaxyproject/galaxy/commit/3aacf9442aff4ddfec6363018a72… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-01-25 (Thu, 25 Jan 2018) Changed paths: M lib/galaxy/tools/data/__init__.py Log Message: ----------- Make TabularToolDataTable._deduplicate_data() faster Another improvement for https://github.com/galaxyproject/galaxy/issues/4783 . Reduces the time to deduplicate `snpeffv_databases.loc` data table (42762 lines) from seconds to milliseconds. Commit: e11048881cb67d1f49e1cdbc7514802e5c970ac7 https://github.com/galaxyproject/galaxy/commit/e11048881cb67d1f49e1cdbc7514… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-01-25 (Thu, 25 Jan 2018) Changed paths: M lib/galaxy/tools/data/__init__.py Log Message: ----------- Merge pull request #5383 from nsoranzo/deduplicate_speedup Make TabularToolDataTable._deduplicate_data() faster Compare: https://github.com/galaxyproject/galaxy/compare/091c5042d99d...e11048881cb6

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[galaxyproject/galaxy] 743432: Constrain tag editor height, minor refactoring. W...
by GitHub 24 Jan '18

24 Jan '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 74343260061e5dc2813efccbff740fe8e3a7b829 https://github.com/galaxyproject/galaxy/commit/74343260061e5dc2813efccbff74… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-01-18 (Thu, 18 Jan 2018) Changed paths: M client/galaxy/style/less/base.less M client/galaxy/style/less/dataset.less M client/galaxy/style/less/history.less Log Message: ----------- Constrain tag editor height, minor refactoring. Will be removed with the conversion to a vue component that can pop out with a more flexible display. Commit: d51ea5d200412af2c0a8a8158a8265530858ebe6 https://github.com/galaxyproject/galaxy/commit/d51ea5d200412af2c0a8a8158a82… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-01-18 (Thu, 18 Jan 2018) Changed paths: M client/galaxy/style/less/base.less Log Message: ----------- Constrain the select2 container for the tags display, instead of the outer box; this prevents the prompt from (in some cases) taking the space. Commit: 091c5042d99d02bfb5d79293bc8b9022c560022a https://github.com/galaxyproject/galaxy/commit/091c5042d99d02bfb5d79293bc8b… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-01-24 (Wed, 24 Jan 2018) Changed paths: M client/galaxy/style/less/base.less M client/galaxy/style/less/dataset.less M client/galaxy/style/less/history.less Log Message: ----------- Merge pull request #5337 from dannon/tag_editor_constraint Tag editor size constraint Compare: https://github.com/galaxyproject/galaxy/compare/d627e5e0b6a1...091c5042d99d

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[galaxyproject/galaxy] a7ee27: Force a new node version when building client for ...
by GitHub 24 Jan '18

24 Jan '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a7ee27614a9253bd61d58090781f555a22010b86 https://github.com/galaxyproject/galaxy/commit/a7ee27614a9253bd61d58090781f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-01-24 (Wed, 24 Jan 2018) Changed paths: M .ci/jenkins/selenium/run_tests.sh Log Message: ----------- Force a new node version when building client for Jenkins. At least one of our Jenkins nodes - possibly more - is failing to build the client without failing the test outright. Commit: d627e5e0b6a1a5a0058c9b3a4a2f94477a6e81b4 https://github.com/galaxyproject/galaxy/commit/d627e5e0b6a1a5a0058c9b3a4a2f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-01-24 (Wed, 24 Jan 2018) Changed paths: M .ci/jenkins/selenium/run_tests.sh Log Message: ----------- Merge pull request #5382 from jmchilton/pin_node_image Force a fixed node image version when building client for Jenkins. Compare: https://github.com/galaxyproject/galaxy/compare/b236140fbf63...d627e5e0b6a1

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[galaxyproject/usegalaxy-playbook] acf14d: Switch back to jetstream-tacc0 for swarm, seems th...
by GitHub 24 Jan '18

24 Jan '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: acf14d868ad323838959f5d6f625d4f0635a3c21 https://github.com/galaxyproject/usegalaxy-playbook/commit/acf14d868ad32383… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-01-24 (Wed, 24 Jan 2018) Changed paths: M env/main/group_vars/galaxywebservers.yml M env/test/group_vars/galaxyservers/vars.yml Log Message: ----------- Switch back to jetstream-tacc0 for swarm, seems there are connection problems for the proxy.

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[galaxyproject/galaxy] 68b3fc: improve docs for config schema options
by GitHub 24 Jan '18

24 Jan '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 68b3fcec27e73787c4e3c0655a72675713e281ce https://github.com/galaxyproject/galaxy/commit/68b3fcec27e73787c4e3c0655a72… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-01-24 (Wed, 24 Jan 2018) Changed paths: M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- improve docs for config schema options Commit: 22489a721e9388b0f516f45c842129d6471b4cde https://github.com/galaxyproject/galaxy/commit/22489a721e9388b0f516f45c8421… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-01-24 (Wed, 24 Jan 2018) Changed paths: M config/galaxy.yml.sample Log Message: ----------- add generated sample Commit: b236140fbf632d9fe5b7a0e0dbc6593851668f41 https://github.com/galaxyproject/galaxy/commit/b236140fbf632d9fe5b7a0e0dbc6… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-01-24 (Wed, 24 Jan 2018) Changed paths: M config/galaxy.yml.sample M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- Merge pull request #5373 from martenson/docs-for-conf-schema improve config options docs Compare: https://github.com/galaxyproject/galaxy/compare/b1483c68c5b6...b236140fbf63

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[galaxyproject/galaxy] 775a9b: Bump conditional Pygments version to 2.2.0 so it m...
by GitHub 24 Jan '18

24 Jan '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 775a9bded50a59684ef87cf4c6f68bdb39214323 https://github.com/galaxyproject/galaxy/commit/775a9bded50a59684ef87cf4c6f6… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-01-24 (Wed, 24 Jan 2018) Changed paths: M lib/galaxy/dependencies/conditional-requirements.txt Log Message: ----------- Bump conditional Pygments version to 2.2.0 so it matches the dev version. Commit: b1483c68c5b665f6b5e807c09682d0add2aeedca https://github.com/galaxyproject/galaxy/commit/b1483c68c5b665f6b5e807c09682… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-01-24 (Wed, 24 Jan 2018) Changed paths: M lib/galaxy/dependencies/conditional-requirements.txt Log Message: ----------- Merge pull request #5376 from natefoo/pygments-version Bump conditional Pygments version to 2.2.0 so it matches the dev Compare: https://github.com/galaxyproject/galaxy/compare/20effb435eb9...b1483c68c5b6

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[galaxyproject/galaxy] 3cc1b2: Fix `make docs` when the virtualenv is not .venv
by GitHub 24 Jan '18

24 Jan '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 3cc1b25c185133fd5ededf3345c178ea863e75c4 https://github.com/galaxyproject/galaxy/commit/3cc1b25c185133fd5ededf3345c1… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-01-24 (Wed, 24 Jan 2018) Changed paths: M doc/Makefile Log Message: ----------- Fix `make docs` when the virtualenv is not .venv Commit: 20effb435eb9ad3fe9bb9e25161c228b52441307 https://github.com/galaxyproject/galaxy/commit/20effb435eb9ad3fe9bb9e25161c… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-01-24 (Wed, 24 Jan 2018) Changed paths: M doc/Makefile Log Message: ----------- Merge pull request #5377 from natefoo/make-docs Fix `make docs` when the virtualenv is not .venv Compare: https://github.com/galaxyproject/galaxy/compare/dd88194e8f56...20effb435eb9

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galaxy-commits January 2018