December 2016 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/infrastructure-playbook] 2f3614: Move from /var/run/sentry to /var/opt/sentry/run f...
by GitHub 12 Dec '16

12 Dec '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 2f36145ba2a3590a4d57dbb02dd742d55c00ad1a https://github.com/galaxyproject/infrastructure-playbook/commit/2f36145ba2a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-12-12 (Mon, 12 Dec 2016) Changed paths: M roles/sentry/defaults/main.yml M taccenv/group_vars/statsservers.yml Log Message: ----------- Move from /var/run/sentry to /var/opt/sentry/run for sentry.sock

1 0

[galaxyproject/galaxy] 4431d7: Extend list of tabular datatypes for bar diagrams
by GitHub 12 Dec '16

12 Dec '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4431d735c8908b19bbcd1ca594ec1a194cf4d299 https://github.com/galaxyproject/galaxy/commit/4431d735c8908b19bbcd1ca594ec… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-12-08 (Thu, 08 Dec 2016) Changed paths: M config/plugins/visualizations/charts/static/repository/build/registry.js M config/plugins/visualizations/charts/static/repository/build/registry.js.map M config/plugins/visualizations/charts/static/repository/visualizations/utilities/tabular-form.js Log Message: ----------- Extend list of tabular datatypes for bar diagrams Commit: 22687410c4829dd9a0e44f55ee93b1020c8eab20 https://github.com/galaxyproject/galaxy/commit/22687410c4829dd9a0e44f55ee93… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2016-12-09 (Fri, 09 Dec 2016) Changed paths: M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Ensure Conda prefix and cached environment are absolute paths Otherwise when Conda commands are executed from the job working directory, they will break. Commit: 879e3d69606e1a4b98bd34f75bf905b9da6edcfa https://github.com/galaxyproject/galaxy/commit/879e3d69606e1a4b98bd34f75bf9… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2016-12-09 (Fri, 09 Dec 2016) Changed paths: M lib/galaxy/tools/deps/__init__.py Log Message: ----------- Skip building cache if force_rebuild is False Also: - re-raise exception if rmtree() fails - change hash(ed)_requirements to hash(ed)_dependencies Commit: 7c9d9d2231ecc113f7d69737a4aa4ec140b7e48c https://github.com/galaxyproject/galaxy/commit/7c9d9d2231ecc113f7d69737a4aa… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-12-09 (Fri, 09 Dec 2016) Changed paths: M templates/webapps/galaxy/workflow/editor.mako Log Message: ----------- Apply a fix similar to 36134bca694c9dc6b2584fb661dfbce4ddb793e6 for the workflow editor. Not ideal, but this is old code we're replacing as the editor is overhauled. Commit: 5a7f9e876e28ea773b79af9bbb887de7cff4aaa7 https://github.com/galaxyproject/galaxy/commit/5a7f9e876e28ea773b79af9bbb88… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2016-12-11 (Sun, 11 Dec 2016) Changed paths: M lib/tool_shed/galaxy_install/install_manager.py Log Message: ----------- Correctly update TS repo status Execute build_dependency_cache() only if using a cached dependency manager. Set tool versions only if the TS repo contains tools. Raise exception if fetch_tool_versions() fails, previously the error message never reached the UI. Commit: 9dda310cd35e18c3ef86c5b09a021fc359fe5011 https://github.com/galaxyproject/galaxy/commit/9dda310cd35e18c3ef86c5b09a02… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-11 (Sun, 11 Dec 2016) Changed paths: M templates/webapps/galaxy/workflow/editor.mako Log Message: ----------- Merge pull request #3296 from dannon/workflow_editor_toolsearch_messagebox_fix [16.10] Workflow editor 'messagebox' fix. Commit: 22c7fcf3fff19ed9f271ada3cd8c007a96444768 https://github.com/galaxyproject/galaxy/commit/22c7fcf3fff19ed9f271ada3cd8c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-11 (Sun, 11 Dec 2016) Changed paths: M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/tool_shed/galaxy_install/install_manager.py Log Message: ----------- Merge pull request #3295 from nsoranzo/release_16.10_tool_install_fixes [16.10] Tool install fixes Commit: 2c833499b130aca72ab78d112692f2a9f0d4d9e6 https://github.com/galaxyproject/galaxy/commit/2c833499b130aca72ab78d112692… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-11 (Sun, 11 Dec 2016) Changed paths: M config/plugins/visualizations/charts/static/repository/build/registry.js M config/plugins/visualizations/charts/static/repository/build/registry.js.map M config/plugins/visualizations/charts/static/repository/visualizations/utilities/tabular-form.js Log Message: ----------- Merge pull request #3287 from guerler/fix_chart_datatypes [16.10] Rely on tabular subclass matching through vizframework layer Commit: 584114a4698076b79d77124b27867d6ea2386188 https://github.com/galaxyproject/galaxy/commit/584114a4698076b79d77124b2786… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2016-12-12 (Mon, 12 Dec 2016) Changed paths: M config/plugins/visualizations/charts/static/repository/build/registry.js M config/plugins/visualizations/charts/static/repository/build/registry.js.map M config/plugins/visualizations/charts/static/repository/visualizations/utilities/tabular-form.js M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/tool_shed/galaxy_install/install_manager.py M templates/webapps/galaxy/workflow/editor.mako Log Message: ----------- Merge branch 'release_16.10' into dev Conflicts: config/plugins/visualizations/charts/static/repository/build/registry.js config/plugins/visualizations/charts/static/repository/build/registry.js.map Compare: https://github.com/galaxyproject/galaxy/compare/c7568a1d871b...584114a46980

1 0

[galaxyproject/galaxy] 28c2ac: Adds a 'make charts' makefile target to make it mo...
by GitHub 12 Dec '16

12 Dec '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 28c2acf17dfc2b73276de0ba7cb73c93d730dde5 https://github.com/galaxyproject/galaxy/commit/28c2acf17dfc2b73276de0ba7cb7… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-12-12 (Mon, 12 Dec 2016) Changed paths: M Makefile Log Message: ----------- Adds a 'make charts' makefile target to make it more obvious how to build these. Not invoked automatically though, since these should very rarely conflict and we don't want to have version build difference conflicts (harmless) all the time. Commit: 8eba2f2f1bbc32a97eb51b97712fb67691723282 https://github.com/galaxyproject/galaxy/commit/8eba2f2f1bbc32a97eb51b97712f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-12-12 (Mon, 12 Dec 2016) Changed paths: M config/plugins/visualizations/charts/webpack.config.js Log Message: ----------- Remove unnecessary require -- webpack is expected as the executor here Commit: a0ae63d8c2983f17aa75b161bd25fa505af20a6c https://github.com/galaxyproject/galaxy/commit/a0ae63d8c2983f17aa75b161bd25… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-12-12 (Mon, 12 Dec 2016) Changed paths: M Makefile Log Message: ----------- Set NODE_MODULES var for 'grunt charts', required due to the execution model here. Commit: 49cdd7082d86c07ab07bb1bee8e4b26baf6b4eb8 https://github.com/galaxyproject/galaxy/commit/49cdd7082d86c07ab07bb1bee8e4… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-12-12 (Mon, 12 Dec 2016) Changed paths: M Makefile Log Message: ----------- Shot in the dark at @nsoranzo's build woes. Commit: 015c32854f2d9ff9402b73f9fe8b291cd2346df5 https://github.com/galaxyproject/galaxy/commit/015c32854f2d9ff9402b73f9fe8b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-12-12 (Mon, 12 Dec 2016) Changed paths: M Makefile Log Message: ----------- Override possible env var use which can break this -- we always want to use Galaxy's modules here anyway Commit: c7568a1d871b8c4c3816130c33a24e1e21e12f29 https://github.com/galaxyproject/galaxy/commit/c7568a1d871b8c4c3816130c33a2… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2016-12-12 (Mon, 12 Dec 2016) Changed paths: M Makefile M config/plugins/visualizations/charts/webpack.config.js Log Message: ----------- Merge pull request #3306 from dannon/charts_makefile_target Adds a 'make charts' makefile target to make it more obvious how to build these. Compare: https://github.com/galaxyproject/galaxy/compare/fc5ac197914b...c7568a1d871b

1 0

[galaxyproject/galaxy] 767c04: Fix SLURM job re-submission.
by GitHub 12 Dec '16

12 Dec '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 767c0400ae92bc541c146ce4ead351b6eacb1fb7 https://github.com/galaxyproject/galaxy/commit/767c0400ae92bc541c146ce4ead3… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-11 (Sun, 11 Dec 2016) Changed paths: M lib/galaxy/jobs/command_factory.py M test/unit/jobs/test_command_factory.py Log Message: ----------- Fix SLURM job re-submission. Approach from @Takadonet - fixes #3289. Commit: fc5ac197914bd1a957fd074424adee115f7a2d96 https://github.com/galaxyproject/galaxy/commit/fc5ac197914bd1a957fd074424ad… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-12-12 (Mon, 12 Dec 2016) Changed paths: M lib/galaxy/jobs/command_factory.py M test/unit/jobs/test_command_factory.py Log Message: ----------- Merge pull request #3290 from jmchilton/clean_working_directory Fix SLURM job re-submission. Compare: https://github.com/galaxyproject/galaxy/compare/f6a573a4191c...fc5ac197914b

1 0

[galaxyproject/galaxy] 32898f: Bring in galaxyproject/galaxy-lib#36 from @bgrueni...
by GitHub 12 Dec '16

12 Dec '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 32898fb6bfada2b0a57ac45813f2751cc77dd7c5 https://github.com/galaxyproject/galaxy/commit/32898fb6bfada2b0a57ac45813f2… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-12 (Mon, 12 Dec 2016) Changed paths: M lib/galaxy/tools/deps/mulled/invfile.lua Log Message: ----------- Bring in galaxyproject/galaxy-lib#36 from @bgruening. Commit: f6a573a4191cf9c90fb4aac78d20064e11cb1c7b https://github.com/galaxyproject/galaxy/commit/f6a573a4191cf9c90fb4aac78d20… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2016-12-12 (Mon, 12 Dec 2016) Changed paths: M lib/galaxy/tools/deps/mulled/invfile.lua Log Message: ----------- Merge pull request #3304 from jmchilton/galaxy-lib-update-4 Bring in galaxyproject/galaxy-lib#36 from @bgruening. Compare: https://github.com/galaxyproject/galaxy/compare/8b9337ffd3f3...f6a573a4191c

1 0

[galaxyproject/galaxy] ef7adc: lexists vs. exists
by GitHub 12 Dec '16

12 Dec '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ef7adcec5300819d411b1fb148baf999f2d54422 https://github.com/galaxyproject/galaxy/commit/ef7adcec5300819d411b1fb148ba… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-12-11 (Sun, 11 Dec 2016) Changed paths: M lib/galaxy/tools/deps/installable.py Log Message: ----------- lexists vs. exists Commit: 8b9337ffd3f3911ed229dcdce1086f682302a4ae https://github.com/galaxyproject/galaxy/commit/8b9337ffd3f3911ed229dcdce108… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-12-12 (Mon, 12 Dec 2016) Changed paths: M lib/galaxy/tools/deps/installable.py Log Message: ----------- Merge pull request #3301 from bgruening/lexists lexists vs. exists Compare: https://github.com/galaxyproject/galaxy/compare/176d4d5cf49a...8b9337ffd3f3

1 0

[galaxyproject/galaxy] 96bd45: Further tighten up GG format.
by GitHub 12 Dec '16

12 Dec '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 96bd4552e1b1a7b18d57f8e0d0f1a5da22b085a1 https://github.com/galaxyproject/galaxy/commit/96bd4552e1b1a7b18d57f8e0d0f1… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-11 (Sun, 11 Dec 2016) Changed paths: M lib/galaxy/datatypes/genetics.py M lib/galaxy/datatypes/sniff.py Log Message: ----------- Further tighten up GG format. I encountered similar input problems to #864 - this helps a little. - Ensure first column is a valid marker as outlined on https://genome.ucsc.edu/goldenpath/help/hgGenomeHelp.html. - Avoid readlines() since it may allocate huge amounts on memory on certain inputs. - Eliminate bare exception. Rebased with bug fixes in original commit and better testing and tighter exception handling as suggested by @nsoranzo. Commit: 176d4d5cf49a5859357ba88f38ef6a2136fb8570 https://github.com/galaxyproject/galaxy/commit/176d4d5cf49a5859357ba88f38ef… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-12-12 (Mon, 12 Dec 2016) Changed paths: M lib/galaxy/datatypes/genetics.py M lib/galaxy/datatypes/sniff.py Log Message: ----------- Merge pull request #3233 from jmchilton/gg_datatype Further tighten up GG format. Compare: https://github.com/galaxyproject/galaxy/compare/e6374bfc211f...176d4d5cf49a

1 0

[galaxyproject/galaxy] 6435db: change nitesh's handle to reflect reality
by GitHub 11 Dec '16

11 Dec '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 6435db510594a48394896a8e5d8d2a7d129b629d https://github.com/galaxyproject/galaxy/commit/6435db510594a48394896a8e5d8d… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-12-01 (Thu, 01 Dec 2016) Changed paths: M doc/source/project/organization.rst Log Message: ----------- change nitesh's handle to reflect reality Commit: e6374bfc211f4192113eea28bbe588a33a197e9a https://github.com/galaxyproject/galaxy/commit/e6374bfc211f4192113eea28bbe5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-11 (Sun, 11 Dec 2016) Changed paths: M doc/source/project/organization.rst Log Message: ----------- Merge pull request #3253 from martenson/procedure-nitesh [PROCEDURES] change Nitesh's handle to reflect reality Compare: https://github.com/galaxyproject/galaxy/compare/06de9d0ae060...e6374bfc211f

1 0

[galaxyproject/galaxy] 4431d7: Extend list of tabular datatypes for bar diagrams
by GitHub 11 Dec '16

11 Dec '16

Branch: refs/heads/release_16.10 Home: https://github.com/galaxyproject/galaxy Commit: 4431d735c8908b19bbcd1ca594ec1a194cf4d299 https://github.com/galaxyproject/galaxy/commit/4431d735c8908b19bbcd1ca594ec… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-12-08 (Thu, 08 Dec 2016) Changed paths: M config/plugins/visualizations/charts/static/repository/build/registry.js M config/plugins/visualizations/charts/static/repository/build/registry.js.map M config/plugins/visualizations/charts/static/repository/visualizations/utilities/tabular-form.js Log Message: ----------- Extend list of tabular datatypes for bar diagrams Commit: 2c833499b130aca72ab78d112692f2a9f0d4d9e6 https://github.com/galaxyproject/galaxy/commit/2c833499b130aca72ab78d112692… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-11 (Sun, 11 Dec 2016) Changed paths: M config/plugins/visualizations/charts/static/repository/build/registry.js M config/plugins/visualizations/charts/static/repository/build/registry.js.map M config/plugins/visualizations/charts/static/repository/visualizations/utilities/tabular-form.js Log Message: ----------- Merge pull request #3287 from guerler/fix_chart_datatypes [16.10] Rely on tabular subclass matching through vizframework layer Compare: https://github.com/galaxyproject/galaxy/compare/22c7fcf3fff1...2c833499b130

1 0

[galaxyproject/galaxy] 226874: Ensure Conda prefix and cached environment are abs...
by GitHub 11 Dec '16

11 Dec '16

Branch: refs/heads/release_16.10 Home: https://github.com/galaxyproject/galaxy Commit: 22687410c4829dd9a0e44f55ee93b1020c8eab20 https://github.com/galaxyproject/galaxy/commit/22687410c4829dd9a0e44f55ee93… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2016-12-09 (Fri, 09 Dec 2016) Changed paths: M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Ensure Conda prefix and cached environment are absolute paths Otherwise when Conda commands are executed from the job working directory, they will break. Commit: 879e3d69606e1a4b98bd34f75bf905b9da6edcfa https://github.com/galaxyproject/galaxy/commit/879e3d69606e1a4b98bd34f75bf9… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2016-12-09 (Fri, 09 Dec 2016) Changed paths: M lib/galaxy/tools/deps/__init__.py Log Message: ----------- Skip building cache if force_rebuild is False Also: - re-raise exception if rmtree() fails - change hash(ed)_requirements to hash(ed)_dependencies Commit: 5a7f9e876e28ea773b79af9bbb887de7cff4aaa7 https://github.com/galaxyproject/galaxy/commit/5a7f9e876e28ea773b79af9bbb88… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2016-12-11 (Sun, 11 Dec 2016) Changed paths: M lib/tool_shed/galaxy_install/install_manager.py Log Message: ----------- Correctly update TS repo status Execute build_dependency_cache() only if using a cached dependency manager. Set tool versions only if the TS repo contains tools. Raise exception if fetch_tool_versions() fails, previously the error message never reached the UI. Commit: 22c7fcf3fff19ed9f271ada3cd8c007a96444768 https://github.com/galaxyproject/galaxy/commit/22c7fcf3fff19ed9f271ada3cd8c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-11 (Sun, 11 Dec 2016) Changed paths: M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/tool_shed/galaxy_install/install_manager.py Log Message: ----------- Merge pull request #3295 from nsoranzo/release_16.10_tool_install_fixes [16.10] Tool install fixes Compare: https://github.com/galaxyproject/galaxy/compare/9dda310cd35e...22c7fcf3fff1

1 0