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

[galaxyproject/galaxy] a547fe: Docker swarm support for interactive environments
by GitHub 20 May '16

20 May '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a547feb9a035c1234bf1e3e506e946f4da3619e8 https://github.com/galaxyproject/galaxy/commit/a547feb9a035c1234bf1e3e506e9… Author: James Taylor <james(a)jamestaylor.org> Date: 2016-05-19 (Thu, 19 May 2016) Changed paths: M config/plugins/interactive_environments/jupyter/config/jupyter.ini.sample M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Docker swarm support for interactive environments Commit: 49b9f8128b4eb8688f416aefd33f922353cc6309 https://github.com/galaxyproject/galaxy/commit/49b9f8128b4eb8688f416aefd33f… Author: James Taylor <james(a)jamestaylor.org> Date: 2016-05-20 (Fri, 20 May 2016) Changed paths: M config/plugins/interactive_environments/jupyter/config/jupyter.ini.sample M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Support Docker Swarm without a configuration parameter Commit: 4f3e0f6d4057848f299f5b10a4e66eb4c0855071 https://github.com/galaxyproject/galaxy/commit/4f3e0f6d4057848f299f5b10a4e6… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-05-20 (Fri, 20 May 2016) Changed paths: M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Merge pull request #2386 from jxtx/gies-swarm Docker swarm support for interactive environments Compare: https://github.com/galaxyproject/galaxy/compare/288498ac84a4...4f3e0f6d4057

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[galaxyproject/galaxy] ad3a65: remove the comment that breaks toc generation
by GitHub 20 May '16

20 May '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/galaxy Commit: ad3a65a6881712b7dcd7e44ca55a6529144e4080 https://github.com/galaxyproject/galaxy/commit/ad3a65a6881712b7dcd7e44ca55a… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-05-18 (Wed, 18 May 2016) Changed paths: M doc/source/releases/index.rst Log Message: ----------- remove the comment that breaks toc generation Commit: d926b3f5099cb0f3153126a59d3a07374e486c80 https://github.com/galaxyproject/galaxy/commit/d926b3f5099cb0f3153126a59d3a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-05-18 (Wed, 18 May 2016) Changed paths: M doc/source/releases/index.rst Log Message: ----------- Merge pull request #2373 from martenson/fix=release-docs [16.04] remove the comment that breaks toc generation Commit: 5f8b9e04baf78f5a4009afc07184327b58b247d3 https://github.com/galaxyproject/galaxy/commit/5f8b9e04baf78f5a4009afc07184… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-05-19 (Thu, 19 May 2016) Changed paths: M templates/webapps/galaxy/workflow/sharing.mako Log Message: ----------- Remove stray print left in workflow sharing which actually throws an exception and breaks sharing when item_name is unicode. Commit: e194c64e262592018429c07ffae931899f130a28 https://github.com/galaxyproject/galaxy/commit/e194c64e262592018429c07ffae9… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2016-05-19 (Thu, 19 May 2016) Changed paths: M templates/webapps/galaxy/workflow/sharing.mako Log Message: ----------- Merge pull request #2377 from dannon/stray_print_breaking_sharing [16.04] Remove stray print left in workflow sharing which actually throws an … Commit: 8d0e1c51df31fa862baac815e24170cceeebb5da https://github.com/galaxyproject/galaxy/commit/8d0e1c51df31fa862baac815e241… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-05-20 (Fri, 20 May 2016) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/runners/pulsar.py Log Message: ----------- Fix Pulsar remote metadata temp files for https://github.com/galaxyproject/galaxy/pull/1688/commits/a2e31403753c407e7… xref #1688 and https://github.com/galaxyproject/galaxy/commit/2a90811ea37e1361d58538f11500… Commit: ac5a328e5f56d395940e29532facc5655f79d8fe https://github.com/galaxyproject/galaxy/commit/ac5a328e5f56d395940e29532fac… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-05-20 (Fri, 20 May 2016) Changed paths: M doc/source/releases/index.rst M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/runners/pulsar.py M templates/webapps/galaxy/workflow/sharing.mako Log Message: ----------- Merge branch 'release_16.04' Compare: https://github.com/galaxyproject/galaxy/compare/f730f2d1abff...ac5a328e5f56

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[galaxyproject/galaxy] 8d0e1c: Fix Pulsar remote metadata temp files for https://...
by GitHub 20 May '16

20 May '16

Branch: refs/heads/release_16.04 Home: https://github.com/galaxyproject/galaxy Commit: 8d0e1c51df31fa862baac815e24170cceeebb5da https://github.com/galaxyproject/galaxy/commit/8d0e1c51df31fa862baac815e241… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-05-20 (Fri, 20 May 2016) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/runners/pulsar.py Log Message: ----------- Fix Pulsar remote metadata temp files for https://github.com/galaxyproject/galaxy/pull/1688/commits/a2e31403753c407e7… xref #1688 and https://github.com/galaxyproject/galaxy/commit/2a90811ea37e1361d58538f11500…

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[galaxyproject/galaxy] 17e829: add edam_data infrastructure to the Galaxy datatyp...
by GitHub 20 May '16

20 May '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 17e82957af9d4a586ee8262f0fb6e98041d436f5 https://github.com/galaxyproject/galaxy/commit/17e82957af9d4a586ee8262f0fb6… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2016-05-20 (Fri, 20 May 2016) Changed paths: M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/registry.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parser/output_objects.py M lib/galaxy/webapps/galaxy/api/datatypes.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- add edam_data infrastructure to the Galaxy datatypes Commit: 8a2b08096ad197df229df8f77eeeed2c4d3e5068 https://github.com/galaxyproject/galaxy/commit/8a2b08096ad197df229df8f77eee… Author: Hervé Ménager <herve.menager(a)gmail.com> Date: 2016-05-20 (Fri, 20 May 2016) Changed paths: M lib/galaxy/datatypes/data.py Log Message: ----------- add basic EDAM data metadata for data.py datatypes Based on agreement with bgruening, jongithub, and fmareuil on the annotation of datatypes with EDAM data concepts. Commit: 5714c85a79d88d4efddcc30f414d376be9a79306 https://github.com/galaxyproject/galaxy/commit/5714c85a79d88d4efddcc30f414d… Author: Hervé Ménager <herve.menager(a)gmail.com> Date: 2016-05-20 (Fri, 20 May 2016) Changed paths: M lib/galaxy/datatypes/sequence.py Log Message: ----------- add basic EDAM data metadata for sequence.py datatypes Based on agreement with bgruening, jongithub, and fmareuil on the annotation of datatypes with EDAM data concepts. Commit: 98e33d0b525db1ce3d7a66e7ee2d8fb63798d366 https://github.com/galaxyproject/galaxy/commit/98e33d0b525db1ce3d7a66e7ee2d… Author: Hervé Ménager <herve.menager(a)gmail.com> Date: 2016-05-20 (Fri, 20 May 2016) Changed paths: M lib/galaxy/datatypes/assembly.py Log Message: ----------- add EDAM data/formats to assembly datatypes Commit: 4ebeb548fdea3d157b62cae7a6e613e7821e292d https://github.com/galaxyproject/galaxy/commit/4ebeb548fdea3d157b62cae7a6e6… Author: Hervé Ménager <hmenager(a)pasteur.fr> Date: 2016-05-20 (Fri, 20 May 2016) Changed paths: M lib/galaxy/datatypes/xml.py Log Message: ----------- add EDAM format and data for Phylo XML Commit: 907950df803e881bbefc4bf16ad8e9a0cff5725d https://github.com/galaxyproject/galaxy/commit/907950df803e881bbefc4bf16ad8… Author: Hervé Ménager <hmenager(a)pasteur.fr> Date: 2016-05-20 (Fri, 20 May 2016) Changed paths: M lib/galaxy/datatypes/triples.py Log Message: ----------- complete EDAM annotations for triple datatypes. Commit: c0867c665306bc59d8353a3fb192f49c87bbd7d7 https://github.com/galaxyproject/galaxy/commit/c0867c665306bc59d8353a3fb192… Author: Hervé Ménager <hmenager(a)pasteur.fr> Date: 2016-05-20 (Fri, 20 May 2016) Changed paths: M lib/galaxy/datatypes/tracks.py Log Message: ----------- complete EDAM annotations for Gene track format Commit: 0002eac91fa644e22aa5b939405e6e4801239384 https://github.com/galaxyproject/galaxy/commit/0002eac91fa644e22aa5b939405e… Author: Hervé Ménager <hmenager(a)pasteur.fr> Date: 2016-05-20 (Fri, 20 May 2016) Changed paths: M lib/galaxy/datatypes/text.py Log Message: ----------- complete EDAM annotations in text datatypes. Commit: 425cee668d3d0ab2b0f4912aabb370b600218199 https://github.com/galaxyproject/galaxy/commit/425cee668d3d0ab2b0f4912aabb3… Author: Hervé Ménager <hmenager(a)pasteur.fr> Date: 2016-05-20 (Fri, 20 May 2016) Changed paths: M lib/galaxy/datatypes/qualityscore.py Log Message: ----------- add EDAM annotations to quality datatypes. Commit: c69aa8b54923b2df4ad6b7a430459a6767fb8f27 https://github.com/galaxyproject/galaxy/commit/c69aa8b54923b2df4ad6b7a43045… Author: Hervé Ménager <hmenager(a)pasteur.fr> Date: 2016-05-20 (Fri, 20 May 2016) Changed paths: M lib/galaxy/datatypes/proteomics.py Log Message: ----------- add EDAM annotation to proteomics datatypes Commit: 0511d72e4a14e8d0c357733564f1ad6cea649723 https://github.com/galaxyproject/galaxy/commit/0511d72e4a14e8d0c357733564f1… Author: Hervé Ménager <hmenager(a)pasteur.fr> Date: 2016-05-20 (Fri, 20 May 2016) Changed paths: M lib/galaxy/datatypes/msa.py Log Message: ----------- add EDAM annotations to msa datatypes. Commit: 2a7436eb630d79072b8f1c4a80ccf1262a195cef https://github.com/galaxyproject/galaxy/commit/2a7436eb630d79072b8f1c4a80cc… Author: Hervé Ménager <hmenager(a)pasteur.fr> Date: 2016-05-20 (Fri, 20 May 2016) Changed paths: M lib/galaxy/datatypes/interval.py Log Message: ----------- add EDAM annotations to interval datatypes. Commit: ec7519b267229ae4c13c6687332d3bb6e467718b https://github.com/galaxyproject/galaxy/commit/ec7519b267229ae4c13c6687332d… Author: Hervé Ménager <hmenager(a)pasteur.fr> Date: 2016-05-20 (Fri, 20 May 2016) Changed paths: M lib/galaxy/datatypes/images.py Log Message: ----------- add EDAM annotations to image datatypes. Commit: 6929cd4cd15e176054bec286c440ca7f97589efe https://github.com/galaxyproject/galaxy/commit/6929cd4cd15e176054bec286c440… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-05-20 (Fri, 20 May 2016) Changed paths: M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/proteomics.py M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/text.py Log Message: ----------- Address review comments by @nsoranzo Commit: 50fe4914339ac6c1f2a80c87eb4ee89967db9297 https://github.com/galaxyproject/galaxy/commit/50fe4914339ac6c1f2a80c87eb4e… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-05-20 (Fri, 20 May 2016) Changed paths: M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/qualityscore.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/webapps/galaxy/api/datatypes.py Log Message: ----------- Fix PEP8 for biotools PR Commit: 2a5b04075cd3d3f467c58f2ef134088931725d6f https://github.com/galaxyproject/galaxy/commit/2a5b04075cd3d3f467c58f2ef134… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-05-20 (Fri, 20 May 2016) Changed paths: M lib/galaxy/datatypes/assembly.py M lib/galaxy/datatypes/images.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Fix some review comments Commit: 9460e6ea4910d086409419b5e17a2ce34da0f15a https://github.com/galaxyproject/galaxy/commit/9460e6ea4910d086409419b5e17a… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-05-20 (Fri, 20 May 2016) Changed paths: M lib/galaxy/datatypes/assembly.py M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/msa.py M lib/galaxy/datatypes/proteomics.py M lib/galaxy/datatypes/qualityscore.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/xml.py Log Message: ----------- More constistent ordering. Remove some blank lines Commit: 1b7c4395e279903a13f61c0789dd868628fc943f https://github.com/galaxyproject/galaxy/commit/1b7c4395e279903a13f61c0789dd… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-05-20 (Fri, 20 May 2016) Changed paths: M lib/galaxy/datatypes/assembly.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/images.py M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/msa.py M lib/galaxy/datatypes/proteomics.py M lib/galaxy/datatypes/qualityscore.py M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/text.py M lib/galaxy/datatypes/tracks.py M lib/galaxy/datatypes/triples.py M lib/galaxy/datatypes/xml.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parser/output_objects.py M lib/galaxy/webapps/galaxy/api/datatypes.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Merge pull request #2387 from nsoranzo/edam_data Add support for EDAM data annotations to datatypes Compare: https://github.com/galaxyproject/galaxy/compare/b6f8e1c7996c...1b7c4395e279

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[galaxyproject/galaxy] ad3a65: remove the comment that breaks toc generation
by GitHub 19 May '16

19 May '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ad3a65a6881712b7dcd7e44ca55a6529144e4080 https://github.com/galaxyproject/galaxy/commit/ad3a65a6881712b7dcd7e44ca55a… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-05-18 (Wed, 18 May 2016) Changed paths: M doc/source/releases/index.rst Log Message: ----------- remove the comment that breaks toc generation Commit: d926b3f5099cb0f3153126a59d3a07374e486c80 https://github.com/galaxyproject/galaxy/commit/d926b3f5099cb0f3153126a59d3a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-05-18 (Wed, 18 May 2016) Changed paths: M doc/source/releases/index.rst Log Message: ----------- Merge pull request #2373 from martenson/fix=release-docs [16.04] remove the comment that breaks toc generation Commit: 5f8b9e04baf78f5a4009afc07184327b58b247d3 https://github.com/galaxyproject/galaxy/commit/5f8b9e04baf78f5a4009afc07184… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-05-19 (Thu, 19 May 2016) Changed paths: M templates/webapps/galaxy/workflow/sharing.mako Log Message: ----------- Remove stray print left in workflow sharing which actually throws an exception and breaks sharing when item_name is unicode. Commit: e194c64e262592018429c07ffae931899f130a28 https://github.com/galaxyproject/galaxy/commit/e194c64e262592018429c07ffae9… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2016-05-19 (Thu, 19 May 2016) Changed paths: M templates/webapps/galaxy/workflow/sharing.mako Log Message: ----------- Merge pull request #2377 from dannon/stray_print_breaking_sharing [16.04] Remove stray print left in workflow sharing which actually throws an … Commit: b6f8e1c7996cdd86e286a7f3f6af62f247428e3a https://github.com/galaxyproject/galaxy/commit/b6f8e1c7996cdd86e286a7f3f6af… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-05-19 (Thu, 19 May 2016) Changed paths: M doc/source/releases/index.rst Log Message: ----------- Merge branch 'release_16.04' into dev Compare: https://github.com/galaxyproject/galaxy/compare/eb430f4078d4...b6f8e1c7996c

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[galaxyproject/galaxy] c453d7: With the removal of Python 2.6 support, the backpo...
by GitHub 19 May '16

19 May '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c453d742effb5bb619c7b8b25181b5967c75c3a4 https://github.com/galaxyproject/galaxy/commit/c453d742effb5bb619c7b8b25181… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-05-19 (Thu, 19 May 2016) Changed paths: M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/conditional-requirements.txt R lib/galaxy/util/backports/importlib/__init__.py M lib/galaxy/web/framework/webapp.py Log Message: ----------- With the removal of Python 2.6 support, the backport of importlib and ordereddict are no longer necessary. Commit: 2b489df04cac987a1e88948fca2df702fedc429a https://github.com/galaxyproject/galaxy/commit/2b489df04cac987a1e88948fca2d… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-05-19 (Thu, 19 May 2016) Changed paths: M lib/galaxy/dependencies/__init__.py Log Message: ----------- Remove import of unused sys.version_info Commit: eb430f4078d496ed020262a7fcddf3094da98680 https://github.com/galaxyproject/galaxy/commit/eb430f4078d496ed020262a7fcdd… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-05-19 (Thu, 19 May 2016) Changed paths: M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/conditional-requirements.txt R lib/galaxy/util/backports/importlib/__init__.py M lib/galaxy/web/framework/webapp.py Log Message: ----------- Merge pull request #2380 from natefoo/remove-py26-deps Remove backported importlib and ordereddict Compare: https://github.com/galaxyproject/galaxy/compare/55c0de689167...eb430f4078d4

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[galaxyproject/galaxy] 49cb1d: Note on updating tool testing
by GitHub 19 May '16

19 May '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 49cb1d6a0ab5e1c57eeb1878ad831c8e40914673 https://github.com/galaxyproject/galaxy/commit/49cb1d6a0ab5e1c57eeb1878ad83… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-05-19 (Thu, 19 May 2016) Changed paths: M scripts/bootstrap_history.py Log Message: ----------- Note on updating tool testing Commit: d1e07e989d32c781344b0c198e96fc172bb74386 https://github.com/galaxyproject/galaxy/commit/d1e07e989d32c781344b0c198e96… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-05-19 (Thu, 19 May 2016) Changed paths: M scripts/bootstrap_history.py Log Message: ----------- Add devteam Commit: 55c0de689167b2335789d91650c106eda560b31e https://github.com/galaxyproject/galaxy/commit/55c0de689167b2335789d91650c1… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-05-19 (Thu, 19 May 2016) Changed paths: M scripts/bootstrap_history.py Log Message: ----------- Merge pull request #2381 from erasche/from-iuc-764 Note on updating tool testing Compare: https://github.com/galaxyproject/galaxy/compare/b44e284be3ed...55c0de689167

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[galaxyproject/galaxy]
by GitHub 19 May '16

19 May '16

Branch: refs/heads/docker_release Home: https://github.com/galaxyproject/galaxy

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[galaxyproject/galaxy] 6e6bfc: Update template to include the release of the Dock...
by GitHub 19 May '16

19 May '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 6e6bfc796d0aa6a7c795debe2be43e82b949590a https://github.com/galaxyproject/galaxy/commit/6e6bfc796d0aa6a7c795debe2be4… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-05-19 (Thu, 19 May 2016) Changed paths: M scripts/bootstrap_history.py Log Message: ----------- Update template to include the release of the Docker container Commit: b44e284be3ed15a3fb3bb77bfac07110ad4ce96d https://github.com/galaxyproject/galaxy/commit/b44e284be3ed15a3fb3bb77bfac0… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-05-19 (Thu, 19 May 2016) Changed paths: M scripts/bootstrap_history.py Log Message: ----------- Merge pull request #2378 from galaxyproject/docker_release Update template to include the release of the Docker container Compare: https://github.com/galaxyproject/galaxy/compare/8cdc1244ef34...b44e284be3ed

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[galaxyproject/galaxy] 6e6bfc: Update template to include the release of the Dock...
by GitHub 19 May '16

19 May '16

Branch: refs/heads/docker_release Home: https://github.com/galaxyproject/galaxy Commit: 6e6bfc796d0aa6a7c795debe2be43e82b949590a https://github.com/galaxyproject/galaxy/commit/6e6bfc796d0aa6a7c795debe2be4… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-05-19 (Thu, 19 May 2016) Changed paths: M scripts/bootstrap_history.py Log Message: ----------- Update template to include the release of the Docker container

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