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:
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Merge pull request #2386 from jxtx/gies-swarm
Docker swarm support for interactive environments
Compare: https://github.com/galaxyproject/galaxy/compare/288498ac84a4...4f3e0f6d4057
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:
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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:
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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:
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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
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