galaxy-commits April 2017

galaxy-commits@lists.galaxyproject.org

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[galaxyproject/galaxy] 77caed: Update text.py Add interaction annotations to Snp...
by GitHub 17 Apr '17

17 Apr '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 77caed9861d3666150c49442df9374b63660c2e5 https://github.com/galaxyproject/galaxy/commit/77caed9861d3666150c49442df93… Author: Jim Johnson <jj(a)umn.edu> Date: 2017-04-17 (Mon, 17 Apr 2017) Changed paths: M lib/galaxy/datatypes/text.py Log Message: ----------- Update text.py Add interaction annotations to SnpEffDb metadata Interaction annotations are now included in SnpEff v4.3 Commit: e9011488f2f5bfe91f542d173a9f7b3132e414ad https://github.com/galaxyproject/galaxy/commit/e9011488f2f5bfe91f542d173a9f… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-04-17 (Mon, 17 Apr 2017) Changed paths: M lib/galaxy/datatypes/text.py Log Message: ----------- Merge pull request #3938 from jj-umn/patch-6 Update text.py Add interaction annotations to SnpEffDb metadata Compare: https://github.com/galaxyproject/galaxy/compare/695293f01563...e9011488f2f5

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[galaxyproject/galaxy] 29331b: Container interface abstraction. Support Docker an...
by GitHub 13 Apr '17

13 Apr '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 29331b36cf4ad350d4919679deeca6f342b1e182 https://github.com/galaxyproject/galaxy/commit/29331b36cf4ad350d4919679deec… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-04-04 (Tue, 04 Apr 2017) Changed paths: M .ci/flake8_docstrings_include_list.txt M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt A config/containers_conf.yml.sample M config/galaxy.ini.sample M lib/galaxy/config.py R lib/galaxy/container/__init__.py R lib/galaxy/container/docker_swarm.py A lib/galaxy/containers/__init__.py A lib/galaxy/containers/docker.py A lib/galaxy/containers/docker_decorators.py A lib/galaxy/containers/docker_model.py A lib/galaxy/containers/docker_swarm.py A lib/galaxy/containers/docker_swarm_manager.py M lib/galaxy/exceptions/__init__.py M lib/galaxy/util/submodules.py M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/web/proxy/__init__.py M lib/galaxy/webapps/galaxy/controllers/interactive_environments.py Log Message: ----------- Container interface abstraction. Support Docker and Docker Swarm mode (>1.12 SwarmKit). Container interface configuration is performed via the containers_conf.yml config file, for which a documented sample is provided. The GIE launcher has been modified to use the container interface if the `enable_beta_containers_interface` option is set in galaxy.ini. This removes some of the previous GIE-specific swarm mode work that was done. The Galaxy docker swarm manager also uses the container interface now. TODO: The API docker interfaces should be done fairly soon before we have many consumers of the docker model objects, because they'll probably be changed to more closely reflect their API representations. Commit: 695293f01563f56637ee6b63db2c96bfd0204f9f https://github.com/galaxyproject/galaxy/commit/695293f01563f56637ee6b63db2c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-04-13 (Thu, 13 Apr 2017) Changed paths: M .ci/flake8_docstrings_include_list.txt M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt A config/containers_conf.yml.sample M config/galaxy.ini.sample M lib/galaxy/config.py R lib/galaxy/container/__init__.py R lib/galaxy/container/docker_swarm.py A lib/galaxy/containers/__init__.py A lib/galaxy/containers/docker.py A lib/galaxy/containers/docker_decorators.py A lib/galaxy/containers/docker_model.py A lib/galaxy/containers/docker_swarm.py A lib/galaxy/containers/docker_swarm_manager.py M lib/galaxy/exceptions/__init__.py M lib/galaxy/util/submodules.py M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/web/proxy/__init__.py M lib/galaxy/webapps/galaxy/controllers/interactive_environments.py Log Message: ----------- Merge pull request #3863 from natefoo/containers-abstraction Container interface abstraction Compare: https://github.com/galaxyproject/galaxy/compare/040635d3dcee...695293f01563

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[galaxyproject/galaxy] c4cf41: Allow explicit workflow scheduler handler process ...
by GitHub 13 Apr '17

13 Apr '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c4cf4164b31249457a4cdb92405006136193b1bb https://github.com/galaxyproject/galaxy/commit/c4cf4164b31249457a4cdb924050… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-04-07 (Fri, 07 Apr 2017) Changed paths: M lib/galaxy/jobs/__init__.py A lib/galaxy/util/handlers.py M lib/galaxy/workflow/scheduling_manager.py M test/integration/test_workflow_handler_configuration.py A test/integration/workflow_handler_configuration_workflow_scheduler_conf.xml Log Message: ----------- Allow explicit workflow scheduler handler process configuration. Refactor job handler stuff to allow this with re-use. Commit: fd216163aec719314fb328b87e5bea6f871a3b0a https://github.com/galaxyproject/galaxy/commit/fd216163aec719314fb328b87e5b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-04-07 (Fri, 07 Apr 2017) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/util/handlers.py M lib/galaxy/workflow/scheduling_manager.py Log Message: ----------- Initial workflow scheduling handler fixes caught by :eagle::eyes:. Commit: 040635d3dcee4c13960170010c8a7c10319c4fd5 https://github.com/galaxyproject/galaxy/commit/040635d3dcee4c13960170010c8a… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-04-13 (Thu, 13 Apr 2017) Changed paths: M lib/galaxy/jobs/__init__.py A lib/galaxy/util/handlers.py M lib/galaxy/workflow/scheduling_manager.py M test/integration/test_workflow_handler_configuration.py A test/integration/workflow_handler_configuration_workflow_scheduler_conf.xml Log Message: ----------- Merge pull request #3844 from jmchilton/dev_workflow_conf Allow explicit configuration of handlers for workflow scheduling. Compare: https://github.com/galaxyproject/galaxy/compare/55c4d5245576...040635d3dcee

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[galaxyproject/galaxy] c134da: Identify and handle runtime values when generating...
by GitHub 13 Apr '17

13 Apr '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c134dac9d5f2ec86f0194d114d42c4742f63e6b9 https://github.com/galaxyproject/galaxy/commit/c134dac9d5f2ec86f0194d114d42… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-04-11 (Tue, 11 Apr 2017) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Identify and handle runtime values when generating displayed text Commit: 7439d03bafe6fad42db950e85c0e329a8f0c8bff https://github.com/galaxyproject/galaxy/commit/7439d03bafe6fad42db950e85c0e… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-04-11 (Tue, 11 Apr 2017) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Remove optional app parameter for text conversion caller Commit: 278030638c50e51e18f712d19a2b8e71c2efc4a1 https://github.com/galaxyproject/galaxy/commit/278030638c50e51e18f712d19a2b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-04-11 (Tue, 11 Apr 2017) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Use new runtime value identifier for select field context values Commit: 18b006cb75ba8f8c088e17ebc7adc52a7b0e11f8 https://github.com/galaxyproject/galaxy/commit/18b006cb75ba8f8c088e17ebc7ad… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-04-11 (Tue, 11 Apr 2017) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/wrappers.py Log Message: ----------- Remove app parameter from text conversion caller Commit: 8ef55bca36673a79974f9f2579543ed6cd15ef3d https://github.com/galaxyproject/galaxy/commit/8ef55bca36673a79974f9f257954… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-04-11 (Tue, 11 Apr 2017) Changed paths: M templates/show_params.mako M templates/webapps/galaxy/workflow/display.mako Log Message: ----------- Remove app parameter from callers used in makos Commit: 9c9a7b97c557444e564c2de6669c28c02226f857 https://github.com/galaxyproject/galaxy/commit/9c9a7b97c557444e564c2de6669c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-04-11 (Tue, 11 Apr 2017) Changed paths: M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/parameters/wrapped.py M lib/galaxy/tools/wrappers.py Log Message: ----------- Remove parsing of app parameter from select field wrapper Commit: 7f111eea528b0be4ad6dfd59bb69076c899ce6aa https://github.com/galaxyproject/galaxy/commit/7f111eea528b0be4ad6dfd59bb69… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-04-11 (Tue, 11 Apr 2017) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Add missing spaces Commit: 735e38d1a3c582727476f8223cdd7c4606e5b413 https://github.com/galaxyproject/galaxy/commit/735e38d1a3c582727476f8223cdd… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-04-11 (Tue, 11 Apr 2017) Changed paths: M test/unit/tools/test_wrappers.py Log Message: ----------- Adjust unit test cases Commit: 55c4d52455763f516aed03795b4a6550ae5744c6 https://github.com/galaxyproject/galaxy/commit/55c4d52455763f516aed03795b4a… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-04-13 (Thu, 13 Apr 2017) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/wrapped.py M lib/galaxy/tools/wrappers.py M templates/show_params.mako M templates/webapps/galaxy/workflow/display.mako M test/unit/tools/test_wrappers.py Log Message: ----------- Merge pull request #3920 from guerler/fix_display_to_text_for_runtime_values Identify and handle runtime values when generating displayed text Compare: https://github.com/galaxyproject/galaxy/compare/d21c8dc8f11c...55c4d5245576

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[galaxyproject/galaxy] 33d662: Fix another tool (GeneBed_Maf_Fasta2) requiring th...
by GitHub 13 Apr '17

13 Apr '17

Branch: refs/heads/release_17.01 Home: https://github.com/galaxyproject/galaxy Commit: 33d6628dabdf75c27979925cb45b94e7ab59d725 https://github.com/galaxyproject/galaxy/commit/33d6628dabdf75c27979925cb45b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-04-13 (Thu, 13 Apr 2017) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Fix another tool (GeneBed_Maf_Fasta2) requiring the legacy Galaxy environment. Commit: 1fe9c4d066e11b61767e22475a1392e0bbacf196 https://github.com/galaxyproject/galaxy/commit/1fe9c4d066e11b61767e22475a13… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-04-13 (Thu, 13 Apr 2017) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Merge pull request #3931 from jmchilton/maf_fix_47 [17.01] Fix another tool (GeneBed_Maf_Fasta2) requiring the legacy Galaxy environment. Compare: https://github.com/galaxyproject/galaxy/compare/93b366d75a99...1fe9c4d066e1

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[galaxyproject/galaxy] 676b5c: Fix inability to raise errors if OS in non en_US
by GitHub 13 Apr '17

13 Apr '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 676b5cb2779eda3f87d62d2ee5dd74244aaa8071 https://github.com/galaxyproject/galaxy/commit/676b5cb2779eda3f87d62d2ee5dd… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2017-04-05 (Wed, 05 Apr 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/visualization.py Log Message: ----------- Fix inability to raise errors if OS in non en_US Commit: d6336b712592809aabef507802d7ce8179a9d2d7 https://github.com/galaxyproject/galaxy/commit/d6336b712592809aabef507802d7… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2017-04-13 (Thu, 13 Apr 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/visualization.py Log Message: ----------- Remove unnecessary print Commit: d21c8dc8f11c2d4c40967ab9f532a5ce6364f2ea https://github.com/galaxyproject/galaxy/commit/d21c8dc8f11c2d4c40967ab9f532… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-04-13 (Thu, 13 Apr 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/visualization.py Log Message: ----------- Merge pull request #3881 from erasche/unicode-viz-errors Fix inability for viz to raise loading with non-ascii messages Compare: https://github.com/galaxyproject/galaxy/compare/23895e9ef0a0...d21c8dc8f11c

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[galaxyproject/galaxy] 4f4efe: Fix library parameter style width to avoid second ...
by GitHub 13 Apr '17

13 Apr '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4f4efe6405b866c419760af465500458d8dafdba https://github.com/galaxyproject/galaxy/commit/4f4efe6405b866c419760af46550… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-04-12 (Wed, 12 Apr 2017) Changed paths: M client/galaxy/style/less/ui.less M static/style/blue/base.css Log Message: ----------- Fix library parameter style width to avoid second line Commit: 23895e9ef0a001d4dafdedc8aee4846f8c7505d7 https://github.com/galaxyproject/galaxy/commit/23895e9ef0a001d4dafdedc8aee4… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-04-13 (Thu, 13 Apr 2017) Changed paths: M client/galaxy/style/less/ui.less M static/style/blue/base.css Log Message: ----------- Merge pull request #3926 from guerler/fix_library_parameter_style Fix library parameter style width to avoid second line Compare: https://github.com/galaxyproject/galaxy/compare/3e191c7ff445...23895e9ef0a0

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[galaxyproject/ansible-galaxy]
by GitHub 13 Apr '17

13 Apr '17

Branch: refs/tags/0.7.3 Home: https://github.com/galaxyproject/ansible-galaxy

1 0

[galaxyproject/ansible-galaxy] 317e92: Handle galaxy_manage_errordocs correctly
by GitHub 13 Apr '17

13 Apr '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/ansible-galaxy Commit: 317e925b8dd4901d7da1069dc2b6e0f80da26e85 https://github.com/galaxyproject/ansible-galaxy/commit/317e925b8dd4901d7da1… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-04-13 (Thu, 13 Apr 2017) Changed paths: M defaults/main.yml M tasks/main.yml Log Message: ----------- Handle galaxy_manage_errordocs correctly

1 0

[galaxyproject/ansible-galaxy]
by GitHub 13 Apr '17

13 Apr '17

Branch: refs/tags/0.7.2 Home: https://github.com/galaxyproject/ansible-galaxy

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galaxy-commits April 2017