December 2015 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/usegalaxy-playbook] 11765e: remove empty section and toolbox beta label
by GitHub 18 Dec '15

18 Dec '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 11765ea5200b3c1b8f63d74e70be5ac469479161 https://github.com/galaxyproject/usegalaxy-playbook/commit/11765ea5200b3c1b… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-12-18 (Fri, 18 Dec 2015) Changed paths: M files/galaxy/usegalaxy.org/config/tool_conf.xml Log Message: ----------- remove empty section and toolbox beta label

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[galaxyproject/galaxy] e06bf5: Allow installation of different repositories with ...
by GitHub 18 Dec '15

18 Dec '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: e06bf5a32052d6cf474cb5c3d195f632ffe8b9e4 https://github.com/galaxyproject/galaxy/commit/e06bf5a32052d6cf474cb5c3d195… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2015-12-18 (Fri, 18 Dec 2015) Changed paths: M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py Log Message: ----------- Allow installation of different repositories with the same name in a single install transaction. Commit: c6fbf987d2c4422eda793fa817f0ce83931d0119 https://github.com/galaxyproject/galaxy/commit/c6fbf987d2c4422eda793fa817f0… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2015-12-18 (Fri, 18 Dec 2015) Changed paths: M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py Log Message: ----------- Whitespaces around operator. Commit: 2c657b98e2945f48e1339f229e7de4de9f40fe4c https://github.com/galaxyproject/galaxy/commit/2c657b98e2945f48e1339f229e7d… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2015-12-18 (Fri, 18 Dec 2015) Changed paths: M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py Log Message: ----------- Break out of loop once we know the repo is already in all_repo_info_dicts. Commit: 9752fa76c54e927918560d474df4fbae6551d4ca https://github.com/galaxyproject/galaxy/commit/9752fa76c54e927918560d474df4… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2015-12-18 (Fri, 18 Dec 2015) Changed paths: M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py Log Message: ----------- Typo Commit: cced5c3378937c14787884d91a613f56112ce7ff https://github.com/galaxyproject/galaxy/commit/cced5c3378937c14787884d91a61… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-12-18 (Fri, 18 Dec 2015) Changed paths: M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py Log Message: ----------- Merge pull request #1366 from mvdbeek/fix_repository_install Allow installation of different repositories with the same name in a … Compare: https://github.com/galaxyproject/galaxy/compare/455372e6bf71...cced5c337893

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[galaxyproject/usegalaxy-playbook] 53613e: update Main mutable confs, and IEs subgits
by GitHub 18 Dec '15

18 Dec '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 53613e12e3fd61b21c12fd6a86938b7d091f9f87 https://github.com/galaxyproject/usegalaxy-playbook/commit/53613e12e3fd61b2… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-12-18 (Fri, 18 Dec 2015) Changed paths: M files/galaxy/usegalaxy.org/var/integrated_tool_panel.xml M files/galaxy/usegalaxy.org/var/migrated_tools_conf.xml M stage/files/interactive_environments/plugins/.ansible_ie_role_current_version M stage/files/interactive_environments/proxy/.ansible_ie_role_current_version Log Message: ----------- update Main mutable confs, and IEs subgits

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[galaxyproject/galaxy] 61f64e: Refactor tool output classes out of galaxy.tools a...
by GitHub 17 Dec '15

17 Dec '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 61f64e828530c54bae6a090580a6e4278b32a699 https://github.com/galaxyproject/galaxy/commit/61f64e828530c54bae6a090580a6… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-16 (Wed, 16 Dec 2015) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/execute.py M lib/galaxy/tools/parser/__init__.py M lib/galaxy/tools/parser/output_actions.py A lib/galaxy/tools/parser/output_objects.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/parser/yaml.py M lib/galaxy/workflow/extract.py M test/unit/tools/test_actions.py M test/unit/tools/test_evaluation.py Log Message: ----------- Refactor tool output classes out of galaxy.tools and into parser module. This makes the galaxy.tool.parser much more portable, it no longer has a dependency on anything in galaxy.tools or submodules except galaxy.tools.loader (which in turn has no dependencies on galaxy.tools or submodules). Commit: 455372e6bf711d64947768f8b05418f8e6b49647 https://github.com/galaxyproject/galaxy/commit/455372e6bf711d64947768f8b054… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2015-12-18 (Fri, 18 Dec 2015) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/execute.py M lib/galaxy/tools/parser/__init__.py M lib/galaxy/tools/parser/output_actions.py A lib/galaxy/tools/parser/output_objects.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/parser/yaml.py M lib/galaxy/workflow/extract.py M test/unit/tools/test_actions.py M test/unit/tools/test_evaluation.py Log Message: ----------- Merge pull request #1353 from jmchilton/output_refactor Refactor tool output classes out of galaxy.tools and into parser module. Compare: https://github.com/galaxyproject/galaxy/compare/80a35c218416...455372e6bf71

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[galaxyproject/galaxy] 50e531: Refactor galaxy.datatypes.checkers into galaxy.uti...
by GitHub 17 Dec '15

17 Dec '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 50e531aa5971bee6f727ad0013b45c4a5d052fc9 https://github.com/galaxyproject/galaxy/commit/50e531aa5971bee6f727ad0013b4… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-17 (Thu, 17 Dec 2015) Changed paths: R lib/galaxy/datatypes/checkers.py M lib/galaxy/datatypes/converters/fastq_to_fqtoc.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/tabular.py A lib/galaxy/util/checkers.py M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/controllers/upload.py M lib/tool_shed/metadata/metadata_generator.py M lib/tool_shed/util/commit_util.py M lib/tool_shed/util/shed_util_common.py M lib/tool_shed/util/tool_util.py M tools/data_source/upload.py Log Message: ----------- Refactor galaxy.datatypes.checkers into galaxy.util.checkers. - Primary reason is because it is used all over the place in contexts that have nothing to do with Galaxy datatype classes or datatype registery or sniffing, most importantly by the code in the tool shed for determining if something is a tool or not. - This code has no dependencies on the datatypes module or any hard dependencies on things not in the Python standard library. Commit: 80a35c21841671907d326e4fb6cedb433389648d https://github.com/galaxyproject/galaxy/commit/80a35c21841671907d326e4fb6ce… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2015-12-18 (Fri, 18 Dec 2015) Changed paths: R lib/galaxy/datatypes/checkers.py M lib/galaxy/datatypes/converters/fastq_to_fqtoc.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/tabular.py A lib/galaxy/util/checkers.py M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/controllers/upload.py M lib/tool_shed/metadata/metadata_generator.py M lib/tool_shed/util/commit_util.py M lib/tool_shed/util/shed_util_common.py M lib/tool_shed/util/tool_util.py M tools/data_source/upload.py Log Message: ----------- Merge pull request #1363 from jmchilton/checkers_refactor Refactor galaxy.datatypes.checkers into galaxy.util.checkers. Compare: https://github.com/galaxyproject/galaxy/compare/e7f4ec9685f3...80a35c218416

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[galaxyproject/usegalaxy-playbook] 14599c: Switch Main to use tool_conf.xml from Ansible, not...
by GitHub 17 Dec '15

17 Dec '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 14599ce512c0292bdca298e0c7bdff9f000a2e6c https://github.com/galaxyproject/usegalaxy-playbook/commit/14599ce512c0292b… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-12-17 (Thu, 17 Dec 2015) Changed paths: A files/galaxy/usegalaxy.org/config/tool_conf.xml M production/group_vars/galaxyservers.yml Log Message: ----------- Switch Main to use tool_conf.xml from Ansible, not the version in the Galaxy distribution

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[galaxyproject/galaxy] 65bd90: Refactor imp_exp toolbox toward more generic entry...
by GitHub 17 Dec '15

17 Dec '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 65bd907e08168daecabd984465b735f50ff0da56 https://github.com/galaxyproject/galaxy/commit/65bd907e08168daecabd984465b7… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-12 (Sat, 12 Dec 2015) Changed paths: M lib/galaxy/app.py M lib/galaxy/tools/imp_exp/__init__.py A lib/galaxy/tools/special_tools.py Log Message: ----------- Refactor imp_exp toolbox toward more generic entry point. Commit: 0180c0525d5f545f67d99c79677a94382ae73ff1 https://github.com/galaxyproject/galaxy/commit/0180c0525d5f545f67d99c79677a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-12 (Sat, 12 Dec 2015) Changed paths: M lib/galaxy/jobs/command_factory.py Log Message: ----------- Improve error log warning for tools with empty commands. Commit: a208961cd3145f90a04e58ac1bb23ed2d91365a4 https://github.com/galaxyproject/galaxy/commit/a208961cd3145f90a04e58ac1bb2… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-12 (Sat, 12 Dec 2015) Changed paths: M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Refactor tool actions for reuse of pieces in downstream actions. Commit: e7f4ec9685f345c13309b16412fd22a6ddadf852 https://github.com/galaxyproject/galaxy/commit/e7f4ec9685f345c13309b16412fd… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2015-12-17 (Thu, 17 Dec 2015) Changed paths: M lib/galaxy/app.py M lib/galaxy/jobs/command_factory.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/imp_exp/__init__.py A lib/galaxy/tools/special_tools.py Log Message: ----------- Merge pull request #1307 from jmchilton/collection_opts_prereq1 Refactor tool stuff for generic model actions Compare: https://github.com/galaxyproject/galaxy/compare/872458f8b9eb...e7f4ec9685f3

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[galaxyproject/galaxy] 7a36b1: PY3 fixes for galaxy.util submodules.
by GitHub 17 Dec '15

17 Dec '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 7a36b141bd72b7fc2c675254c10779dace9be6e1 https://github.com/galaxyproject/galaxy/commit/7a36b141bd72b7fc2c675254c107… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-17 (Thu, 17 Dec 2015) Changed paths: M lib/galaxy/util/aliaspickler.py M lib/galaxy/util/expressions.py M lib/galaxy/util/object_wrapper.py M lib/galaxy/util/odict.py Log Message: ----------- PY3 fixes for galaxy.util submodules. Commit: 872458f8b9ebda4d86863b3d0ca2a9d74e0b53ba https://github.com/galaxyproject/galaxy/commit/872458f8b9ebda4d86863b3d0ca2… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-12-17 (Thu, 17 Dec 2015) Changed paths: M lib/galaxy/util/aliaspickler.py M lib/galaxy/util/expressions.py M lib/galaxy/util/object_wrapper.py M lib/galaxy/util/odict.py Log Message: ----------- Merge pull request #1362 from jmchilton/py3_1 PY3 fixes for galaxy.util submodules. Compare: https://github.com/galaxyproject/galaxy/compare/d9068a808994...872458f8b9eb

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[galaxyproject/galaxy] cdf938: PY3 fixes for galaxy.util.
by GitHub 17 Dec '15

17 Dec '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: cdf9380735878d44fee863c86b69a686ab0fd76f https://github.com/galaxyproject/galaxy/commit/cdf9380735878d44fee863c86b69… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-17 (Thu, 17 Dec 2015) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- PY3 fixes for galaxy.util. Commit: d9068a808994dee2b1c0ea873365846706e03d70 https://github.com/galaxyproject/galaxy/commit/d9068a808994dee2b1c0ea873365… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-12-17 (Thu, 17 Dec 2015) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- Merge pull request #1359 from jmchilton/py3_0 PY3 fixes for galaxy.util. Compare: https://github.com/galaxyproject/galaxy/compare/f6557964b6b8...d9068a808994

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[galaxyproject/galaxy] b0deea: Fix change handler association
by GitHub 17 Dec '15

17 Dec '15

Branch: refs/heads/release_15.10 Home: https://github.com/galaxyproject/galaxy Commit: b0deead9c3260598f83d1ab2ec74b3c3e8974456 https://github.com/galaxyproject/galaxy/commit/b0deead9c3260598f83d1ab2ec74… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-12-17 (Thu, 17 Dec 2015) Changed paths: M client/galaxy/scripts/utils/uploadbox.js M static/maps/utils/uploadbox.js.map M static/scripts/utils/uploadbox.js Log Message: ----------- Fix change handler association Commit: abd51e7f791c99a93062b9f2fee7827dea857c20 https://github.com/galaxyproject/galaxy/commit/abd51e7f791c99a93062b9f2fee7… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-17 (Thu, 17 Dec 2015) Changed paths: M client/galaxy/scripts/utils/uploadbox.js M static/maps/utils/uploadbox.js.map M static/scripts/utils/uploadbox.js Log Message: ----------- Merge pull request #1358 from guerler/fix_same_upload_000 [15.10] Fix change handler association Compare: https://github.com/galaxyproject/galaxy/compare/2d7c2019fba1...abd51e7f791c

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