[galaxy-commits] [galaxyproject/galaxy] f3e06c: iqtree and mldist datatypes

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f3e06cce9aaa34233d406b17f38cab425a4e0099 https://github.com/galaxyproject/galaxy/commit/f3e06cce9aaa34233d406b17f38ca... Author: Mehmet Tekman m.tekman@ucl.ac.uk Date: 2017-10-27 (Fri, 27 Oct 2017)

Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/data.py A lib/galaxy/datatypes/test/example.iqtree A lib/galaxy/datatypes/test/example.mldist

Log Message: ----------- iqtree and mldist datatypes

Commit: b8ce7b516f1a0d66c1ded78b0c93863ad801356c https://github.com/galaxyproject/galaxy/commit/b8ce7b516f1a0d66c1ded78b0c938... Author: Mehmet Tekman m.tekman@ucl.ac.uk Date: 2017-10-28 (Sat, 28 Oct 2017)

Changed paths: M lib/galaxy/datatypes/data.py

Log Message: ----------- added binary file checkers and line count limits

Commit: f993aceee18a44c262d7b2d93345ced17b93cce6 https://github.com/galaxyproject/galaxy/commit/f993aceee18a44c262d7b2d93345c... Author: Mehmet Tekman m.tekman@ucl.ac.uk Date: 2017-11-02 (Thu, 02 Nov 2017)

Changed paths: M .ci/flake8_lint_include_list.txt R .ci/flake8_py3_wrapper.sh M .ci/jenkins/selenium/Dockerfile M .ci/jenkins/selenium/docker-compose.yml M .ci/jenkins/selenium/galaxy.ini M .ci/jenkins/selenium/run_galaxy.bash M .ci/jenkins/selenium/run_tests.sh M .ci/py3_sources.txt M .gitignore M .travis.yml M CITATION M Makefile A client/.babelrc M client/GruntFile.js M client/README.md M client/bower.json M client/galaxy/scripts/admin.toolshed.js M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/apps/login.js M client/galaxy/scripts/apps/panels/admin-panel.js M client/galaxy/scripts/apps/panels/history-panel.js M client/galaxy/scripts/apps/panels/tool-panel.js M client/galaxy/scripts/galaxy.interactive_environments.js M client/galaxy/scripts/galaxy.js M client/galaxy/scripts/galaxy.library.js M client/galaxy/scripts/galaxy.pages.js M client/galaxy/scripts/i18n.js M client/galaxy/scripts/layout/generic-nav-view.js M client/galaxy/scripts/layout/masthead.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/modal.js M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/layout/panel.js M client/galaxy/scripts/layout/router.js M client/galaxy/scripts/layout/scratchbook.js R client/galaxy/scripts/libs/backbone.js R client/galaxy/scripts/libs/bibtex.js R client/galaxy/scripts/libs/d3.js R client/galaxy/scripts/libs/jquery.complexify.js R client/galaxy/scripts/libs/jquery/jquery.cookie.js R client/galaxy/scripts/libs/jquery/jquery.js R client/galaxy/scripts/libs/jquery/jquery.migrate.js R client/galaxy/scripts/libs/jquery/jquery.mousewheel.js R client/galaxy/scripts/libs/raven.js R client/galaxy/scripts/libs/require.js R client/galaxy/scripts/libs/underscore.js M client/galaxy/scripts/mvc/annotation.js M client/galaxy/scripts/mvc/base-mvc.js M client/galaxy/scripts/mvc/base/controlled-fetch-collection.js M client/galaxy/scripts/mvc/citation/citation-model.js M client/galaxy/scripts/mvc/citation/citation-view.js M client/galaxy/scripts/mvc/collection/base-creator.js M client/galaxy/scripts/mvc/collection/collection-li-edit.js M client/galaxy/scripts/mvc/collection/collection-li.js M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/collection/collection-view-edit.js M client/galaxy/scripts/mvc/collection/collection-view.js M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M client/galaxy/scripts/mvc/collection/pair-collection-creator.js M client/galaxy/scripts/mvc/dataset/data.js M client/galaxy/scripts/mvc/dataset/dataset-choice.js M client/galaxy/scripts/mvc/dataset/dataset-edit-attributes.js M client/galaxy/scripts/mvc/dataset/dataset-error.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/dataset/dataset-list.js M client/galaxy/scripts/mvc/dataset/dataset-model.js M client/galaxy/scripts/mvc/dataset/states.js M client/galaxy/scripts/mvc/form/form-data.js M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/form/form-repeat.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/form/form-wrapper.js M client/galaxy/scripts/mvc/grid/grid-model.js M client/galaxy/scripts/mvc/grid/grid-shared.js M client/galaxy/scripts/mvc/grid/grid-template.js M client/galaxy/scripts/mvc/grid/grid-view.js M client/galaxy/scripts/mvc/history/copy-dialog.js M client/galaxy/scripts/mvc/history/hda-li-edit.js M client/galaxy/scripts/mvc/history/hda-li.js M client/galaxy/scripts/mvc/history/hda-model.js M client/galaxy/scripts/mvc/history/hdca-li-edit.js M client/galaxy/scripts/mvc/history/hdca-li.js M client/galaxy/scripts/mvc/history/hdca-model.js M client/galaxy/scripts/mvc/history/history-content-model.js M client/galaxy/scripts/mvc/history/history-contents.js M client/galaxy/scripts/mvc/history/history-list.js M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/history-preferences.js M client/galaxy/scripts/mvc/history/history-structure-view.js M client/galaxy/scripts/mvc/history/history-view-annotated.js M client/galaxy/scripts/mvc/history/history-view-edit-current.js M client/galaxy/scripts/mvc/history/history-view-edit.js M client/galaxy/scripts/mvc/history/history-view.js M client/galaxy/scripts/mvc/history/job-dag.js M client/galaxy/scripts/mvc/history/multi-panel.js M client/galaxy/scripts/mvc/history/options-menu.js M client/galaxy/scripts/mvc/job/job-li.js M client/galaxy/scripts/mvc/job/job-model.js M client/galaxy/scripts/mvc/job/job-params.js A client/galaxy/scripts/mvc/lazy/lazy-limited.js M client/galaxy/scripts/mvc/library/library-dataset-view.js M 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Log Message: ----------- Merge branch 'dev' of github.com:galaxyproject/galaxy into iqtree

Commit: 5cf6452de69c6befc09cbfab1bd310f9a0a94600 https://github.com/galaxyproject/galaxy/commit/5cf6452de69c6befc09cbfab1bd31... Author: Mehmet Tekman m.tekman@ucl.ac.uk Date: 2017-11-02 (Thu, 02 Nov 2017)

Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/data.py

Log Message: ----------- vastly simplified iqtree datatypes

Commit: 94a77f7524f72375bfef02e6e82f3a30e71924d9 https://github.com/galaxyproject/galaxy/commit/94a77f7524f72375bfef02e6e82f3... Author: Mehmet Tekman m.tekman@ucl.ac.uk Date: 2017-11-03 (Fri, 03 Nov 2017)

Changed paths: M config/datatypes_conf.xml.sample R lib/galaxy/datatypes/test/example.mldist

Log Message: ----------- removed obsolete sniffer and test data

Commit: 97fc49db0ce41b264308b0016f2b7f7633bc4a28 https://github.com/galaxyproject/galaxy/commit/97fc49db0ce41b264308b0016f2b7... Author: Mehmet Tekman m.tekman@ucl.ac.uk Date: 2017-11-03 (Fri, 03 Nov 2017)

Changed paths: M lib/galaxy/datatypes/data.py

Log Message: ----------- removed unoverriden methods in subclass, empty lines

Commit: 00ca4f3cdd1af1845ee3920452680ec2548f902f https://github.com/galaxyproject/galaxy/commit/00ca4f3cdd1af1845ee3920452680... Author: Mehmet Tekman m.tekman@ucl.ac.uk Date: 2017-11-04 (Sat, 04 Nov 2017)

Changed paths: M lib/galaxy/datatypes/data.py

Log Message: ----------- quickfix to read

Commit: d9607ce15659b4b26f377c37e7735c7ffa9ba52d https://github.com/galaxyproject/galaxy/commit/d9607ce15659b4b26f377c37e7735... Author: Mehmet Tekman m.tekman@ucl.ac.uk Date: 2017-11-05 (Sun, 05 Nov 2017)

Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/data.py R lib/galaxy/datatypes/test/example.mldist

Log Message: ----------- vastly simplified iqtree datatypes (squashed)

Commit: 77c4ccc655690d4970abe5c0631c1d441d4fd46f https://github.com/galaxyproject/galaxy/commit/77c4ccc655690d4970abe5c0631c1... Author: Mehmet Tekman m.tekman@ucl.ac.uk Date: 2017-11-06 (Mon, 06 Nov 2017)

Log Message: ----------- Merge branch 'iqtree' of github.com:mtekman/galaxy into iqtree

Commit: 5b594ae255b6615bb2d018c85e2e463c77f9cc46 https://github.com/galaxyproject/galaxy/commit/5b594ae255b6615bb2d018c85e2e4... Author: Mehmet Tekman m.tekman@ucl.ac.uk Date: 2017-11-06 (Mon, 06 Nov 2017)

Changed paths: M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/text.py

Log Message: ----------- moved from data to text

Commit: 4bca1a77cca41cb87b0fe2f758657af0e32a46ce https://github.com/galaxyproject/galaxy/commit/4bca1a77cca41cb87b0fe2f758657... Author: Mehmet Tekman m.tekman@ucl.ac.uk Date: 2017-11-06 (Mon, 06 Nov 2017)

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Log Message: ----------- Merge branch 'dev' of github.com:galaxyproject/galaxy into iqtree

Commit: e347aed810f5a67893d4d10b56973ca4a5912962 https://github.com/galaxyproject/galaxy/commit/e347aed810f5a67893d4d10b56973... Author: Mehmet Tekman m.tekman@ucl.ac.uk Date: 2017-11-07 (Tue, 07 Nov 2017)

Changed paths: M config/datatypes_conf.xml.sample

Log Message: ----------- fix to datatype and sniffer

Commit: 3b4b97a2edd4e73d6861e9b749ff75f34014d13d https://github.com/galaxyproject/galaxy/commit/3b4b97a2edd4e73d6861e9b749ff7... Author: John Chilton jmchilton@gmail.com Date: 2017-11-08 (Wed, 08 Nov 2017)

Changed paths: M config/datatypes_conf.xml.sample A lib/galaxy/datatypes/test/example.iqtree M lib/galaxy/datatypes/text.py

Log Message: ----------- Merge pull request #4849 from mtekman/iqtree

Add IQtree datatypes

Compare: https://github.com/galaxyproject/galaxy/compare/855ea1a6a248...3b4b97a2edd4