November 2018 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] c2a49d: Directory datatype for Galaxy.
by GitHub 01 Nov '18

01 Nov '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c2a49de6cee056d6cd942e3b392ffbd15961fb42 https://github.com/galaxyproject/galaxy/commit/c2a49de6cee056d6cd942e3b392f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-10-24 (Wed, 24 Oct 2018) Changed paths: M config/datatypes_conf.xml.sample A lib/galaxy/datatypes/converters/tar_to_directory.xml M lib/galaxy/datatypes/data.py M lib/galaxy/tools/__init__.py M test/functional/tools/sample_datatypes_conf.xml M test/integration/test_upload_configuration_options.py Log Message: ----------- Directory datatype for Galaxy. Commit: dd6b185ab82b7e251ba7ad3b69abbda7ab4018b9 https://github.com/galaxyproject/galaxy/commit/dd6b185ab82b7e251ba7ad3b69ab… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-10-24 (Wed, 24 Oct 2018) Changed paths: M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/util/compression_utils.py M test/api/test_tools.py M test/api/test_tools_upload.py M tools/data_source/upload.py M tools/data_source/upload.xml Log Message: ----------- Implement composite uploads on arbitrary datatypes. Prior to this, composite uploads were only allowed for select data types. As far as I can tell, the framework itself allows arbitrary datatypes to have extra files. This allows the upload API to take in extra files for datatypes that aren't explicitly annotated has having extra files. These may be specified one at a time or in directory structures via tar files. Commit: e3bc005a8602a47e542129b5be53aa6316525e90 https://github.com/galaxyproject/galaxy/commit/e3bc005a8602a47e542129b5be53… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-10-24 (Wed, 24 Oct 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/datasets.py M lib/galaxy/webapps/galaxy/buildapp.py M test/api/test_tools.py M test/base/populators.py Log Message: ----------- Implement API endpoint for indexing extra files in a dataset. Commit: f035d642ceb2a4835d774996f3b3d78588318834 https://github.com/galaxyproject/galaxy/commit/f035d642ceb2a4835d774996f3b3… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-11-01 (Thu, 01 Nov 2018) Changed paths: M config/datatypes_conf.xml.sample A lib/galaxy/datatypes/converters/tar_to_directory.xml M lib/galaxy/datatypes/data.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/util/compression_utils.py M lib/galaxy/webapps/galaxy/api/datasets.py M lib/galaxy/webapps/galaxy/buildapp.py M test/api/test_tools.py M test/api/test_tools_upload.py M test/base/populators.py M test/functional/tools/sample_datatypes_conf.xml M test/integration/test_upload_configuration_options.py M tools/data_source/upload.py M tools/data_source/upload.xml Log Message: ----------- Merge pull request #6844 from jmchilton/compressed_types_and_extra_files Infrastructure/API Support for Composite Uploads/Downloads Compare: https://github.com/galaxyproject/galaxy/compare/c312c1014d0e...f035d642ceb2 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] c3dfdb: Default shed tool installation to database/shed_to...
by GitHub 01 Nov '18

01 Nov '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c3dfdb0dc73bbc5339e285500dcaf345e5c67d60 https://github.com/galaxyproject/galaxy/commit/c3dfdb0dc73bbc5339e285500dca… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-10-29 (Mon, 29 Oct 2018) Changed paths: M config/migrated_tools_conf.xml.sample M config/shed_tool_conf.xml.sample M doc/source/admin/tool_panel.rst M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/tool_shed/galaxy_install/migrate/check.py M lib/tool_shed/util/common_util.py Log Message: ----------- Default shed tool installation to database/shed_tools instead of ../shed_tools Commit: c312c1014d0e85920f630bf3d3e02e508c636b84 https://github.com/galaxyproject/galaxy/commit/c312c1014d0e85920f630bf3d3e0… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-11-01 (Thu, 01 Nov 2018) Changed paths: M config/migrated_tools_conf.xml.sample M config/shed_tool_conf.xml.sample M doc/source/admin/tool_panel.rst M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/tool_shed/galaxy_install/migrate/check.py M lib/tool_shed/util/common_util.py Log Message: ----------- Merge pull request #6937 from natefoo/shed-tools-relocate Default shed tool installation to database/shed_tools Compare: https://github.com/galaxyproject/galaxy/compare/3108bd3b3729...c312c1014d0e **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 2bf5b9: Fix style for legacy toolshed selection page
by GitHub 01 Nov '18

01 Nov '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 2bf5b9b84e5f1391c8a0640255293e23f82042e1 https://github.com/galaxyproject/galaxy/commit/2bf5b9b84e5f1391c8a064025529… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-10-30 (Tue, 30 Oct 2018) Changed paths: M templates/webapps/galaxy/admin/tool_sheds.mako Log Message: ----------- Fix style for legacy toolshed selection page Commit: 3108bd3b37298417df5e9851d7e126c6c1b4878f https://github.com/galaxyproject/galaxy/commit/3108bd3b37298417df5e9851d7e1… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-11-01 (Thu, 01 Nov 2018) Changed paths: M templates/webapps/galaxy/admin/tool_sheds.mako Log Message: ----------- Merge pull request #6910 from guerler/toolshed_selection Fix style for legacy toolshed selection page Compare: https://github.com/galaxyproject/galaxy/compare/3f7425ad9308...3108bd3b3729 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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