Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: da5b72a030d8d07c663566527fc64560e067eb54 https://github.com/galaxyproject/galaxy/commit/da5b72a030d8d07c663566527fc64... Author: Nicola Soranzo nicola.soranzo@earlham.ac.uk Date: 2017-08-22 (Tue, 22 Aug 2017)

Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py R lib/galaxy/datatypes/converters/bcf_bgzip_to_bcf_converter.py R lib/galaxy/datatypes/converters/bcf_bgzip_to_bcf_converter.xml R lib/galaxy/datatypes/converters/bcf_to_bcf_bgzip_converter.py R lib/galaxy/datatypes/converters/bcf_to_bcf_bgzip_converter.xml A lib/galaxy/datatypes/converters/bcf_to_bcf_uncompressed_converter.xml A lib/galaxy/datatypes/converters/bcf_uncompressed_to_bcf_converter.xml A lib/galaxy/datatypes/test/1.bcf A lib/galaxy/datatypes/test/1.bcf_uncompressed

Log Message: ----------- Alias `bcf_bgzip` datatype to `bcf`. Add `bcf_uncompressed` and converters

Since https://bitbucket.org/galaxy/galaxy-central/pull-requests/353 (only) compressed BCF files have been sniffed as `bcf`, so the `bcf_bgzip` datatype (introduced 2 years later in https://github.com/galaxyproject/galaxy/pull/1148 ) is an unused duplicate.

This adds also a distinct `bcf_uncompressed` datatype (and converters) for the rare cases when it may be useful.

Commit: 8dc0e697d3f8841270f6d934d19b271cf23b219e https://github.com/galaxyproject/galaxy/commit/8dc0e697d3f8841270f6d934d19b2... Author: Nicola Soranzo nicola.soranzo@earlham.ac.uk Date: 2017-08-22 (Tue, 22 Aug 2017)

Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/tabular.py M test/functional/tools/sample_datatypes_conf.xml

Log Message: ----------- Fix `vcf_bgzip` datatype

In https://github.com/galaxyproject/galaxy/pull/4254 `vcf_bgzip` was made a proper datatype with the introduction of the `VcfGz` class, but was still described as a subclass in `datatypes_conf.xml` .

Also fix `file_ext` attribute in `BaseVcf` and subclasses.

Commit: a63af63b41e81a104dc177cb13dc2f6f3b4e9e6d https://github.com/galaxyproject/galaxy/commit/a63af63b41e81a104dc177cb13dc2... Author: Nicola Soranzo nicola.soranzo@earlham.ac.uk Date: 2017-08-22 (Tue, 22 Aug 2017)

Changed paths: M lib/galaxy/datatypes/set_metadata_tool.xml

Log Message: ----------- Add requirement for bcftools to set_metadata tool

The `bcftools` binary is used by the `set_meta()` method of the `Bcf` datatype class. Having a `<requirement>` for it in the set_metadata tool makes it possible to use conda to resolve the dependency instead of forcing the admin to install `bcftools` on the PATH of the Galaxy user.

This will also fix errors like https://travis-ci.org/galaxyproject/tools-iuc/jobs/266923024#L1994 when running ``` planemo test --conda_dependency_resolution --conda_auto_install ```

Commit: c89233c7cbbe263d3670fd5d4066a83f537ee173 https://github.com/galaxyproject/galaxy/commit/c89233c7cbbe263d3670fd5d4066a... Author: Dannon Baker dannon.baker@gmail.com Date: 2017-08-24 (Thu, 24 Aug 2017)

Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py R lib/galaxy/datatypes/converters/bcf_bgzip_to_bcf_converter.py R lib/galaxy/datatypes/converters/bcf_bgzip_to_bcf_converter.xml R lib/galaxy/datatypes/converters/bcf_to_bcf_bgzip_converter.py R lib/galaxy/datatypes/converters/bcf_to_bcf_bgzip_converter.xml A lib/galaxy/datatypes/converters/bcf_to_bcf_uncompressed_converter.xml A lib/galaxy/datatypes/converters/bcf_uncompressed_to_bcf_converter.xml M lib/galaxy/datatypes/set_metadata_tool.xml M lib/galaxy/datatypes/tabular.py A lib/galaxy/datatypes/test/1.bcf A lib/galaxy/datatypes/test/1.bcf_uncompressed M test/functional/tools/sample_datatypes_conf.xml

Log Message: ----------- Merge pull request #4477 from nsoranzo/vcf_bcf_fixes

Fixes for VCF/BCF datatypes

Compare: https://github.com/galaxyproject/galaxy/compare/1426225a78d0...c89233c7cbbe