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Fixes for VCF/BCF datatypes #4477

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merged 3 commits into from Aug 25, 2017

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commented Aug 22, 2017

  • Alias bcf_bgzip datatype to bcf. 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 #1148 ) is an unused duplicate.
  • Add a distinct bcf_uncompressed datatype (and converters) for the rare cases when it may be useful.
  • Fix vcf_bgzip datatype. In #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.
  • 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
    

nsoranzo added some commits Aug 22, 2017

Alias `bcf_bgzip` datatype to `bcf`. Add `bcf_uncompressed` and conve…
…rters

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
#1148 ) is an unused duplicate.

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

@nsoranzo nsoranzo added this to the 17.09 milestone Aug 22, 2017

@dannon dannon merged commit c89233c into galaxyproject:dev Aug 25, 2017

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@nsoranzo nsoranzo deleted the nsoranzo:vcf_bcf_fixes branch Aug 25, 2017

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