add tabix version #497
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add tabix version #497
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nsoranzo
reviewed
Nov 22, 2017
| @@ -2,7 +2,7 @@ | |||
| <description>multiple VCF datasets</description> | |||
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| <requirements> | |||
| <requirement type="package">tabix</requirement> | |||
| <requirement type="package" version="0.2.5">tabix</requirement> | |||
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Wouldn't it be better to use:
<requirement type="package" version="1.6">htslib</requirement>
instead? 0.2.5 is pretty ancient and tabix has been distributed as part of htslib for ages.
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I just try to fix the old package. The multicontainer builds are failing because of this. Thats also the reason I have not bumped the tool version number.
Is this ok for you?
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That's not the only problematic requirement in this tool collection:
tool_collections/vcftools/vcftools_annotate/vcftools_annotate.xml
5: <requirement type="binary">echo</requirement>
tool_collections/vcftools/vcftools_isec/vcftools_isec.xml
5: <requirement type="package">tabix</requirement>
tool_collections/vcftools/vcftools_merge/vcftools_merge.xml
5: <requirement type="package">tabix</requirement>
tool_collections/vcftools/vcftools_slice/vcftools_slice.xml
5: <requirement type="binary">echo</requirement>
tool_collections/vcftools/vcftools_subset/vcftools_subset.xml
5: <requirement type="package">tabix</requirement>
Also, tool_collections/vcftools/vcftools_consensus/vcftools_consensus.xml is already using htslib to provide tabix:
<requirement type="package" version="1.3.2">htslib</requirement>
Finally, I noticed that:
- only
vcftools_consensuscites10.1093/bioinformatics/btr330 - documentation links in
<help>could be updated to https://vcftools.github.io/examples.html .
The upstream vcftools seems to be maintained, so it may be worth to use a more sustainable solution?
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xref. #111 |
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