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add tabix version #497

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add tabix version #497

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c836ffd
add tabix version
bgruening Nov 22, 2017
ffc3701
quote filenames
bgruening Nov 22, 2017
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2 changes: 1 addition & 1 deletion tool_collections/vcftools/vcftools_compare/vcftools_compare.xml
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Expand Up @@ -2,7 +2,7 @@
<description>multiple VCF datasets</description>

<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:

The upstream vcftools seems to be maintained, so it may be worth to use a more sustainable solution?

<requirement type="package" version="0.1.11">vcftools</requirement>
</requirements>

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