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add tabix version #497

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add tabix version
bgruening Nov 22, 2017
ffc3701
quote filenames
bgruening Nov 22, 2017
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8 changes: 4 additions & 4 deletions tool_collections/vcftools/vcftools_compare/vcftools_compare.xml
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Original file line number Diff line number Diff line change
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>

Expand All @@ -11,13 +11,13 @@
#set dataset_names = []
#for $input in $inputs:
## Sort file.
sort -k1,1 -k2,2n ${input.file} > ${input.name}.vcf.sorted ;
sort -k1,1 -k2,2n '${input.file}' > '${input.name}.vcf.sorted' ;

## Compress.
bgzip ${input.name}.vcf.sorted ;
bgzip '${input.name}.vcf.sorted' ;

## Index.
tabix -p vcf ${input.name}.vcf.sorted.gz ;
tabix -p vcf '${input.name}.vcf.sorted.gz' ;

#silent dataset_names.append( str($input.name) + '.vcf.sorted.gz' )
#end for
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