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Type:
Task
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Status: Closed
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Priority:
Major
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Resolution: Won't Fix
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Affects Version/s: None
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Fix Version/s: None
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Component/s: None
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Labels:
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Environment:
Linux
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Epic Link:
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Sprint:DEV-40-1, DEV-40-2, DEV-40-3, DEV-40-4, DEV-40-5, DEV-40-RELEASE, DEV-41-1, DEV-41-2, DEV-41-3, DEV-41-4, DEV-41-5, DEV-41-RELEASE, DEV-42-1, DEV-42-2, DEV-42-3, DEV-42-4, DEV-42-5, DEV-42-RELEASE, DEV-43-1
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Affect Type:Userdefined
- vcf-consensus validation is "perl path/to/UGENE/tools/vcftools/vcf-consensus -help".
- Expected message: "vcf-consensus".
- Received message on Windows: "Can't locate Vcf.pm in @INC (you may need to install the Vcf module) (@INC contains: C:/Program Files/Unipro UGENE/tools/perl5/site/lib C:/Program Files/Unipro UGENE/tools/perl5/lib .) at C:\Program Files\Unipro UGENE\tools\vcftools\vcf-consensus line 6.
BEGIN failed--compilation aborted at C:\Program Files\Unipro UGENE\tools\vcftools\vcf-consensus line 6.". - Although the expected message was received, the tool is not valid.
- The message to be displayed is
Usage: cat ref.fa | vcf-consensus [OPTIONS] in.vcf.gz > out.fa Options: -h, -?, --help This help message. -H, --haplotype <int> Apply only variants for the given haplotype (1,2) -i, --iupac-codes Apply variants in the form of IUPAC ambiguity codes -s, --sample <name> If not given, all variants are applied Examples: # Get the consensus for one region. The fasta header lines are then expected # in the form ">chr:from-to". samtools faidx ref.fa 8:11870-11890 | vcf-consensus in.vcf.gz > out.fa
Need to check that the tool is validated correctly on Linux.