perlcpanperlbrewvcf-variant-call-format

Cannot install perl package `Vcf` via CPAN

I'm attempting to install the perl package VCF for my perlbrew installation, which is accessed via vcf-validator

703404669@bioitutil2:~$ vcf-validator 
Can't locate Vcf.pm in @INC (you may need to install the Vcf module) (@INC contains: /home/703404669/Scripts/vcftools-vcftools-ea875e2/src/perl /home/703404669/perl5/perlbrew/perls/perl-5.30.0/lib/site_perl/5.30.0/x86_64-linux /home/703404669/perl5/perlbrew/perls/perl-5.30.0/lib/site_perl/5.30.0 /home/703404669/perl5/perlbrew/perls/perl-5.30.0/lib/5.30.0/x86_64-linux /home/703404669/perl5/perlbrew/perls/perl-5.30.0/lib/5.30.0) at /usr/local/bin/vcf-validator line 9.
BEGIN failed--compilation aborted at /usr/local/bin/vcf-validator line 9.

so I install via CPAN, VCF not Vcf

703404669@bioitutil2:~$ cpan VCF
Loading internal logger. Log::Log4perl recommended for better logging
Reading '/home/703404669/.cpan/Metadata'
  Database was generated on Mon, 23 Sep 2019 11:29:03 GMT
VCF is up to date (1.003).

but still cannot access the module/library:

703404669@bioitutil2:~$ vcf-validator 
Can't locate Vcf.pm in @INC (you may need to install the Vcf module) (@INC contains: /home/703404669/Scripts/vcftools-vcftools-ea875e2/src/perl /home/703404669/perl5/perlbrew/perls/perl-5.30.0/lib/site_perl/5.30.0/x86_64-linux /home/703404669/perl5/perlbrew/perls/perl-5.30.0/lib/site_perl/5.30.0 /home/703404669/perl5/perlbrew/perls/perl-5.30.0/lib/5.30.0/x86_64-linux /home/703404669/perl5/perlbrew/perls/perl-5.30.0/lib/5.30.0) at /usr/local/bin/vcf-validator line 9.
BEGIN failed--compilation aborted at /usr/local/bin/vcf-validator line 9.

I've also tried this 

703404669@bioitutil2:~$ /home/703404669/perl5/perlbrew/perls/perl-5.30.0/bin/perl -e'use VCF'; /home/703404669/perl5/perlbrew/perls/perl-5.30.0/bin/cpan VCF; /home/703404669/perl5/perlbrew/perls/perl-5.30.0/bin/perl -e'VCF'
Loading internal logger. Log::Log4perl recommended for better logging
Reading '/home/703404669/.cpan/Metadata'
  Database was generated on Mon, 23 Sep 2019 11:29:03 GMT
VCF is up to date (1.003).

but am still unable to run the vcf-validator :(

Solution

  • I was able to install the package from GitHub:

    git clone git@github.com:vcftools/vcftools.git
cd vcftools
./autogen.sh
./configure --prefix=/home/hakon/perlbrew/perls/perl-5.28.1
make
make install

    Then I checked if I could run vcf-validator:

    $ vcf-validator --help
Usage: vcf-validator [OPTIONS] file.vcf.gz
Options:
   -d, --duplicates                 Warn about duplicate positions.
   -u, --unique-messages            Output all messages only once.
   -h, -?, --help                   This help message.