perlubuntubioinformaticsvcf-variant-call-formatvcftools

Preparing a Perl file to run with Ubuntu and tabix

I don't know about Ubunto or Perl but still need to install and run a program on it. This is what I am looking at: http://vcftools.sourceforge.net/docs.html

On the installation section it says this:

To build the vcftools executable, type "make" in the vcftools folder.

The Perl scripts require that VCF files are compressed by bgzip and indexed by tabix (both tools are part of the tabix package, available for download here). Both tools must be in directories that are listed in the PATH environment variable. For running the Perl scripts, the PERL5LIB environment variable must be set to include the Vcf.pm module

export PERL5LIB=/path/to/your/installation/perl

so Ok, I extracted and copied their VCFtools folder into ubuntu's home folder. Then I said "make" it gave errors, then I went and downloaded that tabidx tool, but from this point I don't know what to do with it, Ok I download tabidx, but what to do next and how?

Thanks.

Solution 
  • find / -name Vcf.pm

    If that gives one--and only one line--you can do this:

    export PERL5LIB=$( dirname $( find . -name Vcf.pm ))