Question: Bio-DB-HTS installation and ensembl-vep
0
gravatar for felipead66
7 weeks ago by
felipead6630
felipead6630 wrote:

I want to use ensembl-vep with custom annotation. In order to use gff file I need to have library Bio-DB-HTS installed. I downloaded Bio-DB-HTS and used Build.PL with no errors. When I try to install ensembl-vep it still gives an error asking for Bio-DB-HTS library.

How should I install Bio-DB-HTS correctly?

ensembl vep bio-db-hts • 232 views
ADD COMMENTlink modified 7 weeks ago by Emily_Ensembl18k • written 7 weeks ago by felipead6630

How did you install Bio::DB::HTS? Does the VEP know how to find it?

ADD REPLYlink written 7 weeks ago by Emily_Ensembl18k

I installed it both manually from https://github.com/Ensembl/Bio-DB-HTS

and as @cmdcolin suggested i run "cpan Bio::DB::HTS" and seems to work, since I get Bio::DB::HTS is up to date (2.11)

How should I tell VEP how to find it?

ADD REPLYlink written 7 weeks ago by felipead6630

If you've used cpan then Perl should just know where it is. If you install manually, you'll need to add it to your PERL5LIB

ADD REPLYlink written 7 weeks ago by Emily_Ensembl18k

Even using cpan, I still get an error.

Should I use cpan inside ensembl-vep folder?

Alternatively, how to add it to PERL5LIB?

Edit: I am in Ubuntu

ADD REPLYlink modified 7 weeks ago • written 7 weeks ago by felipead6630

Have you tried simply installing it using "cpan Bio::DB::HTS"?

ADD REPLYlink written 7 weeks ago by cmdcolin1.2k

Thank you for your suggestion. I run "cpan Bio::DB::HTS" and I get

Bio::DB::HTS is up to date (2.11)

but still when installing vep and run "perl INSTALL.pl" I get the following:

This module requires htslib (http://htslib/org) Install it if you have not done so already.

This script will attempt to locate htslib by looking for hts.h and libhts.a in:

  1. --htslib command line argument
  2. HTSLIB_DIR environment variable
  3. --prefix command line argument (which also sets installation location)
  4. Alien::HTSlib dependency resolver
  5. pkg-config (extra directories can be set in PKG_CONFIG_PATH environment variable)
  6. common library locations: /usr /usr/local, /usr/share, /opt/local

ERROR: Shared Bio::DB:HTS library not found

ADD REPLYlink written 7 weeks ago by felipead6630
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