Bio-DB-HTS installation and ensembl-vep
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3.3 years ago
felipead66 ▴ 110

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?

Bio-DB-HTS ensembl vep • 5.2k views
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How did you install Bio::DB::HTS? Does the VEP know how to find it?

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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?

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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

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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

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

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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

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In case it can help someone.

With the same issue:

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

The actual problem for me was that the gcc compiler was not compatible with my perl compiler to install DBD::mysql , ExtUtils::CBuilder and other perl libraries. I would get errors such as:

Warning: ExtUtils::CBuilder not installed or no compiler detected
Proceeding with configuration, but compilation may fail during Build

Yet I had multiple gcc compilers. What i ended up doing is installing the modules without compilation, outside my conda env, with apt-get.

sudo apt-get install libdbi-perl sudo apt-get install liblzma-dev sudo apt-get install bioperl sudo apt-get install libdbd-mysql-perl

From what I understand, this way vep's INSTALL.pl won't want to compile some perl libraries that require a specific compiler version, and it doesn't go like no library -> no compiler -> error.

So in the end it looks like Bio::DB:HTS is the issue when in fact it's libraries missing for its installation that cannot be installed because of the compiler's version that are the problem.

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