Failing to install VEP dependencies

Question

I'm trying to install VEP, but am getting stuck installing its dependencies.

I try to install as suggested here https://www.ensembl.org/info/docs/tools/vep/script/index.html

cd ~/bin
git clone https://github.com/Ensembl/ensembl-vep.git
cd ensembl-vep
perl INSTALL.pl

But I get this error:

ERROR: DBI module not found. VEP requires the DBI perl module to function

http://www.ensembl.org/info/docs/tools/vep/script/vep_download.html#requirements

So, I then try and install DBI as suggested here https://www.ensembl.org/info/docs/tools/vep/script/vep_download.html#requirements

cpanm DBI

But I get this error:

Can't write to cpanm home '/Users/michaelflower/.cpanm': You should fix it with chown/chmod first.

How to I 'fix' it with chown/chmod??

Answer 1

On Ubuntu 20.04 this worked for me:

sudo apt install libdbi-perl

But then I ran into a bunch of other errors which I solved sequentially by doing these things (I restarted the installation after every step but I guess if you first do them all, then it should work in 1 go):

sudo apt update # Or you'll more errors
sudo apt install unzip
sudo apt install build-essential
sudo apt install libbz2-dev liblzma-dev zlib1g-dev
sudo apt install libcam-pdf-perl
cpan Bio::DB:HTS # Takes a while as well

This perl modules wants to install

cpan Bio::SeqFeature::Lite # Takes quite a while

Which wants to install:

cpan XML::DOM XML::Parser::PerlSAX XML::Twig

Which then ultimately fails with:

Files=109, Tests=72,  4 wallclock secs ( 0.28 usr  0.09 sys +  2.29 cusr  0.83 csys =  3.49 CPU)
Result: FAIL
Failed 103/109 test programs. 32/72 subtests failed.
make: *** [Makefile:837: test_dynamic] Error 255
  MIROD/XML-Twig-3.52.tar.gz
one dependency not OK (XML::Parser); additionally test harness failed
  /usr/bin/make test -- NOT OK
//hint// to see the cpan-testers results for installing this module, try:
  reports MIROD/XML-Twig-3.52.tar.gz

So I try to install XML::Parser

cpan XML::Parser

and it fails too

Note that if you build against a shareable library in a non-standard location
you may (on some platforms) also have to set your LD_LIBRARY_PATH environment
variable at run time for perl to find the library.

No 'Makefile' created  TODDR/XML-Parser-2.46.tar.gz
  /usr/bin/perl Makefile.PL INSTALLDIRS=site -- NOT OK

I'll ddg some more...

... ok, I just reran to original install command and it crashes with a new message, it wants me to intall LWP::Simple. So I do, on my first attempt it crashed with a permissions error so I add sudo

sudo cpan LWP::Simple

Restarting install...

perl INSTALL.pl

SUCCESS!