Failing to install VEP dependencies - dbi

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!