fixes for VEP easyblock required for VEP v110

[garadar]

I am trying to building vep-110:

cat VEP-110-GCC-11.3.0.eb 
name = 'VEP'
version = '110'

homepage = 'https://www.ensembl.org/info/docs/tools/vep'
description = """Variant Effect Predictor (VEP) determines the effect of your
 variants (SNPs, insertions, deletions, CNVs or structural variants) on genes,
 transcripts, and protein sequence, as well as regulatory regions.
 Includes EnsEMBL-XS, which provides pre-compiled replacements for frequently
 used routines in VEP."""

toolchain = {'name': 'GCC', 'version': '11.3.0'}

source_urls = ['https://github.com/Ensembl/ensembl-vep/archive/release/']
sources = ['%(version)s.tar.gz']

dependencies = [
    ('libnsl', '2.0.0'),
    ('Perl', '5.36.0'),
    ('Archive-Zip', '1.68'),
    ('DBD-mysql', '4.050'),
    ('BioPerl', '1.7.8'),
    ('Bio-DB-HTS', '3.01'),
    # VEP requires Compress::Raw::Zlib >= 2.103
    ('Compress-Raw-Zlib', '2.202'),
]

exts_defaultclass = 'PerlModule'
exts_filter = ("perl -e 'require %(ext_name)s'", "")

exts_list = [
    ('Bio::EnsEMBL::XS', '2.3.2', {
        'source_urls': ['https://github.com/Ensembl/ensembl-xs/archive'],
        'sources': ['%(version)s.tar.gz'],
    }),
]

moduleclass = 'bio'

But I have an issue during the build with the option "--SPECIES all". One of the species files have an typo, the build is failing:

Ensembl/ensembl-vep#1364 (comment)

So I replace in vep.py easyblock, as a workaround, "--SPECIES all" by "--SPECIES cyprinus_carpio_carpio"

But I have Another issue:

== sanity checking...
  >> file 'vep' found: OK
  >> file 'lib/perl5/site_perl/5.36.0/x86_64-linux-thread-multi/Bio/EnsEMBL/XS.pm' found: FAILED
  >> (non-empty) directory 'modules/Bio/EnsEMBL/VEP' found: OK
  >> running command:
	[started at: 2023-10-09 15:27:38]
	[working dir: /opt/ebsofts/VEP/110-GCC-11.3.0/BioEnsEMBLXS/ensembl-xs-2.3.2]
	[output logged in /tmp/eb-zfkep4ya/easybuild-run_cmd-kpjkad31.log]
	perl -MConfig -e 'print $Config::Config{PERL_API_REVISION}'
  >> command completed: exit 0, ran in < 1s
  >> loading modules: GCC/11.3.0, VEP/110...
  >> running command 'vep --help' ...
  >> result for command 'vep --help': OK
  >> running command:
	[started at: 2023-10-09 15:27:43]
	[working dir: /opt/ebsofts/VEP/110-GCC-11.3.0]
	[output logged in /tmp/eb-zfkep4ya/easybuild-run_cmd-cr_97r93.log]
	perl -e 'require Bio::EnsEMBL::XS'

it's checking another version of perl during the sanity check of the extension.

So I have to create a symlink, to make the sanity-check works

(cluster)-[toto@nodexxx site_perl]$ pwd
/opt/ebsofts/VEP/110-GCC-11.3.0/lib/perl5/site_perl
(cluster)-[toto@nodexxx site_perl]$]$ ll
total 4
drwxr-xr-x 3 root root 4096 Oct  9 17:38 5.34.1
lrwxrwxrwx 1 root root    7 Oct  9 17:41 5.36.0 -> 5.34.1/