This page - http://www.bioconductor.org/packages/release/bioc/html/ensemblVEP.html - says that the EnsemblVEP bioconductor package needs v88 of the Ensembl API, but from some of the help pages within ensemblVEP v1.20.0 it looks like maybe v90 is now supported too?
I'm asking because I'm trying to troubleshoot a problem that probably has to do with my installation of the back-end ensembl perl modules and my PERL5LIB variable, rather than bioconductor itself (not sure).
I'm a bit confused, as when I issue what I think is an equivalent unix command-line call to the vep script, it seems to work fine. Does bioconductor make a system call to the vep perl script in order to do the analysis? If so, is there an option within R to show me the command it's trying to run, so I can replicate that and and test it from the command line? Where does bioc take PERL5LIB from (on a linux box) - is it simply taken from my environment when R starts up?
thanks very much,