Not finding pre-existing VEP during install

[tirohia]

Less, I'm thinking, a problem with cpipe and more, most likely, I'm missing something basic.

I have a pre-existing install of VEP, on a server that loads everything as modules (i.e. I don't get to choose where to install VEP). I can load modules for various other things (bedtools, samtools, etc) and in the config.groovy file, put the various locations in. Then when I run ./pipeline/scripts/install.sh, it picks up the location of the pre-existing install and not attempt to reinstall.

With the exception of VEP. The config.groovy file says:

// Set location of Variant Effect Predictor here
// and store it in the local directory called 'vep_cache'
// (you can create a symlink to an existing directory with
// that name if desired).
// See tools/vep/README for more information
VEP_VERSION="90.3"
VEP="/opt/nesi/mahuika/VariantEffectPredictor/ensembl-vep-release-90.3/"

So in addition to the specifying the location of the VEP install here, I've also created a symlink to /opt/nesi/mahuika/VariantEffectPredictor/ensembl-vep-release-90.3/ in the same directory as the config file. That didn't work, so I've now also got symlinks in the current cpipe directory and the pipeline/scripts/ directory.

I don't understand what I'm missing - everything else picks up the current install fine. Anyone know what I might be missing?

Cheers.
Ben.