Downstream.pm should be installed vep's INSTALL.pl

[serge2016]

The new version: https://github.com/Ensembl/VEP_plugins/blob/release/105/Downstream.pm

I use a command like this:

perl INSTALL.pl --NO_TEST --NO_UPDATE --NO_HTSLIB --NO_BIOPERL -a ap --PLUGINSDIR "$SOFT/ensembl-vep-${VEP_VERSION}/Plugins" --PLUGINS ProteinSeqs,Downstream,Conservation,GO,G2P,CADD

So I recommend not to copy the Downstream.pm from this repo but to install it from the official site.

Change should be in this place: https://github.com/ylab-hi/ScanNeo#install-vep-plugins