VEPFlags refuses to accept the scriptPath of VEP

[Rohit-Satyam]

I successfully installed VEP in my ubuntu v.20 and added its path to ~/.bashrc as shown below but still I get the error
.bashrc file content

export PATH="$PATH:/home/subudhak/ensembl-vep-release-108"
alias vep="sudo /home/subudhak/ensembl-vep-release-108/vep"

Error msg

Error in validObject(.Object) : 
  invalid class “VEPFlags” object: Ensembl >=88 requires vep script  (not variant_effect_predictor.pl)

When trying to explicitly define the path the error message persists: (even renamed vep to variant_effect_predictor.pl)

param <- VEPFlags(flags=list(host="useastdb.ensembl.org"), scriptPath = as.character("home/subudhak/ensembl-vep-release-108/variant_effect_predictor.pl"))
Error in validObject(.Object) : 
  invalid class “VEPFlags” object: Ensembl >=88 requires vep script  (not variant_effect_predictor.pl)

[jwokaty]

Sorry it took awhile to get back to this. I was sick most of last week.

It would be helpful to see what code you are executing that produces the error messages so that I can perform the same steps. I don't think you need an alias. After you add the export line to your .bashrc, you need to log out and log back in. (But it also might work in a new terminal window.) If it's working, you should get the path to your vep when doing which vep. Alternatively, if this is your computer, you could also put the same line /etc/profile and logout for it to take effect.

In order to install, I believe I had do something similar to how we set up ensemble-vep on the build machines:

sudo cpan install Archive::Zip
sudo cpan install File::Copy::Recursive
sudo perl INSTALL.pl --NO_HTSLIB
# When asked if you want to install any cache files - say no
# When asked if you want to install any FASTA files - say no
# When asked if you want to install any plugins - say no