[ensembl-dev] VEP installer fails if run from a different working directory

[Michael Yourshaw]

When the VEP installer script is not in the working directory, e.g.,

compute-4-55:~$ perl ~/downloads/variant_effect_predictor/INSTALL.pl --DESTDIR ~/VEP

I get this error:

Testing VEP script
ERROR: Testing VEP script failed with the following error
Can't open perl script "variant_effect_predictor.pl": No such file or directory

Maybe something like

use File::Basename;
my $dirname = dirname(__FILE__);
my $test_vep = `perl $dirname/variant_effect_predictor.pl --help 2>&1`;


Also, I got this, even with --AUTO

The VEP requires the ensembl, ensembl-variation and optionally ensembl-functgenomics modules

Skip to the next step (n) to install cache files

Do you want to continue installing the API (y/n)? y

It would be nice to have complete walk-home-and-ignore for AUTO.


ॐ

Michael Yourshaw, PhD
UCLA Geffen School of Medicine
Department of Human Genetics, Nelson Lab
695 Charles E Young Drive S
Gonda 5554
Los Angeles CA 90095-8348 USA
myourshaw at ucla.edu
970.691.8299

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