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

[Will McLaren]

Hi Michael,

Thanks for the suggestion - I'll add this change to the next VEP version.

I think it's probably OK for now as most users will run INSTALL.pl from
within the VEP directory as per the instructions.

Cheers

Will McLaren
Ensembl Variation

*From: *Michael Yourshaw <myourshaw at ucla.edu>
> *Subject: **[ensembl-dev] VEP installer fails if run from a different
> working directory*
> *Date: *10 January 2014 02:14:33 GMT
> *To: *Ensembl developers list <dev at ensembl.org>
> *Reply-To: *Ensembl developers list <dev at ensembl.org>
>
> 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
>
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>
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