[ensembl-dev] VEP: convert_cache error when using --species all --version all

[Will McLaren]

Hi Cyriac,

It looks like the script is picking up some directories in $VEP_DATA that
are not VEP cache directories, possibly $VEP_DATA/htslib/test ?

I'd suggest moving these as if you use "--species all" the script basically
looks for any directories in --dir and assumes they are VEP caches.

I'll add a fix too to verify the directories before continuing.

Regards

Will McLaren
Ensembl Variation

On 31 October 2015 at 22:58, Cyriac Kandoth <kandoth at cbio.mskcc.org> wrote:

> I normally something like this, after downloading a bunch of caches... and
> it works fine:
> perl convert_cache.pl --species homo_sapiens,mus_musculus --version
> 82_GRCh37,82_GRCh38,82_GRCm38 --dir $VEP_DATA
>
> The documentation states we can use "all" to do all caches found. But
> here's what happen when I do:
> perl convert_cache.pl --species all --version all --dir $VEP_DATA
>
> 2015-10-31 18:54:45 - Processing htslib
> 2015-10-31 18:54:45 - Processing version test
> Can't use an undefined value as an ARRAY reference at convert_cache.pl
> line 176.
>
> Let me know if you need more information to debug.
>
> Cheers!
>
> ~Cyriac
>
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