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

[Cyriac Kandoth]

Yes, that's likely it. I set my vep data folder to be the same as the vep
installation folder.

~Cyriac

On Mon, Nov 2, 2015 at 7:32 AM, Will McLaren <wm2 at ebi.ac.uk> wrote:

> 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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