[ensembl-dev] VEP cache file creation for e74

[Will McLaren]

Hi Jan,

If you add the flag --no_adaptor_cache to your command it should work OK.

This has been fixed in a newer version of VEP, but I guess you're tied to
74.

Regards

Will

More info: it's not the version of Storable that is the issue, it's that
Storable is trying to serialise a DBI object that has an active connection
to the database. The VEP's serialisation code takes care of this by
disconnecting from the DB before the object gets serialised, but in this
case it doesn't work (and FWIW caching in the adaptors is no longer
necessary anyway, this behaviour should have been made the default way
before 74).

On 3 March 2015 at 05:55, Jan Vogel <jan.vogel at gmail.com> wrote:

>
>
> Hello Ensembl and Will,
>
> I’m running into trouble when I am trying to *create / update my cache
> files* for VEP.
>
> My best guess currently is, that the problem is either related to the
> ensembl code, or related to storing references with *Storable.pm* - I’m
> using version *$VERSION = ‘2.41’ of this module.*
>
> *Here’s how to reproduce the error :*
>
> perl  ensembl-tools-release-74/scripts/variant_effect_predictor/
> variant_effect_predictor.pl \
>        -build all -dir tmp --verbose --host <HOST> --user <USER> --pass
> <SECRET> --port 3326
>
> ERROR:
>
> 2015-03-02 20:56:27 - Connected to core version 74 database and variation
> version 74 database
>
> Can't store CODE items at
> …/perl/5.18.2/x86_64-linux-2.6-rhel6/lib/5.18.2/x86_64-linux-thread-multi/Storable.pm
> line 304, at
> variant_effect_predictor/e74_api/ensembl-variation-release-74/modules/Bio/EnsEMBL/Variation/Utils/VEP.pm
> line 4261.
>
>
> So reading trough http://perldoc.perl.org/Storable.html#CODE-REFERENCES suggests
> to serialize code-references with B::Deparse. I’ve added 2 lines to the
> variant_effect_predictor.pl script:
>
> $Storable::Eval=1;
> $Storable::Deparse=1;
>
>
> Now, the script writes the binary cache files - however, the next problem
> occurs when I try to read them.
>
> Depending on which version of the Ensembl API I am using, I get these
> error messages:
>
> *e75: *
>
> 2015-03-02 21:42:33 - Reading cached adaptor data
> code sub {
>     package Bio::EnsEMBL::DBSQL::DBConnection;
>     use strict;
>     $args[0];
> } caused an error: Global symbol "@args" requires explicit package name at
> (eval 108) line 4
>
>
> *e74:*
> 2015-03-02 21:47:40 - Reading cached adaptor data
> code sub {
>     package Bio::EnsEMBL::DBSQL::DBConnection;
>     use strict;
>     $arg;
> } caused an error: Global symbol "$arg" requires explicit package name at
> (eval 130) line 4, at
> /gne/research/apps/ensembl/ensembl-74/ensembl-variation/modules/Bio/EnsEMBL/Variation/Utils/VEP.pm
> line 4281.
>
> I’ve tried various work-arounds and different ensembl versions, but did
> not succeed. Any help welcome.
>
>
> The database I am currently working on is an e67 core which has been
> patched up to e74 ( so i can’t use the e74 cache files from the web).
>
> I tried to build indices with e77 but did not succeed either.
>
>
> Any help welcome
>
>    Jan Vogel
>
>
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