[ensembl-dev] [External] Re: 'Bio::EnsEMBL::Variation::DBSQL::VCFCollectionAdaptor' cannot be found.

Diana Lemos dlemos at ebi.ac.uk
Thu Jul 1 10:57:27 BST 2021


Hi Calum,


You can install Try::Tiny with *cpanm Try::Tiny* (if you have cpan minus 
installed).


The ensembl-vep is missing from @INC. Could you please run:

|export PERL5LIB=${PERL5LIB}:/home/ct194/src/ensembl-vep/modules/|



Best wishes,

Diana



On 30/06/2021 18:30, Tattersfield,Calum (BIDMC - Friedman-Clin Trial 
Nephrol SF) wrote:
> Hi Diana,
>
> Thank you for your reply. Here is my PERL5LIB
>
> ```
> /home/ct194/perl5/lib/perl5:/home/ct194/perl5/lib/perl5:/home/ct194/src/bioperl-1.6.924:/home/ct194/src/ensembl/modules:/home/ct194/src/ensembl-compara/modules:/home/ct194/src/ensembl-variation/modules:/home/ct194/src/ensembl-funcgen/modules:/home/ct194/src/ensembl-taxonomy/modules:/home/ct194/src/ensembl-metadata/modules:/home/ct194/src/ensembl-io/modules:/home/ct194/src/Bio-DB-HTS/lib:/home/ct194/src/Bio-DB-HTS/blib/arch/auto/Bio/DB/HTS/:/home/ct194/src/Bio-DB-HTS/blib/arch/auto/Bio/DB/HTS/Faidx
> ```
> I seem to be getting a new exception now.
> Exception:
> 'Can't locate Try/Tiny.pm in @INC'
>
> Best,
> Calum
>
>
> ------------------------------------------------------------------------
> *From:* Diana Lemos <dlemos at ebi.ac.uk>
> *Sent:* Wednesday, June 30, 2021 12:12 PM
> *To:* Ensembl developers list; Tattersfield,Calum (BIDMC - 
> Friedman-Clin Trial Nephrol SF)
> *Subject:* [External] Re: [ensembl-dev] 
> 'Bio::EnsEMBL::Variation::DBSQL::VCFCollectionAdaptor' cannot be found.
>
> Hello Calum,
>
>
> Can you please share what you have in your PERL5LIB? (echo $PERL5LIB)
>
>
>
> Kind Regards,
>
> Diana
>
>
>
>
> On 30/06/2021 16:19, Tattersfield,Calum (BIDMC - Friedman-Clin Trial 
> Nephrol SF) wrote:
>>
>> Bash on Linux version 7 with Perl/5.24.0. Attempting to access 1000 
>> Genomes population frequencies using example script from
>>
>>
>> https://www.ensembl.info/2015/06/18/1000-genomes-phase-3-frequencies-genotypes-and-ld-data/ 
>> <https://urldefense.com/v3/__https://www.ensembl.info/2015/06/18/1000-genomes-phase-3-frequencies-genotypes-and-ld-data/__;!!CvMGjuU!oaoMjZWRQ3r5bHN6KygbHBZDe01PcoK6slwG76WhSTESwe5EccX_cJ1Cfg3DydU7MoRoy30$>
>>
>>
>> The API version used is 104.
>>
>>
>> Error message is
>>
>> 'Bio::EnsEMBL::Variation::DBSQL::VCFCollectionAdaptor'  cannot be found.
>>
>>
>> Exception is
>>
>> 'Can't locate Bio/DB/HTS/Tabix.pm in @INC'
>>
>>
>> BEGIN failed--compilation aborted at 
>> /src/ensembl-io/modules/Bio/EnsEMBL/IO/TabixParser.pm line 41.
>>
>> BEGIN failed--compilation aborted at 
>> /src/ensembl-io/modules/Bio/EnsEMBL/IO/Parser/VCF4Tabix.pm line 42.
>>
>> Compilation failed in require at 
>> /src/ensembl-variation/modules/Bio/EnsEMBL/Variation/VCFCollection.pm 
>> line 82.
>> BEGIN failed--compilation aborted at 
>> /src/ensembl-variation/modules/Bio/EnsEMBL/Variation/VCFCollection.pm 
>> line 82.
>> Compilation failed in require at 
>> /src/ensembl-variation/modules/Bio/EnsEMBL/Variation/DBSQL/VCFCollectionAdaptor.pm 
>> line 98.
>> BEGIN failed--compilation aborted at 
>> /src/ensembl-variation/modules/Bio/EnsEMBL/Variation/DBSQL/VCFCollectionAdaptor.pm 
>> line 98.
>> Compilation failed in require at (eval 875) line 2.
>>
>>
>> I have been unable to clone tabix from github, but their page says it 
>> has been moved to htslib. I made htslib following api installation 
>> instructions here:
>>
>> https://useast.ensembl.org/info/docs/api/api_installation.html 
>> <https://urldefense.com/v3/__https://useast.ensembl.org/info/docs/api/api_installation.html__;!!CvMGjuU!oaoMjZWRQ3r5bHN6KygbHBZDe01PcoK6slwG76WhSTESwe5EccX_cJ1Cfg3DydU7DS6ergQ$>
>>
>>
>> Thanks,
>>
>> Calum
>>
>>
>> ------------------------------------------------------------------------
>>
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