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

Tattersfield,Calum (BIDMC - Friedman-Clin Trial Nephrol SF) ctatters at bidmc.harvard.edu
Thu Jul 1 20:20:40 BST 2021


Hi Diana,


That has fixed it!


Thank you very much,

Calum

________________________________
From: Diana Lemos <dlemos at ebi.ac.uk>
Sent: Thursday, July 1, 2021 5:57 AM
To: Tattersfield,Calum (BIDMC - Friedman-Clin Trial Nephrol SF); Ensembl developers list
Subject: Re: [External] Re: [ensembl-dev] 'Bio::EnsEMBL::Variation::DBSQL::VCFCollectionAdaptor' cannot be found.


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><mailto: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

________________________________

This message is intended for the use of the person(s) to whom it may be addressed. It may contain information that is privileged, confidential, or otherwise protected from disclosure under applicable law. If you are not the intended recipient, any dissemination, distribution, copying, or use of this information is prohibited. If you have received this message in error, please permanently delete it and immediately notify the sender. Thank you.



_______________________________________________
Dev mailing list    Dev at ensembl.org<mailto:Dev at ensembl.org>
Posting guidelines and subscribe/unsubscribe info: https://lists.ensembl.org/mailman/listinfo/dev_ensembl.org<https://urldefense.com/v3/__https://lists.ensembl.org/mailman/listinfo/dev_ensembl.org__;!!CvMGjuU!oaoMjZWRQ3r5bHN6KygbHBZDe01PcoK6slwG76WhSTESwe5EccX_cJ1Cfg3DydU7yOmgiEc$>
Ensembl Blog: http://www.ensembl.info/<https://urldefense.com/v3/__http://www.ensembl.info/__;!!CvMGjuU!oaoMjZWRQ3r5bHN6KygbHBZDe01PcoK6slwG76WhSTESwe5EccX_cJ1Cfg3DydU7J9J86hk$>

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.ensembl.org/pipermail/dev_ensembl.org/attachments/20210701/063676e9/attachment.html>


More information about the Dev mailing list