[ensembl-dev] ensemb-rest setup

[Javad Karimi]

 Dear Sir/Madam
I'd like to change the gene ID for "SL.2.5" to " 3 " version. I tried but
failed. It would be kind of you to help me about this issue.
Thanks in advance
Javad Karimi

On Wed, Aug 19, 2020 at 1:29 AM Sage Hornung <sage.hornung at neogenomics.com>
wrote:

> Hi,
>
>
>
> I am trying to get ensemble-rest running. I am starting with a VM provided
> by Ensembl. Its on Ubuntu 20.04 and it has VEP working properly. I can pass
> ./verify installation and have also ran a few of the test scripts
> successfully.
>
>
>
> I am using the 100 Version of the API and would like to use the human
> assembly GRCh37
>
> I have pulled the latest from ensemble-rest on git and flowed the
> instructions found here
> https://github.com/Ensembl/ensembl-rest/wiki/REST-Installation-and-Development
>
> I am able to get the dev server running but I get this error.
>
>
>
> 2020/08/18 13:29:19 (1) ReturnError.pm 61> -------------------- EXCEPTION
> --------------------MSG: ERROR: No root_dir or dir specifiedS TACK
> Bio::EnsEMBL::VEP::CacheDir::new
> /home/ensembl/ensembl-api-folder/ensembl-vep/modules/Bio/EnsEMBL/VEP/CacheDir.pm:107STACK
> Bio::EnsEMBL::VEP::AnnotationSourceAdaptor::get_all_from_cache
>
>
>
>
>
>
>
> I have reinstalled VEP with the script inside /VEP and added the cache
> files (I did resize my drive to 80GB) but I still get the error.
>
>
>
> My guess is it has something to do with the registry. I have spent some
> time following the Perl files and tried setting the dir_specified in a few
> files manually to where my cache files were downloaded unsuccessfully.
>
>
>
> I would greatly appreciate and help or suggestions.
>
>
>
> Thank You,
>
>
>
> Sage
>
>
>
>
>
> *Sage Hornung*
>
> *Software Engineer *
>
> *NeoGenomics Laboratories, Inc.*
>
> 2131 Faraday Avenue, Carlsbad, CA 92008
>
> *Phone: *760.516.5114
>
> *Cell: *760.755.3930
>
> sage.hornung at neogenomics.com
>
> neogenomics.com
>
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>
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>
>
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-- 

Javad Karimi , PhD
Entomology Division
Department of Plant Protection
School of Agriculture
Ferdowsi University of Mashhad
Mashhad , Iran
Alternate email jkb at um.ac.ir <javadkarimi10 at gmail.com>
Tel. ( W.): +98-51- 38 80 58 17 ; Cell : +98-911 17 00 817


<https://www.sciencedirect.com/science/article/pii/S0022201117304445?via%3Dihub>
*Microbial insecticides in Iran: History, current status, challenges and
perspective
<https://www.sciencedirect.com/science/article/pii/S0022201117304445?via%3Dihub>*
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