[ensembl-dev] Is Bio::EnsEMBL::Registry needed to connect to database?

[Mahmood Naderan]

H
​i,
Thank you very much. It seems that I missed an export in the previous step.
​

Regards,
Mahmood



On Wed, Jun 28, 2017 at 1:19 AM, Zhicheng Liu <zl at ebi.ac.uk> wrote:

> Hi Mahmood,
>
> Have you tried following the item “3. Set up your environment” under the
> “Installation Procedure” section on this page?
> http://www.ensembl.org/info/docs/api/api_installation.html
>
> The Bio/EnsEMBL/Registry.pm should be located at
> ${HOME}/src/ensembl/modules.
>
> Hope this helps!
>
> Regards,
> Zhicheng
> .
>
> On 27 Jun 2017, at 20:27, Mahmood Naderan <mahmood.nt at gmail.com> wrote:
>
> Hello,
> I finished installing the API according to http://www.ensembl.org/info/
> docs/api/api_installation.html
>
> As I wrote a simple script to connect to the database, I get this error
>
> Can't locate Bio/EnsEMBL/Registry.pm in @INC (@INC contains:
> /opt/perl/lib/site_perl/5.14.2/x86_64-linux-thread-multi
> /opt/perl/lib/site_perl/5.14.2 /opt/perl/lib/5.14.2/x86_64-linux-thread-multi
> /opt/perl/lib/5.14.2 .) at test.pl line 1.
> BEGIN failed--compilation aborted at test.pl line 1.
>
>
> That is correct because there is no Bio::EnsEMBL in the cpan list.
>
> [root at cluster ~]# /opt/perl/bin/cpan -a | grep Bio::EnsEMBL
> [root at cluster ~]#
>
>
> It has not been stated in the installation guide that such package is
> needed. What should I do?
> Is it OK to run "cpanm Bio::EnsEMBL::Registry"? I want to be sure that it
> is safe to do that.
>
> P.S: Sorry for sending a lot of questions. These may seems obvious and
> easy to solve, but for a newbie it takes a while to boot!
>
>
> Regards,
> Mahmood
>
>
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