[ensembl-dev] Installation problem

[mag]

Hi Mahmood,

DBI is a Perl library required to run Ensembl.
You can see the list of Perl libraries required here: 
https://github.com/Ensembl/ensembl/blob/release/90/cpanfile

Libraries can be installed manually using cpan or cpanm, eg cpanm DBI
It is also possible to install all dependencies directly from the 
cpanfile, using installdeps, for example cpanm -v --installdeps --notest 
--cpanfile cpanfile


Hope that helps,
Magali

On 01/09/2017 09:01, Mahmood Naderan wrote:
> Hello,
> I am using the API on a system which is fine. However, as I tried to 
> build the API on another system, I faced some problems. I think I 
> followed all steps, but my script fails to work. Please see the 
> following output
>
>
> mahmood at qemu:~$ echo $PERL5LIB
> :/home/mahmood/src/bioperl-1.6.1:/home/mahmood/src/ensembl/modules:/home/mahmood/src/ensembl-compara/modules:/home/mahmood/src/ensembl-variation/modules:/home/mahmood/src/ensembl-funcgen/modules:/home/mahmood/src/Bio-DB-HTS/lib:/home/mahmood/src/Bio-DB-HTS/blib/arch/auto/Bio/DB/HTS/:/home/mahmood/src/Bio-DB-HTS/blib/arch/auto/Bio/DB/HTS/Faidx:/home/mahmood/src/bioperl-1.6.1:/home/mahmood/src/ensembl/modules:/home/mahmood/src/ensembl-compara/modules:/home/mahmood/src/ensembl-variation/modules:/home/mahmood/src/ensembl-funcgen/modules:/home/mahmood/src/Bio-DB-HTS/lib:/home/mahmood/src/Bio-DB-HTS/blib/arch/auto/Bio/DB/HTS/:/home/mahmood/src/Bio-DB-HTS/blib/arch/auto/Bio/DB/HTS/Faidx
> mahmood at qemu:~$ echo $HTSLIB_DIR
> /home/mahmood/src/htslib
> mahmood at qemu:~$ perl test-new.pl <http://test-new.pl> genes.txt
> Can't locate DBI.pm in @INC (you may need to install the DBI module) 
> (@INC contains: /home/mahmood/src/bioperl-1.6.1 
> /home/mahmood/src/ensembl/modules 
> /home/mahmood/src/ensembl-compara/modules 
> /home/mahmood/src/ensembl-variation/modules 
> /home/mahmood/src/ensembl-funcgen/modules 
> /home/mahmood/src/Bio-DB-HTS/lib 
> /home/mahmood/src/Bio-DB-HTS/blib/arch/auto/Bio/DB/HTS/ 
> /home/mahmood/src/Bio-DB-HTS/blib/arch/auto/Bio/DB/HTS/Faidx 
> /home/mahmood/src/bioperl-1.6.1 /home/mahmood/src/ensembl/modules 
> /home/mahmood/src/ensembl-compara/modules 
> /home/mahmood/src/ensembl-variation/modules 
> /home/mahmood/src/ensembl-funcgen/modules 
> /home/mahmood/src/Bio-DB-HTS/lib 
> /home/mahmood/src/Bio-DB-HTS/blib/arch/auto/Bio/DB/HTS/ 
> /home/mahmood/src/Bio-DB-HTS/blib/arch/auto/Bio/DB/HTS/Faidx /etc/perl 
> /usr/local/lib/x86_64-linux-gnu/perl/5.22.1 
> /usr/local/share/perl/5.22.1 /usr/lib/x86_64-linux-gnu/perl5/5.22 
> /usr/share/perl5 /usr/lib/x86_64-linux-gnu/perl/5.22 
> /usr/share/perl/5.22 /usr/local/lib/site_perl 
> /usr/lib/x86_64-linux-gnu/perl-base .) at 
> /home/mahmood/src/ensembl/modules/Bio/EnsEMBL/DBSQL/DBConnection.pm 
> line 74.
> BEGIN failed--compilation aborted at 
> /home/mahmood/src/ensembl/modules/Bio/EnsEMBL/DBSQL/DBConnection.pm 
> line 74.
> Compilation failed in require at 
> /home/mahmood/src/ensembl/modules/Bio/EnsEMBL/DBSQL/DBAdaptor.pm line 69.
> BEGIN failed--compilation aborted at 
> /home/mahmood/src/ensembl/modules/Bio/EnsEMBL/DBSQL/DBAdaptor.pm line 69.
> Compilation failed in require at 
> /home/mahmood/src/ensembl/modules/Bio/EnsEMBL/Registry.pm line 137.
> BEGIN failed--compilation aborted at 
> /home/mahmood/src/ensembl/modules/Bio/EnsEMBL/Registry.pm line 137.
> Compilation failed in require at test-new.pl <http://test-new.pl> line 1.
> BEGIN failed--compilation aborted at test-new.pl <http://test-new.pl> 
> line 1.
> mahmood at qemu:~$ head -n 3 test-new.pl <http://test-new.pl>
> use Bio::EnsEMBL::Registry;
> use Bio::SeqIO;
> use File::Basename;
> mahmood at qemu:~$
>
>
>
> Which step did I miss? Any thought?
>
> Regards,
> Mahmood
>
>
>
>
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