[ensembl-dev] Installation problem

[Mahmood Naderan]

Thank you very much. I fixed it.

Regards,
Mahmood



On Fri, Sep 1, 2017 at 12:39 PM, mag <mr6 at ebi.ac.uk> wrote:

> 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 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 line 1.
> BEGIN failed--compilation aborted at test-new.pl line 1.
> mahmood at qemu:~$ head -n 3 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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