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Hi Mahmood,<br>
<br>
DBI is a Perl library required to run Ensembl.<br>
You can see the list of Perl libraries required here:
<a class="moz-txt-link-freetext" href="https://github.com/Ensembl/ensembl/blob/release/90/cpanfile">https://github.com/Ensembl/ensembl/blob/release/90/cpanfile</a><br>
<br>
Libraries can be installed manually using cpan or cpanm, eg cpanm
DBI<br>
It is also possible to install all dependencies directly from the
cpanfile, using installdeps, for example cpanm -v --installdeps
--notest --cpanfile cpanfile<br>
<br>
<br>
Hope that helps,<br>
Magali<br>
<br>
<div class="moz-cite-prefix">On 01/09/2017 09:01, Mahmood Naderan
wrote:<br>
</div>
<blockquote type="cite"
cite="mid:CADa2P2VN2tjXuUK+REYbwWDNkpVFferjtedBO__+H+KXmW61QQ@mail.gmail.com">
<div dir="ltr">
<div class="gmail_default" style="font-family:tahoma,sans-serif">Hello,</div>
<div class="gmail_default" style="font-family:tahoma,sans-serif">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</div>
<div class="gmail_default" style="font-family:tahoma,sans-serif"><br>
</div>
<div class="gmail_default" style="font-family:tahoma,sans-serif"><br>
</div>
<div class="gmail_default" style="font-family:tahoma,sans-serif">mahmood@qemu:~$
echo $PERL5LIB<br>
:/home/mahmood/src/bioperl-1.6.1:/home/mahmood/src/ensembl/modules:/home/mahmood/src/ensembl-compara/modules:/home/mahmood/src/ensembl-variation/modules:/home/mahmood/src/ensembl-funcgen/modules:/home/mahmood/src/Bio-DB-HTS/lib:/home/mahmood/src/Bio-DB-HTS/blib/arch/auto/Bio/DB/HTS/:/home/mahmood/src/Bio-DB-HTS/blib/arch/auto/Bio/DB/HTS/Faidx:/home/mahmood/src/bioperl-1.6.1:/home/mahmood/src/ensembl/modules:/home/mahmood/src/ensembl-compara/modules:/home/mahmood/src/ensembl-variation/modules:/home/mahmood/src/ensembl-funcgen/modules:/home/mahmood/src/Bio-DB-HTS/lib:/home/mahmood/src/Bio-DB-HTS/blib/arch/auto/Bio/DB/HTS/:/home/mahmood/src/Bio-DB-HTS/blib/arch/auto/Bio/DB/HTS/Faidx<br>
mahmood@qemu:~$ echo $HTSLIB_DIR<br>
/home/mahmood/src/htslib<br>
mahmood@qemu:~$ perl <a href="http://test-new.pl"
moz-do-not-send="true">test-new.pl</a> genes.txt <br>
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.<br>
BEGIN failed--compilation aborted at
/home/mahmood/src/ensembl/modules/Bio/EnsEMBL/DBSQL/DBConnection.pm
line 74.<br>
Compilation failed in require at
/home/mahmood/src/ensembl/modules/Bio/EnsEMBL/DBSQL/DBAdaptor.pm
line 69.<br>
BEGIN failed--compilation aborted at
/home/mahmood/src/ensembl/modules/Bio/EnsEMBL/DBSQL/DBAdaptor.pm
line 69.<br>
Compilation failed in require at
/home/mahmood/src/ensembl/modules/Bio/EnsEMBL/Registry.pm line
137.<br>
BEGIN failed--compilation aborted at
/home/mahmood/src/ensembl/modules/Bio/EnsEMBL/Registry.pm line
137.<br>
Compilation failed in require at <a href="http://test-new.pl"
moz-do-not-send="true">test-new.pl</a> line 1.<br>
BEGIN failed--compilation aborted at <a
href="http://test-new.pl" moz-do-not-send="true">test-new.pl</a>
line 1.<br>
mahmood@qemu:~$ head -n 3 <a href="http://test-new.pl"
moz-do-not-send="true">test-new.pl</a> <br>
use Bio::EnsEMBL::Registry;<br>
use Bio::SeqIO;<br>
use File::Basename;<br>
mahmood@qemu:~$ <br>
</div>
<div class="gmail_default" style="font-family:tahoma,sans-serif"><br>
</div>
<div class="gmail_default" style="font-family:tahoma,sans-serif"><br>
</div>
<div class="gmail_default" style="font-family:tahoma,sans-serif"><br>
</div>
<div class="gmail_default" style="font-family:tahoma,sans-serif">Which
step did I miss? Any thought?<br>
</div>
<div class="gmail_default" style="font-family:tahoma,sans-serif"><br
clear="all">
</div>
<div>
<div class="gmail_signature">
<div dir="ltr"><font face="tahoma,sans-serif">Regards,<br>
Mahmood</font><br>
<br>
<br>
</div>
</div>
</div>
</div>
<br>
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</pre>
</blockquote>
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