<div dir="ltr"><div class="gmail_default" style="font-family:tahoma,sans-serif">Thank you very much. I fixed it.<br></div></div><div class="gmail_extra"><br clear="all"><div><div class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><font face="tahoma,sans-serif">Regards,<br>Mahmood</font><br><br><br></div></div></div>
<br><div class="gmail_quote">On Fri, Sep 1, 2017 at 12:39 PM, mag <span dir="ltr"><<a href="mailto:mr6@ebi.ac.uk" target="_blank">mr6@ebi.ac.uk</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div text="#000000" bgcolor="#FFFFFF">
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="m_-6685548138973100285moz-txt-link-freetext" href="https://github.com/Ensembl/ensembl/blob/release/90/cpanfile" target="_blank">https://github.com/Ensembl/<wbr>ensembl/blob/release/90/<wbr>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<div><div class="h5"><br>
<br>
<div class="m_-6685548138973100285moz-cite-prefix">On 01/09/2017 09:01, Mahmood Naderan
wrote:<br>
</div>
</div></div><blockquote type="cite"><div><div class="h5">
<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 $PERL5LIB<br>
:/home/mahmood/src/bioperl-1.<wbr>6.1:/home/mahmood/src/ensembl/<wbr>modules:/home/mahmood/src/<wbr>ensembl-compara/modules:/home/<wbr>mahmood/src/ensembl-variation/<wbr>modules:/home/mahmood/src/<wbr>ensembl-funcgen/modules:/home/<wbr>mahmood/src/Bio-DB-HTS/lib:/<wbr>home/mahmood/src/Bio-DB-HTS/<wbr>blib/arch/auto/Bio/DB/HTS/:/<wbr>home/mahmood/src/Bio-DB-HTS/<wbr>blib/arch/auto/Bio/DB/HTS/<wbr>Faidx:/home/mahmood/src/<wbr>bioperl-1.6.1:/home/mahmood/<wbr>src/ensembl/modules:/home/<wbr>mahmood/src/ensembl-compara/<wbr>modules:/home/mahmood/src/<wbr>ensembl-variation/modules:/<wbr>home/mahmood/src/ensembl-<wbr>funcgen/modules:/home/mahmood/<wbr>src/Bio-DB-HTS/lib:/home/<wbr>mahmood/src/Bio-DB-HTS/blib/<wbr>arch/auto/Bio/DB/HTS/:/home/<wbr>mahmood/src/Bio-DB-HTS/blib/<wbr>arch/auto/Bio/DB/HTS/Faidx<br>
mahmood@qemu:~$ echo $HTSLIB_DIR<br>
/home/mahmood/src/htslib<br>
mahmood@qemu:~$ perl <a href="http://test-new.pl" target="_blank">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.<wbr>1
/home/mahmood/src/ensembl/<wbr>modules
/home/mahmood/src/ensembl-<wbr>compara/modules
/home/mahmood/src/ensembl-<wbr>variation/modules
/home/mahmood/src/ensembl-<wbr>funcgen/modules
/home/mahmood/src/Bio-DB-HTS/<wbr>lib
/home/mahmood/src/Bio-DB-HTS/<wbr>blib/arch/auto/Bio/DB/HTS/
/home/mahmood/src/Bio-DB-HTS/<wbr>blib/arch/auto/Bio/DB/HTS/<wbr>Faidx
/home/mahmood/src/bioperl-1.6.<wbr>1
/home/mahmood/src/ensembl/<wbr>modules
/home/mahmood/src/ensembl-<wbr>compara/modules
/home/mahmood/src/ensembl-<wbr>variation/modules
/home/mahmood/src/ensembl-<wbr>funcgen/modules
/home/mahmood/src/Bio-DB-HTS/<wbr>lib
/home/mahmood/src/Bio-DB-HTS/<wbr>blib/arch/auto/Bio/DB/HTS/
/home/mahmood/src/Bio-DB-HTS/<wbr>blib/arch/auto/Bio/DB/HTS/<wbr>Faidx
/etc/perl /usr/local/lib/x86_64-linux-<wbr>gnu/perl/5.22.1
/usr/local/share/perl/5.22.1
/usr/lib/x86_64-linux-gnu/<wbr>perl5/5.22 /usr/share/perl5
/usr/lib/x86_64-linux-gnu/<wbr>perl/5.22 /usr/share/perl/5.22
/usr/local/lib/site_perl /usr/lib/x86_64-linux-gnu/<wbr>perl-base
.) at
/home/mahmood/src/ensembl/<wbr>modules/Bio/EnsEMBL/DBSQL/<wbr>DBConnection.pm
line 74.<br>
BEGIN failed--compilation aborted at
/home/mahmood/src/ensembl/<wbr>modules/Bio/EnsEMBL/DBSQL/<wbr>DBConnection.pm
line 74.<br>
Compilation failed in require at
/home/mahmood/src/ensembl/<wbr>modules/Bio/EnsEMBL/DBSQL/<wbr>DBAdaptor.pm
line 69.<br>
BEGIN failed--compilation aborted at
/home/mahmood/src/ensembl/<wbr>modules/Bio/EnsEMBL/DBSQL/<wbr>DBAdaptor.pm
line 69.<br>
Compilation failed in require at
/home/mahmood/src/ensembl/<wbr>modules/Bio/EnsEMBL/Registry.<wbr>pm line
137.<br>
BEGIN failed--compilation aborted at
/home/mahmood/src/ensembl/<wbr>modules/Bio/EnsEMBL/Registry.<wbr>pm line
137.<br>
Compilation failed in require at <a href="http://test-new.pl" target="_blank">test-new.pl</a> line 1.<br>
BEGIN failed--compilation aborted at <a href="http://test-new.pl" target="_blank">test-new.pl</a>
line 1.<br>
mahmood@qemu:~$ head -n 3 <a href="http://test-new.pl" target="_blank">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="m_-6685548138973100285gmail_signature">
<div dir="ltr"><font face="tahoma,sans-serif">Regards,<br>
Mahmood</font><br>
<br>
<br>
</div>
</div>
</div>
</div>
<br>
<fieldset class="m_-6685548138973100285mimeAttachmentHeader"></fieldset>
<br>
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</pre>
</blockquote>
<br>
</div>
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<br></blockquote></div><br></div>