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<p>Hi Calum,</p>
<p><br>
</p>
<p>You can install Try::Tiny with <b>cpanm Try::Tiny</b> (if you
have cpan minus installed).</p>
<p><br>
</p>
<p>The ensembl-vep is missing from @INC. Could you please run:</p>
<p><code>export
PERL5LIB=${PERL5LIB}:/home/ct194/src/ensembl-vep/modules/</code></p>
<p><br>
</p>
<p><br>
</p>
<p>Best wishes,</p>
<p>Diana <br>
</p>
<p><br>
</p>
<p><br>
</p>
<div class="moz-cite-prefix">On 30/06/2021 18:30, Tattersfield,Calum
(BIDMC - Friedman-Clin Trial Nephrol SF) wrote:<br>
</div>
<blockquote type="cite"
cite="mid:1625074211449.72373@bidmc.harvard.edu">
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<div>Hi Diana,</div>
<div><br>
</div>
<div>Thank you for your reply. Here is my PERL5LIB</div>
<div><br>
</div>
<div>```<br>
</div>
<div>/home/ct194/perl5/lib/perl5:/home/ct194/perl5/lib/perl5:/home/ct194/src/bioperl-1.6.924:/home/ct194/src/ensembl/modules:/home/ct194/src/ensembl-compara/modules:/home/ct194/src/ensembl-variation/modules:/home/ct194/src/ensembl-funcgen/modules:/home/ct194/src/ensembl-taxonomy/modules:/home/ct194/src/ensembl-metadata/modules:/home/ct194/src/ensembl-io/modules:/home/ct194/src/Bio-DB-HTS/lib:/home/ct194/src/Bio-DB-HTS/blib/arch/auto/Bio/DB/HTS/:/home/ct194/src/Bio-DB-HTS/blib/arch/auto/Bio/DB/HTS/Faidx<br>
</div>
<div>```</div>
<div>I seem to be getting a new exception now. </div>
<div>Exception:</div>
<div>'Can't locate Try/Tiny.pm in @INC'</div>
<div><br>
</div>
<div>Best,</div>
<div>Calum<br>
</div>
<p><br>
</p>
<div style="color: rgb(33, 33, 33);">
<hr tabindex="-1" style="display:inline-block; width:98%">
<div id="divRplyFwdMsg" dir="ltr"><font style="font-size:11pt"
face="Calibri, sans-serif" color="#000000"><b>From:</b>
Diana Lemos <a class="moz-txt-link-rfc2396E" href="mailto:dlemos@ebi.ac.uk"><dlemos@ebi.ac.uk></a><br>
<b>Sent:</b> Wednesday, June 30, 2021 12:12 PM<br>
<b>To:</b> Ensembl developers list; Tattersfield,Calum
(BIDMC - Friedman-Clin Trial Nephrol SF)<br>
<b>Subject:</b> [External] Re: [ensembl-dev]
'Bio::EnsEMBL::Variation::DBSQL::VCFCollectionAdaptor'
cannot be found.</font>
<div> </div>
</div>
<div>
<p>Hello Calum,</p>
<p><br>
</p>
<p>Can you please share what you have in your PERL5LIB? (echo
$PERL5LIB)<br>
</p>
<p><br>
</p>
<p><br>
</p>
<p>Kind Regards,</p>
<p>Diana <br>
</p>
<p><br>
</p>
<p><br>
</p>
<p><br>
</p>
<div class="moz-cite-prefix">On 30/06/2021 16:19,
Tattersfield,Calum (BIDMC - Friedman-Clin Trial Nephrol SF)
wrote:<br>
</div>
<blockquote type="cite">
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<p>Bash on Linux version 7 with Perl/5.24.0. Attempting to
access 1000 Genomes population frequencies using example
script from
</p>
<p><br>
</p>
<p><a
href="https://urldefense.com/v3/__https://www.ensembl.info/2015/06/18/1000-genomes-phase-3-frequencies-genotypes-and-ld-data/__;!!CvMGjuU!oaoMjZWRQ3r5bHN6KygbHBZDe01PcoK6slwG76WhSTESwe5EccX_cJ1Cfg3DydU7MoRoy30$"
moz-do-not-send="true">https://www.ensembl.info/2015/06/18/1000-genomes-phase-3-frequencies-genotypes-and-ld-data/</a></p>
<p><br>
</p>
<p>The API version used is 104.</p>
<p><br>
</p>
<p>Error message is </p>
<p>'Bio::EnsEMBL::Variation::DBSQL::VCFCollectionAdaptor'
cannot be found.<br>
</p>
<p><br>
</p>
<p>Exception is </p>
<p>'Can't locate Bio/DB/HTS/Tabix.pm in @INC' </p>
<p><br>
</p>
<p>BEGIN failed--compilation aborted at
/src/ensembl-io/modules/Bio/EnsEMBL/IO/TabixParser.pm line
41.</p>
<p>BEGIN failed--compilation aborted at
/src/ensembl-io/modules/Bio/EnsEMBL/IO/Parser/VCF4Tabix.pm
line 42.</p>
<p>Compilation failed in require at
/src/ensembl-variation/modules/Bio/EnsEMBL/Variation/VCFCollection.pm
line 82.<br>
BEGIN failed--compilation aborted at
/src/ensembl-variation/modules/Bio/EnsEMBL/Variation/VCFCollection.pm
line 82.<br>
Compilation failed in require at
/src/ensembl-variation/modules/Bio/EnsEMBL/Variation/DBSQL/VCFCollectionAdaptor.pm
line 98.<br>
BEGIN failed--compilation aborted at
/src/ensembl-variation/modules/Bio/EnsEMBL/Variation/DBSQL/VCFCollectionAdaptor.pm
line 98.<br>
Compilation failed in require at (eval 875) line 2.<br>
</p>
<p><br>
</p>
<p>I have been unable to clone tabix from github, but their
page says it has been moved to htslib. I made
htslib following api installation instructions here:<br>
</p>
<p><a
href="https://urldefense.com/v3/__https://useast.ensembl.org/info/docs/api/api_installation.html__;!!CvMGjuU!oaoMjZWRQ3r5bHN6KygbHBZDe01PcoK6slwG76WhSTESwe5EccX_cJ1Cfg3DydU7DS6ergQ$"
moz-do-not-send="true">https://useast.ensembl.org/info/docs/api/api_installation.html</a></p>
<p><br>
</p>
<p>Thanks,</p>
<p>Calum<br>
</p>
<br>
<hr>
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