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That seemed to do the trick! I missed .../site_perl from the PERL5LIB path. Thank you :)
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<blockquote type="cite" class="">
<div class="">22. feb. 2016 kl. 10.37 skrev Will McLaren <<a href="mailto:wm2@ebi.ac.uk" class="">wm2@ebi.ac.uk</a>>:</div>
<br class="Apple-interchange-newline">
<div class="">
<div dir="ltr" class="">Hi Johanne,
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</div>
<div class="">It looks like the you have most of the installation working OK, just the Tabix.pm part missing.</div>
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</div>
<div class="">As you followed the blog, I'm assuming you ran the following commands?</div>
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</div>
<div class="">
<pre style="border:0px;font-family:'Courier 10 Pitch',Courier,monospace;font-size:13px;margin-top:0px;margin-bottom:2em;outline:0px;padding:0.75em 2em;vertical-align:baseline;font-stretch:normal;line-height:1.5;overflow:auto;color:rgb(55,55,55);background:rgb(244,244,244)" class="">cd ~/src
git clone git@github.com:samtools/tabix.git
cd tabix
make
cd perl
perl Makefile.PL PREFIX=${HOME}/src/
make && make install</pre>
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<div class="gmail_extra">This should mean you have the Tabix module installed in $HOME/src. It may be that you need to add a couple of paths to PERL5LIB; on my Mac I have /Users/$USER/src/lib/perl5/ and /Users/$USER/src/lib/perl5/site_perl/</div>
<div class="gmail_extra"><br class="">
</div>
<div class="gmail_extra">You can do this as follows:</div>
<div class="gmail_extra"><br class="">
</div>
<div class="gmail_extra">export PERL5LIB=${PERL5LIB}:${HOME}/src/lib/perl5/:${HOME}/src/lib/perl5/site_perl/<br class="">
</div>
<div class="gmail_extra"><br class="">
</div>
<div class="gmail_extra">You can also add this same line to ${HOME}/.profile to have it do this same setup every time you open a terminal.</div>
<div class="gmail_extra"><br class="">
</div>
<div class="gmail_extra">Regards</div>
<div class="gmail_extra"><br class="">
Will McLaren</div>
<div class="gmail_extra">Ensembl Variation</div>
<div class="gmail_extra"><br class="">
<div class="gmail_quote">On 19 February 2016 at 21:42, Johanne Håøy Horn <span dir="ltr" class="">
<<a href="mailto:johannhh@ifi.uio.no" target="_blank" class="">johannhh@ifi.uio.no</a>></span> wrote:<br class="">
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
<div style="word-wrap:break-word" class="">Hello!
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</div>
<div class="">I have a mac with osx 10.11.3, and seem unable to set up the ensemble api correctly. I have followed these guides for installation:</div>
<div class=""><a href="http://www.ensembl.info/blog/2013/09/09/installing-perl-dbdmysql-and-ensembl-on-osx/" target="_blank" class="">http://www.ensembl.info/blog/2013/09/09/installing-perl-dbdmysql-and-ensembl-on-osx/</a></div>
<div class=""><a href="http://www.ensembl.org/info/docs/api/api_installation.html" target="_blank" class="">http://www.ensembl.org/info/docs/api/api_installation.html</a></div>
<div class=""><a href="http://www.ensembl.info/blog/2015/06/18/1000-genomes-phase-3-frequencies-genotypes-and-ld-data/" target="_blank" class="">http://www.ensembl.info/blog/2015/06/18/1000-genomes-phase-3-frequencies-genotypes-and-ld-data/</a></div>
<div class=""><a href="https://raw.githubusercontent.com/Ensembl/ensembl-variation/release/83/C_code/README.txt" target="_blank" class="">https://raw.githubusercontent.com/Ensembl/ensembl-variation/release/83/C_code/README.txt</a></div>
<div class="">Although some tweaking on some terminal commands was needed du to stricter root access in El Capitan than the OS X-installation guide accounted for, I think I have followed the guides and exported all paths correctly (did some of the steps multiple
times to make sure I had downloaded it all)</div>
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</div>
<div class="">When pinging the servers I get:</div>
<div class="">
<div class="">Johanne@Johanne ~/src $ perl ensembl/misc-scripts/<a href="http://ping_ensembl.pl/" target="_blank" class="">ping_ensembl.pl</a></div>
<div class=""><font face="Courier New" class="">Installation is good. Connection to Ensembl works and you can query the human core database</font></div>
<div class=""><br class="">
</div>
<div class="">Johanne@Johanne ~/src $ perl ensembl/misc-scripts/<a href="http://ping_ensembl.pl/" target="_blank" class="">ping_ensembl.pl</a> -ue</div>
<div class=""><font face="Courier New" class="">Installation is good. Connection to Ensembl works and you can query the human core database</font></div>
<div class=""><br class="">
</div>
<div class="">Johanne@Johanne ~/src $ perl ensembl/misc-scripts/<a href="http://ping_ensembl.pl/" target="_blank" class="">ping_ensembl.pl</a> -eg</div>
<div class=""><font face="Courier New" class="">ERROR: Error detected when connecting to Ensembl!</font></div>
<div class=""><font face="Courier New" class=""><span style="white-space:pre-wrap" class=""></span>Looks like you need to setup your PERL5LIB with the Ensembl API. Please consult
<a href="http://www.ensembl.org/info/docs/api/api_installation.html" target="_blank" class="">
http://www.ensembl.org/info/docs/api/api_installation.html</a></font></div>
<div class=""><font face="Courier New" class="">================================================================================</font></div>
<div class=""><font face="Courier New" class="">If the problem persists please send the following error message to
<a href="mailto:helpdesk@ensembl.org" target="_blank" class="">helpdesk@ensembl.org</a></font></div>
<div class=""><font face="Courier New" class="">Can't locate Bio/EnsEMBL/LookUp.pm in @INC (@INC contains: /Users/Johanne/src/lib/perl/5.14.2/ /Users/Johanne/src/ensembl-io/modules /Users/Johanne/src/BioPerl-1.6.1 /Users/Johanne/src/ensembl/modules /Users/Johanne/src/ensembl-compara/modules
/Users/Johanne/src/ensembl-variation/modules /Users/Johanne/src/ensembl-funcgen/modules /Users/Johanne/src/lib64/perl5 /Users/Johanne/src/ensembl-io/modules /Users/Johanne/src/lib/5.14.4/darwin-thread-multi-2level /Users/Johanne/src/lib/5.14.4 /Users/Johanne/src/bioperl-1.6.1
/Users/Johanne/src/ensembl/modules /Users/Johanne/src/ensembl-compara/modules /Users/Johanne/src/ensembl-variation/modules /Users/Johanne/src/ensembl-funcgen/modules /Users/Johanne/src/lib/perl/5.14.2/ /Users/Johanne/src/ensembl-io/modules /Users/Johanne/src/BioPerl-1.6.1/
/Users/Johanne/src/ensembl/modules/ /Users/Johanne/src/ensembl-compara/modules/ /Users/Johanne/src/ensembl-variation/modules/ /Users/Johanne/src/ensembl-funcgen/modules/ /Users/Johanne/src/lib/5.14.4//darwin-thread-multi-2level /Users/Johanne/src/lib/5.14.4/
/Users/Johanne/src/ensembl-io/modules/ /Users/Johanne/src/BioPerl-1.6.1/ /Users/Johanne/src/ensembl/modules/ /Users/Johanne/src/ensembl-compara/modules/ /Users/Johanne/src/ensembl-variation/modules/ /Users/Johanne/src/ensembl-funcgen/modules/ /Users/Johanne/perl5/perlbrew/perls/5.14.4/lib/site_perl/5.14.4/darwin-thread-multi-2level
/Users/Johanne/perl5/perlbrew/perls/5.14.4/lib/site_perl/5.14.4 /Users/Johanne/perl5/perlbrew/perls/5.14.4/lib/5.14.4/darwin-thread-multi-2level /Users/Johanne/perl5/perlbrew/perls/5.14.4/lib/5.14.4 .) at ensembl/misc-scripts/<a href="http://ping_ensembl.pl/" target="_blank" class="">ping_ensembl.pl</a>
line 119.</font></div>
<div class=""><font face="Courier New" class="">================================================================================</font></div>
</div>
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</div>
<div class="">I am able to run the code under «LD calculation» on this page: <a href="http://www.ensembl.org/info/docs/api/variation/variation_tutorial.html#ld" target="_blank" class="">http://www.ensembl.org/info/docs/api/variation/variation_tutorial.html#ld</a></div>
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</div>
<div class="">However, if I run the code on this page: <a href="http://www.ensembl.info/blog/2015/06/18/1000-genomes-phase-3-frequencies-genotypes-and-ld-data/" target="_blank" class="">
http://www.ensembl.info/blog/2015/06/18/1000-genomes-phase-3-frequencies-genotypes-and-ld-data/</a> , I get the error message pasted below:</div>
<div class=""><br class="">
</div>
<div class="">
<div class=""><font face="Courier New" class="">-------------------- WARNING ----------------------</font></div>
<div class=""><font face="Courier New" class="">MSG: 'Bio::EnsEMBL::Variation::DBSQL::VCFCollectionAdaptor' cannot be found.</font></div>
<div class=""><font face="Courier New" class="">Exception Can't locate Tabix.pm in @INC (@INC contains: /Users/Johanne/src/lib/perl/5.14.2/ /Users/Johanne/src/ensembl-io/modules /Users/Johanne/src/BioPerl-1.6.1 /Users/Johanne/src/ensembl/modules /Users/Johanne/src/ensembl-compara/modules
/Users/Johanne/src/ensembl-variation/modules /Users/Johanne/src/ensembl-funcgen/modules /Users/Johanne/src/lib64/perl5 /Users/Johanne/src/ensembl-io/modules /Users/Johanne/src/lib/5.14.4/darwin-thread-multi-2level /Users/Johanne/src/lib/5.14.4 /Users/Johanne/src/bioperl-1.6.1
/Users/Johanne/src/ensembl/modules /Users/Johanne/src/ensembl-compara/modules /Users/Johanne/src/ensembl-variation/modules /Users/Johanne/src/ensembl-funcgen/modules /Users/Johanne/src/lib/perl/5.14.2/ /Users/Johanne/src/ensembl-io/modules /Users/Johanne/src/BioPerl-1.6.1/
/Users/Johanne/src/ensembl/modules/ /Users/Johanne/src/ensembl-compara/modules/ /Users/Johanne/src/ensembl-variation/modules/ /Users/Johanne/src/ensembl-funcgen/modules/ /Users/Johanne/src/lib/5.14.4//darwin-thread-multi-2level /Users/Johanne/src/lib/5.14.4/
/Users/Johanne/src/ensembl-io/modules/ /Users/Johanne/src/BioPerl-1.6.1/ /Users/Johanne/src/ensembl/modules/ /Users/Johanne/src/ensembl-compara/modules/ /Users/Johanne/src/ensembl-variation/modules/ /Users/Johanne/src/ensembl-funcgen/modules/ /Users/Johanne/perl5/perlbrew/perls/5.14.4/lib/site_perl/5.14.4/darwin-thread-multi-2level
/Users/Johanne/perl5/perlbrew/perls/5.14.4/lib/site_perl/5.14.4 /Users/Johanne/perl5/perlbrew/perls/5.14.4/lib/5.14.4/darwin-thread-multi-2level /Users/Johanne/perl5/perlbrew/perls/5.14.4/lib/5.14.4 .) at /Users/Johanne/src/ensembl-io/modules/Bio/EnsEMBL/IO/TabixParser.pm
line 40.</font></div>
<div class=""><font face="Courier New" class="">BEGIN failed--compilation aborted at /Users/Johanne/src/ensembl-io/modules/Bio/EnsEMBL/IO/TabixParser.pm line 40.</font></div>
<div class=""><font face="Courier New" class="">Compilation failed in require at /Users/Johanne/src/ensembl-io/modules/Bio/EnsEMBL/IO/Parser/VCF4Tabix.pm line 41.</font></div>
<div class=""><font face="Courier New" class="">BEGIN failed--compilation aborted at /Users/Johanne/src/ensembl-io/modules/Bio/EnsEMBL/IO/Parser/VCF4Tabix.pm line 41.</font></div>
<div class=""><font face="Courier New" class="">Compilation failed in require at /Users/Johanne/src/ensembl-variation/modules/Bio/EnsEMBL/Variation/VCFCollection.pm line 76.</font></div>
<div class=""><font face="Courier New" class="">BEGIN failed--compilation aborted at /Users/Johanne/src/ensembl-variation/modules/Bio/EnsEMBL/Variation/VCFCollection.pm line 76.</font></div>
<div class=""><font face="Courier New" class="">Compilation failed in require at /Users/Johanne/src/ensembl-variation/modules/Bio/EnsEMBL/Variation/DBSQL/VCFCollectionAdaptor.pm line 95.</font></div>
<div class=""><font face="Courier New" class="">BEGIN failed--compilation aborted at /Users/Johanne/src/ensembl-variation/modules/Bio/EnsEMBL/Variation/DBSQL/VCFCollectionAdaptor.pm line 95.</font></div>
<div class=""><font face="Courier New" class="">Compilation failed in require at (eval 250) line 2.</font></div>
<div class=""><font face="Courier New" class=""><br class="">
</font></div>
<div class=""><font face="Courier New" class=""><br class="">
</font></div>
<div class=""><font face="Courier New" class="">FILE: Bio/EnsEMBL/Registry.pm LINE: 1169</font></div>
<div class=""><font face="Courier New" class="">CALLED BY: EnsEMBL/DBSQL/DBAdaptor.pm LINE: 988</font></div>
<div class=""><font face="Courier New" class="">Date (localtime) = Fri Feb 19 22:32:06 2016</font></div>
<div class=""><font face="Courier New" class="">Ensembl API version = 83</font></div>
<div class=""><font face="Courier New" class="">---------------------------------------------------</font></div>
<div class=""><font face="Courier New" class=""><br class="">
</font></div>
<div class=""><font face="Courier New" class="">-------------------- WARNING ----------------------</font></div>
<div class=""><font face="Courier New" class="">MSG: Could not find VCFCollection adaptor in the registry for homo_sapiens variation</font></div>
<div class=""><font face="Courier New" class=""><br class="">
</font></div>
<div class=""><font face="Courier New" class="">FILE: EnsEMBL/DBSQL/DBAdaptor.pm LINE: 991</font></div>
<div class=""><font face="Courier New" class="">CALLED BY: Variation/DBSQL/SampleGenotypeAdaptor.pm LINE: 287</font></div>
<div class=""><font face="Courier New" class="">Date (localtime) = Fri Feb 19 22:32:06 2016</font></div>
<div class=""><font face="Courier New" class="">Ensembl API version = 83</font></div>
<div class=""><font face="Courier New" class="">---------------------------------------------------</font></div>
<div class=""><font face="Courier New" class=""><br class="">
</font></div>
<div class=""><font face="Courier New" class="">-------------------- EXCEPTION --------------------</font></div>
<div class=""><font face="Courier New" class="">MSG: Could not get adaptor VCFCollection for homo_sapiens variation</font></div>
<div class=""><font face="Courier New" class=""><br class="">
</font></div>
<div class=""><font face="Courier New" class="">STACK Bio::EnsEMBL::DBSQL::DBAdaptor::AUTOLOAD /Users/Johanne/src/ensembl/modules/Bio/EnsEMBL/DBSQL/DBAdaptor.pm:995</font></div>
<div class=""><font face="Courier New" class="">STACK Bio::EnsEMBL::Variation::DBSQL::SampleGenotypeAdaptor::fetch_all_by_Variation /Users/Johanne/src/ensembl-variation/modules/Bio/EnsEMBL/Variation/DBSQL/SampleGenotypeAdaptor.pm:287</font></div>
<div class=""><font face="Courier New" class="">STACK Bio::EnsEMBL::Variation::Variation::get_all_SampleGenotypes /Users/Johanne/src/ensembl-variation/modules/Bio/EnsEMBL/Variation/Variation.pm:987</font></div>
<div class=""><font face="Courier New" class="">STACK Bio::EnsEMBL::Variation::DBSQL::AlleleAdaptor::_fetch_all_by_Variation_from_Genotypes /Users/Johanne/src/ensembl-variation/modules/Bio/EnsEMBL/Variation/DBSQL/AlleleAdaptor.pm:307</font></div>
<div class=""><font face="Courier New" class="">STACK Bio::EnsEMBL::Variation::DBSQL::AlleleAdaptor::fetch_all_by_Variation /Users/Johanne/src/ensembl-variation/modules/Bio/EnsEMBL/Variation/DBSQL/AlleleAdaptor.pm:273</font></div>
<div class=""><font face="Courier New" class="">STACK Bio::EnsEMBL::Variation::Variation::get_all_Alleles /Users/Johanne/src/ensembl-variation/modules/Bio/EnsEMBL/Variation/Variation.pm:861</font></div>
<div class=""><font face="Courier New" class="">STACK toplevel testPerl.pl:17</font></div>
<div class=""><font face="Courier New" class="">Date (localtime) = Fri Feb 19 22:32:06 2016</font></div>
<div class=""><font face="Courier New" class="">Ensembl API version = 83</font></div>
</div>
<div class=""><font face="Courier New" class=""><br class="">
</font></div>
<div class="">Could you help me with the following:</div>
<div class="">1) Have I set up PERL5LIB wrong, as not all pings go through successfully?</div>
<div class="">2) Is there a different way of setting up Tabix and including it in the package when using OSX than described here: <a href="http://www.ensembl.info/blog/2015/06/18/1000-genomes-phase-3-frequencies-genotypes-and-ld-data/" target="_blank" class="">http://www.ensembl.info/blog/2015/06/18/1000-genomes-phase-3-frequencies-genotypes-and-ld-data/</a></div>
<div class="">3) Do you have any suggestions as to how I can set up the installation correctly in order to run the variation script?</div>
<div class=""><br class="">
</div>
<div class="">Any help is greatly appreciated!</div>
<div class=""><br class="">
</div>
<div class="">My apologies if this has been addressed somewhere before. I did not find any other people with the exact same issue when googling around.</div>
<div class=""><br class="">
</div>
<div class="">Best,</div>
<div class="">Johanne Håøy Horn</div>
</div>
<br class="">
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</blockquote>
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