[ensembl-dev] Error while trying to use variation collection (API version 83)

[Johanne Håøy Horn]

That seemed to do the trick! I missed .../site_perl from the PERL5LIB path. Thank you :)

22. feb. 2016 kl. 10.37 skrev Will McLaren <wm2 at ebi.ac.uk<mailto:wm2 at ebi.ac.uk>>:

Hi Johanne,

It looks like the you have most of the installation working OK, just the Tabix.pm part missing.

As you followed the blog, I'm assuming you ran the following commands?


cd ~/src
git clone git at github.com:samtools/tabix.git
cd tabix
make
cd perl
perl Makefile.PL PREFIX=${HOME}/src/
make && make install

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/

You can do this as follows:

export PERL5LIB=${PERL5LIB}:${HOME}/src/lib/perl5/:${HOME}/src/lib/perl5/site_perl/

You can also add this same line to ${HOME}/.profile to have it do this same setup every time you open a terminal.

Regards

Will McLaren
Ensembl Variation

On 19 February 2016 at 21:42, Johanne Håøy Horn <johannhh at ifi.uio.no<mailto:johannhh at ifi.uio.no>> wrote:
Hello!

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:
http://www.ensembl.info/blog/2013/09/09/installing-perl-dbdmysql-and-ensembl-on-osx/
http://www.ensembl.org/info/docs/api/api_installation.html
http://www.ensembl.info/blog/2015/06/18/1000-genomes-phase-3-frequencies-genotypes-and-ld-data/
https://raw.githubusercontent.com/Ensembl/ensembl-variation/release/83/C_code/README.txt
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)

When pinging the servers I get:
Johanne at Johanne ~/src $ perl ensembl/misc-scripts/ping_ensembl.pl<http://ping_ensembl.pl/>
Installation is good. Connection to Ensembl works and you can query the human core database

Johanne at Johanne ~/src $ perl ensembl/misc-scripts/ping_ensembl.pl<http://ping_ensembl.pl/> -ue
Installation is good. Connection to Ensembl works and you can query the human core database

Johanne at Johanne ~/src $ perl ensembl/misc-scripts/ping_ensembl.pl<http://ping_ensembl.pl/> -eg
ERROR: Error detected when connecting to Ensembl!
Looks like you need to setup your PERL5LIB with the Ensembl API. Please consult http://www.ensembl.org/info/docs/api/api_installation.html
================================================================================
If the problem persists please send the following error message to helpdesk at ensembl.org<mailto:helpdesk at ensembl.org>
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/ping_ensembl.pl<http://ping_ensembl.pl/> line 119.
================================================================================

I am able to run the code under «LD calculation» on this page: http://www.ensembl.org/info/docs/api/variation/variation_tutorial.html#ld

However, if I run the code on this page: http://www.ensembl.info/blog/2015/06/18/1000-genomes-phase-3-frequencies-genotypes-and-ld-data/ , I get the error message pasted below:

-------------------- WARNING ----------------------
MSG: 'Bio::EnsEMBL::Variation::DBSQL::VCFCollectionAdaptor' cannot be found.
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.
BEGIN failed--compilation aborted at /Users/Johanne/src/ensembl-io/modules/Bio/EnsEMBL/IO/TabixParser.pm line 40.
Compilation failed in require at /Users/Johanne/src/ensembl-io/modules/Bio/EnsEMBL/IO/Parser/VCF4Tabix.pm line 41.
BEGIN failed--compilation aborted at /Users/Johanne/src/ensembl-io/modules/Bio/EnsEMBL/IO/Parser/VCF4Tabix.pm line 41.
Compilation failed in require at /Users/Johanne/src/ensembl-variation/modules/Bio/EnsEMBL/Variation/VCFCollection.pm line 76.
BEGIN failed--compilation aborted at /Users/Johanne/src/ensembl-variation/modules/Bio/EnsEMBL/Variation/VCFCollection.pm line 76.
Compilation failed in require at /Users/Johanne/src/ensembl-variation/modules/Bio/EnsEMBL/Variation/DBSQL/VCFCollectionAdaptor.pm line 95.
BEGIN failed--compilation aborted at /Users/Johanne/src/ensembl-variation/modules/Bio/EnsEMBL/Variation/DBSQL/VCFCollectionAdaptor.pm line 95.
Compilation failed in require at (eval 250) line 2.


FILE: Bio/EnsEMBL/Registry.pm LINE: 1169
CALLED BY: EnsEMBL/DBSQL/DBAdaptor.pm  LINE: 988
Date (localtime)    = Fri Feb 19 22:32:06 2016
Ensembl API version = 83
---------------------------------------------------

-------------------- WARNING ----------------------
MSG: Could not find VCFCollection adaptor in the registry for homo_sapiens variation

FILE: EnsEMBL/DBSQL/DBAdaptor.pm LINE: 991
CALLED BY: Variation/DBSQL/SampleGenotypeAdaptor.pm  LINE: 287
Date (localtime)    = Fri Feb 19 22:32:06 2016
Ensembl API version = 83
---------------------------------------------------

-------------------- EXCEPTION --------------------
MSG: Could not get adaptor VCFCollection for homo_sapiens variation

STACK Bio::EnsEMBL::DBSQL::DBAdaptor::AUTOLOAD /Users/Johanne/src/ensembl/modules/Bio/EnsEMBL/DBSQL/DBAdaptor.pm:995
STACK Bio::EnsEMBL::Variation::DBSQL::SampleGenotypeAdaptor::fetch_all_by_Variation /Users/Johanne/src/ensembl-variation/modules/Bio/EnsEMBL/Variation/DBSQL/SampleGenotypeAdaptor.pm:287
STACK Bio::EnsEMBL::Variation::Variation::get_all_SampleGenotypes /Users/Johanne/src/ensembl-variation/modules/Bio/EnsEMBL/Variation/Variation.pm:987
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
STACK Bio::EnsEMBL::Variation::DBSQL::AlleleAdaptor::fetch_all_by_Variation /Users/Johanne/src/ensembl-variation/modules/Bio/EnsEMBL/Variation/DBSQL/AlleleAdaptor.pm:273
STACK Bio::EnsEMBL::Variation::Variation::get_all_Alleles /Users/Johanne/src/ensembl-variation/modules/Bio/EnsEMBL/Variation/Variation.pm:861
STACK toplevel testPerl.pl:17
Date (localtime)    = Fri Feb 19 22:32:06 2016
Ensembl API version = 83

Could you help me with the following:
1) Have I set up PERL5LIB wrong, as not all pings go through successfully?
2) Is there a different way of setting up Tabix and including it in the package when using OSX than described here: http://www.ensembl.info/blog/2015/06/18/1000-genomes-phase-3-frequencies-genotypes-and-ld-data/
3) Do you have any suggestions as to how I can set up the installation correctly in order to run the variation script?

Any help is greatly appreciated!

My apologies if this has been addressed somewhere before. I did not find any other people with the exact same issue when googling around.

Best,
Johanne Håøy Horn

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