[ensembl-dev] Error while trying to use variation collection (API version 83)
Will McLaren
wm2 at ebi.ac.uk
Mon Feb 22 09:37:57 GMT 2016
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> 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
> 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 -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 -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
> 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 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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