[ensembl-dev] updating ensembl 79->80 issue

[Will McLaren]

Hi Nathalie,

Your PERL5LIB has the wrong path for BioPerl; you have home/src/bioperl-1.2.3,
it should be home/src/bioperl-live

Regards

Will McLaren
Ensembl Variation

On 17 June 2015 at 13:49, Nathalie Conte <nconte at ebi.ac.uk> wrote:

> hi
> I am updating ensembl from 79 to 80 using git
> $ mkdir src
> $ cd src
> $ git clone https://github.com/bioperl/bioperl-live.git
> $ cd bioperl-live
> $ git checkout bioperl-release-1-6-1
> $ cd -
> $ git clone https://github.com/Ensembl/ensembl-git-tools.git
> $ export PATH=$PWD/ensembl-git-tools/bin:$PATH
> $ git clone https://github.com/Ensembl/ensembl.git
> $ git clone https://github.com/Ensembl/ensembl-variation.git
> $ git clone https://github.com/Ensembl/ensembl-funcgen.git
> $ git clone https://github.com/Ensembl/ensembl-compara.git
>
> I check that everything is installed fine.
>
>
> I get this error message using a script to get LD scores from slice
> objects. the script works well on 79
>
> -------------------- WARNING ----------------------
> MSG: 'Bio::EnsEMBL::DBSQL::SliceAdaptor' cannot be found.
> Exception Can't locate Bio/PrimarySeqI.pm in @INC (@INC contains:
> /homes/perl5lib/lib/perl5/x86_64-linux-thread-multi
> /homes/perl5lib/lib/perl5 home/src home/src/bioperl-1.2.3
> home/src/ensembl/modules home/src/ensembl-compara/modules
> home/src/ensembl-variation/modules home/src/ensembl-functgenomics/modules
> home/src/ensembl-functgenomics/modules
> /ebi/microarray/home/fgpt/sw/lib/perl/RH_prod/lib/x86_64-linux-thread-multi
> /ebi/microarray/home/fgpt/sw/lib/perl/RH_prod/lib
> /ebi/microarray/home/fgpt/sw/lib/perl/RH_prod/lib64
> /ebi/microarray/home/fgpt/sw/lib/perl/RH_prod/lib64/perl5/site_perl
> /nfs/ma/home/svn-database/PhenoBridge/Scripts/BioSD-master/lib
> /usr/local/lib64/perl5 /usr/local/share/perl5 /usr/lib64/perl5/vendor_perl
> /usr/share/perl5/vendor_perl /usr/lib64/perl5 /usr/share/perl5 .) at
> home/src/ensembl/modules/Bio/EnsEMBL/Slice.pm line 74.
> BEGIN failed--compilation aborted at
> home/src/ensembl/modules/Bio/EnsEMBL/Slice.pm line 74.
> Compilation failed in require at
> home/src/ensembl/modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm line 108.
> BEGIN failed--compilation aborted at
> home/src/ensembl/modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm line 108.
> Compilation failed in require at (eval 194) line 3.
>
>
> FILE: Bio/EnsEMBL/Registry.pm LINE: 1040
> CALLED BY: ./testLD.pl  LINE: 19
> Date (localtime)    = Wed Jun 17 12:11:20 2015
> Ensembl API version = 80
> ---------------------------------------------------
> Can't call method "fetch_by_region" on an undefined value at ./testLD.pl
> line 21.
>
> any idea on what is wrong?
> thanks
> Nathalie
>
>
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