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

[Nathalie Conte]

works now, thanks for spotting the error.
Nathalie

On 17 Jun 2015, at 14:00, Will McLaren <wm2 at ebi.ac.uk> wrote:

> 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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