<div dir="ltr">Hi Nathalie,<div><br></div><div>Your PERL5LIB has the wrong path for BioPerl; you have <span style="font-size:12.8000001907349px">home/src/bioperl-1.2.3, it should be </span><span style="font-size:12.8000001907349px">home/src/bioperl-live</span></div><div><span style="font-size:12.8000001907349px"><br></span></div><div><span style="font-size:12.8000001907349px">Regards</span></div><div><span style="font-size:12.8000001907349px"><br></span></div><div><span style="font-size:12.8000001907349px">Will McLaren</span></div><div><span style="font-size:12.8000001907349px">Ensembl Variation</span></div></div><div class="gmail_extra"><br><div class="gmail_quote">On 17 June 2015 at 13:49, Nathalie Conte <span dir="ltr"><<a href="mailto:nconte@ebi.ac.uk" target="_blank">nconte@ebi.ac.uk</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">hi<br>
I am updating ensembl from 79 to 80 using git<br>
$ mkdir src<br>
$ cd src<br>
$ git clone <a href="https://github.com/bioperl/bioperl-live.git" rel="noreferrer" target="_blank">https://github.com/bioperl/bioperl-live.git</a><br>
$ cd bioperl-live<br>
$ git checkout bioperl-release-1-6-1<br>
$ cd -<br>
$ git clone <a href="https://github.com/Ensembl/ensembl-git-tools.git" rel="noreferrer" target="_blank">https://github.com/Ensembl/ensembl-git-tools.git</a><br>
$ export PATH=$PWD/ensembl-git-tools/bin:$PATH<br>
$ git clone <a href="https://github.com/Ensembl/ensembl.git" rel="noreferrer" target="_blank">https://github.com/Ensembl/ensembl.git</a><br>
$ git clone <a href="https://github.com/Ensembl/ensembl-variation.git" rel="noreferrer" target="_blank">https://github.com/Ensembl/ensembl-variation.git</a><br>
$ git clone <a href="https://github.com/Ensembl/ensembl-funcgen.git" rel="noreferrer" target="_blank">https://github.com/Ensembl/ensembl-funcgen.git</a><br>
$ git clone <a href="https://github.com/Ensembl/ensembl-compara.git" rel="noreferrer" target="_blank">https://github.com/Ensembl/ensembl-compara.git</a><br>
<br>
I check that everything is installed fine.<br>
<br>
<br>
I get this error message using a script to get LD scores from slice objects. the script works well on 79<br>
<br>
-------------------- WARNING ----------------------<br>
MSG: 'Bio::EnsEMBL::DBSQL::SliceAdaptor' cannot be found.<br>
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.<br>
BEGIN failed--compilation aborted at home/src/ensembl/modules/Bio/EnsEMBL/Slice.pm line 74.<br>
Compilation failed in require at home/src/ensembl/modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm line 108.<br>
BEGIN failed--compilation aborted at home/src/ensembl/modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm line 108.<br>
Compilation failed in require at (eval 194) line 3.<br>
<br>
<br>
FILE: Bio/EnsEMBL/Registry.pm LINE: 1040<br>
CALLED BY: ./testLD.pl  LINE: 19<br>
Date (localtime)    = Wed Jun 17 12:11:20 2015<br>
Ensembl API version = 80<br>
---------------------------------------------------<br>
Can't call method "fetch_by_region" on an undefined value at ./testLD.pl line 21.<br>
<br>
any idea on what is wrong?<br>
thanks<br>
Nathalie<br>
<br>
<br>
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</blockquote></div><br></div>