[ensembl-dev] runtime errors in latest build of rest server (v86)

ktaylor ktaylor at ebi.ac.uk
Fri Dec 16 10:26:35 GMT 2016


Hi Caleb,

Sorry it's taken a while for someone to get back to you. In release 87 
our REST API was changed to use the newly release VEP 2.0 which you 
rightly surmise is found in www.github.com/Ensembl/ensembl-vep

The revised VEP is configured in similar fashion to the original VEP. 
Do ask again on the mailing list if you need specific help getting VEP 
2.0 working.


Kieron

On 2016-12-13 21:26, Caleb Davis wrote:
> Hi dev-ensembl,
> 
> I built an ensembl rest server (v86) about six weeks ago and it runs
> great. I tried a fresh build using the same recipe yesterday, and I
> got an error about not finding runner.pm [1]. 
> 
> Can't locate Bio/EnsEMBL/VEP/Runner.pm
> 
> Any ideas what's going on? Best I can tell, Bio/EnsEMBL/VEP/Runner.pm
> comes from v87 in ensembl-vep. 
> 
> Many thanks for your time, 
> --Caleb
> 
> OLDER, WORKING INSTALLATION:
> 
> fatal error: Unable to locate credentials
> Use of uninitialized value in subroutine entry at
> /opt/src/ensembl-rest/script/../lib/EnsEMBL/REST/View/TT.pm line 32.
> Use of uninitialized value in subroutine entry at
> /opt/src/ensembl-rest/script/../lib/EnsEMBL/REST/View/HTML.pm line 32.
> Smartmatch is experimental at
> /opt/src/ensembl-rest/script/../lib/EnsEMBL/REST/Controller/VEP.pm
> line 482.
> Smartmatch is experimental at
> /opt/src/ensembl-rest/script/../lib/EnsEMBL/REST/Controller/VEP.pm
> line 483.
> given is experimental at
> /opt/src/ensembl-rest/script/../lib/EnsEMBL/REST/Controller/Xrefs.pm
> line 137.
> when is experimental at
> /opt/src/ensembl-rest/script/../lib/EnsEMBL/REST/Controller/Xrefs.pm
> line 138.
> when is experimental at
> /opt/src/ensembl-rest/script/../lib/EnsEMBL/REST/Controller/Xrefs.pm
> line 150.
> HTTP::Server::PSGI: Accepting connections at http://0:3000/ [2]
> 
> FRESH BUILD, FAILS:
> 
> fatal error: Unable to locate credentials
> keys on reference is experimental at
> /opt/src/ensembl-rest/script/../lib/EnsEMBL/REST/Model/Registry.pm
> line 320.
> Smartmatch is experimental at
> /opt/src/ensembl-rest/script/../lib/EnsEMBL/REST/Model/Registry.pm
> line 321.
> push on reference is experimental at
> /opt/src/ensembl-rest/script/../lib/EnsEMBL/REST/Model/Registry.pm
> line 323.
> Use of uninitialized value in subroutine entry at
> /opt/src/ensembl-rest/script/../lib/EnsEMBL/REST/View/TT.pm line 32.
> Use of uninitialized value in subroutine entry at
> /opt/src/ensembl-rest/script/../lib/EnsEMBL/REST/View/HTML.pm line 32.
> Can't locate Bio/EnsEMBL/VEP/Runner.pm in @INC (you may need to
> install the Bio::EnsEMBL::VEP::Runner module) (@INC contains:
> /opt/src/ensembl-rest/script/../lib /opt/src/bioperl-live
> /opt/src/ensembl/modules /opt/src/ensembl-compara/modules
> /opt/src/ensembl-funcgen/modules /opt/src/ensembl-variation/modules
> /opt/src/ensembl-io/modules /opt/src/ensembl-rest/modules
> /opt/src/ensembl-xs/lib/Bio/EnsEMBL /opt/src/lib/perl/5.18.2
> /opt/src/tabix/perl /opt/perl5/lib/perl5 /opt/src/biodbhts/lib
> /opt/src/biodbhts/blib/arch/auto/Bio/DB/HTS/Faidx
> /opt/src/biodbhts/blib/arch/auto/Bio/DB/HTS /etc/perl
> /usr/local/lib/x86_64-linux-gnu/perl/5.22.1
> /usr/local/share/perl/5.22.1 /usr/lib/x86_64-linux-gnu/perl5/5.22
> /usr/share/perl5 /usr/lib/x86_64-linux-gnu/perl/5.22
> /usr/share/perl/5.22 /usr/local/lib/site_perl
> /usr/lib/x86_64-linux-gnu/perl-base .) at
> /opt/src/ensembl-rest/script/../lib/EnsEMBL/REST/Controller/VEP.pm
> line 28.
> BEGIN failed--compilation aborted at
> /opt/src/ensembl-rest/script/../lib/EnsEMBL/REST/Controller/VEP.pm
> line 28.
> Compilation failed in require at
> /usr/local/share/perl/5.22.1/Catalyst/Utils.pm line 309.
> Compilation failed in require at
> /usr/local/share/perl/5.22.1/Catalyst/ScriptRunner.pm line 50.
> 
> Links:
> ------
> [1] http://runner.pm
> [2] http://0:3000/
> 
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