Ensembl API, something is making it choose an old version

Question

[abascalfederico]

I have re-installed all the ensembl API modules both in my own laptop and in a cluster to run a new script. Curiously, in my laptop the scripts invoke by default the latest Ensembl version (83), whereas in the cluster version 81 is used. Anyone knows how could I remove this 81-ness? (I checked very carefully my bashrc / tcshrc configuration files - nothing odd there)

Many thanks, Federico

Answer 1

[Emily]

Is your PERL5LIB pointing to the correct modules on the cluster?

[abascalfederico]

Yes, they are. I removed all previous Bioperl/ensembl modules, installed the new ones, modified the PERL5LIB accordingly... Everything works fine except that in the cluster the API is using version 81 instead of 83. In case it helps, I have variant_effect_predictor.pl also installed in the cluster, with the following datasets: 81_GRCh37 and 82_GRCh38, but there is nothing in my .bashrc or ENV variables related to VEP. Once more, thanks for your help, Emily

[Emily]

Spoke to our API guys. Here are their suggestions:

What comes to mind is perhaps however this cluster is managed the paths, such as PERL5LIB are set for users as part of starting up a shell on a node when running a job the first question would be to clarify if they see this wrong version when testing the script on the head/login node or only when a job is dispatched the other would be to explicitly set the PERL5LIB (remembering to put the correct path at the start PERL5LIB=newpath:$PERL5LIB) in the job launcher script they're using, really force it to be there and failing all that, harass the cluster admins, usually that's what they're there for (ours were always really good with such issues)

Also they can try the echo ApiVersion trick. That works nicely to debug the problems perl -MBio::EnsEMBL::ApiVersion -e 'warn Bio::EnsEMBL::ApiVersion::software_version()' And for bonus points they can use this snippit to track down their Ensembl installation directory (in-case someone has been naughty and done a farm wide Ensembl install) perl -MBio::EnsEMBL::ApiVersion -e 'warn $INC{"Bio/EnsEMBL/ApiVersion.pm"}' That on my laptop gives me /Users/*username*/Code/ensembl/ensembl/modules/Bio/EnsEMBL/ApiVersion.pm so I know the Ensembl that's being found on my PERL5LIB is in /Users/*username*/Code/ensembl/ensembl/modules

Files

[abascalfederico]

Sorted!! Thank you. These commands revealed that I have another Ensembl's API installation. It is strange because that directory was not explicitly pointed within my PERL5LIB environmental variable, but the parent directory was. Anyhow, its sorted :-) Many thanks!