Ensembl Perl API is not installed

[jvanheld]

The Ensembl Perl APIs are apparently not installed.

This affects all the Ensembl-depending tools :

• supported-organisms-ensembl
• perl-scripts/download-ensembl-features
• perl-scripts/download-ensembl-genome
• perl-scripts/download-ensembl-go-annotations-biomart
• perl-scripts/download-ensembl-variations
• perl-scripts/ensembl-org-info
• perl-scripts/get-all-ensembl-seqs
• perl-scripts/get-ensembl-genome-no-objects.pl
• perl-scripts/get-ensembl-genome-only-objects.pl
• perl-scripts/get-ensembl-genome.pl
• perl-scripts/get-ensembl-one_chrom.pl
• perl-scripts/retrieve-ensembl-seq
• perl-scripts/retrieve-ensembl-seq-norsat.pl
• perl-scripts/supported-organisms-ensembl
• perl-scripts/supported-organisms-ensemblgenomes

Calling any of these scripts returns error like this :

[root@clust-rsat:/opt/rsat-tools/rsat]$ retrieve-ensembl-seq -help
Can't locate Bio/EnsEMBL/Registry.pm in @INC (you may need to install the Bio::EnsEMBL::Registry module) (@INC contains: /opt/rsat-tools/rsat/ext_lib/biomart-perl/lib/ /opt/rsat-tools/rsat/ext_lib/ensemblgenomes-52-105/ensemblgenomes-api/modules /opt/rsat-tools/rsat/ext_lib/ensemblgenomes-52-105/ensembl-variation/modules /opt/rsat-tools/rsat/ext_lib/ensemblgenomes-52-105/ensembl-tools/modules /opt/rsat-tools/rsat/ext_lib/ensemblgenomes-52-105/ensembl-functgenomics/modules /opt/rsat-tools/rsat/ext_lib/ensemblgenomes-52-105/ensembl-external/modules /opt/rsat-tools/rsat/ext_lib/ensemblgenomes-52-105/ensembl-compara/modules /opt/rsat-tools/rsat/ext_lib/ensemblgenomes-52-105/ensembl/modules /opt/rsat-tools/rsat/ext_lib/bioperl-release-/bioperl-live /etc/perl /usr/local/lib/x86_64-linux-gnu/perl/5.30.0 /usr/local/share/perl/5.30.0 /usr/lib/x86_64-linux-gnu/perl5/5.30 /usr/share/perl5 /usr/lib/x86_64-linux-gnu/perl/5.30 /usr/share/perl/5.30 /usr/local/lib/site_perl /usr/lib/x86_64-linux-gnu/perl-base /opt/rsat-tools/rsat/perl-scripts/lib/  /opt/rsat-tools/rsat/ext_lib/ensemblgenomes-52-105/ensembl/modules /opt/rsat-tools/rsat/ext_lib/ensemblgenomes-52-105/ensembl-compara/modules) at /opt/rsat-tools/rsat/perl-scripts/retrieve-ensembl-seq line 28.

[jvanheld]

I currently use a makefile to install Ensembl Perl API.

 make -f makefiles/install_software2.mk install_ensembl_api

[jvanheld]

@FanchTheSystem , the installation via this makefile is a bit heavy, and not very clean. Would it be possible to convert this to an Ansible recipe, so that these Ensembl Perl API would be installed automatically ?

Thanks

[jvanheld]

Ah, en fait il y avait déjà des librairies Ensembl installées, mais comme entretemps j'avais mis à jour les version s d'ENSEMBL_RELEASE et ENSEMBLGENOMES_RELEASE elles n'étaient pas dans le bon dossier.

[jvanheld]

Cependant il manquait une autre librairie : bioperl

make -f makefiles/install_software2.mk install_ensembl_bioperl

[FanchTheSystem]

la version de ensemblgenoms api n'est pas correct (la 52 n'existe pas) https://github.com/rsa-tools/rsat-code/pull/11