Ensembl Perl API is not installed #10
Description
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.