Changing VEP to v92 and adjusting CPUs

[szilvajuhos]

PR checklist

• PR is made against dev branch
• Looks Singularity v2.5 and VEP 91 are not able to work together, so both needed version update
• Ensure the test suite passes (./scripts/test.sh -p docker -t ALL).
• Documentation in docs is updated
• CHANGELOG.md is updated

[szilvajuhos]

I had continuous serialization errors with Singularity 2.5.1 and VEP 91 like:

-------------------- EXCEPTION --------------------
MSG: ERROR: Inappropriate ioctl for device
STACK Bio::EnsEMBL::VEP::AnnotationSource::Cache::BaseSerialized::deserialize_from_file_storable /opt/vep/src/ensembl-vep/modules/Bio/EnsEMBL/VEP/AnnotationSource/Cache/BaseSerialized.pm:134
STACK Bio::EnsEMBL::VEP::AnnotationSource::Cache::BaseSerialized::deserialize_from_file /opt/vep/src/ensembl-vep/modules/Bio/EnsEMBL/VEP/AnnotationSource/Cache/BaseSerialized.pm:103
STACK Bio::EnsEMBL::VEP::AnnotationSource::Cache::BaseSerialized::get_features_by_regions_uncached /opt/vep/src/ensembl-vep/modules/Bio/EnsEMBL/VEP/AnnotationSource/Cache/BaseSerialized.pm:261
STACK Bio::EnsEMBL::VEP::AnnotationSource::get_all_features_by_InputBuffer /opt/vep/src/ensembl-vep/modules/Bio/EnsEMBL/VEP/AnnotationSource.pm:134
STACK Bio::EnsEMBL::VEP::AnnotationType::Transcript::annotate_InputBuffer /opt/vep/src/ensembl-vep/modules/Bio/EnsEMBL/VEP/AnnotationType/Transcript.pm:101
STACK Bio::EnsEMBL::VEP::Runner::_buffer_to_output /opt/vep/src/ensembl-vep/modules/Bio/EnsEMBL/VEP/Runner.pm:402
STACK Bio::EnsEMBL::VEP::Runner::next_output_line /opt/vep/src/ensembl-vep/modules/Bio/EnsEMBL/VEP/Runner.pm:364
STACK Bio::EnsEMBL::VEP::Runner::run /opt/vep/src/ensembl-vep/modules/Bio/EnsEMBL/VEP/Runner.pm:202
STACK toplevel /opt/vep/src/ensembl-vep/vep:224
Date (localtime)    = Fri Oct 26 16:49:30 2018
Ensembl API version = 93

The solution is apparently to

• change to Singularity 2.6
• change to VEP 92

VEP is actually at 94.4, but changing I do not dare to change to it right now. Note, we are running forked version of VEP now, that speeds up processing, but for some reason it is still slow. @maxulysse you have to change the current default vepgrch38 container also.