Bioinformatics

Install VEP ensembl failed

because of file aborted.

2 min readJan 6, 2021

Recently I used VEP for analyzing some data, and faced quite some of difficulties while installing it. So I guess it might help some of you guys.

ERROR: Testing VEP script failed with the following error
Attempt to reload Bio/EnsEMBL/IO/Parser.pm aborted.
Compilation failed in require at /usr/share/perl/5.26/parent.pm line 16.
BEGIN failed--compilation aborted at /home/ubuntu/ensembl-vep/Bio/EnsEMBL/IO/TextParser.pm line 45.
Compilation failed in require at /usr/share/perl/5.26/parent.pm line 16.
BEGIN failed--compilation aborted at /home/ubuntu/ensembl-vep/Bio/EnsEMBL/IO/ColumnBasedParser.pm line 36.
Compilation failed in require at /usr/share/perl/5.26/parent.pm line 16.
BEGIN failed--compilation aborted at /home/ubuntu/ensembl-vep/Bio/EnsEMBL/IO/Parser/BaseVCF4.pm line 45.
Compilation failed in require at /usr/share/perl/5.26/parent.pm line 16.
BEGIN failed--compilation aborted at /home/ubuntu/ensembl-vep/Bio/EnsEMBL/IO/Parser/VCF4.pm line 41.
Compilation failed in require at /home/ubuntu/ensembl-vep/modules/Bio/EnsEMBL/VEP/Parser/VCF.pm line 79.
BEGIN failed--compilation aborted at /home/ubuntu/ensembl-vep/modules/Bio/EnsEMBL/VEP/Parser/VCF.pm line 79.
Compilation failed in require at /home/ubuntu/ensembl-vep/modules/Bio/EnsEMBL/VEP/Parser.pm line 71.
BEGIN failed--compilation aborted at /home/ubuntu/ensembl-vep/modules/Bio/EnsEMBL/VEP/Parser.pm line 71.
Compilation failed in require at /home/ubuntu/ensembl-vep/modules/Bio/EnsEMBL/VEP/Runner.pm line 83.
BEGIN failed--compilation aborted at /home/ubuntu/ensembl-vep/modules/Bio/EnsEMBL/VEP/Runner.pm line 83.
Compilation failed in require at ./vep line 20.
BEGIN failed--compilation aborted at ./vep line 20.

turns out, because of missing Try::Tiny in Perl.

First, go to perl shell mode

perl -MCPAN -e shell

then install

cpan[1]> install Try::Tiny

Try to install VEP again:

perl INSTALL.pl

And we’re good to go

# HGVS
  46: HGVSIntronOffset         - 
  47: SingleLetterAA           - 
# Structural variant data
  48: StructuralVariantOverlap - 
# Protein data
  49: neXtProt                 - Retrieves protein-related data from neXtProt
# Other plugins
  50: CSN                      - Reports Clinical Sequencing Nomenclature (CSN) for variants
  51: miRNA                    - Determines where in the secondary structure of a miRNA a variant falls?All done

Happy coding ~~

PEACE~~