Bioinformatics

Install VEP ensembl failed

because of file aborted.

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Photo by Aaron Burden on Unsplash

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~~

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A passionate automation engineer who strongly believes in “A man can do anything he wants if he puts in the work”.

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