Installing ensembl-vep

Question

[Peerzada]

Hello all ,

I tried installing ensembl-Vep on mu ubuntu using following commands

git clone https://github.com/Ensembl/ensembl-vep
cd ensembl-vep
perl INSTALL.pl

I got the error as :-

ERROR: DBI module not found. VEP requires the DBI perl module to function

I tried installing DBI etc but the error persists . How can I proceed .Please help.

[Arup Ghosh]

VEP requires Archive::Zip and DBI Perl modules, install them using cpanm. More details regarding dependencies are available in the install section of the readme file.

https://github.com/Ensembl/ensembl-vep#install

Answer 1

[tomas4482]

You can either create a new environment using Anaconda3 and download it via conda install -n vep -c bioconda ensembl-vep or install every dependencies manually as described below. I used root user for installation.

# install cpanminus #
sudo apt install build-essential
sudo apt install cpanminus

# install dependencies #
sudo cpanm Archive::Zip
sudo cpanm DBI
sudo apt-get install libmysqlclient-dev
sudo cpanm DBD::mysql
sudo cpanm Bio::Root::Version

# install VEP #
perl INSTALL.pl --AUTO acfp --ASSEMBLY GRCh38 --PLUGINS all --SPECIES homo_sapiens,mus_musculus

Cache files can be huge. You may need to use wget -c or other tools to continuously download them. Otherwise, it may report an installation error when you have any internet interruption during installation.

You can install Plugins manually too. Please read the official document. You may need to chmod 777 ~/.vep to authenticate any modification of the vep file. Otherwise, it will report an error when you install plugins.

[Peerzada]

Thank You Sir