Compilation and Installation

Procedure

1. Use PuTTY to log in to the server as the root user.
2. Decompress the installation package.

   tar -zxvf 104.3.tar.gz

3. Go to the directory generated after the decompression.

   cd ensembl-vep-release-104.3

4. Install and use the cpanm tool to download the dependency package.

   yum install -y perl perl-App-cpanminus.noarch perl-core perl-DBD-MySQL perl-Try-Tiny.noarch
   cpanm Archive::Zip
   cpanm DBI
   cpanm Bio::Root::Version
   cpanm Bio::DB::HTS::Tabix
   cpanm HTTP::Tiny

5. Perform the compilation and installation.

   perl INSTALL.pl  --NO_HTSLIB

   Select n for the three options in the command output.

   Do you want to install any cache files (y/n)? n
   Skipping cache installation
    
   The VEP can use FASTA files to retrieve sequence data for HGVS notations and reference sequence checks.
   FASTA files will be stored in /root/.vep
   Do you want to install any FASTA files (y/n)? n
   Skipping FASTA installation - Exiting
    
   The VEP can use plugins to add functionality and data.
   Plugins will be installed in /root/.vep/Plugins
   Do you want to install any plugins (y/n)? n
   Skipping plugin installation

6. (Optional) Download the cache file.

   cd /root/.vep
   wget http://ftp.ensembl.org/pub/release-104/variation/indexed_vep_cache/homo_sapiens_vep_104_GRCh38.tar.gz --no-check-certificate
   tar homo_sapiens_vep_104_GRCh38.tar.gz