Request: Add Ensembl VEP to Brewsci/bio tap #1982
Description
Hi Brewsci team 👋
🧬 Tool Request: Ensembl VEP
I'd like to kindly request that Ensembl VEP (Variant Effect Predictor) be added to the brewsci/bio tap.
📌 Description
Ensembl VEP is a widely used variant annotation tool maintained by the Ensembl team at EMBL-EBI. It allows researchers to annotate genomic variants with information such as consequences on genes, transcripts, and regulatory regions.
GitHub: https://github.com/Ensembl/ensembl-vep
Website: https://www.ensembl.org/info/docs/tools/vep/index.html
License: Apache 2.0
💡 Motivation
VEP is a standard tool in variant annotation pipelines and is used globally in clinical and research settings. While it's available via:
Manual installation using INSTALL.pl
Docker container
Conda (bioconda::ensembl-vep)
…it is not currently available via Homebrew, which would provide significant benefits:
Simpler install for macOS/Linux users: brew install ensembl-vep
Better integration in reproducible environments or CI
Easier installation in teaching/training environments
Fits naturally with other tools already present in Brewsci (bcftools, samtools, etc.)
🛠️ Installation Considerations
VEP is Perl-based and installs via INSTALL.pl, which handles dependencies and plugins.
A minimal setup could:
Clone a tagged release from GitHub
Place the vep executable in the bin path
Optionally install plugins, caches, and reference data separately
Dependencies:
Perl 5
Perl modules (can be managed via cpan, cpanm, or system packages)
Optionally: htslib, tabix, etc.
The formula could provide the core vep tool, with plugins and reference data downloaded by the user via the existing vep_install script.
🙋 Willing to help
I'm happy to assist in drafting a formula or testing the install process if needed.
Thanks a lot for your amazing work making bioinformatics tools more accessible to the community 🙌
Best regards,
Benjamin Demaille
BIPN Platform – Bioinformatics for Psychiatry and Neurosciences, Paris
https://github.com/bdemaille