Installation¶

pip install vaxrank

Vaxrank requires Python 3.10 or newer.

Reference annotation¶

Vaxrank uses PyEnsembl for reference genome annotation. Install an Ensembl release matching the reference genome your variants were called against:

# GRCh38
pyensembl install --release 113 --species human
# GRCh37 (legacy)
pyensembl install --release 75 --species human

PDF reports¶

PDF generation uses wkhtmltopdf by default. Install a compatible executable and make it available on PATH.

Alternatively, pass --pdf-backend=weasyprint to use WeasyPrint (experimental). It uses system libraries such as Pango:

pip install weasyprint
# macOS also needs: brew install pango

On Apple Silicon, WeasyPrint loads Pango through dyld, which does not search Homebrew's /opt/homebrew/lib by default. Add this to your shell profile:

export DYLD_FALLBACK_LIBRARY_PATH="/opt/homebrew/lib:$DYLD_FALLBACK_LIBRARY_PATH"

Intel macOS already includes Homebrew's /usr/local/lib in dyld's default fallback path.

Isovar version window¶

RNA reconstruction requires a compatible Isovar release; see Isovar support compatibility for the tested range and the measurements Vaxrank retains from it.