Installation

One command, and nothing to compile. Ligase ships as a wheel with the Rust core already built.


pip install ligase-bio

Check it:


python -c "import ligase; print(ligase.version())"
ligase --help

What you need

Python 3.11 or newer. Wheels are published for Linux (manylinux), macOS and Windows, so there is no Rust toolchain and no C compiler involved in installing it.

The tools your pipeline shells out to. Ligase does not bundle an aligner or a variant caller, and does not want to: a step names the tool it runs, and that tool’s real version goes into the cache key and the methods paragraph. Install whatever your pipeline names. For the HIV-1 reference pipeline that is minimap2, samtools and bcftools:


conda install -c bioconda minimap2 samtools bcftools

Ligase itself is also on conda-forge via a Bioconda recipe, and on crates.io as ligase if you want the Rust core directly.

Verifying a step’s tools

A pipeline that names a tool you do not have fails at check, not halfway through an overnight run:


ligase check

That is worth doing on a new machine before anything else.

Where to next

check≠runWrite your first pipeline

Five minutes: two steps, a type error on purpose, then a real run and a cache hit.

ligase≠--helpLook up a command or a flag

Every command and option, generated from the parser so it cannot drift.

Working on Ligase itself

Building from source, running the test suite, fetching the demo data and rebuilding after a Rust change are all in building Ligase. You do not need any of it to use the package.