Installation

Bioconda (binary)

The recommended way to install NGLess is through bioconda:

conda install -c bioconda ngless 

This will install the most recent released version

Using pixi

pixi is an alternative to conda that installs NGLess into a self-contained, per-project environment. The external tools that NGLess drives (bwa, samtools, minimap2, megahit, prodigal) are dependencies of the bioconda package, so they are pulled in automatically.

pixi only reads a manifest named exactly pixi.toml, so create a directory for the install and put the manifest there as pixi.toml (a ready-to-use copy ships in the NGLess repository):

[workspace]
channels = ["conda-forge", "https://conda.anaconda.org/bioconda"]
name = "ngless_test"
platforms = ["linux-64"]
version = "0.1.0"

[dependencies]
ngless = ">=1.6.0,<2"

Then, from that directory, install and run it with:

pixi install
pixi run ngless --version

From source

Since version 1.6, NGLess is written in Rust and builds with a standard Cargo toolchain (see the Rust implementation page for background).

The following sequence of commands should download and build the software

git clone https://github.com/ngless-toolkit/ngless
cd ngless
cargo build --release

This produces the binary at target/release/ngless. The first build takes a while as Cargo downloads and compiles all dependencies; subsequent builds are much faster.

The external tools that NGLess drives (bwa, samtools, minimap2, megahit, prodigal) are not bundled by a source build: they must be available on your $PATH (or pointed to via the NGLESS_<TOOL>_BIN environment variables, e.g. NGLESS_SAMTOOLS_BIN). The versions pinned for testing are listed in pixi.toml.

Cargo commands

• cargo build --release: compile the optimized ngless binary

• cargo test: run the unit tests

• cargo fmt --all -- --check: check formatting (enforced in CI)

The functional/parity test suite is run with run-tests.sh, pointed at the build via the NGLESS_BIN environment variable:

NGLESS_BIN=target/release/ngless ./run-tests.sh