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

Beta releases (via pixi)

Pre-release/beta builds are published as .conda packages on the GitHub releases page before they reach bioconda. The easiest way to install one, together with the external tools that NGLess drives (bwa, samtools, minimap2, megahit, prodigal), is with pixi and a manifest that pins the beta package by URL.

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]
prodigal = ">=2.6.3,<3"
megahit = ">=1.2.9,<2"
samtools = ">=1.23.1,<2"
minimap2 = ">=2.31,<3"
bwa = ">=0.7.19,<0.8"
ngless = { url = "https://github.com/ngless-toolkit/ngless/releases/download/v1.6.0-beta2/ngless-1.6.beta2-ha35fb5c_0.conda" }

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

pixi install
pixi run ngless --version

Update the url to point at the beta release you want to install.

Docker

Alternatively, a docker container with NGLess is available at docker hub:

docker run -v $PWD:/workdir -w /workdir -it nglesstoolkit/ngless:1.4.2 ngless --version

Adapt the mount flags (-v) as needed. You can use the latest tag to get a more up to date version as well.

Linux (binary)

You can download a statically linked version of NGless 1.4.2.

This should work across a wide range of Linux versions (please report any issues you encounter):

curl -L -O https://github.com/ngless-toolkit/ngless/releases/download/v1.4.2/NGLess-v1.4.2-Linux-static-full
chmod +x NGLess-v1.4.2-Linux-static-full
./NGLess-v1.4.2-Linux-static-full

This downloaded file bundles bwa, samtools and megahit (also statically linked).

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