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

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

Stack is the simplest way to install the necessary requirements.

The following sequence of commands should download and build the software

git clone https://github.com/ngless-toolkit/ngless
cd ngless
make

The first time you run this, it will take a while as it will download all dependencies. After this ngless is ready to use and subsequent builds will be much faster.

Make targets

The following are targets in the Makefile.

• make: compiles NGLess and haskell dependencies
• clean: remove local generated files by compilation
• check: run tests
• bench: run benchmarks