Installation¶

Bioconda (binary)¶

The recommended way to install NGLess is through bioconda:

conda install -c bioconda ngless 

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

docker run -v $PWD:/workdir -w /workdir -it quay.io/biocontainers/ngless:0.6.1--py35_0 ngless --version

Adapt the mount flags (-v) as needed.

You can get a statically linked version of NGless 0.6.1 or a nighly build of the latest development code. This should work across a wide range of Linux versions (please report any issues you encounter):

curl -O https://ngless.embl.de/releases/ngless-0.6.0-Linux64
chmod +x ngless-0.6.0-Linux64
./ngless-0.6.0-Linux64

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

If you want to try one of ngless’ builtin modules (motus, specI, …) you can download the full nighly build zip file which includes them.

Stack is the simplest way to install the necessary requirements. You should also have gcc installed (or another C-compiler).

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!

If you use nix, you can easily build and install ngless using it (these scripts also install all necessary dependencies):

nix-env -i -f https://github.com/luispedro/ngless-nix/archive/master.tar.gz

This should download the nix scripts and build ngless.

If you prefer, you can also first clone the repository:

git clone https://github.com/luispedro/ngless-nix
cd ngless-nix
# inspect the default.nix & ngless.nix files if you wish
nix-env -i -f .

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