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 dependenciesclean: remove local generated files by compilationcheck: run testsbench: run benchmarks