Installation

NOTE: As of July 2016, ngless is available only as a pre-release to allow for testing of early versions by fellow scientists. We do not recommend use in production. Please get in touch if you are interested in using ngless in your projects.

At the moment, ngless can be esily obtained in binary form for Windows (experimental) and with either brew or nix (for Mac OS X or Linux). Of course, you can also compile from source.

Windows

Download and run the Windows Installer. The result is a command line utility, so you need to run it on the command line. After running the installer, typing ngless on the terminal should work as the installer will add the right directories to the path variable; you may have to start a new terminal, though. It should also work under Cygwin (but Cygwin is not a dependency).

The Windows package includes bwa and samtools. The bwa and samtools executables are available as ngless-0.0.0-bwa and ngless-0.0.0-samtools, respectively. It has been tested on Windows 10, but this has not had as intensitive testing as the Linux/Mac OS X versions so any bug reports are appreciated.

From source

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/luispedro/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!

With Nix

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 .

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