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.
Download and run the Windows
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
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.
Stack is the simplest way
to install the necessary requirements. You should also have
gcc installed (or
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!
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