NARFMAP

NARFMAP is a fork of the Dragen mapper/aligner Open Source Software.

Installation

Using bioconda

Coming Soon™️

Build from source

Nix

1. Install nix. The Determinate Systems Installer is recommended for Flakes.

curl --proto '=https' --tlsv1.2 -sSf -L https://install.determinate.systems/nix | sh -s -- install

2. Run nix build

If you're feeling bold

We're still using the previous build system under the hood

Prerequisites

Compilation was tested on CentOS 7

• C++17 compatible compiler (e.g gcc-c++ >= 7.1)
• GNU make >= 3.82
• Boost library : boost169-devel >= 1.69.0-1.el7
• For unit tests : googletest (>= v1.6)
• Hardware: x86_86, 64GB RAM minimum
• OS: Centos >= 7.7

Install

The basic procedure is

make

Binary will be generated in ./build/release/

Then optionally, to install to /usr/bin/

make install

By default make will compile and launch unit tests. To disable unit tests, use HAS_GTEST=0, e.g. :

HAS_GTEST=0 make

To compile with unit tests, if google test was installed in user space, it might be required to set GTEST_ROOT and LD_LIBRARY_PATH to where gtest was installed, e.g. :

export GTEST_ROOT=/home/username/lib/gtest
export LD_LIBRARY_PATH=/home/username/lib/gtest/lib

Other variables controlling the build process:

• GCC_BASE
• CXX
• BOOST_ROOT
• BOOST_INCLUDEDIR
• BOOST_LIBRARYDIR

Pull requests

We are accepting pull requests into this repository at this time! For any bug report / recommendation / feature request, please open an issue. Stay tuned for a CONTRIBUTING.md