Installation

To download and compile:

git clone --recursive https://github.com/mcveanlab/mccortex
cd mccortex
make

This generates an executable bin/mccortex31. Running make for the first time requires internet access to fetch some dependencies. First compilation may take some time.

The command ctx31 handles kmer sizes 3-31. To compile for larger values of k (kmer-size), e.g. ctx63 to handle 33-63:

make MAXK=63

Valid MAXK values are 31+32n where n is >= 0. As a short hand to compile at multiple kmer values, you can run the script:

./scripts/multik-build.sh

Dependencies

Most dependencies are fetched automatically by Make. Before you start compilation you will need:

• Make
• git
• bash
• C compiler (e.g. gcc/clang)
• C++ compiler (e.g. g++)
• zlib (a very common compression library)
• perl

The optional perl scripts require the JSON Module. Install with cpanm with: cpanm JSON or with apt-get: sudo apt-get install libjson-pp-perl

Updating

To get the latest version, run in the McCortex directory:

./scripts/update.sh