Clone the repository from github together with Jellyfish submodule (--recursive).

git clone --recursive
cd seed-kraken

The branch with the latest version is seedmod128b_from_0.10.6.

git branch

Building seed-Kraken

Build seed-Kraken and install it into a directory in your $PATH, for example ~/bin. This step requires C++11 enabled GCC with support for auto, so GCC >4.4 is required. ~/bin

Building Jellyfish

cd Jellyfish/build/
autoreconf -i ../
make -j 4

Now, link the seed-modified jellyfish binary to a directory in in your $PATH. Watch out, as this may conflict with another version of Jellyfish you have already installed.

cd bin
ln -s "$(realpath jellyfish)" ~/bin/

Note: this a modified version of Jellyfish v1.11_seedmod made to work with spaced seeds. seed-Kraken calls jellyfish from within its scripts. Make sure that the correct version of jellyfish is in your path:

$ jellyfish --version
jellyfish 1.1.11_seedmod

Setting Paths

Optionally you can setup PATH every time before running seed-Kraken:

export PATH="/directory/to/jellyfish/bin/:$PATH"