Installation
Clone the repository from github together with Jellyfish submodule (--recursive
).
git clone --recursive git@github.com:macieksk/seed-kraken.git
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.
install_kraken.sh ~/bin
Building Jellyfish
cd Jellyfish/build/
autoreconf -i ../
../configure
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"