Companion site for the book chapter "Fast Phylogeny Reconstruction from Genomes of Closely Related Microbes" from the forthcoming third edition of Bacterial Pangenomics.
Bernhard Haubold, Fabian Klötzl, and Beatriz Vieira Mourato
- Run
bash scripts/setup.sh
source ~/.profile
- Install
ectyper
We currently only provide a setup script for Ubuntu. However, that
setup script (scripts/setup.sh) should give you a good idea of
what's required on other systems. You can also start from our Ubuntu
docker, on which we have tested
the code in this repository.
Run
make data
to download the example data into the directory data.
Run
make
This generates the directory tutorial with the scripts and data for
following the tutorial in our chapter. Change into this directory.
cd tutorial
For testing you can run the entire tutorial with one command. If
ectyper was installed in a conda environment, please load it beforehand.
bash ../scripts/cli.sh