Installation

Using pip

To install dRep, simply run

$ pip install drep

OR

$ git clone https://github.com/MrOlm/drep.git

$ cd drep

$ pip install .

That’s it!

Pip is a great package with many options to change the installation parameters in various ways. For details, see pip documentation

Dependencies

dRep requires many other great programs to run. Not all dependencies are needed for all operations

To check which dependencies are installed on your system and accessible by dRep, run

$ dRep bonus testDir --check_dependencies

Near Essential

  • Mash - Makes primary clusters (v1.1.1 confirmed works)
  • MUMmer - Performs ANIm comparison method (v3.23 confirmed works)

Recommended

  • CheckM - Determines contamination and completeness of genomes (v1.0.7 confirmed works)
  • gANI (aka ANIcalculator) - Performs gANI comparison method (v1.0 confirmed works)
  • Prodigal - Used be both checkM and gANI (v2.6.3 confirmed works)

Accessory

  • Centrifuge - Performs taxonomic assignment of bins (v1.0.3 confirmed works)

Programs need to be installed to the system path, so that you can call them from anywhere on your computer.

Testing

To make sure everything is installed correctly you can run the dRep test suite:

$ cd drep/tests

$ python test_suite.py

pyenv

Because dRep is written in python3 and CheckM is written in python2, you may need to use pyenv to be able to call both.

With CheckM installed in a python2 installation of pyenv, and dRep installed in the python3 version, the following command should set allow both python2 and python3 commands to be called:

$ pyenv global 3.5.1 2.7.9

Alternatively, you could add python2 to your CheckM shebang line (though I have not confirmed that this works)