Installation

From conda (new and recommended!) —

Conda is a cross-platform, cross-language package management system. If you haven’t already installed conda, follow these instructions here, and install the python3.6 version. Once you have that done, add the appropriate channels.

conda config --add channels defaults
conda config --add channels conda-forge
conda config --add channels bioconda

and then install riboSeed and all of its dependencies with one command:

conda install riboseed

(Note the lowercase “s”)

From Pypi

riboSeed is on Pypi, so you can install with pip, preferably within a virtualenv:

virtualenv -p python3.5 venv-riboSeed
source venv-riboSeed/bin/activate
pip3.5 install riboSeed

From TestPypi

To install the bleeding-edge version, install from testpypi:

virtualenv -p python3.5 venv-riboSeed
source venv-riboSeed/bin/activate
pip install --extra-index-url https://testpypi.python.org/pypi riboSeed

From GitHub

You can also clone this repository, create a virtual environment, and run python3.5 setup.py install.

Dependencies

External Requirements

riboScan.py

  • Barrnap (must be 0.7 or above)
  • EMBOSS’s Seqret

riboSelect.py

  • None

riboSnag.py

  • PRANK or Mafft
  • BLAST+ suite
  • Barrnap (must be 0.7 or above)

riboSeed.py

  • SPAdes v3.8 or higher
  • BWA (tested with 0.7.12-r1039)
  • SAMTools (must be 1.3.1 or above)
  • QUAST (tested with 4.1)

NOTE: barrnap has certain Perl requirements that may not be included on your machine. Ensure barrnap runs fine before trying riboSeed. Or try python barrnap.