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.