Setting up GraphBin
Dependencies
GraphBin installation requires python 3 (tested on Python 3.6 and 3.7). The following dependencies are required to run GraphBin and related support scripts.
- python-igraph - version 0.7.1
- biopython - version 1.74
- cairocffi
Setting up GraphBin
Method 1: conda install
You can install GraphBin using the bioconda distribution. You can download
Anaconda or Miniconda which contains conda
.
Now let's add the required conda channels so we know the locations where packages are stored.
conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge
Once you have added the channels, you can install GraphBin directly from the bioconda distribution using the command
conda install -c bioconda graphbin
You can also create a new conda environment and install GraphBin from bioconda using the following commands.
# create conda environment
conda create -n graphbin
# activate conda environment
conda activate graphbin
# install graphbin
conda install -c bioconda graphbin
Method 2: pip install
You can install GraphBin using pip
from the PyPI distribution.
pip install graphbin
After setup, check if GraphBin is properly installed by typing graphbin -h
on the command line. You should see the usage options as shown in section Using GraphBin
Now let's prepare our results to run GraphBin.