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.

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.