Installation

PhiSpy can be installed using several methods. We recommend using either conda (easiest) or pip.

Conda (Recommended)

The easiest way to install PhiSpy for all users is to use bioconda:

conda install -c bioconda phispy

This method handles all dependencies automatically and works across different platforms.

To install PhiSpy using pip, you need a C++ compiler and the Python header files.

On Ubuntu/Debian systems:

sudo apt install -y build-essential python3-dev python3-pip
python3 -m pip install --user PhiSpy

On macOS (requires Xcode Command Line Tools):

xcode-select --install
python3 -m pip install --user PhiSpy

The pip installation will place PhiSpy.py in ~/.local/bin which should be in your $PATH. If it’s not, see the Tips and Tricks section.

For advanced users, you can clone the git repository and install from source:

git clone https://github.com/linsalrob/PhiSpy.git
cd PhiSpy
python3 -m pip install --user .

If you want to track installed files for easy uninstallation:

git clone https://github.com/linsalrob/PhiSpy.git
cd PhiSpy
python3 setup.py install --user --record installed_files.txt

To uninstall later:

cat installed_files.txt | xargs rm -f

If you have root access and want to install globally:

git clone https://github.com/linsalrob/PhiSpy.git
cd PhiSpy
python3 -m pip install .

PhiSpy requires the following programs to be installed. Most of these are installed automatically when using conda or pip:

For HMM-based prophage detection:

To verify that PhiSpy is installed correctly:

PhiSpy.py --version

You should see the version number printed. If you get a “command not found” error, see the Tips and Tricks section.