Table of contents
- Installing PhyloPyPruner
- Upgrading PhyloPyPruner
- Removing PhyloPyPruner
The easiest way to install PhyloPyPruner is by using the package manager for Python, pip:
pip install phylopypruner # install for all users pip install --user phylopypruner # install for the current user only
Once installed, the program is located within
$HOME/.local/bin. Depending on
your OS, you might have to add the directory to your
$PATH to avoid typing
the entire path. Once in your path, you run the program like this:
If you want to upgrade to the latest version, use pip with the flag
--upgrade like so:
pip install --upgrade phylopypruner # upgrade for all users pip install --user --upgrade phylopypruner # upgrade for the current user only
To remove PhyloPyPruner from your system, use pip with the command
pip uninstall phylopypruner # remove for all users pip uninstall --user phylopypruner # remove for the current user only
If you get the error message
No module named phylopypruner when trying to run PhyloPyPruner, try running it with a different version. This error message arise when pip installs phylopypruner for a different version of Python than what is in your path.
There are no external dependencies, but the the plotting library Matplotlib may be installed for generating the paralogy frequency- and occupancy plots.
This software runs under both Python 3 and 2.7. To see what version of Python is on your machine, type
python --version Enter into the command line. Multiple versions of Python may be installed on the same machine. In such cases, different version are kept apart by having different names such as
python3. Too see all versions of Python that are installed on your system, type
python and press Tab in the command line.
If you need to install Python, I recommend the Python distribution Anaconda as Anaconda is tailor-made for scientific computing and data science.
To see if Matplotlib is installed and what version is on your system, enter
pip list | grep matplotlib into the command line. To install Matplotlib, you can use the Python package manager pip by typing:
pip install matplotlib. To upgrade to the latest version, type
pip install --upgrade matplotlib into the command line.
Note: A GUI is required in order to generate plots. If you are connecting to a remote machine via SSH, use the option
-Xto enable X11 forwarding.
To see if pip is installed on your machine, type
which pip Enter into the command line. If pip is installed and is in your path, then which returns the path to pip. If not, which does not return anything. You can download and install pip by entering the commands below, but you should also consider upgrading your Python version as newer versions of Python comes with pip installed by default.
curl https://bootstrap.pypa.io/get-pip.py -o get-pip.py python get-pip.py
Note that different versions of pip may be installed on your system. These versions are generally differentiated by having different names such as
pip3. To see what version of pip is installed on your system, type
pip --version Enter into the command line. This will also tell you which version of Python that pip is associated with.