PhageTerm installation notes

Installing Phage Term

PhageTerm is a tool to analyse the structure of phage assemblies based on the sequence coverage.

A common way to use it is via a Galaxy server, but a version is available to install as a tool.

Get the tool

The tool can be downloaded from Source Forge.

After downloading the package and extracting it, it's important to take note of the path where the script is, that we will later refer to as {INSTALL_DIR}.

Install the requirements

Using Miniconda we can create a dedicated conda environment to run PhageTerm:

mamba create -n phageterm  \
  python=2.7 matplotlib numpy pandas scikit-learn scipy statsmodels reportlab

Run the program

First, we need to activate the environment:

conda activate phageterm

Then we can run the program as:

python2 {INSTALL_DIR}/PhageTerm.py \
  -f {FORWARD_READS} -p {REVERSE_READS} \
  -r {REF_GENOME} -c {CORES} -n {PHAGE_NAME}