Installation

The pdm_utils package is written for Python >=3.7 and can be installed on MacOS and Linux platforms. There are several third-party general dependencies that need to be installed in advance, and there are several dependencies that are only needed for a subset of pdm_utils tools. Below is a general step- by-step installation guide.

Required

The following software should be installed in the order indicated:

1. MySQL

2. Anaconda

3. pdm_utils Python package

4. MySQL phage genomics database instance

Optional

Several pdm_utils tools have specific dependencies. Install the following software as needed:

• ARAGORN (importing tRNA and tmRNA data)

• Infernal (importing tRNA and tmRNA data)

• tRNAScan-SE (importing tRNA and tmRNA data)

• MMseqs2 (creating gene phamilies)

• NCBI Blast+ (finding conserved domains)

• NCBI Conserved Domain Database (finding conserved domains)

• Markov Clustering (creating gene phamilies)

• pdm_utils repository (source code, MySQL scripts, tests)