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Installation guide for PhageScanner
PhageScanner incorporates several command line tools within its pipeline, many of which are designed for Unix systems, common in bioinformatics for use on HPCs. This guide outlines installation steps for multiple operating systems. The necessary tools include:
- CD-HIT - Clusters proteins in the
database
pipeline to avoid duplicates during testing and training. - BLAST - Blast is used as a pseudo model in both the
train
andpredict
pipelines. - Megahit - Assembles reads in the
predict
pipeline. - Phanotate - Used to identify open reading frames in the
predict
pipeline.
NOTE: PhageScanner is optimized for 64-bit macOS and Ubuntu Linux. Windows users can utilize the tool via the Docker image or by installing the Ubuntu Windows Subsystem for Linux (WSL). This workaround is necessary because some dependencies, such as cd-hit, phanotate, and megahit, rely on C++ libraries not natively supported on Windows. For the best experience, we recommend using PhageScanner on macOS or Linux.
Directions for installing these dependencies are provided for Mac, Linux, and Windows:
- Installation Directions for Linux and Mac
- Installation Directions for Windows
For Mac or Linux (including WSL/WSL2), Anaconda simplifies the installation of command line tool dependencies. Start by installing miniconda. Then, create a new virtual environment (e.g., conda create -n phagescanner python==3.12.3
) and install the following tools:
CD-HIT (see CDHIT package here)
conda install bioconda::cd-hit
BLAST (see BLAST package here)
conda install bioconda::blast
Megahit (see Megahit package here)
conda install bioconda::megahit
PHANOTATE (see Phanotate package here)
conda install bioconda::phanotate
There are couple of ways we recommend using PhageScanner on Windows. One method is to download the Windows Linux Subsystem (WSL) or to create a docker container for the dependencies. This guide walks through both of these options.
Docker can be used to install PhageScanner locally any on operating system. For questions on using Docker please visit the Docker Guide. In addition, there may be an interest in the resource that docker containers can use, please see here. For any questions about problems with Docker, visit the corresponding stack overflow page here.
- Download Docker:
- Installation Instructions for Mac: https://docs.docker.com/desktop/install/mac-install/
- Installation Instructions for Ubuntu: https://docs.docker.com/engine/install/ubuntu/
- Installation Instructions for Windows: https://docs.docker.com/desktop/install/windows-install/
PhageScanner is available on DockerHub, simplifying its deployment on Windows:
- Download the Docker image:
docker pull dreyceyalbin/phagescanner
- Verify the installation:
docker run --rm dreyceyalbin/phagescanner --help
The docker image can be built locally to allow for more flexibility. There are two steps involved in this process:
- Navigate to the
Docker/
directory and build the image:
docker build -t dreyceyalbin/phagescanner .
- Test the image:
docker run --rm dreyceyalbin/phagescanner --help
Another option is using the Windows Subsystem for Linux:
- Install WSL with Ubuntu 22.00.0+ following these directions..
- Install the dependencies using the Linux and Mac directions above. Make sure to follow the steps to verify the dependencies have been correctly installed.
- Install Python v12 and PhageScanner:
- Install Phage scanner using
python -m pip install -r requirements.txt
from the root directory.
- Install Phage scanner using
After these steps, your system should be ready to test the examples provided by PhageScanner.