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README.md

PhageRage-Docker

Advances in sequencing technology provide the opportunity to explore viral diversity in a variety of ecological niches. Analysis of complex viral samples presents unique bioinformatic challenges, punctuated by the paucity of available viral genomes relative to their richness in the environment. PhageRage has been developed for the comprehensive examination of viral metagenomic data. PhageRage is a UNIX-based solution for the comprehensive examination of viral metagenomic data from assembly through analysis. It was developed with agility in mind; tools databases and modules can be customized and controlled by the user (even those without any programming savvy). PhageRage can also be run locally.

Getting Started

Clone project:

git clone github.com/thatzopoulos/PhageRage-docker.git

Move files that you want to run to inputFiles (raw read files, .fastq) and files/folders used for the homology detection tool to the all_gbk folder prior to building the docker image.

From within the project folder run:

sudo docker build -t phage_rage .
sudo docker run -v /pathToLocalFolder/runName:/phageRageDockerOutputFolder -i -t phage_rage

To pull up phageRage help for parameters while in the docker container:

python3 phage-rage.py -h

For documentation using phageRage, refer to here. Note: 'phageRageDockerOutputFolder' (the folder where Docker expects output to be written) must be the same folder specified when running phage-rage.py, the -o option.

Prerequisites

Docker is the only prerequisite for this program to run, all other dependencies are handled by the Dockerfile.

Authors

  • Jonathon Brenner
  • Thomas Hatzopoulos
  • Zach Romer
  • Jonathan Felipe Xavier
  • Catherine Putonti

License

This project is licensed under the MIT License

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