PATRIC

Description

patric website

PATRIC is an integration of different types of data and software tools that support research on bacterial pathogens. The typical biologist seeking access to the PATRIC data and tools will usually explore the web-based user interface. However, there are many instances in which programatic or command-line interfaces are more suitable. For users that wish command-line access to PATRIC, we provide the tools described in this document. We call these tools the P3-scripts. They are intended to run on your machine, going over the network to access the services provided by PATRIC.

Environment Modules

Run module spider patric to find out what environment modules are available for this application.

Environment Variables

• HPC_PATRIC_DIR - installation directory
• HPC_PATRIC_BIN - executable directory

Citation

If you publish research that uses patric you have to cite it as follows:

Brettin, T., J. J. Davis, T. Disz, R. A. Edwards, S. Gerdes, G. J. Olsen, R. Olson, R. Overbeek, B. Parrello, G. D. Pusch, M. Shukla, J. A. Thomason, 3rd, R. Stevens, V. Vonstein, A. R. Wattam and F. Xia. RASTtk: a modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes. Sci Rep. 2015. 5: 8365. PMID: 25666585. PMCID: PMC4322359.

Categories

machine_learning