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Corbata: CORe microBiome Analysis Tools


In order to run the Corbata scripts, you will need to install (or confirm that you have installed) a Unix version of R. You can download the latest version of R from: http://www.r-project.org

R is an awesome statistics package that everybody who handles data should at least be a little familiar with. Because the potentially interested users of Corbata may range in their bioinformatics experiences, it was decided to leave the Corbata scripts in their original command line form, instead of converting them into R libraries. As command line scripts, they can easily be run from a Unix prompt by specifying the input file and sometimes a few extra parameters. At JCVI, we frequently process large datasets on our compute grid, so R scripts are preferred over R's interactive console interface. (As an R library, which is not provided, new users to R may have some issues understanding how the R environment works and may have difficulties preparing the data objects to be passed into the function calls. Unfortunately, this means Windows users will be at a disadvantage, since Windows does not have a command line interface. You will need to modify the scripts if you want to run them on that platform.  Fortunately, most of the scripts are not very long or complicated, so learning to do so would not be too challenging.)

If R is already installed on your Unix system, the R scripts will auto-detect your installation (with the help of the #!/usr/bin/env Rscript on the first line of each of the Corbata scripts).

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