Usage

Pita has to be called from the command line with a fairly simple syntax. A general use example:

$ pita -c config.yaml -i indexdir/

The -c option defines the location of the configuration file in yaml format. More information of how to make this file can be found in the subsection (Needs to be added). The -i option defines the location of the directory with a genome index generated by gimmemotifs. Using the syntax:

$ gimme index [-h] <subcommand> [options] [-i DIR] FASTADIR INDEXNAME