RepeatRunner Documentation:

To run repeat_runner do the following:

  1. download and install CGL from (;
  2. set the REPEAT_RUNNER_LIB environment varible to point at the repeat_runner/lib directory
  3. If you havent' done so already, install wu-blast and set the necessary enviroment varibles, such as WUBLASTFILTER, WUBLASTMATRIX
  4. If you are using the te_protein.fasta as a blastx database (by default this is true), format it using the wu-blast setdb command, e.g. setdb repeat_runner/sample_data/te_proteins.fasta
  5. Customize the paramters.cfg file in repeat_runner/config. To do this set the paths to the various executables and databases on your machine.
  6. type ./bin/repeat_runner for a usage statement.