RepeatRunner Documentation

RepeatRunner

TO RUN REPEAT_RUNNER, DO THE FOLLOWING:

  1. Download and install CGL from (www.yandell-lab.org/cgl);

  2. Set the REPEAT_RUNNER_LIB environment varible to point at the repeat_runner/lib directory

  3. If you haven’t’\ 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.