| 5. Install RepeatMasker. Download from http://www.repeatmasker.org |
| a. The most current version of RepeatMasker requires a program called TRF. |
| This can be downloaded from http://tandem.bu.edu/trf/trf.html |
| b. The TRF download will contain a single executable file. You will need to |
| [
](http://malachite.genetics.utah.edu/projects/maker/browser/INSTALL#L122) |
rename the file from whatever it is to just 'trf' (all lower case). |
| [
](http://malachite.genetics.utah.edu/projects/maker/browser/INSTALL#L123) |
c. Make TRF executable by typing chmod +x+u trf. You can then move this file |
| wherever you want. I just put it in the /RepeatMasker directory. |
| d. Unpack RepeatMasker to the directory of your choice (i.e. /usr/local). |
| e. If you do not have WuBlast installed, you will need to install the program |
| RMBlast. We do not recomend using cross_match, as RepeatMasker |
| performance will suffer. |
| f. Now in the RepeatMasker directory type perl ./configure in the command |
| line. You will be asked to identify the location of perl, wublast, and |
| trf. The script expects the paths to the folders containing the |
| executables (because you are pointing to a folder the path must end in a |
| '/' character or the configuration script throws a fit). |
| g. Add the location where you installed RepeatMasker to your PATH variable in |
| .bash_profile (i.e. export PATH="/usr/local/RepeatMasker:$PATH"). |
| h. You must register at http://www.girinst.org and download the Repbase |
| repeat database, Repeat Masker edition, for RepeatMasker to work. |
| i. Unpack the contents of the RepBase tarball into the RepeatMasker/Libraries |
| directory. |