RepeatMasker Installation Notes
===============================

Pre-requisites
--------------

  - A UNIX based operating system.

  - Perl 5.8.0 or higher installed.

  - TRF 4.09 or higher ( http://tandem.bu.edu/trf/trf.html )
  
  - A search engine.  We currently support:

       crossmatch : http://www.phrap.org
       rmblast :  http://www.repeatmasker.org/RMBlast.html
       nhmmer : Pre release version - 
              ftp://selab.janelia.org/pub/pickup/hmmer3.1-snap20121016.1.tgz 
              ( Dfam required )
       abblast/wublast : http://blast.advbiocomp.com/licensing/

  - Dfam and/or RepeatMasker libraries.  Dfam 3.1 is
    included in this release.
    Updates can be found at: www.dfam.org.
    The RepBase RepeatMasker Library can be obtained
    at: http://www.girinst.org
       

Installation 
------------

  1. Unpack the files to the directory you wish to install
     them in.

  2. Configure the distribution by invoking Perl on the
     the "configure" script, i.e.:
  
            perl ./configure

     The configure script will prompt you for all the
     information needed to setup the RepeatMasker suite of
     programs.


Library Cache Directories
-------------------------

Since version 3.0 RepeatMasker creates species-specific libraries
on the fly.  These libraries are cached in the first writable 
directory in the programs library path.  The default path is:

  1. The RepeatMasker installation "Library" directory.
  2. The ".RepeatMaskerCache" subdirectory of the users home
     directory.
  3. The temporary processing directory "RM_#" created
     in the same directory as the sequence file and 
     removed at the end of the run.
  
NOTE: If the program cannot save libraries in either path 1 or 2, the
libraries will need to be created each time the program runs.  This
will slow down runs on shorter sequences.
