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

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

  - A UNIX based operating system ( or cygwin unix emulation
    system for windows ).

  - Perl 5.8.0 or higher installed.


Installation - Automated
------------------------

  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.

Installation - By Hand
----------------------

  1. Change line 1 in the RepeatMasker, ProcessRepeats and DateRepeats scripts, 
     if Perl is not in the /usr/local/bin directory.

     For Windows w/Cygwin port:  Cygwin perl is located in /bin/perl
     Alternatively, providing some flexibility and access from different systems,
     you can replace the first line and invoke perl like:
             #!/bin/env perl 
             $^W = 1;
     We have not defaulted to this as it doesn't always work properly.

  2. Edit the configuration section of the RepeatMasker and DateRepeats scripts.  
     This is the section starting with the following text:

     ##----------------------------------------------------------------------##
     ##     CONFIGURE THE FOLLOWING PARAMETERS FOR YOUR INSTALLATION         ##

     In this section you will need to indicate the location
     of the cross_match executable and the RepeatMasker directory.
     If you are using WUBlast, you will also need to indicate the 
     location of thes executables here.

  3. Include RepeatMasker in every user's path (e.g. by making an alias in
    /usr/local/bin) or change an existing alias to RepeatMasker to indicate
    the new directory name.



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.