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

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

  - A UNIX based operating system.

  - Perl 5.8.0 or higher installed.

  - Python 3.0 installed.

  - h5py HDF5 library for Python
      See https://docs.h5py.org/en/latest/build.html for installation
      instructions.

  - 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.  The curated families from
    Dfam 3.1 are included in this release. Updates and the complete
    (curated & uncrated) Dfam libraries can be found at: www.dfam.org.
    The RepBase RepeatMasker Library can be obtained at: 
    http://www.girinst.org
       

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

  1. Unpack the distribution in your home directory or in a location where it 
     may be shared with other users of your system ( ie. /usr/local/ ). Make 
     sure you do not extract in a directory already containing a pre-existing
     directory called "RepeatMasker" as it will attempt to overwrite files 
     contained within.  For example:

         % cp RepeatMasker-open-4-#-#.tar.gz /usr/local
         % cd /usr/local
         % gunzip RepeatMasker-open-4-#-#.tar.gz
         % tar xvf RepeatMasker-open-4-#-#.tar

  2. RepeatMasker comes with a copy of the curated portion of 
     Dfam ( Libraries/Dfam.h5 ).  This is a small library ( at 
     this time ).  There are two options for supplementing the
     main RepeatMasker library:

       - The complete Dfam ( curated and uncurated families ) library
         may be downloaded from www.dfam.org in famdb HDF5 format and
         used to replace the distributed "Libraries/dfam.h5" file. For
         example:

             % wget https://www.dfam.org/releases/Dfam_3.2/families/Dfam.h5.gz
             % gunzip Dfam.h5.gz
             ## NOTE: This will overwrite the distributed Dfam.h5 file.
             % mv Dfam.h5 /usr/local/RepeatMasker/Libraries

     and/or

       - The RepBase RepeatMasker Edition ( final version 10/26/2018 )
         may be downloaded from www.girinst.org and unpaked in the
         RepeatMasker directory.  For example:

             % cp RepBaseRepeatMaskerEdition-20181026.tar.gz /usr/local/RepeatMasker/
             % cd /usr/local/RepeatMasker
             % gunzip RepBaseRepeatMaskerEdition-20181026.tar.gz
             % tar xvf RepBaseRepeatMaskerEdition-20181026.tar
             % rm RepBaseRepeatMaskerEdition-20181026.tar
               
  3. 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.