##
## INSTRUCTIONS TO INSTALL GFF2APLOT v2.0
##
##
## $Id: INSTALL,v 1.1 2003/03/17 17:58:46 jabril Exp $
##

    GFF2APLOT v2.0

    a program to visualize the alignment of two genomic sequences
    together with their annotations. From GFF-format input files
    it produces PostScript figures for that alignment.
    

      Copyright (C) 1999-2003 - Josep Francesc ABRIL FERRANDO
                                        Thomas WIEHE
                                       Roderic GUIGO SERRA

-------------------------------------------------------------------------------
  Installing GFF2APLOT v2.0
-------------------------------------------------------------------------------

+ PROGRAM's PRE-REQUISITES:

  gff2aplot needs the following Perl modules installed in your system,
  we used those available from the standard Perl distribution. Those
  that are not in the standard distribution are marked with an '(*)',
  although this will change from one installation to another. In such
  cases make sure that you already have downloaded them from
  CPAN (http://www.perl.com/CPAN) and get them installed.

    "Getopt::Long" - processing command-line options.
       "Benchmark" - checking and comparing running times of code.
    "Data::Dumper" - pretty printing data structures for debugging (*?).


+ INSTALLING SOFTWARE:

  You will find a Makefile in the distribution directory that you may need
  to edit in order to install GFF2APLOT. In principle, you only need to
  modify the INSTALLDIR variable, although you can achieve the same effect
  from command-line, as shown latter in this document.
  Depending on the system, you may also have to modify/update the ali2gff 
  Makefile that can be found at the src/ali2gff directory.

  GFF2APLOT Makefiles were developed and tested on a Red Hat Linux box
  running GNU Make version 3.79.1.

  Once you have set up the makefile, just type:

     make

  and then:

     make install

  By default, the latter command will move all the scripts to /usr/local/bin
  but if you want to place all the exec files into another directory, just
  define the new installation path as follows:

     make INSTALLDIR=/your/path/bin install

  Another way of doing that is modifying that variable on the Makefile
  accordingly to your needs.

  Our apologies but there is not a 'make test' yet...

  Thanks for using GFF2APLOT, we hope you will enjoy it and it will
  be useful for your research.


+ SETTING ENVIRONMENT VARIABLES:

  There are two environmental variables that can be set by users to their
  preferences:

     + You can specify the path where gff2aplot can find the default
       files with the shell variable "GFF2APLOT_CUSTOMPATH". Default
       value is the path where you are running gff2aplot.

     + You can also define the default custom filename you will like
       with the variable "GFF2APLOT_CUSTOMFILE", program default filename
       for custom file is ".gff2aplotrc".

     + Now gff2aplot does not need to write any temporary file, so that
       previous versions default temporary directory path variable
       ("GFF2APLOT_TMP") is no longer used.

     + Setting those vars in Bourne-shell and C-shell:

       o Using a Bourne-Shell (e.g. bash):

            export GFF2APLOT_CUSTOMPATH="path"
            export GFF2APLOT_CUSTOMFILE="file_name"

       o Using a C-Shell:

            setenv GFF2APLOT_CUSTOMPATH "path"
            setenv GFF2APLOT_CUSTOMFILE "file_name"

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