NAME
    Bio Legato - A customizable GUI for running programs

VERSION
    Version @VERSION@

SYNOPSIS
    biolegato [options] [files]

DESCRIPTION
    BioLegato is a customizable GUI for running programs.  Its initial intent is
    to be a replacement for GDE; however with its large plugin API, it may be
    customized to run more than just CLI programs.

    With the versatility of BioLegato's plugin interface, it supports a wide
    range of file formats which may be added to at any time through addition of
    plugins.

OPTIONS
  NOTE: All command line parameters are case insensitive and may optionally
        begin with -, --, or / to prevent confusion with filenames.  Options
        which are synonymous (e.g. --help and --h mean the same thing), are
        listed below, separated by commas.

    help,h,?
        Displays usage information for using BioLegato.
    manpage,man
        Displays the manpage entry for BioLegato (this screen).
    optionlist
        Displays the list of options for using BioLegato.
    version,v
        Displays the version information for BioLegato.
    debug
        Enables BioLegato's debug mode.
    plugins
        Displays a list of loaded plugins.
    pipe
        Pipes data from the input stream into BioLegato.
    exec-properties,ep
        Executes a command and reads the output as a
        properties file content for BioLegato.

USAGE EXAMPLES
    biolegato

    biolegato insequence.gb

    biolegato --debug
    biolegato /debug
    biolegato -debug

    biolegato --plugins --properties --debug

    biolegato --plugins /properties -debug insequence.gb

ENVIRONMENT VARIABLES
    BioLegato searches for the following environment variables.
    If they don't exist BioLegato sets them to defaults.

      BL_HOME
        Default: the path where BioLegato resides
        Description: the path to reference BioLegato from

      BL_PROPERTIES
        Default: $BL_HOME/properties
        Description: the locations to load the BioLegato properties file from

      BL_DEBUG
        Default: uses .blproperties value OR command switch --debug
        Description: set to "true" to enable debug mode

      NOTE: in properties files, BL_DIR points to the directory where
            BioLegato is stored

PROPERTIES
    BioLegato general properties:
      Property             Description
        debug                Determines whether to display debug information.
        plugins              Sets the plugin search path.
        temp                 Sets the temporary files directory.
        pcd.menus.path       Sets the path(s) to read BioPCD menus from.
        font.size            Determines the default font size for objects in
                             BioLegato.

    Sequence canvas-specific properties:
      Property             Description
        seqcolourdirs        The location to load the default sequence colour
                             masks from.  Please note that a default colour mask
                             may be specified by naming a colour mask file
                             "default" (with any extension).

    This properties class will read properties files from the directory
    containing BioLegato, the user directory and finally the directory BioLegato
    was launched from.  Please note that this behaviour can be changed using the
    BL_PROPERTIES environment variable.

    NOTE: for path properties BioLegato will replace all $'s with the
          appropriate environment variables if set.

SUPPORTED PLUGINS
    For information about plugins, please consult the BioLegato API

FILE FORMATS
    All file formats in BioLegato are supported through plugins.  File format
    support is different for each canvas.  The following is a list of standard
    file types supported by the GDE canvas:

        BioLegato flatfiles
        FastA files
        GDE flatfiles
        GDE format files
        GenBank files (2008 standard compliant)

    The following is a list of files supported by the Table canvas:
        CSV (Comma Separated Values) spreadsheet files
        TSV (Tab Separated Values) spreadsheet files

AUTHORS
    Dr. Brian Fristensky
    Department of Plant Science
    University of Manitoba
    Winnipeg, MB  Canada R3T 2N2

    Email: frist@cc.umanitoba.ca
    Web: http://home.cc.umanitoba.ca/~frist

    Graham Alvare
    Department of Plant Science
    University of Manitoba
    Winnipeg, MB  Canada R3T 2N2

    Email: alvare@cc.umanitoba.ca
    Web: http://home.cc.umanitoba.ca/~alvare