fastHmm/fastBlast Configuration Files
$Id: README,v 1.2 2007/10/16 20:13:19 whuang Exp $

Overview

The fastHmm/fastBlast configuration files contain key=value macros, which
define a number of parameters used with the various tools bundled or
required by fastHmm and fastBlast.  We believe these parameters are optimal
in balancing accuracy of results with running time, however you may change
these values at your discretion.

Some parameters are global in that they apply to most, if not all tools
required by fastHmm or fastBlast.  These macros include the number of
concurrent analysis threads (NUMTHREADS), for example.  Most other macros
are grouped by specific tools (indicated by their all-uppercase prefix)
and occasionally subdivided into different scenarios in which the tools
are run.  Thus, the macro names cannot be arbitrarily named and should
use the following format:

TOOLNAME_arg = value
-or-
TOOLNAME_scenario_arg = value

The TOOLNAME and "scenario" names are fixed and examples are provided in the
existing configuration files.  Creating new TOOLNAME's or scenario names
will not negatively affect fastHmm or fastBlast, though these macros will
never be used.  "arg" refers to the tool-specific argument whose value you'd
like to set.  These arguments are formed and concatenated as "-arg <value>",
with the exception of the special "arg" keyword "FLAGS".  These macros are
used to pass valueless flags to the specified tool and these are added to
the tool command-line as is.  For example:

TOOLNAME_FLAGS = -flag1 -flag2 -flag3

will add "-flag1 -flag2 -flag3" as parameters when running "TOOLNAME" in
fastHmm or fastBlast.  It is important that the case of "arg" and the flags
specified in "FLAGS" are consistent with what the tool expects.  There is
no error checking to ensure parameters passed to the tool make sense or
that they're even acceptable to the tool.  Therefore, you should refer to
the tool-specific documentation for assistance with additional parameters.
Specifying invalid parameters will cause most of the tools not to run, and
therefore will cause fastHmm and/or fastBlast not to run properly.

Some tools may be used in fastHmm and fastBlast however parameters are never
shared between the two configuration files.  The fastHmm configuration file
contains only parameters used in fastHmm and similarly, the fastBlast
configuration file contains only parameters used in fastBlast.

Please see the individual configuration files and accompanying comments for
more information.  If you've made changes to the configuration files and
either fastHmm or fastBlast are no longer working properly, you should
revert your changes or replace the configuration files with those from the
original distribution.  Always keep backup configuration files if you choose
to make changes.

For additional assistance, please contact the fastHmm/fastBlast team at
http://microbesonline.org/fasthmm or by email to fasthmm@microbesonline.org.
