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README

cndsrc: Colin N. Dewey's Source Code (2005-12-04)

CONTENTS 
-------- 
This package includes the source code for the many utility programs
that I have written as well as for the mercator, parametricAlign, and
recombination programs.  Makefiles are included for compilation of
these programs so that they may be used and distributed.

PREREQUISITES
-------------
In order to successfully compile the programs in this package, you
must have a couple of external packages installed.  These are:

- Optik: http://optik.sourceforge.net/
  - Only required if your version of python is < 2.3.
    This python library must be installed system-wide or in your
    personal python library directory (e.g. $HOME/lib/python).

- BLAT: http://www.cse.ucsc.edu/~kent/
  - Only required if you wish to generate input for the
    mercator program using the makeMercatorInput script.

- Genscan: http://genes.mit.edu/GENSCAN.html
  - Only required if you wish to run the makeMavidConstraints script
    for generating constraints for the MAVID multiple alignment
    program

- Polymake: http://www.math.tu-berlin.de/polymake/
  - Only required if you wish to build the parametricAlign program.
  - If installed, the environment variable POLYMAKE_PATH should be set
    to the directory in which you have installed the polymake package
    (using both the "make install" and "make install-devel" commands in
    the unpacked polymake directory)

INSTALLATION
------------

1. Make sure that all prerequisites have been installed correctly

2. Unpack the source code tarball: 

   tar zxf cndsrc-XXXX.XX.XX.tar.gz

3. Change to the cndsrc directory:

   cd cndsrc-XXXX.XX.XX

4. Build all programs:

   make

5. Install programs to the "bin" directory in the directory specified
   by the --prefix option (in this example the programs will be installed
   in /usr/local/cndsrc-XXXX-XX-XX/bin): 

   make install prefix=/usr/local/cndsrc-XXXX-XX-XX"

RUNNING UTILITY PROGRAMS
------------------------

Most of the small utility programs (e.g. faReformat) are fairly simple and
you can get the usage information for each of these programs by
running them with the "--help" option.  For example:

$ faReformat --help
Usage: faReformat [options] < fastaInput
Reformat fasta input

Options: 
  -?, --help                  Display this help message
  -s, --strip-title           truncate the title for each record at the first
                              whitespace character
  -g, --remove-gaps           remove gaps from sequences
  -w, --width=NUM             number of characters at which sequence is wrapped
                              (default: 60)


RUNNING APPLICATIONS
--------------------

For instructions on running the larger applications (i.e. mercator,
parametricAlign, and recombination programs), please read the README
files in the appropriate subdirectory of the "apps" directory.