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.