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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.