GenomeHistory installation instructions: Basic Instructions: The following 5 commands should generate the GenomeHistory package from GenomeHistory.tar-- the % indicates your prompt--don't type it :) If you downloaded the gzipped binaries, type % gunzip GenomeHistory_bin.tar.gz If you downloaded the compressed archive (GenomeHistory_src.tar.Z), type % uncompress GenomeHistory_src.tar.Z If you downloaded the gzipped archive (GenomeHistory_src.tar.gz), type % gunzip GenomeHistory_src.tar.gz If your system doesn't include gzip/gunzip, you can download the compressed archive (GenomeHistory.tar.Z), or the uncompressed archive (GenomeHistory.tar) If you downloaded the GenomeHistory binaries type: % tar xvf GenomeHistory_bin.tar Otherwise type % tar xvf GenomeHistory_src.tar Now, if you downloaded the GenomeHistory source rather than the binaries, you will need to make the package. Otherwise, skip to the step where you add GenomeHistory to your path. *****BUILDING GenomeHistory****** This will create a new directory called GenomeHistory. % cd GenomeHistory The configure.pl script will identify your compiler: % configure.pl You can now make all of the needed programs by typing % make *****ADDING GenomeHistory TO YOUR PATH****** The next step is to add GenomeHistory.pl and the other relevant programs to your path. WARNING: Changing your startup files as described below can occasionally have serious side-effects, especially if you have a complicated computing environment. You may want to ask your local wizard for help. Find out where GenomeHistory is: type: % pwd and write down the results--you will need this when you see in the instructions below First, you need to know your shell--type: % echo $SHELL You should get something like /bin/bash or /bin/tcsh Instructions for BASH shell (/bin/bash) and CSH (/bin/csh or /bin/tcsh) follow Instructions for BASH shell (/bin/bash) type % cd This will take you to your home directory. Now type % cp .bash_profile .bash_profile_GenomeHistory to save your current .bash_profile file (if you don't have one, this will generate an error--ignore it) Now type % vi .bash_profile This will open a vi screen, which may or may not be empty, depending on your current setup. (If you prefer another editor, feel free to use it.) For the following vi commands, the ` character tells you where to begin and stop typing--don't type the ` character itself. Go to the last line of the file if it is not empty and type 'a'--this will take you to insert mode. Now type 'export PATH=$PATH:' followed by the Escape key. You should see what you just typed on your screen. Type ':wq' to leave vi. type % source .bash_profile % which GenomeHistory.pl If everything has worked, the which command should tell you where you installed GenomeHistory. Otherwise, use % cp .bash_profile_GenomeHistory .bash_profile to restore your original setup Instructions for C-shell and TC-shell (/bin/csh and /bin/tcsh) type % cd This will take you to your home directory. Now type % cp .cshrc .cshrc_GenomeHistory to save your current .cshrc file (if you don't have one, this will generate an error--ignore it) Now type: % vi .cshrc This will open a vi screen, which may or may not be empty, depending on your current setup. (If you prefer another editor, feel free to use it.) For the following vi commands, the ` character tells you where to begin and stop typing--don't type the ` character itself. Go to the last line of the file if it is not empty and type 'a'--this will take you to insert mode. Now type 'set path=( $path )' followed by the Escape key. You should see what you just typed on your screen. Type ':wq' to leave vi. type % source .cshrc % which GenomeHistory.pl If everything has worked, the which command should tell you where you installed GenomeHistory. Otherwise, use % cp .cshrc_GenomeHistory .csrch to restore your original setup Please see the GenomeHistory documentation (GenomeHistory.html) for instructions and tips on using GenomeHistory Comments on basic installation process: To build and use the package, you will need a c and a c++ compiler (preferably the GNu gcc and g++), the Washington University implementation of BLAST, and clustalw. The make command will build liblapack (a partial lapack library), libf2c (because lapack was originally built in Fortran), liblikelihood and libdnafuncs (two of my libraries that have many generic functions), like_pair_dist (which calculates Ks/Ka), aligndna_new (which creates a nucleotide alignment from a protein alignment), and calc_percent_diff (which calculates the percentage difference for all pairs of sequences in an alignment). You will need to add the GenomeHistory directory to your path. You can then run the program by typing GenomeHistory.pl where is a input file with the parameters for the run. An example input file with descriptions of each command is included at GenomeHistory/test_analysis.txt Other platforms: This package was developed and tested on a RedHat 6.2 Linux machines with the gcc compilers. It should work on other platforms, but has not been tested on them. Use configure.pl or edit the file GenomeHistory/make.inc to change the name of your c and c++ compiler.