RAPID is a software package that can compute pairwise identity by descent and perform linkage analysis for individuals in very large and complex pedigrees. All code is written in ISO C99 and should compile on any platform with a compliant compiler. Building RAPID is very simple and can be done by typing the command './build_rapid.sh' in the directory that contains this INSTALL file, but, for optimal speed, RAPID should be built to use the ATLAS numerical libraries. Following are instructions to install both ATLAS and RAPID. If you are unwilling or unable to install ATLAS, skip past the 'External libraries' section. External libraries ================== Although the program can be built with no external dependencies, computation time can be considerably shorter if CBLAS and CLAPACK numerical libraries are available. A freely available implementation of these is the ATLAS project. The default installation assumes that ATLAS has already been installed and is available. Some platforms already have ATLAS based libraries available with no additional work for the user, in which case installing ATLAS is optional, though you may still need to figure out where your CBLAS and CLAPACK libraries are installed. Macs running OS X, for instance, have these libraries available and do not need to install ATLAS (although you can get a more optimized, faster version by installing it yourself). A. Using already installed libraries. If you are on Mac OS X and do not wish to install ATLAS, execute the command './build_rapid.sh', answer the questions, and RAPID will be installed (ie you are done and ready to use the program). If you are on any other platform and with to use an already installed ATLAS, figure out the directory where libatlas.a is and the directory where cblas.h is, take note of these, then execute the command './build_rapid.sh', answer the questions, and you are done and ready to use the program. If you are not on Mac OS X and wish to use a non-ATLAS implementation of CBLAS and CLAPACK, you must figure out where the libraries and header files are, then you can use './build_rapid.sh' to install RAPID. I cannot guarantee that RAPID will build correctly or even that it will run properly in this case, so I don't recommend this final option. B. Installing ATLAS yourself. To install ATLAS, go to http://math-atlas.sourceforge.net and download the latest version. Do not be intimidated by the rather lengthy installation instructions on the web site! You can, in fact, get a perfectly good installation very simply. If you want to eke out every last bit of performance, go ahead and read the instructions. The following instructions work for ATLAS version 3.8.0 and should work with a reasonably recent version of the gcc compiler, and possibly other compilers as well. After downloading, type in the following commands in a terminal application from the directory containing the ATLAS package you downloaded. (The % is the computer prompt and should not be typed.) % gunzip -c atlas3.8.0.tar.gz | tar xvf - % cd ATLAS % mkdir Build % cd Build % ../configure --nof77 --prefix=~/ATLAS3.8.0 % make build % make check % make install The 'make check' step is actually optional, but it will allow you to verify that the library built correctly. A different directory may be specified after the '--prefix=' argument (ie instead of ~/ATLAS3.8.0), but remember what this is as it will be used when building RAPID. Build RAPID =========== If you have the gcc compiler (almost certainly the case for Linux, Mac, and most types of Unix), then from the directory that contains this file type the command: ./build_rapid.sh You will be asked whether you have ATLAS installed. If you installed ATLAS, the directory that that has the ATLAS libraries and header files will be '~/ATLAS3.8.0/lib' and '~/ATLAS3.8.0/include', respectively. If you specified a different directory after the '--prefix=' option while installing ATLAS, substitute this directory for '~/ATLAS3.8.0'. You should end up with an executable file called 'rapid', which may be moved to anywhere you see fit. If you did not install ATLAS, just answer 'no' and RAPID will be built without it. If you use a compiler other than gcc, you will have to edit Makefile to specify the correct compiler and options.