Installing Libraries for JESAM

Alignment Server Dependencies

JESAM uses three libraries that are free to academics and most developers PVM, SleepyCat's version of the BerkeleyDB routines, and OOC's ORBacus. Compiling the alignment server code requires a C, and a C++ compiler, but no Java compiler. Only the first two are needed before you can start calculating sequence overlaps. It is only the alignment publishing and clustering code that uses C++ and CORBA. Once all these libraries are compiled and installed, it is possible to start compiling the JESAM tools. Note that depending upon your compilation choices for the three libraries (static/dynamic) you may need to edit both your PATH, and LD_LIBRARY_PATH or LD_LIBRARYN32_PATH(SGI) environment variables before being able to compile or use the JESAM tools. PVM also requires access to two or three main environment variables including $PVM_ROOT, and $PVM_ARCH which must be specified during PVM library compilation.