February 21, 1992 Installation instructions for the BLAST application and utility programs. o Start by installing the skeletal ncbi library posted beneath /pub/ncbi, or installing the complete library posted in /toolbox/ncbi_tools/ncbi.tar.Z. The skeletal library contains just C language header files for various computing platforms, as it is unnecessary at this time to use any object files from the ncbi library to link the BLAST application programs. Read the installation instructions that accompany either version of the library. The complete library is posted with a separate PostScript-format documentation file. o FTP the source code for the "gish" and "dfa" libraries from the directories "/pub/gish" and "/pub/dfa" respectively. Follow the installation instructions provided with those libraries. o As necessary, edit the blast Makefile in order to: indicate which of the compile-time options you wish to enable: REFINED_STATS -- perform more precise statistical estimates (recommended) USE_SHM -- support for shared memory database files using System V interprocess communication facilities. This requires that the SYSV_SHM_AVAIL macro be defined in the ncbilcl.h header provided by the ncbi library. USE_MPROC -- support for multiprocessing (only on Silicon Graphics Inc. IRIX 3.3+ and 4.0+ platforms). CLEAN8MERS -- weed out uninformative 8-mers from nucleotide query sequences in BLASTN. Do not define the USE_SHM or USE_MPROC macros in the Makefile unless your computing platform supports these options. adapt the Makefile to wherever you may have installed the ncbi, gish, and dfa libraries; as provided, the Makefiles expect these libraries to be located relative to the blast directory in ../ncbi, ../gish, and ../dfa; these expected locations can be changed by changing the Makefile settings for the variables NCBI, GISH, and DFA. o If you wish to maintain the BLAST databases and substitution matrix files in directories other than the defaults (/usr/ncbi/blast/db and /usr/ncbi/blast/pam, respectively), edit the BLASTDB and BLASTPAM macros defined in the header file include/blast.h. The user can override these defaults by setting the environment variables BLASTDB and BLASTPAM to whichever directories they wish, but regardless, the BLAST programs will still look first in the user's current working directory for database and substitition matrix files. #define BLASTDB /usr/ncbi/blast/db #define BLASTPAM /usr/ncbi/blast/pam o After the ncbi, gish, and dfa libraries have been made, do a "make depend" then "make all" in the blast directory. o Read the introductory comments in setdb.c and pressdb.c to see how databases are prepared for searching with the BLAST application programs. o See the blast.1 and blast3.1 manual pages for instructions on using the BLAST application programs.