April 14, 1993

Installation instructions for the BLAST application and utility programs.

o Start by installing a skeletal version of the NCBI core library that is
posted beneath /pub/ncbi.  (The complete NCBI core library is posted in
/toolbox/ncbi_tools/ncbi.tar.Z, but its version may be incompatible with the
posted BLAST software).  The skeletal library presently contains only C
language header (.h) files to adapt the BLAST software to various computing
platforms; it is unnecessary at this time to use any object files from the core
library to link the BLAST application programs.  Be sure to read the
installation instructions that accompany the skeletal library.

Some computing platforms offer symmetric multiprocessing (SMP) capabilities
with different application programming interfaces.  At the time of this writing,
the list of platforms for which the NCBI provides at least marginal support for
SMP in the BLAST programs includes:  Silicon Graphics, Inc., IRIX; SunSoft
Solaris 2.2; and Digital Equipment Corp. OSF/1.  In order to activate or employ
this feature in the BLAST programs, the MPROC_AVAIL macro must have been
previously #defined in the platform-specific ncbilcl.h file prior to compiling
and linking the source code distributed in the "gish" and "blast" archives.
(Again, see the instructions for installing the skeletal ncbi library).


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 Individual Makefiles are provided for a few computing platforms, including a
"generic" Makefile named "Makefile.gen".  As may be necessary, edit the
appropriate blast Makefile in order to:

  indicate which of the compile-time options you wish to enable:

     REFINED_STATS -- perform more precise statistical estimates (recommended)

     CLEAN8MERS -- weed out uninformative 8-mers from nucleotide query
                   sequences in BLASTN.

  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.

  If multiprocessing or multithreads are to be used, set the MPLIB make
  variable to an appropriate directive (e.g., "-lthreads") with which to
  link the programs on your multiprocessing computing platform; otherwise,
  leave the MPLIB variable unset.  (See also the installation instructions for
  the skeletal ncbi core library).


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/matrix, respectively), edit the BLASTDB and BLASTMAT (formerly
called BLASTPAM) macros defined in the header file include/blastapp.h.  The
user can override these defaults by setting the environment variables BLASTDB
and BLASTMAT to whichever directories they wish but, regardless, the BLAST
programs will still look first in the user's current working directory for
database and substitution matrix files.

  #define BLASTDB "/usr/ncbi/blast/db/"
  #define BLASTMAT "/usr/ncbi/blast/matrix/"

The terminal / on these path names is important!

o After the ncbi, gish, and dfa libraries have been made (in that order), issue
a "make -f Makefile depend" then "make all" in the blast directory.  On some
systems, the "make depend" may fail horribly; in any case, the "make depend"
step can be skipped if desired.

o Install the substitution matrix files distributed beneath the matrix
subdirectory.  (See above for a description of their proper installed
location).

o Read the introductory comments in setdb.c and pressdb.c to see how databases
are prepared for searching with the BLAST application programs.  Input to the
"setdb" and "pressdb" programs must be in FASTA format.  The utility programs
"gb2fasta", "pir2fasta", "sp2fasta", and "gt2fasta" are provided to reformat
the sequence records from GenBank, PIR, SWISS-PROT and EMBL flat files into
FASTA format, for subsequent processing by "setdb" and "pressdb".

o See the blast.1 and blast3.1 manual pages for instructions on using the BLAST
application programs.  These files are in UNIX manual page format.  PostScript
versions are also available in the files blast.1ps and blast.3ps.