HMMER 2.0 
Installation instructions 
SRE, Mon Jan 19 07:09:37 1998
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1) Edit the top of the Makefile. 
   Set the paths and other make variables to suit your system.

   The only variables you should need to set are BINDIR
   and MANDIR.

   If you are installing in directories called bin/ and man/ in your
   home directory, you don't need to change anything.

   If you have a source-only distribution, check the compiler (CC)
   and compiler flags (CFLAGS).

   The default Makefile is configured for cc (your vendor's compiler) 
   and -O optimization. The package builds "out of the box" on
   SGI IRIX, Sun Solaris, GNU/Linux/Intel, or DEC Alpha/Digital Unix
   platforms without any special modifications.

   On SunOS 4.1.x systems, you will have to use GNU's gcc,
   because SunOS cc is not ANSI-compliant.

   You can play with the compiler options in CFLAGS to
   try to get more speed, if you're compiler-fluent.

2) If you have a source-only distribution, type 'make' to build the programs.
   If you have a binary distribution, skip this step.

3) Optional; type 'make test' to compile and run a test suite.
   Some of the tests require that you have Perl installed.

4) type 'make install' to install the programs and man pages. 
   You may have to become root, depending on where you're installing.

5) type 'make clean' to clean up.


Note on environment variables:

   HMMER reads three environment variables:
      HMMERDB  - directory location of HMM databases (e.g. PFAM)
      BLASTDB  - directory location of FASTA-formatted sequence databases
      BLASTMAT - directory location of PAM scoring matrices

   If you have installed BLAST, you probably already have these 
   environment variables set in system-wide or user-specific
   .cshrc files. They are optional. If they are set up, you
   can simplify command lines to:
      > hmmpfam pfam my.query
      > hmmsearch my.hmm swiss35
   instead of
      > hmmpfam   /some/long/path/to/databases/pfam my.query
      > hmmsearch my.hmm /some/long/path/to/databases/swiss35

- Sean Eddy
  eddy@genetics.wustl.edu
