HMMER 1.8
Installation instructions 
Sean Eddy, 16 April 1995
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Obtaining and unpacking a distribution:
---------------------------------------

The current version of the HMMER source distribution can be obtained
by anonymous FTP from ftp://genome.wustl.edu/pub/eddy/hmmer.tar.Z. To
choose and download a precompiled version for your machine, see
http://genome.wustl.edu/eddy/hmmer.html.

hmmer.tar.Z or a precompiled distribution like hmmer-sgi-irix62.tar.Z
are compressed UNIX tar files. To unpack:
 	> uncompress hmmer.tar.Z
	> tar xf hmmer.tar.Z
You will now see a new directory called hmmer-1.8.3 or something
similar. Go into it (if you're reading this, you're probably already
there...)



Installing a precompiled executable distribution:
-------------------------------------------------

You don't need to do anything; the programs are ready to run. Read
Userguide.ps (a PostScript file) to see a tutorial and some demos.

To install the HMMER programs and man pages permanently on your
system, follow steps 1), 3), and 4) below.



Compiling a source code distribution:
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1) Edit the top of the Makefile. 
   Set the installation paths to suit your system.
   Generally you should not need to do any other configuration.
   For SunOS, you need to specify an ANSI-compliant compiler such as gcc.

2) type 'make' to build the programs.

3) type 'make test' to run a battery of exercises on the
   programs. You need Perl installed to do this. Running
   the tests is optional, but you may find it comforting
   to see that the programs run and pass some rudimentary
   checks.

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

   Note on man pages: If you can install unformatted man pages,
   set INSTMAN to be "cp" in the Makefile. If you can't -- for
   instance, many SGIs don't have nroff installed -- I've
   provided my Perl script "instman.pl" that uses the same
   command-line syntax as cp, but uses groff to format the
   .man file before installing it.
 
4) type 'make clean' to clean up.

   And if you haven't already, print out the User's Guide, Userguide.ps,
   using "lpr" or whatever you do to print PostScript documents:

5) lpr Userguide.ps


### Note on environment variables:

   HMMER reads two environment variables:
      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:
      > hmmls my.hmm swiss31
   instead of
      > hmmls my.hmm /some/long/path/to/databases/swiss31

### Notes on compilation and portability:

This code should compile on any UNIX platform without modification
simply by unpacking it and typing `make'. If it does not, please
report it as a bug. I have tested this version on the following
platforms:

	  SGI Indigo2       	IRIX 6.2
	  Sun UltraSparc 1  	Solaris 5.5
	  DEC Alpha 3000/500	OSF/1 5.60
	  Intel Pentium PC  	Linux 2.0.18

HMMER has also been reported to compile with minor modifications on
MacOS, DOS/Win95, and VAX platforms. However, I don't have access to
any of these platforms and so I don't promise anything about them.

The code is currently maintained under IRIX 6.2 on an Indigo2 R4400.

- Sean Eddy
  eddy@genetics.wustl.edu
   
