Installation instructions

1. Edit the top of the Makefile.

   Set the paths and other make variables to suit your system. The default Makefile is configured for SGI IRIX or DEC Alpha OSF/1 platforms, using the vendor's cc compiler. However, it is easily reconfigured for other UNIX systems and other compilers. Just follow the instructions in the Makefile. For SunOS, you need to specify an ANSI-compliant compiler such as gcc. For Solaris, you need to specify the -DNORANDOM cflag, as instructed in the Makefile.

2. type 'make' to build the programs
3. type 'make test' to run a battery of exercises on the programs. You need Perl to do this. If Perl is not in /usr/local/bin/perl you will have to change the path in the first line of the script Testsuite/Run_Tests. 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.

5. 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:

6. lpr Userguide.ps

This package has been built and tested on the following systems:

• Sun SPARCstations running SunOS 4.1.x and Solaris 2.x
• Silicon Graphics Indigo and 340/VGX running IRIX 4.0.x and 5.x
• DEC 5000 running Ultrix 4.2
• DEC Alphas running OSF/1
• Alliant FX/2800 running Concentrix 2.2

I expect it should build on any UNIX platform; if it doesn't, email me, and I'll fix it.

I would port it to Mac, PC, and VAX platforms, except that I don't have access to any of these machines and I have no experience with them. There are few UNIX-specific functions in the package so it should be straightforward to port to other ANSI C environments. Email me if you're interested in running the HMM code on a non-UNIX platform.

HMMER is currently maintained under IRIX on an Indigo2 R4400.