INSTALL

Brief installation instructions 
HMMER 3.0; March 2010
SRE, Mon Mar 24 09:29:34 2008
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These are quick installation instructions. For complete documentation,
including customization and troubleshooting, see the Installation
chapter in the HMMER User's Guide (Userguide.pdf).

Starting from a source distribution, hmmer-3.0.tar.gz:
 uncompress:                uncompress hmmer-3.0.tar.gz  
 unpack:                    tar xf hmmer-3.0.tar
 move into new directory:   cd hmmer-3.0
 configure:                 ./configure
 build:                     make
 automated tests:           make check
 automated install:         make install

HMMER is developed primarily on Linux and Mac OS/X systems. It is
tested on a variety of UNIX and UNIX-like operating systems. It is
written in ANSI C99 conforming to POSIX standards. It is meant to be
portable to any POSIX-compliant system with an ANSI C99 compiler,
including all UNIX and Macintosh systems. It should also build on
Windows systems with optional POSIX compatibility software installed,
such as Cygwin.

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Starting from a Subversion (SVN) working copy:

If you have checked HMMER out from its Subversion repository, there's
some additional stuff you need to do one-time-only in your new working
directory:

   ln -s easel/aclocal.m4 aclocal.m4
   autoconf
   (cd easel; autoconf)

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Brief notes on different ways we configure HMMER during development:

for production:      ./configure CC=icc LDFLAGS="-static"
   icc (Intel C compiler) is best, for optimal performance

for debugging:       ./configure --enable-debugging

for profiling:       ./configure CFLAGS="-g -pg -O"
                     make
                     (run benchmark program; then gprof the program)

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The HMMER development team
HHMI Janelia Farm Research Campus
http://hmmer.org/