[WashU] HMMER
User's Guide


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Next: Environment variable configuration Up: Installation Previous: Installing a precompiled distribution

Compiling from a source-only distribution

1.
Download the distribution from http://hmmer.wustl.edu/.

2.
Uncompress and un-tar it:
> uncompress hmmer.tar.Z
> tar xf hmmer.tar
A new directory hmmer-xx is created, where ``xx'' is the HMMER version number.

3.
Go to the top level directory and run the configure script.
> cd hmmer-xx
> ./configure
If you want to include the optional PVM support, do:
> ./configure -with-pvm
If you include PVM, the system that you're compiling on must already be set up for PVM; specifically, the environment variables PVM_ROOT and PVM_ARCH must be set, so HMMER can find the PVM headers and library.

If you want to disable POSIX threads support, do:
> ./configure -disable-threads

If you want to change the choice of compilation flags (CFLAGS) or the compiler (CC), set these as environment variables:
> env CC=gcc CFLAGS="-O6" ./configure
For other generic configuration options, see the documentation for GNU autoconf 2.12. - but it may be easier to just edit the Makefile (see below).

4.
Edit the top of the Makefile.

To build and test HMMER in its source directory, you don't need to edit the Makefile at all.

To permanently install HMMER on your system, set the make variables BINDIR and MANDIR to be the directories where you want HMMER executables and man pages to be installed. If you are installing the programs in /usr/local/bin and the man pages in /usr/local/man/man1, you don't need to change anything.

The default Makefile gets configured into a reliable but not necessarily optimal choice of compiler and compilation flags. The package is known to build "out of the box" on SGI IRIX, Sun Solaris, GNU/Linux, FreeBSD, or DEC Digital Unix platforms without any special modifications. However, you may want to change the CC or CFLAGS variables to suit your system. In particular, you can play with the compiler options in CFLAGS to try to get more speed, if you're compiler-fluent. The Makefile includes some hints for various platforms.

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

5.
Type make to build the programs.

6.
(Optional) Type make check to compile and run a test suite. Some of the tests require that you have Perl installed. None of these tests should fail.

7.
Type make install to install the programs and man pages. You may have to become root, depending on where you're installing.

8.
Type make clean to clean up.


next up previous contents
Next: Environment variable configuration Up: Installation Previous: Installing a precompiled distribution


Direct comments and questions to <eddy@genetics.wustl.edu>