8 Clustal-Omega needs argtable2 (http://argtable.sourceforge.net/). If
9 argtable2 is installed in a non-standard directory you might have to
10 point configure to its installation directory. For example, if you are
11 on a Mac and have argtable installed via MacPorts then you should use
12 the following command line:
14 $ ./configure CFLAGS='-I/opt/local/include' LDFLAGS='-L/opt/local/lib'
16 ClustalO will automatically support multi-threading if your compiler
17 supports OpenMP. For some reason automake's OpenMP detection for
18 Apple's gcc is broken. You can force OpenMP detection by calling configure
21 $ ./configure OPENMP_CFLAGS='-fopenmp' CFLAGS='-DHAVE_OPENMP'
23 You could use a non-Apple gcc installed via MacPorts, adding
25 CC=/opt/local/bin/gcc-mp-4.5
27 to the configure call (you will have to change the exact string to match
30 See below for generic installation instructions:
32 ----------------------------------------------------------------------
36 Installation Instructions
37 *************************
39 Copyright (C) 1994, 1995, 1996, 1999, 2000, 2001, 2002, 2004, 2005,
40 2006, 2007, 2008, 2009 Free Software Foundation, Inc.
42 Copying and distribution of this file, with or without modification,
43 are permitted in any medium without royalty provided the copyright
44 notice and this notice are preserved. This file is offered as-is,
45 without warranty of any kind.
50 Briefly, the shell commands `./configure; make; make install' should
51 configure, build, and install this package. The following
52 more-detailed instructions are generic; see the `README' file for
53 instructions specific to this package. Some packages provide this
54 `INSTALL' file but do not implement all of the features documented
55 below. The lack of an optional feature in a given package is not
56 necessarily a bug. More recommendations for GNU packages can be found
57 in *note Makefile Conventions: (standards)Makefile Conventions.
59 The `configure' shell script attempts to guess correct values for
60 various system-dependent variables used during compilation. It uses
61 those values to create a `Makefile' in each directory of the package.
62 It may also create one or more `.h' files containing system-dependent
63 definitions. Finally, it creates a shell script `config.status' that
64 you can run in the future to recreate the current configuration, and a
65 file `config.log' containing compiler output (useful mainly for
66 debugging `configure').
68 It can also use an optional file (typically called `config.cache'
69 and enabled with `--cache-file=config.cache' or simply `-C') that saves
70 the results of its tests to speed up reconfiguring. Caching is
71 disabled by default to prevent problems with accidental use of stale
74 If you need to do unusual things to compile the package, please try
75 to figure out how `configure' could check whether to do them, and mail
76 diffs or instructions to the address given in the `README' so they can
77 be considered for the next release. If you are using the cache, and at
78 some point `config.cache' contains results you don't want to keep, you
79 may remove or edit it.
81 The file `configure.ac' (or `configure.in') is used to create
82 `configure' by a program called `autoconf'. You need `configure.ac' if
83 you want to change it or regenerate `configure' using a newer version
86 The simplest way to compile this package is:
88 1. `cd' to the directory containing the package's source code and type
89 `./configure' to configure the package for your system.
91 Running `configure' might take a while. While running, it prints
92 some messages telling which features it is checking for.
94 2. Type `make' to compile the package.
96 3. Optionally, type `make check' to run any self-tests that come with
97 the package, generally using the just-built uninstalled binaries.
99 4. Type `make install' to install the programs and any data files and
100 documentation. When installing into a prefix owned by root, it is
101 recommended that the package be configured and built as a regular
102 user, and only the `make install' phase executed with root
105 5. Optionally, type `make installcheck' to repeat any self-tests, but
106 this time using the binaries in their final installed location.
107 This target does not install anything. Running this target as a
108 regular user, particularly if the prior `make install' required
109 root privileges, verifies that the installation completed
112 6. You can remove the program binaries and object files from the
113 source code directory by typing `make clean'. To also remove the
114 files that `configure' created (so you can compile the package for
115 a different kind of computer), type `make distclean'. There is
116 also a `make maintainer-clean' target, but that is intended mainly
117 for the package's developers. If you use it, you may have to get
118 all sorts of other programs in order to regenerate files that came
119 with the distribution.
121 7. Often, you can also type `make uninstall' to remove the installed
122 files again. In practice, not all packages have tested that
123 uninstallation works correctly, even though it is required by the
124 GNU Coding Standards.
126 8. Some packages, particularly those that use Automake, provide `make
127 distcheck', which can by used by developers to test that all other
128 targets like `make install' and `make uninstall' work correctly.
129 This target is generally not run by end users.
131 Compilers and Options
132 =====================
134 Some systems require unusual options for compilation or linking that
135 the `configure' script does not know about. Run `./configure --help'
136 for details on some of the pertinent environment variables.
138 You can give `configure' initial values for configuration parameters
139 by setting variables in the command line or in the environment. Here
142 ./configure CC=c99 CFLAGS=-g LIBS=-lposix
144 *Note Defining Variables::, for more details.
146 Compiling For Multiple Architectures
147 ====================================
149 You can compile the package for more than one kind of computer at the
150 same time, by placing the object files for each architecture in their
151 own directory. To do this, you can use GNU `make'. `cd' to the
152 directory where you want the object files and executables to go and run
153 the `configure' script. `configure' automatically checks for the
154 source code in the directory that `configure' is in and in `..'. This
155 is known as a "VPATH" build.
157 With a non-GNU `make', it is safer to compile the package for one
158 architecture at a time in the source code directory. After you have
159 installed the package for one architecture, use `make distclean' before
160 reconfiguring for another architecture.
162 On MacOS X 10.5 and later systems, you can create libraries and
163 executables that work on multiple system types--known as "fat" or
164 "universal" binaries--by specifying multiple `-arch' options to the
165 compiler but only a single `-arch' option to the preprocessor. Like
168 ./configure CC="gcc -arch i386 -arch x86_64 -arch ppc -arch ppc64" \
169 CXX="g++ -arch i386 -arch x86_64 -arch ppc -arch ppc64" \
170 CPP="gcc -E" CXXCPP="g++ -E"
172 This is not guaranteed to produce working output in all cases, you
173 may have to build one architecture at a time and combine the results
174 using the `lipo' tool if you have problems.
179 By default, `make install' installs the package's commands under
180 `/usr/local/bin', include files under `/usr/local/include', etc. You
181 can specify an installation prefix other than `/usr/local' by giving
182 `configure' the option `--prefix=PREFIX', where PREFIX must be an
185 You can specify separate installation prefixes for
186 architecture-specific files and architecture-independent files. If you
187 pass the option `--exec-prefix=PREFIX' to `configure', the package uses
188 PREFIX as the prefix for installing programs and libraries.
189 Documentation and other data files still use the regular prefix.
191 In addition, if you use an unusual directory layout you can give
192 options like `--bindir=DIR' to specify different values for particular
193 kinds of files. Run `configure --help' for a list of the directories
194 you can set and what kinds of files go in them. In general, the
195 default for these options is expressed in terms of `${prefix}', so that
196 specifying just `--prefix' will affect all of the other directory
197 specifications that were not explicitly provided.
199 The most portable way to affect installation locations is to pass the
200 correct locations to `configure'; however, many packages provide one or
201 both of the following shortcuts of passing variable assignments to the
202 `make install' command line to change installation locations without
203 having to reconfigure or recompile.
205 The first method involves providing an override variable for each
206 affected directory. For example, `make install
207 prefix=/alternate/directory' will choose an alternate location for all
208 directory configuration variables that were expressed in terms of
209 `${prefix}'. Any directories that were specified during `configure',
210 but not in terms of `${prefix}', must each be overridden at install
211 time for the entire installation to be relocated. The approach of
212 makefile variable overrides for each directory variable is required by
213 the GNU Coding Standards, and ideally causes no recompilation.
214 However, some platforms have known limitations with the semantics of
215 shared libraries that end up requiring recompilation when using this
216 method, particularly noticeable in packages that use GNU Libtool.
218 The second method involves providing the `DESTDIR' variable. For
219 example, `make install DESTDIR=/alternate/directory' will prepend
220 `/alternate/directory' before all installation names. The approach of
221 `DESTDIR' overrides is not required by the GNU Coding Standards, and
222 does not work on platforms that have drive letters. On the other hand,
223 it does better at avoiding recompilation issues, and works well even
224 when some directory options were not specified in terms of `${prefix}'
230 If the package supports it, you can cause programs to be installed
231 with an extra prefix or suffix on their names by giving `configure' the
232 option `--program-prefix=PREFIX' or `--program-suffix=SUFFIX'.
234 Some packages pay attention to `--enable-FEATURE' options to
235 `configure', where FEATURE indicates an optional part of the package.
236 They may also pay attention to `--with-PACKAGE' options, where PACKAGE
237 is something like `gnu-as' or `x' (for the X Window System). The
238 `README' should mention any `--enable-' and `--with-' options that the
241 For packages that use the X Window System, `configure' can usually
242 find the X include and library files automatically, but if it doesn't,
243 you can use the `configure' options `--x-includes=DIR' and
244 `--x-libraries=DIR' to specify their locations.
246 Some packages offer the ability to configure how verbose the
247 execution of `make' will be. For these packages, running `./configure
248 --enable-silent-rules' sets the default to minimal output, which can be
249 overridden with `make V=1'; while running `./configure
250 --disable-silent-rules' sets the default to verbose, which can be
251 overridden with `make V=0'.
256 On HP-UX, the default C compiler is not ANSI C compatible. If GNU
257 CC is not installed, it is recommended to use the following options in
258 order to use an ANSI C compiler:
260 ./configure CC="cc -Ae -D_XOPEN_SOURCE=500"
262 and if that doesn't work, install pre-built binaries of GCC for HP-UX.
264 On OSF/1 a.k.a. Tru64, some versions of the default C compiler cannot
265 parse its `<wchar.h>' header file. The option `-nodtk' can be used as
266 a workaround. If GNU CC is not installed, it is therefore recommended
271 and if that doesn't work, try
273 ./configure CC="cc -nodtk"
275 On Solaris, don't put `/usr/ucb' early in your `PATH'. This
276 directory contains several dysfunctional programs; working variants of
277 these programs are available in `/usr/bin'. So, if you need `/usr/ucb'
278 in your `PATH', put it _after_ `/usr/bin'.
280 On Haiku, software installed for all users goes in `/boot/common',
281 not `/usr/local'. It is recommended to use the following options:
283 ./configure --prefix=/boot/common
285 Specifying the System Type
286 ==========================
288 There may be some features `configure' cannot figure out
289 automatically, but needs to determine by the type of machine the package
290 will run on. Usually, assuming the package is built to be run on the
291 _same_ architectures, `configure' can figure that out, but if it prints
292 a message saying it cannot guess the machine type, give it the
293 `--build=TYPE' option. TYPE can either be a short name for the system
294 type, such as `sun4', or a canonical name which has the form:
298 where SYSTEM can have one of these forms:
303 See the file `config.sub' for the possible values of each field. If
304 `config.sub' isn't included in this package, then this package doesn't
305 need to know the machine type.
307 If you are _building_ compiler tools for cross-compiling, you should
308 use the option `--target=TYPE' to select the type of system they will
311 If you want to _use_ a cross compiler, that generates code for a
312 platform different from the build platform, you should specify the
313 "host" platform (i.e., that on which the generated programs will
314 eventually be run) with `--host=TYPE'.
319 If you want to set default values for `configure' scripts to share,
320 you can create a site shell script called `config.site' that gives
321 default values for variables like `CC', `cache_file', and `prefix'.
322 `configure' looks for `PREFIX/share/config.site' if it exists, then
323 `PREFIX/etc/config.site' if it exists. Or, you can set the
324 `CONFIG_SITE' environment variable to the location of the site script.
325 A warning: not all `configure' scripts look for a site script.
330 Variables not defined in a site shell script can be set in the
331 environment passed to `configure'. However, some packages may run
332 configure again during the build, and the customized values of these
333 variables may be lost. In order to avoid this problem, you should set
334 them in the `configure' command line, using `VAR=value'. For example:
336 ./configure CC=/usr/local2/bin/gcc
338 causes the specified `gcc' to be used as the C compiler (unless it is
339 overridden in the site shell script).
341 Unfortunately, this technique does not work for `CONFIG_SHELL' due to
342 an Autoconf bug. Until the bug is fixed you can use this workaround:
344 CONFIG_SHELL=/bin/bash /bin/bash ./configure CONFIG_SHELL=/bin/bash
346 `configure' Invocation
347 ======================
349 `configure' recognizes the following options to control how it
354 Print a summary of all of the options to `configure', and exit.
358 Print a summary of the options unique to this package's
359 `configure', and exit. The `short' variant lists options used
360 only in the top level, while the `recursive' variant lists options
361 also present in any nested packages.
365 Print the version of Autoconf used to generate the `configure'
369 Enable the cache: use and save the results of the tests in FILE,
370 traditionally `config.cache'. FILE defaults to `/dev/null' to
375 Alias for `--cache-file=config.cache'.
380 Do not print messages saying which checks are being made. To
381 suppress all normal output, redirect it to `/dev/null' (any error
382 messages will still be shown).
385 Look for the package's source code in directory DIR. Usually
386 `configure' can determine that directory automatically.
389 Use DIR as the installation prefix. *note Installation Names::
390 for more details, including other options available for fine-tuning
391 the installation locations.
395 Run the configure checks, but stop before creating any output
398 `configure' also accepts some other, not widely useful, options. Run
399 `configure --help' for more details.