--- /dev/null
+The impatient can try:\r
+\r
+$ ./configure\r
+$ make\r
+$ make install\r
+\r
+\r
+Clustal-Omega needs argtable2 (http://argtable.sourceforge.net/). If\r
+argtable2 is installed in a non-standard directory you might have to\r
+point configure to its installation directory. For example, if you are\r
+on a Mac and have argtable installed via MacPorts then you should use\r
+the following command line:\r
+\r
+$ ./configure CFLAGS='-I/opt/local/include' LDFLAGS='-L/opt/local/lib'\r
+\r
+ClustalO will automatically support multi-threading if your compiler\r
+supports OpenMP. For some reason automake's OpenMP detection for\r
+Apple's gcc is broken. You can force OpenMP detection by calling configure \r
+like so:\r
+\r
+$ ./configure OPENMP_CFLAGS='-fopenmp' CFLAGS='-DHAVE_OPENMP'\r
+\r
+You could use a non-Apple gcc installed via MacPorts, adding\r
+\r
+CC=/opt/local/bin/gcc-mp-4.5\r
+\r
+to the configure call (you will have to change the exact string to match\r
+your gcc version).\r
+\r
+See below for generic installation instructions:\r
+\r
+----------------------------------------------------------------------\r
+\r
+\r
+\r
+Installation Instructions\r
+*************************\r
+\r
+Copyright (C) 1994, 1995, 1996, 1999, 2000, 2001, 2002, 2004, 2005,\r
+2006, 2007, 2008, 2009 Free Software Foundation, Inc.\r
+\r
+ Copying and distribution of this file, with or without modification,\r
+are permitted in any medium without royalty provided the copyright\r
+notice and this notice are preserved. This file is offered as-is,\r
+without warranty of any kind.\r
+\r
+Basic Installation\r
+==================\r
+\r
+ Briefly, the shell commands `./configure; make; make install' should\r
+configure, build, and install this package. The following\r
+more-detailed instructions are generic; see the `README' file for\r
+instructions specific to this package. Some packages provide this\r
+`INSTALL' file but do not implement all of the features documented\r
+below. The lack of an optional feature in a given package is not\r
+necessarily a bug. More recommendations for GNU packages can be found\r
+in *note Makefile Conventions: (standards)Makefile Conventions.\r
+\r
+ The `configure' shell script attempts to guess correct values for\r
+various system-dependent variables used during compilation. It uses\r
+those values to create a `Makefile' in each directory of the package.\r
+It may also create one or more `.h' files containing system-dependent\r
+definitions. Finally, it creates a shell script `config.status' that\r
+you can run in the future to recreate the current configuration, and a\r
+file `config.log' containing compiler output (useful mainly for\r
+debugging `configure').\r
+\r
+ It can also use an optional file (typically called `config.cache'\r
+and enabled with `--cache-file=config.cache' or simply `-C') that saves\r
+the results of its tests to speed up reconfiguring. Caching is\r
+disabled by default to prevent problems with accidental use of stale\r
+cache files.\r
+\r
+ If you need to do unusual things to compile the package, please try\r
+to figure out how `configure' could check whether to do them, and mail\r
+diffs or instructions to the address given in the `README' so they can\r
+be considered for the next release. If you are using the cache, and at\r
+some point `config.cache' contains results you don't want to keep, you\r
+may remove or edit it.\r
+\r
+ The file `configure.ac' (or `configure.in') is used to create\r
+`configure' by a program called `autoconf'. You need `configure.ac' if\r
+you want to change it or regenerate `configure' using a newer version\r
+of `autoconf'.\r
+\r
+ The simplest way to compile this package is:\r
+\r
+ 1. `cd' to the directory containing the package's source code and type\r
+ `./configure' to configure the package for your system.\r
+\r
+ Running `configure' might take a while. While running, it prints\r
+ some messages telling which features it is checking for.\r
+\r
+ 2. Type `make' to compile the package.\r
+\r
+ 3. Optionally, type `make check' to run any self-tests that come with\r
+ the package, generally using the just-built uninstalled binaries.\r
+\r
+ 4. Type `make install' to install the programs and any data files and\r
+ documentation. When installing into a prefix owned by root, it is\r
+ recommended that the package be configured and built as a regular\r
+ user, and only the `make install' phase executed with root\r
+ privileges.\r
+\r
+ 5. Optionally, type `make installcheck' to repeat any self-tests, but\r
+ this time using the binaries in their final installed location.\r
+ This target does not install anything. Running this target as a\r
+ regular user, particularly if the prior `make install' required\r
+ root privileges, verifies that the installation completed\r
+ correctly.\r
+\r
+ 6. You can remove the program binaries and object files from the\r
+ source code directory by typing `make clean'. To also remove the\r
+ files that `configure' created (so you can compile the package for\r
+ a different kind of computer), type `make distclean'. There is\r
+ also a `make maintainer-clean' target, but that is intended mainly\r
+ for the package's developers. If you use it, you may have to get\r
+ all sorts of other programs in order to regenerate files that came\r
+ with the distribution.\r
+\r
+ 7. Often, you can also type `make uninstall' to remove the installed\r
+ files again. In practice, not all packages have tested that\r
+ uninstallation works correctly, even though it is required by the\r
+ GNU Coding Standards.\r
+\r
+ 8. Some packages, particularly those that use Automake, provide `make\r
+ distcheck', which can by used by developers to test that all other\r
+ targets like `make install' and `make uninstall' work correctly.\r
+ This target is generally not run by end users.\r
+\r
+Compilers and Options\r
+=====================\r
+\r
+ Some systems require unusual options for compilation or linking that\r
+the `configure' script does not know about. Run `./configure --help'\r
+for details on some of the pertinent environment variables.\r
+\r
+ You can give `configure' initial values for configuration parameters\r
+by setting variables in the command line or in the environment. Here\r
+is an example:\r
+\r
+ ./configure CC=c99 CFLAGS=-g LIBS=-lposix\r
+\r
+ *Note Defining Variables::, for more details.\r
+\r
+Compiling For Multiple Architectures\r
+====================================\r
+\r
+ You can compile the package for more than one kind of computer at the\r
+same time, by placing the object files for each architecture in their\r
+own directory. To do this, you can use GNU `make'. `cd' to the\r
+directory where you want the object files and executables to go and run\r
+the `configure' script. `configure' automatically checks for the\r
+source code in the directory that `configure' is in and in `..'. This\r
+is known as a "VPATH" build.\r
+\r
+ With a non-GNU `make', it is safer to compile the package for one\r
+architecture at a time in the source code directory. After you have\r
+installed the package for one architecture, use `make distclean' before\r
+reconfiguring for another architecture.\r
+\r
+ On MacOS X 10.5 and later systems, you can create libraries and\r
+executables that work on multiple system types--known as "fat" or\r
+"universal" binaries--by specifying multiple `-arch' options to the\r
+compiler but only a single `-arch' option to the preprocessor. Like\r
+this:\r
+\r
+ ./configure CC="gcc -arch i386 -arch x86_64 -arch ppc -arch ppc64" \\r
+ CXX="g++ -arch i386 -arch x86_64 -arch ppc -arch ppc64" \\r
+ CPP="gcc -E" CXXCPP="g++ -E"\r
+\r
+ This is not guaranteed to produce working output in all cases, you\r
+may have to build one architecture at a time and combine the results\r
+using the `lipo' tool if you have problems.\r
+\r
+Installation Names\r
+==================\r
+\r
+ By default, `make install' installs the package's commands under\r
+`/usr/local/bin', include files under `/usr/local/include', etc. You\r
+can specify an installation prefix other than `/usr/local' by giving\r
+`configure' the option `--prefix=PREFIX', where PREFIX must be an\r
+absolute file name.\r
+\r
+ You can specify separate installation prefixes for\r
+architecture-specific files and architecture-independent files. If you\r
+pass the option `--exec-prefix=PREFIX' to `configure', the package uses\r
+PREFIX as the prefix for installing programs and libraries.\r
+Documentation and other data files still use the regular prefix.\r
+\r
+ In addition, if you use an unusual directory layout you can give\r
+options like `--bindir=DIR' to specify different values for particular\r
+kinds of files. Run `configure --help' for a list of the directories\r
+you can set and what kinds of files go in them. In general, the\r
+default for these options is expressed in terms of `${prefix}', so that\r
+specifying just `--prefix' will affect all of the other directory\r
+specifications that were not explicitly provided.\r
+\r
+ The most portable way to affect installation locations is to pass the\r
+correct locations to `configure'; however, many packages provide one or\r
+both of the following shortcuts of passing variable assignments to the\r
+`make install' command line to change installation locations without\r
+having to reconfigure or recompile.\r
+\r
+ The first method involves providing an override variable for each\r
+affected directory. For example, `make install\r
+prefix=/alternate/directory' will choose an alternate location for all\r
+directory configuration variables that were expressed in terms of\r
+`${prefix}'. Any directories that were specified during `configure',\r
+but not in terms of `${prefix}', must each be overridden at install\r
+time for the entire installation to be relocated. The approach of\r
+makefile variable overrides for each directory variable is required by\r
+the GNU Coding Standards, and ideally causes no recompilation.\r
+However, some platforms have known limitations with the semantics of\r
+shared libraries that end up requiring recompilation when using this\r
+method, particularly noticeable in packages that use GNU Libtool.\r
+\r
+ The second method involves providing the `DESTDIR' variable. For\r
+example, `make install DESTDIR=/alternate/directory' will prepend\r
+`/alternate/directory' before all installation names. The approach of\r
+`DESTDIR' overrides is not required by the GNU Coding Standards, and\r
+does not work on platforms that have drive letters. On the other hand,\r
+it does better at avoiding recompilation issues, and works well even\r
+when some directory options were not specified in terms of `${prefix}'\r
+at `configure' time.\r
+\r
+Optional Features\r
+=================\r
+\r
+ If the package supports it, you can cause programs to be installed\r
+with an extra prefix or suffix on their names by giving `configure' the\r
+option `--program-prefix=PREFIX' or `--program-suffix=SUFFIX'.\r
+\r
+ Some packages pay attention to `--enable-FEATURE' options to\r
+`configure', where FEATURE indicates an optional part of the package.\r
+They may also pay attention to `--with-PACKAGE' options, where PACKAGE\r
+is something like `gnu-as' or `x' (for the X Window System). The\r
+`README' should mention any `--enable-' and `--with-' options that the\r
+package recognizes.\r
+\r
+ For packages that use the X Window System, `configure' can usually\r
+find the X include and library files automatically, but if it doesn't,\r
+you can use the `configure' options `--x-includes=DIR' and\r
+`--x-libraries=DIR' to specify their locations.\r
+\r
+ Some packages offer the ability to configure how verbose the\r
+execution of `make' will be. For these packages, running `./configure\r
+--enable-silent-rules' sets the default to minimal output, which can be\r
+overridden with `make V=1'; while running `./configure\r
+--disable-silent-rules' sets the default to verbose, which can be\r
+overridden with `make V=0'.\r
+\r
+Particular systems\r
+==================\r
+\r
+ On HP-UX, the default C compiler is not ANSI C compatible. If GNU\r
+CC is not installed, it is recommended to use the following options in\r
+order to use an ANSI C compiler:\r
+\r
+ ./configure CC="cc -Ae -D_XOPEN_SOURCE=500"\r
+\r
+and if that doesn't work, install pre-built binaries of GCC for HP-UX.\r
+\r
+ On OSF/1 a.k.a. Tru64, some versions of the default C compiler cannot\r
+parse its `<wchar.h>' header file. The option `-nodtk' can be used as\r
+a workaround. If GNU CC is not installed, it is therefore recommended\r
+to try\r
+\r
+ ./configure CC="cc"\r
+\r
+and if that doesn't work, try\r
+\r
+ ./configure CC="cc -nodtk"\r
+\r
+ On Solaris, don't put `/usr/ucb' early in your `PATH'. This\r
+directory contains several dysfunctional programs; working variants of\r
+these programs are available in `/usr/bin'. So, if you need `/usr/ucb'\r
+in your `PATH', put it _after_ `/usr/bin'.\r
+\r
+ On Haiku, software installed for all users goes in `/boot/common',\r
+not `/usr/local'. It is recommended to use the following options:\r
+\r
+ ./configure --prefix=/boot/common\r
+\r
+Specifying the System Type\r
+==========================\r
+\r
+ There may be some features `configure' cannot figure out\r
+automatically, but needs to determine by the type of machine the package\r
+will run on. Usually, assuming the package is built to be run on the\r
+_same_ architectures, `configure' can figure that out, but if it prints\r
+a message saying it cannot guess the machine type, give it the\r
+`--build=TYPE' option. TYPE can either be a short name for the system\r
+type, such as `sun4', or a canonical name which has the form:\r
+\r
+ CPU-COMPANY-SYSTEM\r
+\r
+where SYSTEM can have one of these forms:\r
+\r
+ OS\r
+ KERNEL-OS\r
+\r
+ See the file `config.sub' for the possible values of each field. If\r
+`config.sub' isn't included in this package, then this package doesn't\r
+need to know the machine type.\r
+\r
+ If you are _building_ compiler tools for cross-compiling, you should\r
+use the option `--target=TYPE' to select the type of system they will\r
+produce code for.\r
+\r
+ If you want to _use_ a cross compiler, that generates code for a\r
+platform different from the build platform, you should specify the\r
+"host" platform (i.e., that on which the generated programs will\r
+eventually be run) with `--host=TYPE'.\r
+\r
+Sharing Defaults\r
+================\r
+\r
+ If you want to set default values for `configure' scripts to share,\r
+you can create a site shell script called `config.site' that gives\r
+default values for variables like `CC', `cache_file', and `prefix'.\r
+`configure' looks for `PREFIX/share/config.site' if it exists, then\r
+`PREFIX/etc/config.site' if it exists. Or, you can set the\r
+`CONFIG_SITE' environment variable to the location of the site script.\r
+A warning: not all `configure' scripts look for a site script.\r
+\r
+Defining Variables\r
+==================\r
+\r
+ Variables not defined in a site shell script can be set in the\r
+environment passed to `configure'. However, some packages may run\r
+configure again during the build, and the customized values of these\r
+variables may be lost. In order to avoid this problem, you should set\r
+them in the `configure' command line, using `VAR=value'. For example:\r
+\r
+ ./configure CC=/usr/local2/bin/gcc\r
+\r
+causes the specified `gcc' to be used as the C compiler (unless it is\r
+overridden in the site shell script).\r
+\r
+Unfortunately, this technique does not work for `CONFIG_SHELL' due to\r
+an Autoconf bug. Until the bug is fixed you can use this workaround:\r
+\r
+ CONFIG_SHELL=/bin/bash /bin/bash ./configure CONFIG_SHELL=/bin/bash\r
+\r
+`configure' Invocation\r
+======================\r
+\r
+ `configure' recognizes the following options to control how it\r
+operates.\r
+\r
+`--help'\r
+`-h'\r
+ Print a summary of all of the options to `configure', and exit.\r
+\r
+`--help=short'\r
+`--help=recursive'\r
+ Print a summary of the options unique to this package's\r
+ `configure', and exit. The `short' variant lists options used\r
+ only in the top level, while the `recursive' variant lists options\r
+ also present in any nested packages.\r
+\r
+`--version'\r
+`-V'\r
+ Print the version of Autoconf used to generate the `configure'\r
+ script, and exit.\r
+\r
+`--cache-file=FILE'\r
+ Enable the cache: use and save the results of the tests in FILE,\r
+ traditionally `config.cache'. FILE defaults to `/dev/null' to\r
+ disable caching.\r
+\r
+`--config-cache'\r
+`-C'\r
+ Alias for `--cache-file=config.cache'.\r
+\r
+`--quiet'\r
+`--silent'\r
+`-q'\r
+ Do not print messages saying which checks are being made. To\r
+ suppress all normal output, redirect it to `/dev/null' (any error\r
+ messages will still be shown).\r
+\r
+`--srcdir=DIR'\r
+ Look for the package's source code in directory DIR. Usually\r
+ `configure' can determine that directory automatically.\r
+\r
+`--prefix=DIR'\r
+ Use DIR as the installation prefix. *note Installation Names::\r
+ for more details, including other options available for fine-tuning\r
+ the installation locations.\r
+\r
+`--no-create'\r
+`-n'\r
+ Run the configure checks, but stop before creating any output\r
+ files.\r
+\r
+`configure' also accepts some other, not widely useful, options. Run\r
+`configure --help' for more details.\r
+\r
git://source.jalview.org / jabaws.git / blobdiff