JWS-112 Bumping version of ClustalO (src, binaries and windows) to version 1.2.4.

[jabaws.git] / binaries / src / clustalo / INSTALL

diff --git a/binaries/src/clustalo/INSTALL b/binaries/src/clustalo/INSTALL
index ede75b5..2099840 100644 (file)
--- a/binaries/src/clustalo/INSTALL
+++ b/binaries/src/clustalo/INSTALL
@@ -1,43 +1,8 @@
-The impatient can try:
-
-$ ./configure
-$ make
-$ make install
-
-
-Clustal-Omega needs argtable2 (http://argtable.sourceforge.net/). If
-argtable2 is installed in a non-standard directory you might have to
-point configure to its installation directory. For example, if you are
-on a Mac and have argtable installed via MacPorts then you should use
-the following command line:
-
-$ ./configure CFLAGS='-I/opt/local/include' LDFLAGS='-L/opt/local/lib'
-
-ClustalO will automatically support multi-threading if your compiler
-supports OpenMP. For some reason automake's OpenMP detection for
-Apple's gcc is broken. You can force OpenMP detection by calling configure 
-like so:
-
-$ ./configure OPENMP_CFLAGS='-fopenmp' CFLAGS='-DHAVE_OPENMP'
-
-You could use a non-Apple gcc installed via MacPorts, adding
-
-CC=/opt/local/bin/gcc-mp-4.5
-
-to the configure call (you will have to change the exact string to match
-your gcc version).
-
-See below for generic installation instructions:
-
-----------------------------------------------------------------------
-
-
-
 Installation Instructions
 *************************
 
-Copyright (C) 1994, 1995, 1996, 1999, 2000, 2001, 2002, 2004, 2005,
-2006, 2007, 2008, 2009 Free Software Foundation, Inc.
+Copyright (C) 1994-1996, 1999-2002, 2004-2013 Free Software Foundation,
+Inc.
 
    Copying and distribution of this file, with or without modification,
 are permitted in any medium without royalty provided the copyright
@@ -47,8 +12,8 @@ without warranty of any kind.
 Basic Installation
 ==================
 
-   Briefly, the shell commands `./configure; make; make install' should
-configure, build, and install this package.  The following
+   Briefly, the shell command `./configure && make && make install'
+should configure, build, and install this package.  The following
 more-detailed instructions are generic; see the `README' file for
 instructions specific to this package.  Some packages provide this
 `INSTALL' file but do not implement all of the features documented
@@ -261,6 +226,11 @@ order to use an ANSI C compiler:
 
 and if that doesn't work, install pre-built binaries of GCC for HP-UX.
 
+   HP-UX `make' updates targets which have the same time stamps as
+their prerequisites, which makes it generally unusable when shipped
+generated files such as `configure' are involved.  Use GNU `make'
+instead.
+
    On OSF/1 a.k.a. Tru64, some versions of the default C compiler cannot
 parse its `<wchar.h>' header file.  The option `-nodtk' can be used as
 a workaround.  If GNU CC is not installed, it is therefore recommended
@@ -339,9 +309,10 @@ causes the specified `gcc' to be used as the C compiler (unless it is
 overridden in the site shell script).
 
 Unfortunately, this technique does not work for `CONFIG_SHELL' due to
-an Autoconf bug.  Until the bug is fixed you can use this workaround:
+an Autoconf limitation.  Until the limitation is lifted, you can use
+this workaround:
 
-     CONFIG_SHELL=/bin/bash /bin/bash ./configure CONFIG_SHELL=/bin/bash
+     CONFIG_SHELL=/bin/bash ./configure CONFIG_SHELL=/bin/bash
 
 `configure' Invocation
 ======================
@@ -397,4 +368,3 @@ operates.
 
 `configure' also accepts some other, not widely useful, options.  Run
 `configure --help' for more details.
-