[EMBOSS] EMBOSS 2.8.0 released

[Alan Bleasby]

EMBOSS 2.8.0 is available for download from:

  http://www.uk.embnet.org/Software/EMBOSS
  ftp://ftp.uk.embnet.org/pub/EMBOSS

Details of changes from 2.7.1 are, as usual, available in the
ChangeLog file.

Note that large file support is now the default compilation mode. The
original indexing system is, however, still used in 2.8.0 so
should not be used on individual database flat files >2Gb. We expect
to release a new indexing system in 2.9.0 (in fact the code is
distributed for this in 2.8.0 but is not yet integrated).

GUI developers who did not pick up the pre-2.8.0 release should note
that there have been significant changes to the ACD files in this
release.


COMPILATION:

1) Systems where gcc is not the system compiler (e.g. AIX,HP-UX,IRIX,Tru64,
   Solaris)

   We recommend using the default compiler for each platform. The
   configure scripts, being GNU, will preferentially use the gcc
   compiler by default. To use the system compiler type:
                 setenv CC cc
   or the 'sh' equivalent before configuration.

2) Systems where gcc is the default compiler (e.g. Linux,MacOSX)
   No pre-configuration commands are required.

EMBOSS should compile with gcc on systems even when it isn't the manufacturer
supplied compiler for the platform however, using the recommended
compiler will ensure that all compilation optimisations are applied.
Use of the manufacturer's compiler also allows the --enable-64 switch to be
used, should 64-bit pointers be necessary for any of your applications (and
the architecture allows them). The --enable-64 flag is not necessary for
normal EMBOSS operation and is therefore off by default.

3) IRIX systems
   You should:
     setenv CC cc
   as above. There is also a configuration switch for IRIX which you
   should use (--with-sgiabi=). This allows you to select 32/64-bit
   libraries and the MIPS level (3 or 4). The values accepted by the
   switch are:
      n32m3
      n32m4
      64m3
      64m4
   An example configuration line is:
      ./configure --with-sgiabi=n32m3   [etc]
   The --enable-64 flag is meaningless for IRIX as the use/non-use of
   64-bit pointers is controlled by the --with-sgiabi switch.

EMBASSY

Note that, because of the ACD changes mentioned above, those sites who
install the EMBASSY packages (also in ftp://ftp.uk.embnet.org/pub/EMBOSS/)
will need to re-ftp and build them.


SYSTEMS NOT DIRECTLY SUPPORTED BY THE CORE DEVELOPMENT TEAM

Compilation of EMBOSS should still work. We patently have no way
of testing this though. The compilation may not build in large file
support for those platforms. Large file support is not strictly necessary
for 2.8.0 but will be required when the new indexing system is released.
We will be happy to hear from people, with experience of systems aspects
of such platforms, and collaborate to make as many platforms as possible
ready for the next release (email emboss-bug at embnet.org).


Alan