General Users.
-------------


GCC and CC compilers
--------------------

The 'configure' script looks for a working GNU C compiler (gcc) and uses it
by default if it is found. You can force 'configure' to use the
standard C compiler (cc) by either adding a line to the 'configure'
script:

     CC=cc

or by defining an environment variable:

     setenv CC cc

The file 'config.cache' seems to retain the value for this option. If you
have already run 'configure' you may need to delete the 'config.cache' file
when changing back to the gcc compiler.


Shared libraries
----------------

By default, the configure script builds shared libraries using
libtool. While this is very nice for making usable binaries, it can be
a pain when trying to debug a program. For that reason, compilation of
shared libraries can be turned off by specifying the
'--disable-shared' option to 'configure'.

PLplot graphics
---------------

EMBOSS now comes with a stripped down version of PLPlot which
is now compiled under the same system as EMBOSS.

The full PLplot can be obtained from http://www.plplot.org/
and by FTP from ftp://plplot.sourceforge.net/pub/plplot/

PLplot is a scientific graphics library distributed under the GNU
Library license. This license is a requirement to integrate a graphics
library into EMBOSS while allowing third party packages (for example
PHYLIP) to be integrated with the EMBOSS libraries. We are interested
in any other GNU Library licensed scientific graphics packages.

The only major thing to know about PLplot for the normal user are the
device types. These consist of various plotters e.g.
"xterm","xwin","ps" (postscipt) ,"psc" (colour postscript).

X devices. 
----------

To get xterm you must have X installed or else PLplot will not build the
required driver.

PNG driver.
-----------

To get the PNG driver you will need to have installed the z, png and
gd libraries. In particular gd version >= 2.0.28 must be used.  If for
some reason you do not have the required libraries and your system
support group will not update these then install all three latest
versions (z, gd, png) to a new directory and then add this new
directory to your configure line for EMBOSS.

     ./configure --with-pngdriver=my_dir

as gd (and the others) were installed using --prefix=my_dir 
in their ./configure commands. On Linux distributions the
above is not usually necessary as PNG graphics will be detected
automatically as long as both the library and development
RPMs/PKGs have been installed.



Other graphics libraries
------------------------

We have considered other graphics libraries, including the GNU libplot
library. The problem with GNU libplot currently is that it uses the
full GNU license which is not suitable for the non-EMBOSS applications.
We understand that there will be a future release of GNU libplot under
the GNU Library license. We also intend separating graphics by making
the applications produce XML output which can then be rendered using
a separate OpenGL-based graphics engine.

Third party applications
------------------------

A few applications are wrappers to third-party applications which must
be installed and in one case customised.

clustalw release 1.8.0 or later, or 2 or later, should be installed in
the path with the name clustalw. EMBOSS application emma is a wrapper
to launch clustalw.

primer3 from the Whitehead institute must be installed in one or two versions.

EMBOSS application eprimer3 launches primer3_core and expects this to
be version 1.x of the program.

EMBOSS application eprimer32 launches primer32_core and expects this
to be a renamed primer3_core from version 2.x of the program.

primer3's configuration files also need to be installed. The original
application looks by default in /opt/primer3_config

Installation.
-------------

If you have copied the binaries to another directory instead, or
made other changes to the file locations, you can also use
environment variables or the embossrc file(s) to tell the programs
where to look

You will need to use this command:

     setenv EMBOSS_ACDROOT $(prefix)/share/EMBOSS/acd

or in your site emboss.default file (in the share/EMBOSS install
directory or under emboss/ in the original source directory) or in
~/.embossrc file put

     env emboss_acdroot $(prefix)/share/EMBOSS/acd


Compilation problems for the CVS developers version
---------------------------------------------------

On some systems there may be compatibility problems with different
automake, autoconf or libtool versions. Always make sure that you keep
up to date with releases of these tools and let us know of any
problems you experience ([email protected]). If a libtool problem
does arise you can try deleting the following files:

   config.cache
   ltmain.sh
   ltconfig
   libtool

and then type

   aclocal -I m4
   autoconf
   automake -a

and then retry the make.