HowTo for compiling emboss under windows

[David Starks-Browning]

Olivier,

Just a few comments:

> 1) install cygwin (http://www.cygwin.com). That's surely possible to 
> compile without it, but it's making everything easier. 

No, you cannot compile EMBOSS as distributed without a POSIX emulation
layer like Cygwin.  There are other comparable systems like MKS (all
commercial, I believe), but to do a native Windows port, you would
need to modify EMBOSS.  Someone has posted to this list in the past
few months about this, check the archives.

> procedure:
> ./configure --without-x CFLAGS=-s
> make
> make install
>  
> --without-x because at one point the X11 library is required (even if 
> useless) and without this flag the compilation would stop.
> CFLAGS=-s to make the binaries smaller.

Cygwin does also provide X, though it's a big download if you don't
otherwise need it.  Can you generate graphics without X?  I know that
Cygwin provides libpng, for example, but I haven't investigated
whether EMBOSS can use it.

> 5) text files are different between windows and linux. If you save 
> (for ex.) emboss.default from, say, wordpad, EMBOSS programs parsing
> this file won't be able to pass the first line and they will crash.
> To overcome this, use notepad instead

I think you might have this backwards.  Wordpad can handle UNIX
end-of-line characters, but notepad cannot.  And Cygwin provides vi
and emacs. :-)

> 6) EMBOSS has then been built with cygwin. To use it from a ms-dos cmd
> instead of the cygwin bash the cygwin1.dll has to be in your windows
> PATH (ex: C:\windows\system32).

Putting cygwin1.dll in your Windows path (e.g. C:\windows\system32) is
*strongly discouraged* by the Cygwin folks.  You end up with a Cygwin
installation that cannot be maintained by the normal Cygwin Setup program.

If you want to run EMBOSS programs from the Windows command line,
then add C:\cygwin\bin to your Windows PATH somehow.  (But why not use
Cygwin bash if you've got it?)

Regards,
David