Cygwin
I tried a few times to install EMBOSS in my cygwin. It takes a lot of recompiling and reading the net to find what the compilation errors are. The basic steps are as for any distribution, ie
% ./configure --prefix=/usr/local/emboss
% make
% make install
I first had the compiler complaining because it could not find a shared library related to 'ajax' () and was then complaining about not finding the x11 libraries. They recommend anyway to use '--without-X' in the emboss website so I went with it. The way to fix the shared library problem is using the '--disable-shared' option. After all, your command should look like:
%./configure --without-x CFLAGS=-s --disable-shared
Linux
when just doing % ./configure you get:
'/usr/lib/gcc-lib/i586-suse-linux/3.3.3/../../../../i586-suse-linux/bin/ld: cannot find -lX11'
This can be avoided by adding the option '--without-x' so that you end up running
./configure --without-x --prefix=/usr/local/emboss
Note: Remember that everytime a failed attempt to recompile happens, you need to do 'make clean' before re-running './configure'