It's assumed that you have native gcc compiler in your Cygwin/Linux installation (e.g. gcc 3.x.x/4.x.x and tools like: autoconf, make etc..). Just launch the Cygwin setup to download and install missing tools.
Under Ubuntu get "build-essentials" package (install it from Synaptic or type in console 'sudo apt-get install build-essentials'.

To build m68k cross assembler you will need daily snapshot of VASM which can be found here.
Download it and extract for example in your $HOME folder in "vasm" directory. Go to 'vasm' directory by typing 'cd vasm'.

After that type in the console:
$ make CPU=m68k SYNTAX=mot

After that gcc will build two files:
  • vasmm68k_mot
  • vobjdump

Rename them and move them to Cygwin /bin directory:
$ mv vasmm68k_mot /bin/vasm68k_mot.exe
$ mv vobjdump /bin/vobjdump.exe

NOTE: above step is only for Cygwin, under Linux renaming of files is not needed. But of course you will still have to copy those files to be system wide usable like this:
$ sudo cp vasmm68k_mot /usr/local/bin
$ sudo cp vobjdump /usr/local/bin

Now you can check if the VASM is usable in your Cygwin/Linux environment by typing in bash:
$ cd ~
$ vasmm68k_mot

The following message should appear:
vasm 1.3d (c) in 2002-2009 Volker Barthelmann
vasm M68k/CPU32/ColdFire cpu backend 1.0c (c) 2002-2009 Frank Wille
vasm motorola syntax module 2.7d (c) 2002-2009 Frank Wille
vasm test output module 1.0 (c) 2002 Volker Barthelmann

fatal error 16: no input file specified

Now to compile with VASM file "test.s" just type in:
vasmm68k_mot -Ftos test.s -o test.tos