CGEN is written in Scheme, and is usually run via a Scheme interpreter such as Guile. Therefore, no explicit configure/compile step is required for cgen itself.
Normally, the interpreted cgen sources, as well as files generated by cgen, all sit within in a common source tree that also includes the cgen-generated tools (the opcodes library and the various simulators). In a build tree configured from such a source tree, cgen rarely needs to be run: only when its inputs (.cpu/.opc description files, or .scm cgen sources) are changed. Even in such cases, cgen is rarely run by hand: instead, cgen is invoked via the make program in the generated tools directories.

See also:

    http://www.airs.com/ian/configure
    http://www.fsf.org/software/guile
    http://sources.redhat.com/fom/cgen?file=7

 =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
  Jakob Nielsen                 jakob.nielsen@dspfactory.com
  Senior DSP Engineer
  Dspfactory Ltd.                Tel: +1-519-884-9696 x252
  80 King Street S., Suite 206   Fax: +1-519-884-0228
  Waterloo, ONT, CANADA          http://www.dspfactory.com/
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       $(SHELL) $(srcdir)/cgen.sh opcodes $(srcdir) $(CGEN) \
         $(CGENDIR) "$(CGENFLAGS)" $(arch) $(prefix) $(archfile) $(opcfile) \
         "$(options)" "$(extrafiles)"
         touch stamp-${prefix} 

From George Varughese:

If you want to run cgen scripts in a different directory other than
binutils/opcodes (GNU binutils),

copy binutils/opcodes/cgen.sh to the new directory, and create a makefile
(Makefile) as follows:

####### Makefile begin
srcdir=.
cgendir = ./cgen/src/cgen
CGEN = "guile -L $(cgendir) -l ${cgendir}/guile.scm -s"
# directory where all cgen .scm files are
CGENDIR = `pwd`/cgen/src/cgen
CGENFLAGS = -v
arch=tp01
prefix = tp01
archfile = `pwd`/tp01.cpu
opcfile = `pwd`/tp01.opc
extrafiles =
options =

# remember to use use tab where necessary
run-cgen:
       $(SHELL) $(srcdir)/cgen.sh opcodes $(srcdir) $(CGEN) \
         $(CGENDIR) "$(CGENFLAGS)" $(arch) $(prefix) $(archfile) $(opcfile) \
         "$(options)" "$(extrafiles)"
         touch stamp-${prefix}

###### Makefile end

and run make. This example assumes that your cgen inputs are tp01.cpu, and
tp01.opc.

Following text shows how cgen is called from binutils.
   
If you have gnu binutils downloaded and configured, cd to opcodes directory
run
   
make -n stamp-m32r
or
make stamp-m32r
   
to see how m32r related files  are generated using cgen.

opcodes directory contains a shell script "cgen.sh". If you insert
set -x
in this file, at the top, and run "make stamp-m32r", you will see how cgen guile
scripts are called.