To run cygwin shell as emacs shell try the following in your .emacs
c:\.emacs default location, read ntemacs FAQ for full details
Replace d:/cygwin with wherever cygwin is installed in your environment.

;# http://www.cs.washington.edu/homes/voelker/ntemacs.html
;How do I use a shell in Emacs?
;http://www.gnu.org/software/emacs/windows/faq7.html#shell

;#set |grep COMSPEC
;#COMSPEC=C:\WINNT\system32\cmd.exe

;; For the interactive shell
(setq explicit-shell-file-name "d:/cygwin/bin/bash.exe")

;; For subprocesses invoked via the shell (e.g., "shell -c command")
(setq shell-file-name "d:/cygwin/bin/bash.exe")

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