To convert files from windows (or DOS) type line endings to UNIX or Mac flavor use “flip”

Convert DOS or Windows line endings to Unix or Mac

flip -d <filename>

Convert Unix line endings to Windows

flip -u <filename>

To install flip on Mac:

sudo port install flip

To install flip on Ubuntu Linux

sudo apt-get install flip

How do you know your line endings are DOS or Windows flavor? Open your text file with a plain text editor. If you see a “^M” at the end of every line then your line endings are DOS/Windows.

From the flip Usage instructions

Usage: flip [-t|-u|-d|-m] filename[s]
   Converts ASCII files between Unix, MS-DOS/Windows, or Macintosh newline formats
 
   Options: 
      -u  =  convert file(s) to Unix newline format (newline)
      -d  =  convert file(s) to MS-DOS/Windows newline format (linefeed + newline)
      -m  =  convert file(s) to Macintosh newline format (linefeed)
      -t  =  display current file type, no file modifications