I you copy files from windows to a unix system, you have to take care about the line endings.
This is a quicktip how you can convert all files in a directory from windows to unix line endings. You need the program dos2unix, if it’s not installed on your system you can install it with
apt-get install dos2unix
Then you can convert all the files in your current directory with:
find . -type f -exec dos2unix {} \;