Fix all color 'ls' output issues in make_copy().

Sorry Brad, the previous pull request is not a total clean up of the code.
Now I just updated all code in custom folder, make sure 'ls' in make_copy() is corrected for no color output.
Now I just stopped at the step of the installation of 'gemini', and I have reported the error [https://github.com/arq5x/gemini/issues/264] to gemini. It looks like the problem of anaconda, and I met the same error in the installation of bcbio-nextgen.