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PATH=$PATH:/Applications/alphamelts:/Users/Zack/bin
run_alphamelts.command -f alphamelts_settings.txt -b mybatch

import os

# Go to the directory where the alphaMELTS input files are.
os.chdir('/Users/Zack/Desktop/Testcmd')

# Run the shell script.
process = subprocess.Popen('./runit', shell=True)
process.wait()

print 'done'