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[haoqichen20]

1. usage_cli: At the end of this section you have a block of bash code to run phuego, in which the following line is included. Here, $results_dir variable should be used instead

# Create the experiment dir. exp_dir="$pub_dir/$experiment"

2. Update damping factor to -ds flag.
3. Update parameter input when running phuEGO from bash file

• double quote escape for fisher geneset input
• avoid using space between the floats of damping factors