Thanks, Nate! I wasn't so sure before if using mkdir would do the trick.
Actually, my main goal is to implement a slightly modified velveth in our
galaxy. According to how  it's run, I need to provide a directory. I was
wondering how I could save the data in the created directory, since all the
data that galaxy generates get stored in the database/files/000 folder. I
also need to be able to use these data for velvetg.

In line with my question, I found this in the galaxy version of velveth:

velveth_jgi_wrapper.pl $output $output.extra_files_path

Can you explain to me what $output.extra_files_path pertains to here?

Cheers,

CL
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