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