How to call mothur in a shell script


I want to write a shell script to process a batch of data using a loop. In each cycle of the loop, I want to call mothur to run its commands. However, it seems shell does not allow me to call a foreign system like mothur in the script. Is there any way to fix or go around this?

Thanks in advance.


If you are running mothur on a mac/linux box you would do the following (assuming mothur is in the PATH):

mothur “#screen.seqs(fasta=something.fasta, maxhomop=8);summary.seqs()”

Can you do that?