Running "GAST" in Mac OS

Hi, everybody
I am freshman of MOTHUR

I am trying to use a perl script “GAST” in Mac OS for classifying pyrosequencing reads into known taxa
Mothur is to be used during the run

The question is how to let the script know the exact folder of my Mothur

how to modify this following line in the GAST script

my $mothur_cmd = “mothur “#unique.seqs(fasta=$in_filename);””;

Did you try my $mothur_cmd = “fullPathToMothur/mothur “#unique.seqs(fasta=$in_filename);””; If your path contains spaces you will need to use escape quotes around it.

thank you for your reply

I found my mistake that the folder path should be carefully capitalized