Update MANUAL.md

MANUAL.md

@@ -11,6 +11,8 @@ To determine if aTRAM can run on your computer:
 ######perl configure.pl 
 
   This script will determine if BLAST, muscle, mafft and other de novo assembly software are available. It will create a text file called configure.txt in the lib folder with the paths to the programs. They can be available in your $PATH by adding them directly to the appropriate folder (e.g. /usr/bin) or add the path to the programs to your $PATH. Alternatively, the configure.txt file can be edited directly with the path to the programs after configure.pl is run. BLAST is required and at least one of the de novo assemblers are required Trinity or Velvet.
+
+If you have problems running configure.pl for the first time, delete lib/config.txt.
 
 ## Running aTRAM