--- a/SeqSero2_package.py	Thu Oct 03 06:29:10 2019 -0400
+++ b/SeqSero2_package.py	Thu Oct 03 07:04:21 2019 -0400
@@ -1264,7 +1264,8 @@
   #database="H_and_O_and_specific_genes.fasta"
   dirpath = os.path.abspath(os.path.dirname(os.path.realpath(__file__)))
   ex_dir = os.path.abspath(os.path.join(os.path.dirname(os.path.dirname(__file__)),'seqsero2_db')) # ed_SL_09152019: add ex_dir for packaging
-  database=dirpath+"/seqsero2_db/H_and_O_and_specific_genes.fasta" # ed_SL_09152019: change path to database for packaging
+  #database=ex_dir+"/seqsero2_db/H_and_O_and_specific_genes.fasta" # ed_SL_09152019: change path to database for packaging
+  database="H_and_O_and_specific_genes.fasta"
   note="Note:"
   NA_note=" This predicted serotype is not in the Kauffman-White scheme." # ed_SL_09272019: add for new output format
   if len(sys.argv)==1:
@@ -1280,8 +1281,8 @@
       subprocess.check_call(["mkdir",make_dir])
     #subprocess.check_call("cp "+dirpath+"/"+database+" "+" ".join(input_file)+" "+make_dir,shell=True)
     #subprocess.check_call("ln -sr "+dirpath+"/"+database+" "+" ".join(input_file)+" "+make_dir,shell=True)
-    subprocess.check_call("ln -f -s "+database+" "+" ".join(input_file)+" "+make_dir,shell=True) # ed_SL_09152019: change path to database for packaging 
-    #subprocess.check_call("ln -f -s "+dirpath+"/"+database+" "+" ".join(input_file)+" "+make_dir,shell=True) ### ed_SL_05282019: use -f option to force the replacement of links, remove -r and use absolute path instead to avoid link issue (use 'type=os.path.abspath' in -i argument).
+    #subprocess.check_call("ln -f -s "+database+" "+" ".join(input_file)+" "+make_dir,shell=True) # ed_SL_09152019: change path to database for packaging 
+    subprocess.check_call("ln -f -s "+dirpath+"/seqsero2_db/"+database+" "+" ".join(input_file)+" "+make_dir,shell=True) ### ed_SL_05282019: use -f option to force the replacement of links, remove -r and use absolute path instead to avoid link issue (use 'type=os.path.abspath' in -i argument).
   ############################begin the real analysis 
     if analysis_mode=="a":
       if data_type in ["1","2","3"]:#use allele mode