moved taxonomy db directory to config file

moved temp directory to config file
added these parameters & run directory to logfile

create_snap_nt_db.sh

@@ -0,0 +1,43 @@
+#!/bin/bash
+#
+#	create_snap_nt_db.sh
+#
+# 	This script will create SNAP databases from the NCBI NT database.
+#	1. download NCBI nt database 
+#	2. split NT into chunks
+#	3. create SNAP databases from each chunk
+#	Chiu Laboratory
+#	University of California, San Francisco
+#	January, 2014
+#
+# Copyright (C) 2014 Scot Federman - All Rights Reserved
+# Permission to copy and modify is granted under the BSD license 
+# Last revised 4/21/2014  
+
+number_of_chunks="15"
+targetsize="3950"
+SNAP_seed=20
+SNAP_O=1000
+SNAP_version="snap_1.0b10"
+
+START=$(date +%s)
+
+curl -O "ftp://ftp.ncbi.nih.gov/blast/db/FASTA/nt.gz.md5"
+curl -O "ftp://ftp.ncbi.nih.gov/blast/db/FASTA/nt.gz"
+
+# check md5sum
+
+gunzip nt.gz
+
+#strip headers from nt
+sed "s/\(>gi|[0-9]*|\).*/\1/g" nt > nt.stripped_header.fasta
+
+#split fasta file into chunks
+# gt splitfasta -numfiles $number_of_chunks nt.stripped_header.fasta
+gt splitfasta -targetsize $targetsize nt.stripped_header.fasta
+
+#use SNAP to index each chunk
+for f in nt.stripped_header.fasta.*
+do
+	$SNAP_version index $f snap_index_042214.$f -s $SNAP_seed -O$SNAP_O 
+done