--- a/README.txt	Mon Aug 03 05:45:16 2015 -0400
+++ b/README.txt	Mon Aug 03 06:00:51 2015 -0400
@@ -10,17 +10,17 @@
    - change "/path/to/VN_genomes_varfiles_lists_hg18" to the location of the directory containing files with the locations of all the Complete Genomics
      varfiles to be used as a virtual normal. This file should contain 1 file location per line, e.g.
      
-	    /path/to/normal-varfile-1
-		/path/to/normal-varfile-2
-		/path/to/normal-varfile-3
-		/path/to/normal-varfile-4
-		/path/to/normal-varfile-5
-		/path/to/normal-varfile-6
-		/path/to/normal-varfile-7
-		/path/to/normal-varfile-8
+            /path/to/normal-varfile-1
+            /path/to/normal-varfile-2
+            /path/to/normal-varfile-3
+            /path/to/normal-varfile-4
+            /path/to/normal-varfile-5
+            /path/to/normal-varfile-6
+            /path/to/normal-varfile-7
+            /path/to/normal-varfile-8
    			...
    			
-   - edit the tool xml file to offer sets of virtual normals
+   - edit the tool xml file to offer one or more different sets of virtual normals: 
 
 	[..]
 		<!-- edit these options to reflect sets of normal you have available. The values must name files within the directories specified in data_table_conf.xml file -->
@@ -38,29 +38,24 @@
      So if your .loc file looks like this:
 
 
-		#loc file for annovar tool
+		#loc file for virtual normal tool
+		# <columns>value, dbkey, name, VN_genomes_varfiles_lists_location, VN_genomes_junctionfile_lists_location, reference_crr_cgatools</columns>
 
-		# <columns>value, dbkey, name, VN_genomes_varfiles_list, VN_genomes_junctionfile_list, reference_crr_cgatools</columns>
-
-		hg18	hg18	Virtual Normal hg18	/path/to/VN_genomes_varfiles_lists_hg18	/path/to/VN_genomes_junctionfiles_lists_hg18	/path/to/hg18.crr
-		hg19	hg19	Virtual_Normal hg19	/path/to/VN_genomes_varfiles_lists_hg19	/path/to/VN_genomes_junctionfiles_lists_hg19	/path/to/hg19.crr
+		hg18	hg18	Virtual Normal hg18	/path/to/VN_genomes_varfiles_lists_hg18/	/path/to/VN_genomes_junctionfiles_lists_hg18/	/path/to/hg18.crr
+		hg19	hg19	Virtual_Normal hg19	/path/to/VN_genomes_varfiles_lists_hg19/	/path/to/VN_genomes_junctionfiles_lists_hg19/	/path/to/hg19.crr
 
      And your xml file like the example above, then the tool expects the following files to exist:
 		 /path/to/VN_genomes/varfiles_list_hg18/46_diversity.txt 	
      		 /path/to/VN_genomes/varfiles_list_hg18/433_1000g.txt
-		etc
-     and containing a 1-per-line list of locations of the varfiles of the normal genomes.
+		       ...etc..
 
-
- 
+     and each of these files must contain a 1-per-line list of locations of the varfiles of the normal genomes (or junction files in case of SV analysis).
 
      Varfiles can be in compressed or uncompressed form. For example, Complete Genomics' Diversity panel can be used.
      (can be downloaded from ftp://ftp2.completegenomics.com/)		
-   
-   - change	"/path/to/VN_genomes_junctionfiles_lists_hg18" to the location of the file containing the locations of all the Complete Genomics
-     junctionfiles to be used as a virtual normal. This file should contain 1 file location per line.  For example, Complete Genomics' 
-	 Diversity panel can be used. (can be downloaded from ftp://ftp2.completegenomics.com/)
+
+
      
- 2) restart Galaxy for changes to take effect
+ 2) restart Galaxy for changes to take effect (alternatively, in the admin panel these setting can be reloaded without the need to restart your galaxy instance)
  
  After this initial setup, additional normals can be added to the lists without having to restart Galaxy.