diff README.txt @ 0:1209f18a5a83 draft

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author saskia-hiltemann
date Mon, 03 Aug 2015 05:01:15 -0400
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children 885ba15c2564
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+Installs VirtualNormal Correction Tool
+
+After installing this tool via admin panel, manually configure the following:
+
+1) edit virtual_normal_correction.loc file
+
+   - change "/path/to/hg18.crr" to the location of the Complete Genomics reference crr file on your system
+     (can be downloaded from ftp://ftp.completegenomics.com/ReferenceFiles/ )
+     
+   - change "/path/to/VN_genomes_varfiles_hg18.txt" to the location of the file containing 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
+   			...
+   			
+   	 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_hg18.txt" 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
+ 
+ After this initial setup, additional normals can be added to the lists without having to restart Galaxy.