--- a/README	Fri Jan 04 13:29:03 2013 -0600
+++ b/README	Fri Jan 04 15:01:19 2013 -0600
@@ -9,6 +9,7 @@
 
 The included tool_dependencies.xml will download and install the defuse code.  
 It will set the environment variable: "DEFUSE_PATH" to the location of the defuse install.  
+The tool_dependencies.xml also has the download for bowtie.
 
 
 The defuse.pl command relies on a configuration file to specifiy options, the location of reference data, and other applications that it depends upon: bowtie, bowtie-build, samtools, blat, fatotwobit, R, and Rscript.
@@ -32,4 +33,19 @@
 These datasets should be referenced in the tool-data/defuse.loc file. 
 
 
+External Tools
+deFuse relies on other publically available tools as part of its pipeline. Some of these tools are not included with the deFuse download. Obtain these tools as detailed below.
+Download bowtie: 
+The latest version of bowtie can be downloaded from sourceforge: http://sourceforge.net/projects/bowtie-bio/files/bowtie/. deFuse has been tested on version 0.12.5.
+Set the bowtie_bin and bowtie_build_bin entries in config.txt to the fully qualified paths of the bowtie and bowtie-build binaries.
+Download blat and faToTwoBit
+The latest blat tool suite can be downloaded from the ucsc website: http://hgdownload.cse.ucsc.edu/admin/exe/. Download blat and faToTwoBit and set the blat_bin and fatotwobit_bin entries in config.txt to the fully qualified paths of the blat and faToTwoBit binaries.
+Download R
+The latest version of R can be downloaded from the R project website: http://www.r-project.org/. Install R and then locate the R and Rscript executables, and set the r_bin and rscript_bin entries in config.txt to the path of those executables.
+Install the kernlab package. Run R, then at the prompt type install.packages("kernlab")
+Creating required derivative files
+Once the required files and tools have been downloaded, the create_reference_dataset.pl script will build any derivative files including bowtie indices and 2bit files. Run the following command. Expect this step to take at least 12 hours.
+create_reference_dataset.pl -c config.txt
 
+
+