--- a/defuse.xml	Sun Jan 13 13:48:56 2013 -0600
+++ b/defuse.xml	Mon Jan 14 11:26:17 2013 -0600
@@ -197,6 +197,18 @@
 #except
 __GMAP_BIN__
 #end try
+gmap_bin = #slurp
+#try
+$ref_dict['gmap_bin']
+#except
+__GMAP_BIN__
+#end try
+gmap_setup_bin = #slurp
+#try
+$ref_dict['gmap_setup_bin']
+#except
+__GMAP_SETUP_BIN__
+#end try
 r_bin = #slurp
 #try
 $ref_dict['r_bin']
@@ -210,6 +222,15 @@
 __RSCRIPT_BIN__
 #end try
 
+# Directory where you want your dataset
+gmap_index_directory = #slurp
+#try
+$ref_dict['gmap_index_directory']
+#except
+$(dataset_directory)/gmap
+#end try
+
+
 #raw
 # Dataset files
 dataset_prefix       = $(dataset_directory)/defuse
@@ -559,6 +580,7 @@
 if `grep __BLAT_BIN__ $defuse_config ${gt} /dev/null` ${amp}${amp} BLAT_BIN=`which blat`;then sed -i'.tmp' "s#__BLAT_BIN__#\${BLAT_BIN}#" $defuse_config; fi
 if `grep __FATOTWOBIT_BIN__ $defuse_config ${gt} /dev/null` ${amp}${amp} FATOTWOBIT_BIN=`which faToTwoBit`;then sed -i'.tmp' "s#__FATOTWOBIT_BIN__#\${FATOTWOBIT_BIN}#" $defuse_config; fi
 if `grep __GMAP_BIN__ $defuse_config ${gt} /dev/null` ${amp}${amp} GMAP_BIN=`which gmap`;then sed -i'.tmp' "s#__GMAP_BIN__#\${GMAP_BIN}#" $defuse_config; fi
+if `grep __GMAP_SETUP_BIN__ $defuse_config ${gt} /dev/null` ${amp}${amp} GMAP_SETUP_BIN=`which gmap_setup`;then sed -i'.tmp' "s#__GMAP_SETUP_BIN__#\${GMAP_SETUP_BIN}#" $defuse_config; fi
 if `grep __R_BIN__ $defuse_config ${gt} /dev/null` ${amp}${amp} R_BIN=`which R`;then sed -i'.tmp' "s#__R_BIN__#\${R_BIN}#" $defuse_config; fi
 if `grep __RSCRIPT_BIN__ $defuse_config ${gt} /dev/null` ${amp}${amp} RSCRIPT_BIN=`which Rscript`;then sed -i'.tmp' "s#__RSCRIPT_BIN__#\${RSCRIPT_BIN}#" $defuse_config; fi