--- a/config_sub.sh	Wed Oct 18 16:55:57 2017 -0400
+++ b/config_sub.sh	Thu Oct 19 10:05:54 2017 -0400
@@ -11,9 +11,11 @@
 GMAP_SETUP_BIN=$GMAP_BUILD_BIN
 R_BIN=`which R`
 RSCRIPT_BIN=`which Rscript`
-
-cat $1 | sed "s#__SAMTOOLS_BIN__#${SAMTOOLS_BIN}#"| \
-sed "s#__BOWTIE_BIN__#${BOWTIE_BIN}#"| \
+DEFUSE_BIN=`which defuse_run.pl`
+DEFUSE_PATH=`python -c "import os.path;  print os.path.dirname(os.path.dirname(os.path.realpath(\"$DEFUSE_BIN\")))"`
+cat $1 | sed "s#__DEFUSE_PATH__#${DEFUSE_PATH}#" | \
+sed "s#__SAMTOOLS_BIN__#${SAMTOOLS_BIN}#" | \
+sed "s#__BOWTIE_BIN__#${BOWTIE_BIN}#" | \
 sed "s#__BOWTIE_BUILD_BIN__#${BOWTIE_BUILD_BIN}#" | \
 sed "s#__BLAT_BIN__#${BLAT_BIN}#"| \
 sed "s#__FATOTWOBIT_BIN__#${FATOTWOBIT_BIN}#" | \
@@ -23,5 +25,5 @@
 sed "s#__GMAP_BUILD_BIN__#${GMAP_BUILD_BIN}#" | \
 sed "s#__R_BIN__#${R_BIN}#" | \
 sed "s#__RSCRIPT_BIN__#${RSCRIPT_BIN}#" > $2
-
-## if `grep __DEFUSE_PATH__ $defuse_config ${gt} /dev/null`;then sed -i'.tmp' "s#__DEFUSE_PATH__#\${DEFUSE_PATH}#" $defuse_config; fi
+export DATASET_DIRECTORY=`grep '^dataset_directory' $1 | awk '{print \$NF}'`
+echo "$DATASET_DIRECTORY"