diff --git a/ag_gbs_qc_prism.sh b/ag_gbs_qc_prism.sh
index bfd75ef..2c5de08 100755
--- a/ag_gbs_qc_prism.sh
+++ b/ag_gbs_qc_prism.sh
@@ -122,6 +122,7 @@ function echo_opts() {
 function configure_env() {
    cd $GBS_PRISM_BIN
    cp ag_gbs_qc_prism.sh $OUT_ROOT
+   cp ag_gbs_qc_prism.mk $OUT_ROOT
    cp demultiplex_prism.sh $OUT_ROOT
    cp genotype_prism.sh $OUT_ROOT
    cp get_cohort_fastq_filenames.psql $OUT_ROOT
@@ -156,7 +157,7 @@ function get_targets() {
    for ((j=0;$j<$NUM_COHORTS;j=$j+1)) do
       cohort=${cohorts_array[$j]}
       cohort_moniker=${RUN}.$cohort
-      echo $OUT_ROOT/$cohort_moniker.ag_gbs_qc_prism >> $OUT_ROOT/ag_gbs_qc_targets.txt
+      echo $OUT_ROOT/$cohort_moniker.ag_gbs_qc_prism >> $OUT_ROOT/ag_gbs_qc_prism_targets.txt
       script=$OUT_ROOT/${cohort_moniker}.sh
       if [ -f $script ]; then
          if [ ! $FORCE == yes ]; then
@@ -176,16 +177,13 @@ function get_targets() {
 
       $GBS_PRISM_BIN/list_keyfile.sh -s $libname -f $fcid -e $enzyme -g $gbs_cohort -q $qc_cohort -t qc > $OUT_ROOT/${cohort_moniker}.key
       $GBS_PRISM_BIN/list_keyfile.sh -s $libname -f $fcid -e $enzyme -g $gbs_cohort -q $qc_cohort -t unblind_script  > $OUT_ROOT/${cohort_moniker}.unblind.sed
-
-      # get the name of the fastq files
-      #fastq_filenames=""
-      
-      
+      $GBS_PRISM_BIN/list_keyfile.sh -s $libname -f $fcid -e $enzyme -g $gbs_cohort -q $qc_cohort -t files  > $OUT_ROOT/${cohort_moniker}.filenames
 
       echo "#!/bin/bash
 cd $OUT_ROOT
-#./demultiplex_prism.sh  [-h] [-n] [-d] [-x gbsx|tassel3_qc|tassel3] [-l sample_info ]  [-e enzymeinfo] -O outdir input_file_name(s)
+mkdir -p $cohort
 # run demultiplexing
+./demultiplex_prism.sh -x tassel3_qc -l $OUT_ROOT/${cohort_moniker}.key  -e $enzyme -O $OUT_ROOT/$cohort \`cat $OUT_ROOT/${cohort_moniker}.filenames | awk '{print \$2}' -\`
 # run genotyping
      " > $script
       chmod +x $script
@@ -203,7 +201,7 @@ function fake_prism() {
 function run_prism() {
    # do genotyping
    cd $OUT_ROOT
-   make -f ag_gbs_qc_prism.sh -d -k  --no-builtin-rules -j 16 `cat $OUT_ROOT/ag_gbs_qc_prism_targets.txt` > $OUT_ROOT/ag_gbs_qc_prism.log 2>&1
+   make -f ag_gbs_qc_prism.mk -d -k  --no-builtin-rules -j 16 `cat $OUT_ROOT/ag_gbs_qc_prism_targets.txt` > $OUT_ROOT/ag_gbs_qc_prism.log 2>&1
 
    # run summaries
 }
diff --git a/demultiplex_prism.mk b/demultiplex_prism.mk
new file mode 100644
index 0000000..9a58333
--- /dev/null
+++ b/demultiplex_prism.mk
@@ -0,0 +1,24 @@
+# genotype_priosm main makefile
+#***************************************************************************************
+# references:
+#***************************************************************************************
+# make: 
+#     http://www.gnu.org/software/make/manual/make.html
+#
+
+
+%.demultiplex_prism:
+	$*.sh
+	date > $@
+	
+##############################################
+# specify the intermediate files to keep 
+##############################################
+.PRECIOUS: %.log %.genotype_priosm
+
+##############################################
+# cleaning - not yet doing this using make  
+##############################################
+clean:
+	echo "no clean for now" 
+
diff --git a/demultiplex_prism.sh b/demultiplex_prism.sh
index 7bfd3ca..a11403c 100755
--- a/demultiplex_prism.sh
+++ b/demultiplex_prism.sh
@@ -149,10 +149,9 @@ function echo_opts() {
 #
 function configure_env() {
    # copy scripts we need to outfolder
-   cd $SEQ_PRISMS_BIN
-   cp ../demultiplex_prism.sh $OUT_DIR
-   cp ../seq_prisms/data_prism.py $OUT_DIR
-   cp ../gbs_prism.mk $OUT_DIR
+   cd $GBS_PRISM_BIN
+   cp demultiplex_prism.sh $OUT_DIR
+   cp demultiplex_prism.mk $OUT_DIR
    cp $SAMPLE_INFO $OUT_DIR
    cp $ENZYME_INFO $OUT_DIR
 
@@ -175,6 +174,11 @@ function check_env() {
       echo "SEQ_PRISMS_BIN not set - exiting"
       exit 1
    fi
+   if [ -z "$GBS_PRISM_BIN" ]; then
+      echo "GBS_PRISM_BIN not set - exiting"
+      exit 1
+   fi
+
 }
 
 function get_targets() {
@@ -342,7 +346,7 @@ function fake_prism() {
 
 function run_prism() {
    # do genotyping
-   make -f gbs_prism.mk -d -k  --no-builtin-rules -j 16 `cat $OUT_DIR/demultiplex_targets.txt` > $OUT_DIR/demultiplex_prism.log 2>&1
+   make -f demultiplex_prism.mk -d -k  --no-builtin-rules -j 16 `cat $OUT_DIR/demultiplex_targets.txt` > $OUT_DIR/demultiplex_prism.log 2>&1
 
    # run summaries
 }
diff --git a/genotype_prism.mk b/genotype_prism.mk
index a2a1b32..e6a6a0f 100644
--- a/genotype_prism.mk
+++ b/genotype_prism.mk
@@ -7,11 +7,7 @@
 #
 
 
-%.genotype_priosm:
-	$*.sh
-	date > $@
-
-%.demultiplex_prism:
+%.genotype_prism:
 	$*.sh
 	date > $@