diff --git a/README b/README
index 187232f..6dea733 100755
--- a/README
+++ b/README
@@ -16,6 +16,7 @@ R packages (HiddenMarkov 1.3-1, zoo 1.6-2, R.methodsS3 1.2.0 and R.oo 1.7.3)
 ### Installation instructions ###
 git clone git://github.com/JaneliaSciComp/msg.git
 cd msg
+copy or link version 0.1.9 of samtools into the msg directory
 make
 
 ### Toy Example ###
diff --git a/make-pileups.sh b/make-pileups.sh
index 22b9e48..f870165 100755
--- a/make-pileups.sh
+++ b/make-pileups.sh
@@ -17,6 +17,8 @@ true=0
 false="false"
 
 all=$false
+script_dir=$(dirname $0)
+
 
 while getopts "ai:d:p:q:" opt
 do 
@@ -44,19 +46,19 @@ species=par1
 file=$dir/aln_${indiv}_${species}-filtered
 echo "$file"
 
-[ -e $parent1.fai ] || samtools faidx $parent1
+[ -e $parent1.fai ] || $script_dir/samtools faidx $parent1
 [ -e $file-sorted.bam ] || {
     echo "samtools view -bt $parent1.fai $file.sam | samtools sort - $file-sorted"
-    samtools view -bt $parent1.fai $file.sam | samtools sort - $file-sorted
+    $script_dir/samtools view -bt $parent1.fai $file.sam | $script_dir/samtools sort - $file-sorted
 }
-[ -e $file-sorted.bam.bai ] || samtools index $file-sorted.bam
+[ -e $file-sorted.bam.bai ] || $script_dir/samtools index $file-sorted.bam
 
 for ref in $refs ; do
     [ -e $file-$ref-sorted.pileup ] || {
         echo "Making pileup for $species contig $ref"
-        samtools view -bu $file-sorted.bam $ref | samtools sort - $file-$ref-sorted
-        samtools index $file-$ref-sorted.bam
-        samtools pileup -cf $parent1 $file-$ref-sorted.bam > $file-$ref-sorted.pileup
+        $script_dir/samtools view -bu $file-sorted.bam $ref | samtools sort - $file-$ref-sorted
+        $script_dir/samtools index $file-$ref-sorted.bam
+        $script_dir/samtools pileup -cf $parent1 $file-$ref-sorted.bam > $file-$ref-sorted.pileup
         rm $file-$ref-sorted.bam $file-$ref-sorted.bam.bai
     }
 done
diff --git a/msg.pl b/msg.pl
index 8683a37..548b1e2 100755
--- a/msg.pl
+++ b/msg.pl
@@ -16,8 +16,8 @@ sub system_call {
 
 GetOptions(
 	'barcodes|b=s' => \$barcodes,
-   're_cutter=s' => \$re_cutter,
-   'linker_system=s' => \$linker_system,
+	're_cutter=s' => \$re_cutter,
+	'linker_system=s' => \$linker_system,
 	'reads|i=s' => \$raw_read_data,
 	'update|u' => \$update_genomes,
 	'parent1=s' => \$parent1_genome,
@@ -116,7 +116,7 @@ sub system_call {
 
 			&system_call("bwa", "index", "-a", $genome_index{$sp}, "$genomes_fa{$sp}.msg") 
 				unless( -e "$genomes_fa{$sp}.msg.bwt" and -e "$genomes_fa{$sp}.msg.ann" );
-			&system_call("samtools", "faidx", "$genomes_fa{$sp}.msg") ;
+			&system_call("$src/samtools", "faidx", "$genomes_fa{$sp}.msg") ;
 
 			unless (-e "$out.sam") {
 				&system_call("bwa", "aln", "-t", $update_nthreads, "$genomes_fa{$sp}.msg", $reads_for_updating_fq{$sp}, "> $out.sai") ;
@@ -125,10 +125,10 @@ sub system_call {
 
 			&system_call("$src/filter-sam.py", "-i", "$out.sam", "-o", "$out.filtered.sam") ;
 
-			&system_call("samtools", "view", "-bt", "$genomes{$sp}.msg.fai", "-o $out.bam", "$out.filtered.sam") ;
-			&system_call("samtools", "sort", "$out.bam", "$out.bam.sorted") ;
-			&system_call("samtools", "index", "$out.bam.sorted.bam") ;
-			&system_call("samtools", "pileup", "-f", "$genomes_fa{$sp}.msg", "$out.bam.sorted.bam", "-c", "> $out.pileup") ;
+			&system_call("$src/samtools", "view", "-bt", "$genomes{$sp}.msg.fai", "-o $out.bam", "$out.filtered.sam") ;
+			&system_call("$src/samtools", "sort", "$out.bam", "$out.bam.sorted") ;
+			&system_call("$src/samtools", "index", "$out.bam.sorted.bam") ;
+			&system_call("$src/samtools", "pileup", "-f", "$genomes_fa{$sp}.msg", "$out.bam.sorted.bam", "-c", "> $out.pileup") ;
 
 		}
 
diff --git a/test_dependencies_executable.sh b/test_dependencies_executable.sh
index e8b5029..966970d 100644
--- a/test_dependencies_executable.sh
+++ b/test_dependencies_executable.sh
@@ -20,9 +20,15 @@ if ! which bwa >/dev/null 2>/dev/null ; then
 	exit 1
 fi
 
-if ! which samtools >/dev/null 2>/dev/null ; then
-	echo "Please install samtools somewhere in your PATH"
-	exit 1
+samtools_required_version="Version: 0.1.9 (r783)"
+if ! [ -e $(dirname $0)/samtools ] ; then
+        echo "Please install samtools ($samtools_required_version) within the msg directory"
+	    exit 1
+fi
+samtools_version=`$(dirname $0)/samtools 2>&1 | grep 'Version:'`
+if [ "$samtools_version" != "$samtools_required_version" ] ; then
+    echo "The samtools found within the msg directory is $samtools_version.  It must be $samtools_required_version" 
+    exit 1
 fi
 
 echo "All required executables found in PATH"