Description: Adjust pbhoney example script for Debian
 * Use /bin/sh rather than /bin/bash (unnecessarily)
 * s/Honey.py/Honey/
 * Fix error in example
 (reference parameter doesn't exist for one command but is required for another)
 * Replace sam2bam script (not packaged) with the actual samtools commands
Author: Afif Elghraoui <afif@ghraoui.name>
Forwarded: no
Last-Update: 2016-02-08
--- pbsuite.orig/docs/honeyExample/workflow.sh
+++ pbsuite/docs/honeyExample/workflow.sh
@@ -1,18 +1,20 @@
-#!/bin/bash
+#!/bin/sh
 
 #Set the inputReads and reference -- change at your leisure
 inputReads=filtered_subreads.fastq
 reference=lambda_modified.fasta
 
 echo "PIEMapping"
-Honey.py pie $inputReads $reference
+Honey pie $inputReads $reference -o mappingFinal.sam
 
 echo "Sam To Bam"
-sam2bam $reference mapping.tails.sam
+samtools view -bt $reference mappingFinal.sam |
+    samtools sort - > mappingFinal.bam
+samtools index mappingFinal.bam
 
 echo "Calling Tails"
-Honey.py tails mappingFinal.bam --reference $reference
+Honey tails mappingFinal.bam
 
 echo "Calling Spots"
-Honey.py spots mappingFinal.bam
+Honey spots --reference $reference mappingFinal.bam