[med-svn] [pbsuite] 07/11: Fix pbhoney example workflow script

[Afif Elghraoui]

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commit d43b78dabe8c6ef110520f221242043bc1a9d316
Author: Afif Elghraoui <afif at ghraoui.name>
Date:   Tue Feb 9 00:16:35 2016 -0800

    Fix pbhoney example workflow script
---
 debian/patches/fix-example.patch | 37 +++++++++++++++++++++++++++++++++++++
 debian/patches/series            |  1 +
 2 files changed, 38 insertions(+)

diff --git a/debian/patches/fix-example.patch b/debian/patches/fix-example.patch
new file mode 100644
index 0000000..110e05e
--- /dev/null
+++ b/debian/patches/fix-example.patch
@@ -0,0 +1,37 @@
+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 at 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
+ 
diff --git a/debian/patches/series b/debian/patches/series
index 330b576..689e1f6 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,3 +1,4 @@
 fix-syntax-error.patch
 intervaltree-import-statement.patch
 rm-intervaltree-dependency.patch
+fix-example.patch

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