From 9999dd07fa83308c36d8cde82d340507204af414 Mon Sep 17 00:00:00 2001
From: Bjoern Gruening <bjoern.gruening@gmail.com>
Date: Tue, 21 Jan 2014 18:57:47 +0100
Subject: [PATCH 1/2] Add missing requirement tags.

---
 lib/galaxy/datatypes/converters/bam_to_bai.xml | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/lib/galaxy/datatypes/converters/bam_to_bai.xml b/lib/galaxy/datatypes/converters/bam_to_bai.xml
index 42943966f89..3f6d363db4f 100644
--- a/lib/galaxy/datatypes/converters/bam_to_bai.xml
+++ b/lib/galaxy/datatypes/converters/bam_to_bai.xml
@@ -1,4 +1,7 @@
 <tool id="CONVERTER_Bam_Bai_0" name="Bam to Bai" hidden="true">
+  <requirements>
+      <requirement type="package">samtools</requirement>
+  </requirements>
   <command>samtools index $input1 $output1</command>
   <inputs>
     <page>
@@ -10,4 +13,4 @@
    </outputs>
   <help>
   </help>
-</tool>
\ No newline at end of file
+</tool>

From 16dfc5e851a1c9512faf77e778a9f27288e90e32 Mon Sep 17 00:00:00 2001
From: Bjoern Gruening <bjoern.gruening@gmail.com>
Date: Tue, 21 Jan 2014 18:58:25 +0100
Subject: [PATCH 2/2] Add missing requirement tags.

---
 lib/galaxy/datatypes/converters/sam_to_bam.xml | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/lib/galaxy/datatypes/converters/sam_to_bam.xml b/lib/galaxy/datatypes/converters/sam_to_bam.xml
index 1a5ce77b794..8d743d8ad7a 100644
--- a/lib/galaxy/datatypes/converters/sam_to_bam.xml
+++ b/lib/galaxy/datatypes/converters/sam_to_bam.xml
@@ -5,6 +5,9 @@
          To fix this: (a) merge sam_to_bam tool in tools with this conversion (like fasta_to_len 
          conversion); and (b) define a datatype-specific way to set converter parameters.
       -->
+    <requirements>
+        <requirement type="package">samtools</requirement>
+    </requirements>
     <command interpreter="python">sam_to_bam.py $input1 $output</command>
     <inputs>
         <param name="input1" type="data" format="sam" label="SAM file"/>