# HG changeset patch
# User biomonika <biomonika@psu.edu>
# Date 1408993789 14400
# Node ID 9c08f9866ce60a9f268c53c1ec03b17afdcaffcb
# Parent  7558fc0db1cfb71b1c4c52f1b190f4da27780421
d7

diff -r 7558fc0db1cf -r 9c08f9866ce6 test_dependency.xml
--- a/test_dependency.xml	Mon Aug 25 14:55:16 2014 -0400
+++ b/test_dependency.xml	Mon Aug 25 15:09:49 2014 -0400
@@ -6,8 +6,9 @@
         <requirement type="package" version="0.1.19">samtools</requirement>
       </requirements>
       </requirements>
-      <command interpreter="bash">test_dependency.sh $output</command>
+      <command interpreter="bash">test_dependency.sh $output $input1</command>
       <inputs>
+        <param format="fastq" name="input1" type="data" label="Reference"/>
       </inputs>
       <outputs>
         <data format="txt" name="output" />
diff -r 7558fc0db1cf -r 9c08f9866ce6 tool_dependencies.xml
--- a/tool_dependencies.xml	Mon Aug 25 14:55:16 2014 -0400
+++ b/tool_dependencies.xml	Mon Aug 25 15:09:49 2014 -0400
@@ -7,6 +7,7 @@
         <install version="1.0">
             <actions>
                 <action type="download_by_url">http://sourceforge.net/projects/samtools/files/samtools/0.1.19/samtools-0.1.19.tar.bz2</action>
+                <action type="shell_command">sed -i .bak -e 's/O2/O2 -fPIC/‘ Makefile</action>
                 <action type="shell_command">make</action>
                 <action type="set_environment">
                     <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable>