# HG changeset patch
# User biomonika <biomonika@psu.edu>
# Date 1408987782 14400
# Node ID 480491c2ce1cb2e2ca749842d8ab0ea7a39e5f02
# Parent  5573c2fa98241ceb9b9d504af4de6ca31b75a48e
freebayes_inspired

diff -r 5573c2fa9824 -r 480491c2ce1c tool_dependencies.xml
--- a/tool_dependencies.xml	Mon Aug 25 12:51:30 2014 -0400
+++ b/tool_dependencies.xml	Mon Aug 25 13:29:42 2014 -0400
@@ -2,13 +2,28 @@
     <set_environment version="1.0">
         <environment_variable name="LINKYX_PATH" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable>
     </set_environment>
-    <package name="samtools_fPIC" version="1.1">
+
+    <package name="samtools" version="0.1.18">
         <install version="1.0">
             <actions>
-                <action type="download_by_url">http://sourceforge.net/projects/samtools/files/samtools/0.1.19/samtools-0.1.19.tar.bz2</action>
-                <action type="shell_command">sed -i 's/O2/O2 -fPIC/‘ Makefile </action>
-                <action type="shell_command">make </action>
-                <action type="make_directory">$INSTALL_DIR/bin</action>
+                <action type="download_by_url">http://sourceforge.net/projects/samtools/files/samtools/0.1.18/samtools-0.1.18.tar.bz2</action>
+                <action type="shell_command">sed -i 's/O2/O2 -fPIC/‘ Makefile</action>
+                <action type="shell_command">make</action>
+                <action type="move_file">
+                    <source>samtools</source>
+                    <destination>$INSTALL_DIR/bin</destination>
+                </action>
+                <action type="move_file">
+                    <source>libbam.a</source>
+                    <destination>$INSTALL_DIR/bin</destination>
+                </action>
+               <action type="move_file">
+                    <source>bam.h</source>
+                    <destination>$INSTALL_DIR/bin</destination>
+                </action>
+                <action type="set_environment">
+                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
+                </action>
                 <action type="set_environment">
                     <environment_variable name="SAMTOOLS" action="set_to">$INSTALL_DIR/bin</environment_variable>
                 </action>