# HG changeset patch
# User devteam
# Date 1380565229 14400
# Node ID c0f72bdba484c176ccfb9c1e5125e83866d3af78
# Parent  ecf4ca7388a5c08586b37f5a9f3a6e006304a2cb
Uploaded updated tool dependency definition that copies header files to INSTALL_DIR/include/bam/

diff -r ecf4ca7388a5 -r c0f72bdba484 tool_dependencies.xml
--- a/tool_dependencies.xml	Tue Sep 24 16:19:53 2013 -0400
+++ b/tool_dependencies.xml	Mon Sep 30 14:20:29 2013 -0400
@@ -4,28 +4,28 @@
         <install version="1.0">
             <actions_group>
                 <actions os="linux" architecture="i386">
-                    <action type="download_by_url">http://depot.galaxyproject.org/package/linux/i386/samtools/samtools-0.1.18-linux-i386.tgz</action>
+                    <action type="download_by_url" target_filename="samtools-0.1.18.tgz">http://depot.galaxyproject.org/package/linux/i386/samtools/samtools-0.1.18-linux-i386.tgz</action>
                     <action type="move_directory_files">
                         <source_directory>.</source_directory>
                         <destination_directory>$INSTALL_DIR</destination_directory>
                     </action>
                 </actions>
                 <actions os="linux" architecture="x86_64">
-                    <action type="download_by_url">http://depot.galaxyproject.org/package/linux/x86_64/samtools/samtools-0.1.18-linux-x86_64.tgz</action>
+                    <action type="download_by_url" target_filename="samtools-0.1.18.tgz">http://depot.galaxyproject.org/package/linux/x86_64/samtools/samtools-0.1.18-linux-x86_64.tgz</action>
                     <action type="move_directory_files">
                         <source_directory>.</source_directory>
                         <destination_directory>$INSTALL_DIR</destination_directory>
                     </action>
                 </actions>
                 <actions os="darwin" architecture="i386">
-                    <action type="download_by_url">http://depot.galaxyproject.org/package/darwin/i386/samtools/samtools-0.1.18-Darwin-i386.tgz</action>
+                    <action type="download_by_url" target_filename="samtools-0.1.18.tgz">http://depot.galaxyproject.org/package/darwin/i386/samtools/samtools-0.1.18-Darwin-i386.tgz</action>
                     <action type="move_directory_files">
                         <source_directory>.</source_directory>
                         <destination_directory>$INSTALL_DIR</destination_directory>
                     </action>
                 </actions>
                 <actions os="darwin" architecture="x86_64">
-                    <action type="download_by_url">http://depot.galaxyproject.org/package/darwin/x86_64/samtools/samtools-0.1.18-Darwin-x86_64.tgz</action>
+                    <action type="download_by_url" target_filename="samtools-0.1.18.tgz">http://depot.galaxyproject.org/package/darwin/x86_64/samtools/samtools-0.1.18-Darwin-x86_64.tgz</action>
                     <action type="move_directory_files">
                         <source_directory>.</source_directory>
                         <destination_directory>$INSTALL_DIR</destination_directory>
@@ -43,10 +43,15 @@
                         <source>libbam.a</source>
                         <destination>$INSTALL_DIR/lib</destination>
                     </action>
+                    <action type="move_directory_files">
+                        <source_directory>src</source_directory>
+                        <destination_directory>$INSTALL_DIR/include/bam</destination_directory>
+                    </action>
                 </actions>
                 <action type="set_environment">
                     <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
                     <environment_variable name="BAM_LIB_PATH" action="set_to">$INSTALL_DIR/lib</environment_variable>
+                    <environment_variable name="BAM_ROOT" action="set_to">$INSTALL_DIR</environment_variable>
                 </action>
             </actions_group>
         </install>