# HG changeset patch
# User devteam
# Date 1380120673 14400
# Node ID fd1537dcbe4a5cc2e7023a32cacfe2f7fedd5049
# Parent  a7936f4ea40582f960a29010f1cd8b9a84f808e7
Uploaded an updated tool_dependencies.xml that first attempts to download a precompiled binary for SAMTools 0.1.18.

diff -r a7936f4ea405 -r fd1537dcbe4a tool_dependencies.xml
--- a/tool_dependencies.xml	Tue Feb 05 14:17:55 2013 -0500
+++ b/tool_dependencies.xml	Wed Sep 25 10:51:13 2013 -0400
@@ -2,18 +2,53 @@
 <tool_dependency>
     <package name="samtools" version="0.1.18">
         <install version="1.0">
-            <actions>
-                <action type="download_by_url">http://downloads.sourceforge.net/project/samtools/samtools/0.1.18/samtools-0.1.18.tar.bz2</action>
-                <action type="shell_command">sed -i.bak 's/-lcurses/-lncurses/' Makefile</action>
-                <action type="shell_command">make</action>
-                <action type="move_file">
-                    <source>samtools</source>
-                    <destination>$INSTALL_DIR/bin</destination>
-                </action>
+            <actions_group>
+                <actions os="linux" architecture="i386">
+                    <action type="download_by_url" target_filename="samtools-0.1.18.tgz">http://depot.galaxyproject.org/package/linux/i386/samtools/samtools-0.1.18-linux-i386.tgz</action>
+                    <action type="move_directory_files">
+                        <source_directory>.</source_directory>
+                        <destination_directory>$INSTALL_DIR</destination_directory>
+                    </action>
+                </actions>
+                <actions os="linux" architecture="x86_64">
+                    <action type="download_by_url" 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>$INSTALL_DIR</destination_directory>
+                    </action>
+                </actions>
+                <actions os="darwin" architecture="i386">
+                    <action type="download_by_url" target_filename="samtools-0.1.18.tgz">http://depot.galaxyproject.org/package/darwin/i386/samtools/samtools-0.1.18-Darwin-i386.tgz</action>
+                    <action type="move_directory_files">
+                        <source_directory>.</source_directory>
+                        <destination_directory>$INSTALL_DIR</destination_directory>
+                    </action>
+                </actions>
+                <actions os="darwin" architecture="x86_64">
+                    <action type="download_by_url" 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>$INSTALL_DIR</destination_directory>
+                    </action>
+                </actions>
+                <actions>
+                    <action type="download_by_url">http://depot.galaxyproject.org/package/source/samtools/samtools-0.1.18.tar.bz2</action>
+                    <action type="shell_command">sed -i.bak 's/-lcurses/-lncurses/' Makefile</action>
+                    <action type="shell_command">make</action>
+                    <action type="move_file">
+                        <source>samtools</source>
+                        <destination>$INSTALL_DIR/bin</destination>
+                    </action>
+                    <action type="move_file">
+                        <source>libbam.a</source>
+                        <destination>$INSTALL_DIR/lib</destination>
+                    </action>
+                </actions>
                 <action type="set_environment">
                     <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
+                    <environment_variable name="BAM_LIB_PATH" action="set_to">$INSTALL_DIR/lib</environment_variable>
                 </action>
-            </actions>
+            </actions_group>
         </install>
         <readme>
 Program: samtools (Tools for alignments in the SAM format)