diff tool_dependencies.xml @ 95:1b8b1c9cf1a8 draft

Uploaded

--- a/tool_dependencies.xml	Tue Nov 27 11:41:33 2012 -0500
+++ b/tool_dependencies.xml	Tue Nov 27 15:12:54 2012 -0500
@@ -3,18 +3,20 @@
     <set_environment version="1.0">
         <environment_variable name="SCRIPT_PATH" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable>
     </set_environment>
-    <package name="samtools" version="0.1.18">
+    <package name="samtools" version="0.1.12">
         <install version="1.0">
             <actions>
-                <action type="download_by_url">http://sourceforge.net/projects/samtools/files/samtools/0.1.18/samtools-0.1.18.tar.bz2</action>
-                <action type="shell_command">sed -i.bak -e 's/-lcurses/-lncurses/g' Makefile</action>
-                <action type="shell_command">make</action>
+                <action type="download_by_url">http://ec2-184-73-120-244.compute-1.amazonaws.com/modENCODE_Galaxy/tool_dependencies/samtools/samtools</action>
+                <action type="shell_command">chmod ago+x samtools</action>
                 <action type="move_file">
                     <source>samtools</source>
                     <destination>$INSTALL_DIR/bin</destination>
                 </action>
+
+                <action type="download_by_url">http://ec2-184-73-120-244.compute-1.amazonaws.com/modENCODE_Galaxy/tool_dependencies/samtools/maq2sam-long</action>
+                <action type="shell_command">chmod ago+x maq2sam-long </action>
                 <action type="move_file">
-                    <source>misc/maq2sam-long</source>
+                    <source>maq2sam-long</source>
                     <destination>$INSTALL_DIR/bin</destination>
                 </action>
                 <action type="set_environment">