# HG changeset patch
# User bernhardlutz
# Date 1386276598 18000
# Node ID 7fe7c27092e084dd3c3d850dadcff06a834951cf
# Parent  1d177cf141efc3fe25f80b333d3f93b9a11cac74
Uploaded

diff -r 1d177cf141ef -r 7fe7c27092e0 tool_dependencies.xml
--- a/tool_dependencies.xml	Thu Dec 05 14:55:37 2013 -0500
+++ b/tool_dependencies.xml	Thu Dec 05 15:49:58 2013 -0500
@@ -1,21 +1,23 @@
-<?xml version="1.0"?>
 <tool_dependency>
-    <package name="spectral_hk" version="0.1">
+    <package name="vienna_rna" version="1.8.5">
         <install version="1.0">
             <actions>
-                <action type="shell_command">git clone https://bitbucket.org/ncgc/spectral_hk.git</action>
-                <action type="shell_command">git reset --hard 4c2d2f36708798bbe49a4633df246fa065e2268a</action>
-                <action type="shell_command">make</action>
-                <action type="move_file">
-                    <source>spectral_hk</source>
-                    <destination>$INSTALL_DIR/bin</destination>
-                </action>
+                <action type="download_by_url">http://www.tbi.univie.ac.at/~ivo/RNA/ViennaRNA-1.8.5.tar.gz</action>
+                <action type="command">./configure --prefix $INSTALL_DIR</action>
+                <action type="change_directory">Perl</action>
+                <action type="command">perl Makefile.PL PREFIX=$INSTALL_DIR/perl</action>
+                <action type="change_directory">..</action>
+                <action type="make_install" />
+
                 <action type="set_environment">
+                    <environment_variable name="LIBRARY_PATH" action="prepend_to">$INSTALL_DIR/lib</environment_variable>
+                    <environment_variable name="LD_LIBRARY_PATH" action="prepend_to">$INSTALL_DIR/lib</environment_variable>
                     <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
+                    <environment_variable name="C_INCLUDE_PATH" action="prepend_to">$INSTALL_DIR/include</environment_variable>
+                    <environment_variable name="PERL5LIB" action="prepend_to">$INSTALL_DIR/perl/lib</environment_variable>
                 </action>
             </actions>
         </install>
-        <readme>Compiling spectral_hk requires a C compiler (typically gcc)</readme>
+        <readme>Compiling ViennaRNA requires a C compiler (typically gcc)</readme>
     </package>
 </tool_dependency>
-