# HG changeset patch
# User rnateam
# Date 1383051339 14400
# Node ID e9a43f76591a473795673ae06ff8d7c1622ab060

Uploaded

diff -r 000000000000 -r e9a43f76591a tool_dependencies.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Tue Oct 29 08:55:39 2013 -0400
@@ -0,0 +1,64 @@
+<?xml version='1.0' encoding='utf-8'?>
+<tool_dependency>
+    <package name="rnashapes" version="2.1.6">
+        <install version="1.0">
+            <actions_group>
+                <!-- Download the binaries for RNAshapes compatible with 32-bit OSX. -->
+                <actions os="darwin" architecture="i386">
+                    <action type="download_by_url">http://bibiserv.techfak.uni-bielefeld.de/spool/download/bibiserv_1383039523_10840/RNAshapes-2.1.6-osx.tar.gz</action>
+                    <action type="move_file">
+                        <source>RNAshapes</source>
+                        <destination>$INSTALL_DIR/bin/</destination>
+                    </action>
+                </actions>
+                <!-- Download the binaries for RNAshapes compatible with 32-bit Linux (i386). -->
+                <actions os="linux" architecture="i386">
+                    <action type="download_by_url">http://bibiserv.techfak.uni-bielefeld.de/spool/download/bibiserv_1383039480_10830/RNAshapes-2.1.6-i386-linux.tar.gz</action>
+                    <action type="move_file">
+                        <source>RNAshapes</source>
+                        <destination>$INSTALL_DIR/bin/</destination>
+                    </action>
+                </actions>
+                <!-- Download the binaries for RNAshapes compatible with 32-bit Linux (i686). -->
+                <actions os="linux" architecture="i686">
+                    <action type="download_by_url">http://bibiserv.techfak.uni-bielefeld.de/spool/download/bibiserv_1383039480_10830/RNAshapes-2.1.6-i386-linux.tar.gz</action>
+                    <action type="move_file">
+                        <source>RNAshapes</source>
+                        <destination>$INSTALL_DIR/bin/</destination>
+                    </action>
+                </actions>
+                <!-- This actions tag is only processed if none of the above tags resulted in a successful installation. -->
+                <actions>
+                    <action type="download_by_url">http://bibiserv.techfak.uni-bielefeld.de/spool/download/bibiserv_1383039313_10782/RNAshapes-2.1.6.tar.gz</action>
+                    <action type="autoconf" />
+                </actions>
+                <!-- The $PATH environment variable is only set if one of the above <actions> tags resulted in a successful installation. -->
+                <action type="set_environment">
+                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
+                </action>
+            </actions_group>
+        </install>
+        <readme>
+Downloads the precompiled 32bit Linux, or Mac OS X RNAshapes
+binaries, which is faster than performing a local compliation,
+avoids any issues with build dependencies, and is more reproducible between
+installations as there is no variability from the compiler or library versions.
+
+RNA shape abstraction maps structures to a tree-like domain of shapes, retaining adjacency and nesting of structural features, 
+but disregarding helix lengths. Shape abstraction integrates well with dynamic programming algorithms, 
+and hence it can be applied during structure prediction rather than afterwards. 
+This avoids exponential explosion and can still give us a non-heuristic and complete account of properties of the molecule's folding space.
+
+RNAshapes offers three powerful RNA analysis tools in one single software package:
+
+- Computation of a small set of representative structures of different shapes, complete in a well-defined sense.
+- Computation of accumulated shape probabilities.
+- Comparative prediction of consensus structures, as an alternative to the over-expensive Sankoff Algorithm.
+
+
+For more details, see:
+http://bibiserv.techfak.uni-bielefeld.de/rnashapes/
+        </readme>
+    </package>
+</tool_dependency>
+