Mercurial > repos > iuc > package_randfold_2_0

changeset 0:b34d2c942c79 draft

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Imported from capsule None
author iuc
date Tue, 27 Jan 2015 09:01:30 -0500
parents
children 53e370639b89
files tool_dependencies.xml
diffstat 1 files changed, 45 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Tue Jan 27 09:01:30 2015 -0500
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+<?xml version="1.0"?>
+<tool_dependency>
+  <package name="squid" version="1.9g">
+      <repository changeset_revision="c1b72442ee05" name="package_squid_1_9g" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="randfold" version="2.0">
+      <install version="1.0">
+          <actions>
+              <action type="download_by_url">http://bioinformatics.psb.ugent.be/supplementary_data/erbon/nov2003/downloads/randfold-2.0.tar.gz</action>
+                <action type="set_environment_for_install">
+                  <repository changeset_revision="c1b72442ee05" name="package_squid_1_9g" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
+                      <package name="squid" version="1.9g" />
+                    </repository>
+                </action>
+                <action type="shell_command">make</action>
+                <action type="move_file">
+                  <source>randfold</source>
+                    <destination>$INSTALL_DIR/bin</destination>
+                </action>
+                <action type="set_environment">
+                  <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
+                </action>
+            </actions>
+        </install>
+        <readme>
+
+RANDFOLD - A randsomization test for sequence secondary structure 
+Copyright (C) 2005 Eric Bonnet - Bioinformatics &amp;amp; Evolutionary Genomics - VIB
+-----------------------------------------------------------------------------
+
+This is RANDFOLD version 2. The software compute the probability that, for a 
+given sequence, the Minimum Free Energy (MFE) of the secondary structure is 
+different from MFE computed with random sequences. 
+
+For more information, see the paper published in Bioinformatics:
+
+Bonnet E, Wuyts J, Rouze P, Van de Peer Y.
+Evidence that microRNA precursors, unlike other non-coding RNAs, have lower 
+folding free energies than random sequences.
+Bioinformatics. 2004 Nov 22;20(17):2911-7.
+PMID: 15217813
+
+        </readme>
+    </package>
+</tool_dependency>