Mercurial > repos > hogart > unafold

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README.md	Tue Mar 10 05:45:08 2015 -0400
@@ -0,0 +1,527 @@
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+    <div id="readme" class="blob instapaper_body">
+    <article class="markdown-body entry-content" itemprop="mainContentOfPage"><h1>
+<a id="user-content-galaxy-tool-wrapper-for-unafold" class="anchor" href="#galaxy-tool-wrapper-for-unafold" aria-hidden="true"><span class="octicon octicon-link"></span></a>Galaxy Tool wrapper for UNAFold</h1>
+
+<p>This is the <a href="http://usegalaxy.org">Galaxy</a> wrapper for the <a href="http://mfold.rna.albany.edu/?q=DINAMelt/software">UNAFold</a>. UNAFold software was developed for nucleic acid folding and hybridization prediction (<a href="http://dx.doi.org/10.1007/978-1-60327-429-6_1">doi: 10.1007/978-1-60327-429-6_1</a>, <a href="http://dx.doi.org/10.1093/nar/gki591">doi: 10.1093/nar/gki591</a>). This wrapper is not yet deposited in the Tool-Shed repository, so this is the single place where it can downloaded.</p>
+
+<h2>
+<a id="user-content-installation" class="anchor" href="#installation" aria-hidden="true"><span class="octicon octicon-link"></span></a>Installation</h2>
+
+<ul class="task-list">
+<li><p>Save <a href="http://mfold.rna.albany.edu/?q=DINAMelt/software">UNAFold.pl</a> in your $PATH, that is accesable to the Galaxy.</p></li>
+<li><p>Create the directory <code>unafold</code> in <code>$GALAXY_DIR/tools/</code> and copy <code>unafold.xml</code> and <code>unafold.sh</code> files into it.</p></li>
+<li>Add the Galaxy tool definition to the <code>tools_conf.xml</code>:</li>
+</ul>
+
+<div class="highlight highlight-html"><pre>    &lt;<span class="pl-ent">section</span> <span class="pl-e">id</span>=<span class="pl-s1"><span class="pl-pds">"</span>unafold_tool<span class="pl-pds">"</span></span> <span class="pl-e">name</span>=<span class="pl-s1"><span class="pl-pds">"</span>UNAFold<span class="pl-pds">"</span></span>&gt;
+        &lt;<span class="pl-ent">tool</span> <span class="pl-e">file</span>=<span class="pl-s1"><span class="pl-pds">"</span>unafold/unafold.xml<span class="pl-pds">"</span></span> /&gt;
+    &lt;/<span class="pl-ent">section</span>&gt;`</pre></div>
+
+<ul class="task-list">
+<li>Please, be sure that <code>zip</code> datatype is registered in your Galaxy instance. If not, add the following string to the <code>datatypes_conf.xml</code> file:</li>
+</ul>
+
+<div class="highlight highlight-html"><pre>    &lt;<span class="pl-ent">datatype</span> <span class="pl-e">extension</span>=<span class="pl-s1"><span class="pl-pds">"</span>zip<span class="pl-pds">"</span></span> <span class="pl-e">type</span>=<span class="pl-s1"><span class="pl-pds">"</span>galaxy.datatypes.binary:Binary<span class="pl-pds">"</span></span> <span class="pl-e">mimetype</span>=<span class="pl-s1"><span class="pl-pds">"</span>application/zip<span class="pl-pds">"</span></span> <span class="pl-e">subclass</span>=<span class="pl-s1"><span class="pl-pds">"</span>True<span class="pl-pds">"</span></span> /&gt;</pre></div>
+
+<ul class="task-list">
+<li>Reload the Galaxy instance.</li>
+</ul>
+</article>
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