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author hogart
date Tue, 10 Mar 2015 05:54:18 -0400
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1 # Galaxy Tool wrapper for UNAFold #
1 2
3 This is the [Galaxy](http://usegalaxy.org) wrapper for the [UNAFold](http://mfold.rna.albany.edu/?q=DINAMelt/software). UNAFold software was developed for nucleic acid folding and hybridization prediction ([doi: 10.1007/978-1-60327-429-6_1](http://dx.doi.org/10.1007/978-1-60327-429-6_1), [doi: 10.1093/nar/gki591](http://dx.doi.org/10.1093/nar/gki591)). This wrapper is not yet deposited in the Tool-Shed repository, so this is the single place where it can downloaded.
2 4
5 ## Installation ##
3 6
4 <!DOCTYPE html> 7 * Save [UNAFold.pl](http://mfold.rna.albany.edu/?q=DINAMelt/software) in your $PATH, that is accesable to the Galaxy.
5 <html lang="en" class="">
6 <head prefix="og: http://ogp.me/ns# fb: http://ogp.me/ns/fb# object: http://ogp.me/ns/object# article: http://ogp.me/ns/article# profile: http://ogp.me/ns/profile#">
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12 <title>galaxy-tools-unafold/README.md at master · DrHogart/galaxy-tools-unafold · GitHub</title>
13 <link rel="search" type="application/opensearchdescription+xml" href="/opensearch.xml" title="GitHub">
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21 <meta content="@github" name="twitter:site" /><meta content="summary" name="twitter:card" /><meta content="DrHogart/galaxy-tools-unafold" name="twitter:title" /><meta content="galaxy-tools-unafold - Galaxy Tool wrapper for UNAFold" name="twitter:description" /><meta content="https://avatars1.githubusercontent.com/u/651214?v=3&amp;s=400" name="twitter:image:src" /> 9 * Create the directory `unafold` in `$GALAXY_DIR/tools/` and copy `unafold.xml` and `unafold.sh` files into it.
22 <meta content="GitHub" property="og:site_name" /><meta content="object" property="og:type" /><meta content="https://avatars1.githubusercontent.com/u/651214?v=3&amp;s=400" property="og:image" /><meta content="DrHogart/galaxy-tools-unafold" property="og:title" /><meta content="https://github.com/DrHogart/galaxy-tools-unafold" property="og:url" /><meta content="galaxy-tools-unafold - Galaxy Tool wrapper for UNAFold" property="og:description" /> 10 * Add the Galaxy tool definition to the `tools_conf.xml`:
23 <meta name="browser-stats-url" content="/_stats"> 11 ```html
24 <link rel="assets" href="https://assets-cdn.github.com/"> 12 <section id="unafold_tool" name="UNAFold">
25 <link rel="conduit-xhr" href="https://ghconduit.com:25035"> 13 <tool file="unafold/unafold.xml" />
26 14 </section>`
27 <meta name="pjax-timeout" content="1000"> 15 ```
28
29 16
30 <meta name="msapplication-TileImage" content="/windows-tile.png"> 17 * Please, be sure that `zip` datatype is registered in your Galaxy instance. If not, add the following string to the `datatypes_conf.xml` file:
31 <meta name="msapplication-TileColor" content="#ffffff"> 18 ```html
32 <meta name="selected-link" value="repo_source" data-pjax-transient> 19 <datatype extension="zip" type="galaxy.datatypes.binary:Binary" mimetype="application/zip" subclass="True" />
33 <meta name="google-analytics" content="UA-3769691-2"> 20 ```
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413 <article class="markdown-body entry-content" itemprop="mainContentOfPage"><h1>
414 <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>
415
416 <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>
417
418 <h2>
419 <a id="user-content-installation" class="anchor" href="#installation" aria-hidden="true"><span class="octicon octicon-link"></span></a>Installation</h2>
420
421 <ul class="task-list">
422 <li><p>Save <a href="http://mfold.rna.albany.edu/?q=DINAMelt/software">UNAFold.pl</a> in your $PATH, that is accesable to the Galaxy.</p></li>
423 <li><p>Create the directory <code>unafold</code> in <code>$GALAXY_DIR/tools/</code> and copy <code>unafold.xml</code> and <code>unafold.sh</code> files into it.</p></li>
424 <li>Add the Galaxy tool definition to the <code>tools_conf.xml</code>:</li>
425 </ul>
426
427 <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;
428 &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;
429 &lt;/<span class="pl-ent">section</span>&gt;`</pre></div>
430
431 <ul class="task-list">
432 <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>
433 </ul>
434
435 <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>
436
437 <ul class="task-list">
438 <li>Reload the Galaxy instance.</li>
439 </ul>
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