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author | hogart |
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date | Tue, 10 Mar 2015 05:45:08 -0400 |
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js-update-url-with-hash">Blame</a> <a href="/DrHogart/galaxy-tools-unafold/commits/master/README.md" class="minibutton " rel="nofollow">History</a> </div><!-- /.button-group --> <a class="octicon-button disabled tooltipped tooltipped-w" href="#" aria-label="You must be signed in to make or propose changes"><span class="octicon octicon-pencil"></span></a> <a class="octicon-button danger disabled tooltipped tooltipped-w" href="#" aria-label="You must be signed in to make or propose changes"> </a> </div><!-- /.actions --> <div class="file-info"> 23 lines (16 sloc) <span class="file-info-divider"></span> 1.239 kb </div> </div> <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> <<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>> <<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> /> </<span class="pl-ent">section</span>>`</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> <<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> /></pre></div> <ul class="task-list"> <li>Reload the Galaxy instance.</li> </ul> </article> </div> </div> <a href="#jump-to-line" rel="facebox[.linejump]" data-hotkey="l" style="display:none">Jump to Line</a> <div id="jump-to-line" style="display:none"> <form accept-charset="UTF-8" class="js-jump-to-line-form"> <input class="linejump-input js-jump-to-line-field" type="text" placeholder="Jump to line…" autofocus> <button type="submit" class="button">Go</button> </form> </div> </div> </div><!-- /.repo-container --> <div class="modal-backdrop"></div> </div><!-- /.container --> </div><!-- /.site --> </div><!-- /.wrapper --> <div class="container"> <div class="site-footer" role="contentinfo"> <ul class="site-footer-links right"> <li><a href="https://status.github.com/" data-ga-click="Footer, go to status, text:status">Status</a></li> <li><a href="https://developer.github.com" data-ga-click="Footer, go to api, text:api">API</a></li> <li><a href="http://training.github.com" data-ga-click="Footer, go to training, text:training">Training</a></li> <li><a href="http://shop.github.com" data-ga-click="Footer, go to shop, text:shop">Shop</a></li> <li><a href="https://github.com/blog" data-ga-click="Footer, go to blog, text:blog">Blog</a></li> <li><a href="https://github.com/about" data-ga-click="Footer, go to about, text:about">About</a></li> </ul> <a href="https://github.com" aria-label="Homepage"> <span class="mega-octicon octicon-mark-github" title="GitHub"></span> </a> <ul class="site-footer-links"> <li>© 2015 <span title="0.04783s from github-fe143-cp1-prd.iad.github.net">GitHub</span>, Inc.</li> <li><a href="https://github.com/site/terms" data-ga-click="Footer, go to terms, text:terms">Terms</a></li> <li><a href="https://github.com/site/privacy" data-ga-click="Footer, go to privacy, text:privacy">Privacy</a></li> <li><a href="https://github.com/security" data-ga-click="Footer, go to security, text:security">Security</a></li> <li><a href="https://github.com/contact" data-ga-click="Footer, go to contact, text:contact">Contact</a></li> </ul> </div> </div> <div class="fullscreen-overlay js-fullscreen-overlay" id="fullscreen_overlay"> <div class="fullscreen-container js-suggester-container"> <div class="textarea-wrap"> <textarea name="fullscreen-contents" id="fullscreen-contents" class="fullscreen-contents js-fullscreen-contents" placeholder=""></textarea> <div class="suggester-container"> <div class="suggester fullscreen-suggester js-suggester js-navigation-container"></div> </div> </div> </div> <div class="fullscreen-sidebar"> <a href="#" class="exit-fullscreen js-exit-fullscreen tooltipped tooltipped-w" aria-label="Exit Zen Mode"> <span class="mega-octicon octicon-screen-normal"></span> </a> <a href="#" class="theme-switcher js-theme-switcher tooltipped tooltipped-w" aria-label="Switch themes"> <span class="octicon octicon-color-mode"></span> </a> </div> </div> <div id="ajax-error-message" class="flash flash-error"> <span class="octicon octicon-alert"></span> <a href="#" class="octicon octicon-x flash-close js-ajax-error-dismiss" aria-label="Dismiss error"></a> Something went wrong with that request. 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