Mercurial > repos > hogart > unafold
changeset 2:75a1e3d0842f draft
Uploaded README.md
author | hogart |
---|---|
date | Tue, 10 Mar 2015 05:45:08 -0400 |
parents | 51baa0ab6def |
children | 188b9cec6b79 |
files | README.md |
diffstat | 1 files changed, 527 insertions(+), 0 deletions(-) [+] |
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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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