Mercurial > repos > hogart > unafold
diff README.md @ 4:bda10049b902 draft
Uploaded correct files instead of GitHub fetched
author | hogart |
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date | Tue, 10 Mar 2015 05:54:18 -0400 |
parents | 75a1e3d0842f |
children | 5f95a9afe2ee |
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<link href="https://github.com/DrHogart/galaxy-tools-unafold/commits/master.atom" rel="alternate" title="Recent Commits to galaxy-tools-unafold:master" type="application/atom+xml"> - - </head> - +# Galaxy Tool wrapper for UNAFold # - <body class="logged_out env-production vis-public page-blob"> - <a href="#start-of-content" tabindex="1" class="accessibility-aid js-skip-to-content">Skip to content</a> - <div class="wrapper"> - - - - - - - - <div class="header header-logged-out" role="banner"> - <div class="container clearfix"> - - <a class="header-logo-wordmark" href="https://github.com/" data-ga-click="(Logged out) Header, go to homepage, icon:logo-wordmark"> - <span class="mega-octicon octicon-logo-github"></span> - </a> - - <div class="header-actions" role="navigation"> - <a class="button primary" href="/join" data-ga-click="(Logged out) Header, clicked Sign up, text:sign-up">Sign up</a> - <a class="button" href="/login?return_to=%2FDrHogart%2Fgalaxy-tools-unafold%2Fblob%2Fmaster%2FREADME.md" data-ga-click="(Logged out) Header, clicked Sign in, text:sign-in">Sign in</a> - </div> - - <div class="site-search repo-scope js-site-search" role="search"> - <form accept-charset="UTF-8" action="/DrHogart/galaxy-tools-unafold/search" class="js-site-search-form" data-global-search-url="/search" data-repo-search-url="/DrHogart/galaxy-tools-unafold/search" method="get"><div style="margin:0;padding:0;display:inline"><input name="utf8" type="hidden" value="✓" /></div> - <input type="text" - class="js-site-search-field is-clearable" - data-hotkey="s" - name="q" - placeholder="Search" - data-global-scope-placeholder="Search GitHub" - data-repo-scope-placeholder="Search" - tabindex="1" - autocapitalize="off"> - <div class="scope-badge">This repository</div> -</form> - </div> - - <ul class="header-nav left" role="navigation"> - <li class="header-nav-item"> - <a class="header-nav-link" href="/explore" data-ga-click="(Logged out) Header, go to explore, text:explore">Explore</a> - </li> - <li class="header-nav-item"> - <a class="header-nav-link" href="/features" data-ga-click="(Logged out) Header, go to features, text:features">Features</a> - </li> - <li class="header-nav-item"> - <a class="header-nav-link" href="https://enterprise.github.com/" data-ga-click="(Logged out) Header, go to enterprise, text:enterprise">Enterprise</a> - </li> - <li class="header-nav-item"> - <a class="header-nav-link" href="/blog" data-ga-click="(Logged out) Header, go to blog, text:blog">Blog</a> - </li> - </ul> - - </div> -</div> - - - - <div id="start-of-content" class="accessibility-aid"></div> - <div class="site" itemscope itemtype="http://schema.org/WebPage"> - <div id="js-flash-container"> - - </div> - <div class="pagehead repohead instapaper_ignore readability-menu"> - <div class="container"> - -<ul class="pagehead-actions"> +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. - <li> - <a href="/login?return_to=%2FDrHogart%2Fgalaxy-tools-unafold" - class="minibutton with-count tooltipped tooltipped-n" - aria-label="You must be signed in to watch a repository" rel="nofollow"> - <span class="octicon octicon-eye"></span> - Watch - </a> - <a class="social-count" href="/DrHogart/galaxy-tools-unafold/watchers"> - 1 - </a> - - </li> - - <li> - <a href="/login?return_to=%2FDrHogart%2Fgalaxy-tools-unafold" - class="minibutton with-count tooltipped tooltipped-n" - aria-label="You must be signed in to star a repository" rel="nofollow"> - <span class="octicon octicon-star"></span> - Star - </a> - - <a class="social-count js-social-count" href="/DrHogart/galaxy-tools-unafold/stargazers"> - 0 - </a> - - </li> - - <li> - <a href="/login?return_to=%2FDrHogart%2Fgalaxy-tools-unafold" - class="minibutton with-count tooltipped tooltipped-n" - aria-label="You must be signed in to fork a repository" rel="nofollow"> - 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<div class="file-history-tease-header"> - Fetching contributors… - </div> +* Create the directory `unafold` in `$GALAXY_DIR/tools/` and copy `unafold.xml` and `unafold.sh` files into it. +* Add the Galaxy tool definition to the `tools_conf.xml`: +```html + <section id="unafold_tool" name="UNAFold"> + <tool file="unafold/unafold.xml" /> + </section>` +``` - <div class="participation"> - <p class="loader-loading"><img alt="" height="16" src="https://assets-cdn.github.com/assets/spinners/octocat-spinner-32-EAF2F5-0bdc57d34b85c4a4de9d0d1db10cd70e8a95f33ff4f46c5a8c48b4bf4e5a9abe.gif" width="16" /></p> - <p class="loader-error">Cannot retrieve contributors at this time</p> - </div> -</include-fragment> -<div class="file"> - <div class="file-header"> - <div class="file-actions"> - <div class="button-group"> - <a href="/DrHogart/galaxy-tools-unafold/raw/master/README.md" class="minibutton " id="raw-url">Raw</a> - <a href="/DrHogart/galaxy-tools-unafold/blame/master/README.md" class="minibutton 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> +* Please, be sure that `zip` datatype is registered in your Galaxy instance. If not, add the following string to the `datatypes_conf.xml` file: +```html + <datatype extension="zip" type="galaxy.datatypes.binary:Binary" mimetype="application/zip" subclass="True" /> +``` - </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. Please try again. - </div> - - - <script crossorigin="anonymous" src="https://assets-cdn.github.com/assets/frameworks-4bf9533935259bb898a8d60e1958f4d047968c430eae889800a187e279faf38f.js"></script> - <script async="async" crossorigin="anonymous" src="https://assets-cdn.github.com/assets/github-9d83860b0798bdd794d00b491fc7cb4ab9ea416cc8c511f719e253faa86e635b.js"></script> - - - - </body> -</html> - +* Reload the Galaxy instance.