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Changed the layout again, added more content, added the command-line tutorial page, downloads, about, user guides, admin page, developers guide
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‎about/index.html

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<!DOCTYPE HTML>
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<html lang="en">
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<head>
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<meta charset="utf-8">
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<title>SeqWare - About</title>
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<link rel="stylesheet" type="text/css" href="/style.css" media="screen">
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<meta name="generator" content="nanoc 3.3.6">
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</head>
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<body>
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<div id="homepic">
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<a href="/"><img src="/pictures/seqware_logo.png"/></a>
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</div>
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<div id="main">
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<h1 id="seqware">SeqWare</h1>
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<p>The open source SeqWare project is a portable software infrastructure designed to analyze massive genomics datasets produced by contemporary and emerging technologies, in particular Next Generation Sequencing (NGS) platforms. It consists of a comprehensive suite of tools focused on enabling the end-to-end analysis of sequence data – from from raw base calling to analyzed variants ready for interpretation by users.</p>
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<p>SeqWare currently provides four tools specifically designed to support massively parallel sequencing technologies. All four tools can be used together or separately. </p>
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<ul>
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<li><strong>Portal</strong>: a LIMS-like web application to manage samples, record computational events, and present results back to end users. </li>
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<li><strong>Pipeline</strong>: a workflow engine that is capable of wrapping and combining other tools (BFAST, BWA, SAMtools, etc) into complex pipelines, recording metadata about the analysis, and facilitates automation of pipelines based on metadata. </li>
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<li><strong>Query Engine</strong>: a query tool to store and query variants and other events inferred from sequence data. </li>
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<li><strong>MetaDB</strong>: provides a common database to store metadata used by all components. </li>
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</ul>
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<p>SeqWare is currently used by a variety of NGS users including the <a href="http://unclineberger.org/">Lineberger Comprehensive Cancer Center at UNC</a>, at the <a href="http://oicr.on.ca/">Ontario Institute for Cancer Research in Toronto</a> and by our commercial partner <a href="http://nimbusinformatics.com/">Nimbus Informatics</a>.</p>
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<h2 id="citation">Citation</h2>
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<p>O’Connor, B. D., B. Merriman, and S. F. Nelson. <a href="http://www.biomedcentral.com/1471-2105/11/S12/S2">SeqWare Query Engine: storing and searching sequence data in the cloud</a>. BMC Bioinformatics 2010, 11(Suppl 12):S2</p>
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</div>
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<div id="sidebar">
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<ul>
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<li><a href="/about/"><span>About SeqWare</span></a></li>
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<li><a href="/download/"><span>Download</span></a></li>
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</ul>
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<h2><span>Quick Reference</span></h2>
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<ul>
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<li><a href="/users/"><span>User Guide</span></a></li>
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<li><a href="/administrators/"><span>Administrator Guide</span></a></li>
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<li><a href="/source/"><span>Developers Guide</span></a></li>
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<li><a href="http://sourceforge.net/apps/mediawiki/seqware/index.php?title=Main_Page"><span>Old Wiki</span></a></li>
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</ul>
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<h2><span>APIs</span></h2>
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<ul>
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<li><a href="/webservice-api/"><span>Web Service API</span></a></li>
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<li><a href="/queryengine-api/"><span>Query Engine API</span></a></li>
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</ul>
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<h2><span>Contact</span></h2>
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<ul>
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<li><a href="http://sourceforge.net/mail/?group_id=239239"><span>Mailing Lists</span></a></li>
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<li><a href="mailto:[email protected]"><span>JIRA Bug Tracker</span></a></li>
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</ul>
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</div>
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</body>
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</html>

‎administrators/index.html

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<!DOCTYPE HTML>
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<html lang="en">
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<head>
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<meta charset="utf-8">
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<title>SeqWare - </title>
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<link rel="stylesheet" type="text/css" href="/style.css" media="screen">
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<meta name="generator" content="nanoc 3.3.6">
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</head>
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<body>
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<div id="homepic">
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<a href="/"><img src="/pictures/seqware_logo.png"/></a>
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</div>
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<div id="main">
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<p><a href="http://sourceforge.net/apps/mediawiki/seqware/index.php?title=Creating_a_SeqWare_VM">Creating a SeqWare VM</a></p>
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</div>
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<div id="sidebar">
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<ul>
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<li><a href="/about/"><span>About SeqWare</span></a></li>
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<li><a href="/download/"><span>Download</span></a></li>
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</ul>
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<h2><span>Quick Reference</span></h2>
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<ul>
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<li><a href="/users/"><span>User Guide</span></a></li>
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<li><a href="/administrators/"><span>Administrator Guide</span></a></li>
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<li><a href="/source/"><span>Developers Guide</span></a></li>
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<li><a href="http://sourceforge.net/apps/mediawiki/seqware/index.php?title=Main_Page"><span>Old Wiki</span></a></li>
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</ul>
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<h2><span>APIs</span></h2>
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<ul>
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<li><a href="/webservice-api/"><span>Web Service API</span></a></li>
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<li><a href="/queryengine-api/"><span>Query Engine API</span></a></li>
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</ul>
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<h2><span>Contact</span></h2>
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<ul>
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<li><a href="http://sourceforge.net/mail/?group_id=239239"><span>Mailing Lists</span></a></li>
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<li><a href="mailto:[email protected]"><span>JIRA Bug Tracker</span></a></li>
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</ul>
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</div>
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</body>
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</html>

‎download/index.html

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<!DOCTYPE HTML>
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<html lang="en">
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<head>
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<meta charset="utf-8">
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<title>SeqWare - Downloads</title>
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<link rel="stylesheet" type="text/css" href="/style.css" media="screen">
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<meta name="generator" content="nanoc 3.3.6">
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</head>
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<body>
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<div id="homepic">
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<a href="/"><img src="/pictures/seqware_logo.png"/></a>
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</div>
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<div id="main">
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<h1 id="downloads">Downloads</h1>
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<h2 id="seqware-pipeline">SeqWare Pipeline</h2>
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<p>The latest version of the pipeline jar is always available on our continuous build server. Please choose the jar that has the -full suffix, e.g. <a href="http://jenkins.res.oicr.on.ca/job/seqware/lastStableBuild/net.sourceforge.seqware$seqware-distribution/">seqware-distribution-0.12.5-SNAPSHOT-full.jar</a>.</p>
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<h2 id="source-code">Source Code</h2>
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<p>We are currently in the process of migrating from SourceForge to GitHub, so our code is distributed between two locations:</p>
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<ol>
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<li><a href="http://sourceforge.net/scm/?type=svn&amp;group_id=239239">Subversion on SourceForge</a> : All of our SeqWare Pipeline, MetaDB, Portal and archetype code</li>
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<li><a href="https://github.com/SeqWare/seqware">Git on GitHub</a> : Our query engine code and website documentation (including this site!)</li>
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</ol>
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<p>Please be patient with us as we transition, and send any of your questions or comments to one of our <a href="http://sourceforge.net/mail/?group_id=239239">mailing lists</a>.</p>
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<h2 id="virtual-machines-vms-and-amis">Virtual Machines (VMs) and AMIs</h2>
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<p>….</p>
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</div>
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<div id="sidebar">
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<ul>
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<li><a href="/about/"><span>About SeqWare</span></a></li>
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<li><a href="/download/"><span>Download</span></a></li>
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</ul>
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<h2><span>Quick Reference</span></h2>
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<ul>
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<li><a href="/users/"><span>User Guide</span></a></li>
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<li><a href="/administrators/"><span>Administrator Guide</span></a></li>
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<li><a href="/source/"><span>Developers Guide</span></a></li>
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<li><a href="http://sourceforge.net/apps/mediawiki/seqware/index.php?title=Main_Page"><span>Old Wiki</span></a></li>
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</ul>
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<h2><span>APIs</span></h2>
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<ul>
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<li><a href="/webservice-api/"><span>Web Service API</span></a></li>
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<li><a href="/queryengine-api/"><span>Query Engine API</span></a></li>
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</ul>
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<h2><span>Contact</span></h2>
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<ul>
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<li><a href="http://sourceforge.net/mail/?group_id=239239"><span>Mailing Lists</span></a></li>
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<li><a href="mailto:[email protected]"><span>JIRA Bug Tracker</span></a></li>
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</ul>
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</div>
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</body>
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</html>

‎index.html

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<meta name="generator" content="nanoc 3.3.6">
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</head>
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<body>
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<div id="homepic">
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<a href="/"><img src="/pictures/seqware_logo.png"/></a>
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</div>
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<div id="main">
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<div id="homepic">
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<a href="/"><img src="pictures/seqware_logo.png"/></a>
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</div>
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<h1>Next-Generation Sequencing Analysis on the Grid and in the Cloud</h1>
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<h1>Next-Generation Sequencing Analysis on the Grid and in the Cloud</h1>
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<p>The open source SeqWare project is a portable software infrastructure designed to analyze massive genomics datasets produced by contemporary and emerging technologies, in particular Next Generation Sequencing (NGS) platforms. It consists of a comprehensive suite of tools focused on enabling the end-to-end analysis of sequence data -- from from raw base calling to analyzed variants ready for interpretation by users.</p>
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<table>
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<tr>
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<th>Users</th>
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<th>Administrators</th>
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<th>Developers</th>
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<th><a href="/users/">Users</a></th>
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<th><a href="/administrators/">Administrators</a></th>
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<th><a href="/source/">Developers</a></th>
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</tr>
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<tr>
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<td><img src="pictures/Use.png"/></td>
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<td><img src="pictures/Deploy.png"/></td>
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<td><img src="pictures/Develop.png"/></td>
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<td><a href="/users/"><img src="pictures/Use.png" /></a></td>
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<td><a href="/administrators/"><img src="pictures/Deploy.png" /></a></td>
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<td><a href="/source/"><img src="pictures/Develop.png" /></a></td>
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</tr>
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<tr>
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<td width="200">Create and run workflows either using a web application or command line interface</td>
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</tr>
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</table>
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<p>SeqWare is currently used by a variety of NGS users including the <a href="http://unclineberger.org/">Lineberger Comprehensive Cancer Center at UNC</a>, at the <a href="http://oicr.on.ca/">Ontario Institute for Cancer Research in Toronto</a> and by our commercial partner <a href="http://nimbusinformatics.com/">Nimbus Informatics.</a></p>
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</div>
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<div id="sidebar">
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<ul>
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<li><a href="/about/"><span>About SeqWare</span></a></li>
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<li><a href="/download/"><span>Download</span></a></li>
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</ul>
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<h2><span>Quick Reference</span></h2>
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<ul>
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<li><a href="http://nanoc.stoneship.org/docs/3-getting-started/"><span>Installing SeqWare</span></a></li>
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<li><a href="http://sourceforge.net/apps/mediawiki/seqware/index.php?title=How_to_Write_a_Bundled_Workflow"><span>Writing Bundled Workflows</span></a></li>
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<li><a href="/users/"><span>User Guide</span></a></li>
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<li><a href="/administrators/"><span>Administrator Guide</span></a></li>
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<li><a href="/source/"><span>Developers Guide</span></a></li>
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<li><a href="http://sourceforge.net/apps/mediawiki/seqware/index.php?title=Main_Page"><span>Old Wiki</span></a></li>
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</ul>
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<h2><span>APIs</span></h2>
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<ul>
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<li><a href="/webservice-api/"><span>Web Service API</span></a></li>
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<li><a href="/queryengine-api/"><span>Query Engine API</span></a></li>
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</ul>
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<h2><span>Community</span></h2>
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<ul>
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<li><a href="http://sourceforge.net/mail/?group_id=239239"><span>Mailing Lists</span></a></li>
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<li><a href="source.html"><span>Source Code</span></a></li>
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<li><a href="http://sourceforge.net/apps/mediawiki/seqware/index.php?title=Main_Page"><span>Old Wiki</span></a></li>
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</ul>
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<h2><span>Contact</span></h2>
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<ul>
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<li><a href=""><span>Submit a bug</span></a></li>
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<li><a href="http://sourceforge.net/mail/?group_id=239239"><span>Mailing Lists</span></a></li>
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<li><a href="mailto:[email protected]"><span>JIRA Bug Tracker</span></a></li>
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</ul>
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</div>
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</body>

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