Commit f736f16e authored by Matej Lexa's avatar Matej Lexa
Browse files

Fixed webpage to fit on a page better; fixed deployment script to require argument

parent ce53ebab

_site.yml

+6 −7
Original line number Diff line number Diff line 
name: "Coronavirus"

output_dir: "."

navbar:

  title: "Coronavirus student project (PB051)"

  left:

    - text: "Home"

      href: index.html

    - text: "Page 1 - Sequence data"

    - text: "p1: Sequence data"

      href: page1.html

    - text: "Page 2 - HMM Alignment"

    - text: "p2: HMM Alignment"

      href: page2.html

    - text: "Page 3 - Related sequences"

    - text: "p3: Related sequences"

      href: page3.html

    - text: "Page 4 - Phylogenetic trees"

    - text: "p4: Phylogenetic trees"

      href: page4.html

    - text: "Page 5 - Phylogeography"

    - text: "p5: Phylogeography"

      href: page5.html

    - text: "Page 6 - Time series"

    - text: "p6: Time series"

      href: page6.html

deploy.sh

+6 −0
Original line number Diff line number Diff line
@@ -6,6 +6,12 @@ 
# Note:

# To deploy up-to-date static webpages, run RMarkdown render_site() command in R first



# poor man's help message

if [ -z "$1" ]; then

       	echo "Warning: use scp compliant server:path argument to specify deployment target"

	exit 

fi



#cp *.html /mnt/lexa/public_html/pa055/.

#cp -R images /mnt/lexa/public_html/pa055/.

#cp -R site_libs /mnt/lexa/public_html/pa055/.

index.html

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<!DOCTYPE html>



<html>



<head>



<meta charset="utf-8" />

<meta name="generator" content="pandoc" />

<meta http-equiv="X-UA-Compatible" content="IE=EDGE" />









<title>Coronavirus student project</title>



<script src="site_libs/jquery-1.11.3/jquery.min.js"></script>

<meta name="viewport" content="width=device-width, initial-scale=1" />

<link href="site_libs/bootstrap-3.3.5/css/bootstrap.min.css" rel="stylesheet" />

<script src="site_libs/bootstrap-3.3.5/js/bootstrap.min.js"></script>

<script src="site_libs/bootstrap-3.3.5/shim/html5shiv.min.js"></script>

<script src="site_libs/bootstrap-3.3.5/shim/respond.min.js"></script>

<script src="site_libs/navigation-1.1/tabsets.js"></script>

<link href="site_libs/highlightjs-9.12.0/default.css" rel="stylesheet" />

<script src="site_libs/highlightjs-9.12.0/highlight.js"></script>



<style type="text/css">code{white-space: pre;}</style>

<style type="text/css">

  pre:not([class]) {

    background-color: white;

  }

</style>

<script type="text/javascript">

if (window.hljs) {

  hljs.configure({languages: []});

  hljs.initHighlightingOnLoad();

  if (document.readyState && document.readyState === "complete") {

    window.setTimeout(function() { hljs.initHighlighting(); }, 0);

  }

}

</script>







<style type="text/css">

h1 {

  font-size: 34px;

}

h1.title {

  font-size: 38px;

}

h2 {

  font-size: 30px;

}

h3 {

  font-size: 24px;

}

h4 {

  font-size: 18px;

}

h5 {

  font-size: 16px;

}

h6 {

  font-size: 12px;

}

.table th:not([align]) {

  text-align: left;

}

</style>









<style type = "text/css">

.main-container {

  max-width: 940px;

  margin-left: auto;

  margin-right: auto;

}

code {

  color: inherit;

  background-color: rgba(0, 0, 0, 0.04);

}

img {

  max-width:100%;

}

.tabbed-pane {

  padding-top: 12px;

}

.html-widget {

  margin-bottom: 20px;

}

button.code-folding-btn:focus {

  outline: none;

}

summary {

  display: list-item;

}

</style>





<style type="text/css">

/* padding for bootstrap navbar */

body {

  padding-top: 51px;

  padding-bottom: 40px;

}

/* offset scroll position for anchor links (for fixed navbar)  */

.section h1 {

  padding-top: 56px;

  margin-top: -56px;

}

.section h2 {

  padding-top: 56px;

  margin-top: -56px;

}

.section h3 {

  padding-top: 56px;

  margin-top: -56px;

}

.section h4 {

  padding-top: 56px;

  margin-top: -56px;

}

.section h5 {

  padding-top: 56px;

  margin-top: -56px;

}

.section h6 {

  padding-top: 56px;

  margin-top: -56px;

}

.dropdown-submenu {

  position: relative;

}

.dropdown-submenu>.dropdown-menu {

  top: 0;

  left: 100%;

  margin-top: -6px;

  margin-left: -1px;

  border-radius: 0 6px 6px 6px;

}

.dropdown-submenu:hover>.dropdown-menu {

  display: block;

}

.dropdown-submenu>a:after {

  display: block;

  content: " ";

  float: right;

  width: 0;

  height: 0;

  border-color: transparent;

  border-style: solid;

  border-width: 5px 0 5px 5px;

  border-left-color: #cccccc;

  margin-top: 5px;

  margin-right: -10px;

}

.dropdown-submenu:hover>a:after {

  border-left-color: #ffffff;

}

.dropdown-submenu.pull-left {

  float: none;

}

.dropdown-submenu.pull-left>.dropdown-menu {

  left: -100%;

  margin-left: 10px;

  border-radius: 6px 0 6px 6px;

}

</style>



<script>

// manage active state of menu based on current page

$(document).ready(function () {

  // active menu anchor

  href = window.location.pathname

  href = href.substr(href.lastIndexOf('/') + 1)

  if (href === "")

    href = "index.html";

  var menuAnchor = $('a[href="' + href + '"]');



  // mark it active

  menuAnchor.parent().addClass('active');



  // if it's got a parent navbar menu mark it active as well

  menuAnchor.closest('li.dropdown').addClass('active');

});

</script>



<!-- tabsets -->



<style type="text/css">

.tabset-dropdown > .nav-tabs {

  display: inline-table;

  max-height: 500px;

  min-height: 44px;

  overflow-y: auto;

  background: white;

  border: 1px solid #ddd;

  border-radius: 4px;

}



.tabset-dropdown > .nav-tabs > li.active:before {

  content: "";

  font-family: 'Glyphicons Halflings';

  display: inline-block;

  padding: 10px;

  border-right: 1px solid #ddd;

}



.tabset-dropdown > .nav-tabs.nav-tabs-open > li.active:before {

  content: "&#xe258;";

  border: none;

}



.tabset-dropdown > .nav-tabs.nav-tabs-open:before {

  content: "";

  font-family: 'Glyphicons Halflings';

  display: inline-block;

  padding: 10px;

  border-right: 1px solid #ddd;

}



.tabset-dropdown > .nav-tabs > li.active {

  display: block;

}



.tabset-dropdown > .nav-tabs > li > a,

.tabset-dropdown > .nav-tabs > li > a:focus,

.tabset-dropdown > .nav-tabs > li > a:hover {

  border: none;

  display: inline-block;

  border-radius: 4px;

  background-color: transparent;

}



.tabset-dropdown > .nav-tabs.nav-tabs-open > li {

  display: block;

  float: none;

}



.tabset-dropdown > .nav-tabs > li {

  display: none;

}

</style>



<!-- code folding -->









</head>



<body>





<div class="container-fluid main-container">









<div class="navbar navbar-default  navbar-fixed-top" role="navigation">

  <div class="container">

    <div class="navbar-header">

      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">

        <span class="icon-bar"></span>

        <span class="icon-bar"></span>

        <span class="icon-bar"></span>

      </button>

      <a class="navbar-brand" href="index.html"></a>

    </div>

    <div id="navbar" class="navbar-collapse collapse">

      <ul class="nav navbar-nav">

        <li>

  <a href="index.html">Home</a>

</li>

<li>

  <a href="page1.html">p1: Sequence data</a>

</li>

<li>

  <a href="page2.html">p2: HMM Alignment</a>

</li>

<li>

  <a href="page3.html">p3: Related sequences</a>

</li>

<li>

  <a href="page4.html">p4: Phylogenetic trees</a>

</li>

<li>

  <a href="page5.html">p5: Phylogeography</a>

</li>

<li>

  <a href="page6.html">p6: Time series</a>

</li>

      </ul>

      <ul class="nav navbar-nav navbar-right">

        

      </ul>

    </div><!--/.nav-collapse -->

  </div><!--/.container -->

</div><!--/.navbar -->



<div class="fluid-row" id="header">







<h1 class="title toc-ignore">Coronavirus student project</h1>



</div>





<p>A PB051 bioinformatics project at the Faculty of Informatics at MU in Brno.</p>

<div id="goals-with-web-pages-to-create" class="section level3">

<h3>Goals (with web pages to create):</h3>

<ol style="list-style-type: decimal">

<li>Collect as many coronavirus sequences as possible (Page 1 - Sequence data)</li>

<li>Using HMMER create a profile-HMM of coronavirus sequence and/or its important subsequences (Page 2 - HMM Alignment)</li>

<li>Find other related sequences in public sequence databases (Page 3 - Related sequences)</li>

<li>Create a labeled phylogenetic tree of the aligned sequences (Page 4 - Phylogenetic trees)</li>

<li>Phylogeographic analysis (Page 5 - Phylogeography)</li>

<li>Time series analysis (Page 6 - Time series)</li>

</ol>

</div>

<div id="sources-of-relevant-data" class="section level2">

<h2>Sources of relevant data</h2>

<p><a href="https://www.ncbi.nlm.nih.gov/genbank/sars-cov-2-seqs/">NCBI: SARS-CoV-2 (Severe acute respiratory syndrome coronavirus 2) Sequences</a></p>

<p><a href="https://ourworldindata.org/coronavirus#up-to-date-n-co-v-2019-data-working-group-data">University of Oxford: Our World in Data COVID-19 page</a></p>

<p><a href="https://www.who.int/emergencies/diseases/novel-coronavirus-2019/situation-reports/">WHO Situation reports</a></p>

<p><a href="https://github.com/CSSEGISandData/COVID-19">John Hopkins University Data and Links</a></p>

</div>

<div id="software" class="section level2">

<h2>Software</h2>

<p><a href="http://hmmer.org/">HMMER 3.0</a></p>

</div>

<div id="references" class="section level2">

<h2>References</h2>

<p><a href="https://en.wikipedia.org/wiki/Severe_acute_respiratory_syndrome_coronavirus_2">Wikipedia background information</a></p>

<p><a href="https://www.sciencemag.org/news/2020/01/mining-coronavirus-genomes-clues-outbreak-s-origins">Cohen (2020): Mining coronavirus genomes for clues to the outbreak’s origins</a></p>

<p><a href="https://yulab-smu.github.io/treedata-book/">Data integration, manipulation and visualization of phylogenetic trees</a></p>

<p><a href="https://guides.github.com/introduction/git-handbook/">GIT Handbook</a></p>

<p><a href="https://rmarkdown.rstudio.com/lesson-1.html">RMarkdown information</a></p>

</div>









</div>



<script>



// add bootstrap table styles to pandoc tables

function bootstrapStylePandocTables() {

  $('tr.header').parent('thead').parent('table').addClass('table table-condensed');

}

$(document).ready(function () {

  bootstrapStylePandocTables();

});





</script>



<!-- tabsets -->



<script>

$(document).ready(function () {

  window.buildTabsets("TOC");

});



$(document).ready(function () {

  $('.tabset-dropdown > .nav-tabs > li').click(function () {

    $(this).parent().toggleClass('nav-tabs-open')

  });

});

</script>



<!-- code folding -->





<!-- dynamically load mathjax for compatibility with self-contained -->

<script>

  (function () {

    var script = document.createElement("script");

    script.type = "text/javascript";

    script.src  = "https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML";

    document.getElementsByTagName("head")[0].appendChild(script);

  })();

</script>



</body>

</html>

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