Documentation - html and markdown updates

DerrickWood · Feb 18, 2015 · 39f7e93 · 39f7e93
1 parent 6a7e388
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Showing 10 changed files with 1,178 additions and 755 deletions.
diff --git a/CHANGELOG b/CHANGELOG
@@ -13,6 +13,8 @@ v0.10.5-beta:
 * added kraken-translate for getting taxonomic names for each sequence
 * added a --rebuild option to kraken-build
 * turned off default name checking for PE reads; added --check-names option
+* added plasmids to --download-library options
+* added HTML manual, redirecting README to that
 
 v0.10.4-beta:
 * use GRCh38 for human genome library

diff --git a/README b/README
diff --git a/README.md b/README.md
@@ -0,0 +1,10 @@
+Kraken taxonomic sequence classification system
+===============================================
+
+Please see the [Kraken webpage] or the [Kraken manual]
+for information on installing and operating Kraken.
+A local copy of the [Kraken manual] is also present here
+in the `docs/` directory (`MANUAL.html` and `MANUAL.markdown`).
+
+[Kraken webpage]:   http://ccb.jhu.edu/software/kraken/
+[Kraken manual]:    http://ccb.jhu.edu/software/kraken/MANUAL.html
diff --git a/docs/MANUAL.html b/docs/MANUAL.html
diff --git a/docs/MANUAL.markdown b/docs/MANUAL.markdown
diff --git a/docs/Makefile b/docs/Makefile
@@ -0,0 +1,9 @@
+all:
+	pandoc --title-prefix "Kraken Manual" \
+	       --include-in-header head.html \
+               --include-before-body top.html \
+	       --from markdown --to html \
+	       --table-of-contents \
+	       --css kraken.css \
+               --output MANUAL.html \
+	       < MANUAL.markdown
diff --git a/docs/bar-bg.png b/docs/bar-bg.png
diff --git a/docs/head.html b/docs/head.html
@@ -0,0 +1 @@
+<link href='http://fonts.googleapis.com/css?family=Ubuntu:400,700,400italic' rel='stylesheet' type='text/css'>
diff --git a/docs/kraken.css b/docs/kraken.css
@@ -0,0 +1,45 @@
+body {
+  background: #f0f0f0 url("bar-bg.png") top left repeat-y;
+  color: #333;
+  margin: 10px;
+  margin-left: 50px;
+  margin-bottom: 20px;
+  font-family: 'Ubuntu', sans-serif;
+}
+
+a         { color: #00b0f0; }
+a:visited { color: #0090f0; }
+a:hover   { color: #00d0ff; }
+a:active  { color: #00f0ff; }
+
+.pretoc {
+  text-align: center;
+  font-size: 1.2em;
+}
+.title {
+  font-size: 2em;
+  font-weight: bold;
+  margin-bottom: 0;
+}
+.version {
+  font-size: 0.9em;
+}
+h1 {
+  color: #0090f0;
+  border-bottom: 1px #0090f0 solid;
+  margin-left: -10px;
+  margin-bottom: 3px;
+}
+h1 a {
+  color: #0090f0;
+  text-decoration: none;
+}
+div#confidence-score-table table th {
+  width: 7em;
+}
+pre {
+  margin-left: 4em;
+}
+code {
+  font-size: 1.2em;
+}
diff --git a/docs/top.html b/docs/top.html
@@ -0,0 +1,9 @@
+<div class="pretoc">
+  <p class="title">Kraken taxonomic sequence classification system</p>
+
+  <p class="version">Version 0.10.5-beta</p>
+
+  <p>Operating Manual</p>
+</div>
+
+<h1>Table of Contents</h1>
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		@@ -0,0 +1 @@
		<link href='http://fonts.googleapis.com/css?family=Ubuntu:400,700,400italic' rel='stylesheet' type='text/css'>