First setup of Faqs and Docs for R2

.gitignore

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+/.project

docs/Faqs.md

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+<a id="r2_faqs"> </a>
+
+
+Frequently Asked Questions (FAQs)
+===========================================
+
+*A collections of questions about the R2 platform*
+
+
+Subheader (H2) also appears in TOC
+-----
+
+-  A bulleted list is created by a minus, plus or asterisk followed by two spaces
+-  Next item
+  -  Subitem by two spaces
+
+
+Third subheader 
+-----
+
+1.  This will give a numbered list
+2.  Next item
+
+	To continue numbering after enter or figure, indent the whole paragraph with a tab, or more tabs when in sublist
+
+3.  And the third continues
+
+Any text between restarts numbering
+
+4.  Next list
+  1. Two spaces create a sublist
+  *  They can be mixed
+
+Images are formatted as follows:
+
+![Figure 11: the extra settings Panel](_static/images/OneGene_Adapting.png)
+
+[**Figure 11: the extra settings Panel**](_static/images/OneGene_Adapting.png)
+
+Note the enter between the lines; this is to guarantee proper formatting in pdf
+
+The Did you know box is formatted as follows
+
+---------
+  ![](_static/images/R2d2_logo.png)**Did you know box**
+
+
+> *Three or more minusses preceded by a return create a line; the > sign in front of a paragraph indents the whole paragraph and the single asterisks put it in italic*
+
+---------
+
+You'll have to get used to the use of spaces and enters in Markdown; these are used for formatting
+
+
+  Two spaces at the start of a line creates a paragraph
+Type on here below  
+
+
+
+
+
+
+
+
+
+

docs/Workflows.md

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+<a id="r2_workflows"> </a>
+
+
+Workflows
+===========================================
+
+*Typical workflows that explore the combinations of analysis possible in R2*
+
+
+Subheader (H2) also appears in TOC
+-----
+
+-  A bulleted list is created by a minus, plus or asterisk followed by two spaces
+-  Next item
+  -  Subitem by two spaces
+
+
+Third subheader 
+-----
+
+1.  This will give a numbered list
+2.  Next item
+
+	To continue numbering after enter or figure, indent the whole paragraph with a tab, or more tabs when in sublist
+
+3.  And the third continues
+
+Any text between restarts numbering
+
+4.  Next list
+  1. Two spaces create a sublist
+  *  They can be mixed
+
+Images are formatted as follows:
+
+![Figure 11: the extra settings Panel](_static/images/OneGene_Adapting.png)
+
+[**Figure 11: the extra settings Panel**](_static/images/OneGene_Adapting.png)
+
+Note the enter between the lines; this is to guarantee proper formatting in pdf
+
+The Did you know box is formatted as follows
+
+---------
+  ![](_static/images/R2d2_logo.png)**Did you know box**
+
+
+> *Three or more minusses preceded by a return create a line; the > sign in front of a paragraph indents the whole paragraph and the single asterisks put it in italic*
+
+---------
+
+You'll have to get used to the use of spaces and enters in Markdown; these are used for formatting
+
+
+  Two spaces at the start of a line creates a paragraph
+Type on here below  
+
+
+
+
+
+
+
+
+
+

docs/_static/css/r2tutorials.css

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+/*
+Creates an image in a box with text below and shadowed outline 
+Use as follows:
+<div class="polaroid">
+  <img src="rock600x400.jpg" alt="Norway" style="width:100%">
+  <div class="container">
+    <p>The Troll's tongue in Hardanger, Norway</p>
+  </div>
+</div>
+
+*/
+div.polaroid {
+  width: 80%;
+  background-color: white;
+  box-shadow: 0 4px 8px 0 rgba(0, 0, 0, 0.2), 0 6px 20px 0 rgba(0, 0, 0, 0.19);
+  margin-bottom: 25px;
+}
+
+div.container {
+  text-align: center;
+  padding: 10px 20px;
+}
+
+div.noshow{
+	display: none;
+}
+
+/* 
+Creates an R2 did you know box; a table containing header with R2D2 image
+*/
+
+div.r2didyouknow table {
+	border-collapse:collapse;
+	border-left:solid 1px black;
+	border-right:solid 1px black;
+	border-top:solid 1px black;
+	border-bottom:solid 1px black;
+	margin:auto;
+	background-color:#f2f2f2;
+	width: 85%; 
+	cellpadding: 6px;
+}
+div.r2didyouknow th {
+	color:#C45A58;
+	height: 32px;
+	border-bottom:solid 1px black;
+	background-image: url("../images/R2d2_logo.png");
+	background-repeat: no-repeat; 
+	background-position: left; 
+}
+
+
+
+
+/* 
+Images are parsed into an reference external class; we want these centered and block just
+like their annotation text in strong
+*/
+a.reference.external strong{
+	display: block;
+	text-align: center;
+  	padding: 10px 10px;	
+}
+
+img{
+	display: block;
+    margin-left: auto;
+    margin-right: auto; 
+  	padding: 10px 10px;	
+}
+
+/*
+Except for the logo
+*/
+
+img[src="_images/R2d2_logo.png"]{
+	display: inline;
+	float: left;
+}
+

docs/_templates/R2_Chapter_Template.md

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+<a id="r2_chapter_template"> </a>
+
+
+This is the header (H1) that will appear as title in the TOC
+===========================================
+
+*Subtitle between asterisk creates italic style*
+
+
+Subheader (H2) also appears in TOC
+-----
+
+-  A bulleted list is created by a minus, plus or asterisk followed by two spaces
+-  Next item
+  -  Subitem by two spaces
+
+
+Third subheader 
+-----
+
+1.  This will give a numbered list
+2.  Next item
+
+	To continue numbering after enter or figure, indent the whole paragraph with a tab, or more tabs when in sublist
+
+3.  And the third continues
+
+Any text between restarts numbering
+
+4.  Next list
+  1. Two spaces create a sublist
+  *  They can be mixed
+
+Images are formatted as follows:
+
+![Figure 11: the extra settings Panel](_static/images/OneGene_Adapting.png)
+
+[**Figure 11: the extra settings Panel**](_static/images/OneGene_Adapting.png)
+
+Note the enter between the lines; this is to guarantee proper formatting in pdf
+
+The Did you know box is formatted as follows
+
+---------
+  ![](_static/images/R2d2_logo.png)**Did you know box**
+
+
+> *Three or more minusses preceded by a return create a line; the > sign in front of a paragraph indents the whole paragraph and the single asterisks put it in italic*
+
+---------
+
+You'll have to get used to the use of spaces and enters in Markdown; these are used for formatting
+
+
+  Two spaces at the start of a line creates a paragraph
+Type on here below  
+
+
+
+
+
+
+
+
+
+

docs/_templates/layout.html

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+{% extends "!layout.html" %}
+{% set css_files = css_files + [ "_static/css/r2tutorials.css" ] %}

docs/conf.py

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+import datetime
+
+extensions = []
+templates_path = ['_templates']
+
+master_doc = 'index'
+
+project = u'R2 Faqs and Workflows'
+copyright = u'2016, Jan Koster'
+author = u'R2 support team'
+
+version = datetime.date.today().strftime('%Y-%m-%d')
+release = '1.0.0.a'
+language = None
+
+exclude_patterns = ['_build']
+pygments_style = 'sphinx'
+
+import sphinx_rtd_theme
+html_theme = "sphinx_rtd_theme"
+html_theme_path = [sphinx_rtd_theme.get_html_theme_path()]
+def setup(app):
+  app.add_stylesheet( "css/r2tutorials.css" )
+# from http://stackoverflow.com/questions/32079200/how-do-i-set-up-custom-styles-for-restructuredtext-sphinx-readthedocs-etc/32079202#32079202
+
+html_static_path = ['_static']
+html_show_sourcelink = True
+htmlhelp_basename = 'Testdoc'
+html_logo = '_static/images/r2_logo_128.png'
+html_favicon = '_static/images/r2favicon.ico'
+
+latex_elements = {
+# The paper size ('letterpaper' or 'a4paper').
+# Changed this to a4; we're in Europe ;-)
+'papersize': 'a4paper',
+
+# The font size ('10pt', '11pt' or '12pt').
+#'pointsize': '10pt',
+
+# Additional stuff for the LaTeX preamble.
+#'preamble': '',
+
+# Latex figure (float) alignment
+# default below is float; we want position as is: H
+#'figure_align': 'htbp', 
+'figure_align': 'H', 
+}
+
+latex_documents = [
+  (master_doc, 'Test.tex', u'R2 Faqs and Workflows',
+   u'The R2 support team', 'manual'),
+]
+
+man_pages = [
+    (master_doc, 'test', u'R2 Faqs and Workflows',
+     [author], 1)
+]
+
+texinfo_documents = [
+  (master_doc, 'Test', u'R2 Faqs and Workflows',
+   author, 'Test', 'R2 Faqs and Workflows',
+   'Miscellaneous'),
+]
+
+from recommonmark.parser import CommonMarkParser
+
+# The suffix of source filenames.
+source_suffix = ['.rst', '.md']
+
+source_parsers = {
+	'.md': CommonMarkParser,
+}

docs/index.rst

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+R2 Faqs and Workflows: |version|
+====================
+
+This contains a collection of Frequently Asked Questions and Workflows for R2; a biologist friendly, web based genomics analysis and visualization application developed by Jan Koster at the department of Oncogenomics in the Academic Medical Center (AMC) Amsterdam, the Netherlands.
+For citations, please include the following webcite: 'R2: Genomics Analysis and Visualization Platform (http://r2.amc.nl http://r2platform.com)'
+
+Copyright (c) 2006-2016 Jan Koster
+
+.. rubric:: Table of Contents
+
+.. toctree::
+   :maxdepth: 2
+   :numbered: 2
+
+   Faqs
+   Workflows
+
+..   
+   

docs/requirements.txt

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+sphinx-rtd-theme
+sphinx
+recommonmark