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2 parents a1c1423 + ca3525f commit 2bb2e402ae578daf0fed692590275fd4d3cce075 @michaelbarton committed Mar 11, 2013
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58 Gemfile.lock
@@ -0,0 +1,58 @@
+GEM
+ remote: http://rubygems.org/
+ specs:
+ adsf (1.1.1)
+ rack (>= 1.0.0)
+ colored (1.2)
+ cri (2.3.0)
+ colored (>= 1.2)
+ execjs (1.4.0)
+ multi_json (~> 1.0)
+ fssm (0.2.10)
+ haml (4.0.0)
+ tilt
+ json (1.7.7)
+ listen (0.7.2)
+ multi_json (1.6.1)
+ nanoc (3.5.0)
+ cri (~> 2.2)
+ nokogiri (1.5.6)
+ rack (1.5.2)
+ rack-contrib (1.1.0)
+ rack (>= 0.9.1)
+ rainpress (1.0)
+ rake (10.0.3)
+ rb-fsevent (0.9.3)
+ rdiscount (2.0.7)
+ rubypants (0.2.0)
+ sass (3.2.5)
+ tilt (1.3.3)
+ typogruby (1.0.15)
+ rubypants
+ uglifier (1.3.0)
+ execjs (>= 0.3.0)
+ multi_json (~> 1.0, >= 1.0.2)
+ w3c_validators (1.2)
+ json
+ nokogiri
+
+PLATFORMS
+ ruby
+
+DEPENDENCIES
+ adsf (~> 1.1.0)
+ fssm (~> 0.2.0)
+ haml (~> 4.0.0)
+ listen (~> 0.7.2)
+ nanoc (~> 3.5.0)
+ nokogiri (~> 1.5.0)
+ rack (~> 1.5.0)
+ rack-contrib (~> 1.1.0)
+ rainpress (~> 1.0.0)
+ rake (~> 10.0.0)
+ rb-fsevent (~> 0.9.1)
+ rdiscount (~> 2.0.0)
+ sass (~> 3.2.0)
+ typogruby (~> 1.0.15)
+ uglifier (~> 1.3.0)
+ w3c_validators (~> 1.2.0)
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5 config.yaml
@@ -10,11 +10,14 @@ site:
analytics_token: "UA-1362555-4"
navigation:
'about': "/"
- 'install': "/install/"
'scaffold format': "/scaffold-format/"
'troubleshooting': "/troubleshooting/"
'mailing list': "/mailing-list/"
'contribute': "/contribute/"
+ guides:
+ 'installing': "/install/"
+ 'genome annotations': "/managing-annotations/"
+ 'a simple genome': "/a-simple-genome/"
author:
url: "http://www.michaelbarton.me.uk"
name: "Michael Barton"
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5 content/markup/a-simple-genome.markdown
@@ -0,0 +1,5 @@
+---
+ title: Completing a simple genome
+---
+
+<%= youtube 'jVn62pMnIRA' %>
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195 content/markup/getting-started.markdown
@@ -1,195 +0,0 @@
----
- title: "Getting Started"
----
-
-This page provides a quick introduction to installing scaffolder and creating
-a simple scaffold from three nucleotide sequences. Scaffolder has been tested
-on Debian and OS X but there may differences on Windows. If you have any
-questions or comments feel free to ask on the [scaffolder mailing list][email].
-
-### Installation
-
-Scaffolder requires both [Ruby][] and [RubyGems][] to run. These are usually
-already installed or can be installed easy on Mac OS X and Linux distributions.
-The software can be tested by running the following commands on the console or
-terminal (excluding the '$' sign):
-
-<%= highlight %>
-
-$ ruby -v
-$ gem -v
-
-<%= endhighlight %>
-
-If both of these return without error, scaffolder can be installed via RubyGems
-using the following command:
-
-<%= highlight %>
-
-$ gem install scaffolder scaffolder-tools
-
-<%= endhighlight %>
-
-The install can be tests by running the following command. This should print
-the list of available scaffolder options.
-
-<%= highlight %>
-
-$ scaffolder
-
-<%= endhighlight %>
-
-If this fails or returns an error the RubyGems executable directory may not be
-in your shell path. The location of this can found using the following command,
-the result of which should be added to the $PATH variable in your shell login
-script. Examples of updating the shell path are available [for OS X][osx_path]
-and [for Linux][linux_path]
-
-<%= highlight %>
-
-# Add the output of this your $PATH
-$ gem env | grep "EXECUTABLE DIRECTORY" | cut -d : -f 2
-
-<%= endhighlight %>
-
-### Creating a simple scaffold
-
-To begin creating a scaffold, create a text file named 'sequences.fna'
-containing the following nucleotide sequences. These will be our example
-sequences which we wish to build a scaffold with. The following steps will
-progress through creating a simple scaffold.
-
-<%= highlight %>
-
->sequence1
-AAAAAAAAAAAA
->sequence2
-TTTTTTTTTTTT
->sequence3
-GGGGG
-
-<%= endhighlight %>
-
-Create the file 'scaffold.yml' and add the content below. This is the scaffold
-file specifying how our nucleotide sequences should be joined together.
-
-<%= highlight %>
-
----
- - sequence:
- source: 'sequence1'
-
-<%= endhighlight %>
-
-The scaffold is written in the [YAML][] format. YAML is data serialisation
-format which is useful to pass information between computer software but which
-also can be easily edited by hand. YAML formatted documents should begin with
-three dashes ('---'). The scaffold file is represented as a list of sequence
-entries. Using the YAML format each entry is defined by starting with a dash
-('-') then indented by two spaces for the remaining lines of the entry.
-
-As you can see in the code above this scaffold file has only one entry. The
-'sequence' tag specifies that this entry is a sequence. The 'source' tag
-identifies the name of the sequence to use. The source tag should match the
-first space delimited word in the corresponding sequence fasta header.
-
-The sequence for this simple scaffold is produced by running the scaffolder
-sequence command giving the locations of the two files we have just created.
-
-<%= highlight %>
-
-$ scaffolder sequence scaffold.yml sequences.fna
-
-<%= endhighlight %>
-
-This returns the nucleotide sequence of sequence1. This is as expected as the
-scaffold only contains one sequence entry.
-
-<%= highlight %>
-
->.
-AAAAAAAAAAAA
-
-<%= endhighlight %>
-
-### Adding additional sequences to the scaffold
-
-A scaffold with only a single sequence is rather simple. Update the scaffold
-file so that it now resembles the text below. Here we have added a second
-sequence from the fasta file and an unknown region between these two sequences.
-
-<%= highlight %>
-
----
- - sequence:
- source: 'sequence1'
- - unresolved:
- length: 5
- - sequence:
- source: 'sequence2'
-
-<%= endhighlight %>
-
-Running the scaffolder command again will generate following super sequence.
-This contains the two sequences joined by the 5bp region of 'N' characters we
-specified. These unresolved regions can be used for joining contigs by
-approximate distances.
-
-<%= highlight %>
-
->.
-AAAAAAAAAAAANNNNNTTTTTTTTTTTT
-
-<%= endhighlight %>
-
-### Replacing regions of sequence in the scaffold
-
-Imagine there is a region in sequence1 which we wish to replace. For example
-the start of region on is poor quality or it is an already scaffolded set of
-contigs containing gaps. Performing PCR would determine the correct sequence in
-this area but we need a way to update sequence1 in the scaffold. We can do this
-by updating the scaffold file as follows:
-
-<%= highlight %>
-
----
- - sequence:
- source: 'sequence1'
- inserts:
- - source: 'sequence3'
- open: 3
- close: 5
- - unresolved:
- length: 5
- - sequence:
- source: 'sequence2'
-
-<%= endhighlight %>
-
-Here we have added an insert to sequence1 using the "inserts" tag. This
-replaces the region in the range 3...5 (specified by the open and close
-coordinates) with sequence3. Running the scaffolder command again we can see
-that this is now the case where four guanine bases have been inserted
-
-<%= highlight %>
-
->.
-AAGGGGGAAAAAAANNNNNTTTTTTTTTTTT
-
-<%= endhighlight %>
-
-This is a brief tutorial for creating a simple scaffold. More complex scaffolds
-can be created by adding further sequences and inserts to the scaffold. More
-details about the scaffolder format can be found at [the scaffolder API][api]
-and the [scaffolder-format man page][format]. Details on the available
-scaffolder commands can be found on [the man pages][man].
-
-[Ruby]: http://www.ruby-lang.org/
-[RubyGems]: http://rubygems.org/
-[osx_path]: http://stackoverflow.com/questions/135688/setting-environment-variables-in-os-x
-[linux_path]: http://www.troubleshooters.com/linux/prepostpath.htm
-[man]: /man
-[api]: http://rubydoc.info/gems/scaffolder/0.4.1/Scaffolder
-[email]: http://groups.google.com/group/scaffolder
-[yaml]: http://www.yaml.org/
-[format]: /man/scaffolder-format/
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5 content/markup/managing-annotations.markdown
@@ -0,0 +1,5 @@
+---
+ title: Managing genome annotations
+---
+
+<%= youtube 'U3HnVWMUb90' %>
View
1 content/stylesheets/styles.css
@@ -320,6 +320,7 @@ section {
/* Footer */
footer {
+ font-size: 12px;
width:170px;
float:left;
position:fixed;
View
2 layouts/_footer.haml
@@ -1,4 +1,4 @@
%footer
%p
%small
- Hosted on <a href="http://www.heroku.com/">Heroku</a> using the <a href="https://github.com/broccolini/dinky">Dinky theme</a> and built with <a href="http://nanoc.ws/">Nanoc</a>.
+ Built with <a href="https://github.com/broccolini/dinky">Dinky</a> and <a href="http://nanoc.ws/">Nanoc</a>.
View
7 layouts/_title.haml
@@ -10,3 +10,10 @@
%a{:href => navigation_link(href)}
%li
= name
+ %p.header
+ = "Video Guides"
+ %ul
+ - @site.config[:site][:guides].each do |name,href|
+ %a{:href => navigation_link(href)}
+ %li
+ = name
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4 lib/content.rb
@@ -5,3 +5,7 @@ def increase_markdown_header(line)
def anchor(text,id)
"<h3 id='#{id}'>#{text}</h3>"
end
+
+def image(url,width=400)
+ "<img src='#{relative_path_to(url)}' width=#{width}>"
+end
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12 lib/default.rb
@@ -1,14 +1,2 @@
include Nanoc3::Helpers::Rendering
include Nanoc3::Helpers::LinkTo
-
-def highlight
- "<pre class=\"class=prettyprint\">"
-end
-
-def endhighlight
- "</pre>"
-end
-
-def image(url,width=400)
- "<img src='#{relative_path_to(url)}' width=#{width}>"
-end
View
2 lib/header.rb
@@ -39,5 +39,5 @@ def favicon
end
def site_title
- [@item[:title],@site.config[:site][:title],@site.config[:author][:name]].compact.uniq * " | "
+ @site.config[:site][:title] + " &middot; " + @item[:title]
end

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