DAseq website

gem 'github-pages'

source 'https://rubygems.org'

To the extent possible under law,

[Karl Broman](https://github.com/kbroman)

has waived all copyright and related or neighboring rights to

“[simple site](https://github.com/kbroman/simple_site)”.

This work is published from the United States.

<br/>

[![CC0](https://i.creativecommons.org/p/zero/1.0/88x31.png)](https://creativecommons.org/publicdomain/zero/1.0/)

require "rubygems"

require 'rake'

require 'yaml'

require 'time'

SOURCE = "."

CONFIG = {

  'version' => "0.3.0",

  'themes' => File.join(SOURCE, "_includes", "themes"),

  'layouts' => File.join(SOURCE, "_layouts"),

  'posts' => File.join(SOURCE, "_posts"),

  'post_ext' => "md",

  'theme_package_version' => "0.1.0"

}

# Path configuration helper

module JB

  class Path

    SOURCE = "."

    Paths = {

      :layouts => "_layouts",

      :themes => "_includes/themes",

      :theme_assets => "assets/themes",

      :theme_packages => "_theme_packages",

      :posts => "_posts"

    }

    def self.base

      SOURCE

    end

    # build a path relative to configured path settings.

    def self.build(path, opts = {})

      opts[:root] ||= SOURCE

      path = "#{opts[:root]}/#{Paths[path.to_sym]}/#{opts[:node]}".split("/")

      path.compact!

      File.__send__ :join, path

    end

  end #Path

end #JB

# Usage: rake post title="A Title" [date="2012-02-09"] [tags=[tag1, tag2]]

desc "Begin a new post in #{CONFIG['posts']}"

task :post do

  abort("rake aborted: '#{CONFIG['posts']}' directory not found.") unless FileTest.directory?(CONFIG['posts'])

  title = ENV["title"] || "new-post"

  tags = ENV["tags"] || "[]"

  slug = title.downcase.strip.gsub(' ', '-').gsub(/[^\w-]/, '')

  begin

    date = (ENV['date'] ? Time.parse(ENV['date']) : Time.now).strftime('%Y-%m-%d')

  rescue Exception => e

    puts "Error - date format must be YYYY-MM-DD, please check you typed it correctly!"

    exit -1

  end

  filename = File.join(CONFIG['posts'], "#{date}-#{slug}.#{CONFIG['post_ext']}")

  if File.exist?(filename)

    abort("rake aborted!") if ask("#{filename} already exists. Do you want to overwrite?", ['y', 'n']) == 'n'

  end

  puts "Creating new post: #{filename}"

  open(filename, 'w') do |post|

    post.puts "---"

    post.puts "layout: post"

    post.puts "title: \"#{title.gsub(/-/,' ')}\""

    post.puts 'description: ""'

    post.puts "category: "

    post.puts "tags: []"

    post.puts "---"

    post.puts "{% include JB/setup %}"

  end

end # task :post

# Usage: rake page name="about.html"

# You can also specify a sub-directory path.

# If you don't specify a file extention we create an index.html at the path specified

desc "Create a new page."

task :page do

  name = ENV["name"] || "new-page.md"

  filename = File.join(SOURCE, "#{name}")

  filename = File.join(filename, "index.html") if File.extname(filename) == ""

  title = File.basename(filename, File.extname(filename)).gsub(/[\W\_]/, " ").gsub(/\b\w/){$&.upcase}

  if File.exist?(filename)

    abort("rake aborted!") if ask("#{filename} already exists. Do you want to overwrite?", ['y', 'n']) == 'n'

  end

  mkdir_p File.dirname(filename)

  puts "Creating new page: #{filename}"

  open(filename, 'w') do |post|

    post.puts "---"

    post.puts "layout: page"

    post.puts "title: \"#{title}\""

    post.puts 'description: ""'

    post.puts "---"

    post.puts "{% include JB/setup %}"

  end

end # task :page

desc "Launch preview environment"

task :preview do

  system "jekyll --auto --server"

end # task :preview

# Public: Alias - Maintains backwards compatability for theme switching.

task :switch_theme => "theme:switch"

namespace :theme do

  # Public: Switch from one theme to another for your blog.

  #

  # name - String, Required. name of the theme you want to switch to.

  #        The the theme must be installed into your JB framework.

  #

  # Examples

  #

  #   rake theme:switch name="the-program"

  #

  # Returns Success/failure messages.

  desc "Switch between Jekyll-bootstrap themes."

  task :switch do

    theme_name = ENV["name"].to_s

    theme_path = File.join(CONFIG['themes'], theme_name)

    settings_file = File.join(theme_path, "settings.yml")

    non_layout_files = ["settings.yml"]

    abort("rake aborted: name cannot be blank") if theme_name.empty?

    abort("rake aborted: '#{theme_path}' directory not found.") unless FileTest.directory?(theme_path)

    abort("rake aborted: '#{CONFIG['layouts']}' directory not found.") unless FileTest.directory?(CONFIG['layouts'])

    Dir.glob("#{theme_path}/*") do |filename|

      next if non_layout_files.include?(File.basename(filename).downcase)

      puts "Generating '#{theme_name}' layout: #{File.basename(filename)}"

      open(File.join(CONFIG['layouts'], File.basename(filename)), 'w') do |page|

        if File.basename(filename, ".html").downcase == "default"

          page.puts "---"

          page.puts File.read(settings_file) if File.exist?(settings_file)

          page.puts "---"

        else

          page.puts "---"

          page.puts "layout: default"

          page.puts "---"

        end 

        page.puts "{% include JB/setup %}"

        page.puts "{% include themes/#{theme_name}/#{File.basename(filename)} %}" 

      end

    end

    puts "=> Theme successfully switched!"

    puts "=> Reload your web-page to check it out =)"

  end # task :switch

  # Public: Install a theme using the theme packager.

  # Version 0.1.0 simple 1:1 file matching.

  #

  # git  - String, Optional path to the git repository of the theme to be installed.

  # name - String, Optional name of the theme you want to install.

  #        Passing name requires that the theme package already exist.

  #

  # Examples

  #

  #   rake theme:install git="https://github.com/jekyllbootstrap/theme-twitter.git"

  #   rake theme:install name="cool-theme"

  #

  # Returns Success/failure messages.

  desc "Install theme"

  task :install do

    if ENV["git"]

      manifest = theme_from_git_url(ENV["git"])

      name = manifest["name"]

    else

      name = ENV["name"].to_s.downcase

    end

    packaged_theme_path = JB::Path.build(:theme_packages, :node => name)

    abort("rake aborted!

      => ERROR: 'name' cannot be blank") if name.empty?

    abort("rake aborted! 

      => ERROR: '#{packaged_theme_path}' directory not found.

      => Installable themes can be added via git. You can find some here: http://github.com/jekyllbootstrap

      => To download+install run: `rake theme:install git='[PUBLIC-CLONE-URL]'`

      => example : rake theme:install git='git@github.com:jekyllbootstrap/theme-the-program.git'

    ") unless FileTest.directory?(packaged_theme_path)

    manifest = verify_manifest(packaged_theme_path)

    # Get relative paths to packaged theme files

    # Exclude directories as they'll be recursively created. Exclude meta-data files.

    packaged_theme_files = []

    FileUtils.cd(packaged_theme_path) {

      Dir.glob("**/*.*") { |f| 

        next if ( FileTest.directory?(f) || f =~ /^(manifest|readme|packager)/i )

        packaged_theme_files << f 

      }

    }

    # Mirror each file into the framework making sure to prompt if already exists.

    packaged_theme_files.each do |filename|

      file_install_path = File.join(JB::Path.base, filename)

      if File.exist? file_install_path and ask("#{file_install_path} already exists. Do you want to overwrite?", ['y', 'n']) == 'n'

        next

      else

        mkdir_p File.dirname(file_install_path)

        cp_r File.join(packaged_theme_path, filename), file_install_path

      end

    end

    puts "=> #{name} theme has been installed!"

    puts "=> ---"

    if ask("=> Want to switch themes now?", ['y', 'n']) == 'y'

      system("rake switch_theme name='#{name}'")

    end

  end

  # Public: Package a theme using the theme packager.

  # The theme must be structured using valid JB API.

  # In other words packaging is essentially the reverse of installing.

  #

  # name - String, Required name of the theme you want to package.

  #        

  # Examples

  #

  #   rake theme:package name="twitter"

  #

  # Returns Success/failure messages.

  desc "Package theme"

  task :package do

    name = ENV["name"].to_s.downcase

    theme_path = JB::Path.build(:themes, :node => name)

    asset_path = JB::Path.build(:theme_assets, :node => name)

    abort("rake aborted: name cannot be blank") if name.empty?

    abort("rake aborted: '#{theme_path}' directory not found.") unless FileTest.directory?(theme_path)

    abort("rake aborted: '#{asset_path}' directory not found.") unless FileTest.directory?(asset_path)

    ## Mirror theme's template directory (_includes)

    packaged_theme_path = JB::Path.build(:themes, :root => JB::Path.build(:theme_packages, :node => name))

    mkdir_p packaged_theme_path

    cp_r theme_path, packaged_theme_path

    ## Mirror theme's asset directory

    packaged_theme_assets_path = JB::Path.build(:theme_assets, :root => JB::Path.build(:theme_packages, :node => name))

    mkdir_p packaged_theme_assets_path

    cp_r asset_path, packaged_theme_assets_path

    ## Log packager version

    packager = {"packager" => {"version" => CONFIG["theme_package_version"].to_s } }

    open(JB::Path.build(:theme_packages, :node => "#{name}/packager.yml"), "w") do |page|

      page.puts packager.to_yaml

    end

    puts "=> '#{name}' theme is packaged and available at: #{JB::Path.build(:theme_packages, :node => name)}"

  end

end # end namespace :theme

# Internal: Download and process a theme from a git url.

# Notice we don't know the name of the theme until we look it up in the manifest.

# So we'll have to change the folder name once we get the name.

#

# url - String, Required url to git repository.

#        

# Returns theme manifest hash

def theme_from_git_url(url)

  tmp_path = JB::Path.build(:theme_packages, :node => "_tmp")

  abort("rake aborted: system call to git clone failed") if !system("git clone #{url} #{tmp_path}")

  manifest = verify_manifest(tmp_path)

  new_path = JB::Path.build(:theme_packages, :node => manifest["name"])

  if File.exist?(new_path) && ask("=> #{new_path} theme package already exists. Override?", ['y', 'n']) == 'n'

    remove_dir(tmp_path)

    abort("rake aborted: '#{manifest["name"]}' already exists as theme package.")

  end

  remove_dir(new_path) if File.exist?(new_path)

  mv(tmp_path, new_path)

  manifest

end

# Internal: Process theme package manifest file.

#

# theme_path - String, Required. File path to theme package.

#        

# Returns theme manifest hash

def verify_manifest(theme_path)

  manifest_path = File.join(theme_path, "manifest.yml")

  manifest_file = File.open( manifest_path )

  abort("rake aborted: repo must contain valid manifest.yml") unless File.exist? manifest_file

  manifest = YAML.load( manifest_file )

  manifest_file.close

  manifest

end

def ask(message, valid_options)

  if valid_options

    answer = get_stdin("#{message} #{valid_options.to_s.gsub(/"/, '').gsub(/, /,'/')} ") while !valid_options.include?(answer)

  else

    answer = get_stdin(message)

  end

  answer

end

def get_stdin(message)

  print message

  STDIN.gets.chomp

end

#Load custom rake scripts

Dir['_rake/*.rake'].each { |r| load r }

## DA-seq website

Please visit our website for DA-seq [here](https://klugerlab.github.io/DAseq/).

# This is the default format.

# For more see: https://github.com/mojombo/jekyll/wiki/Permalinks

permalink: /:categories/:year/:month/:day/:title

exclude: [".rvmrc", ".rbenv-version", "ReadMe.md", "Rakefile", "changelog.md", "License.md"]

highlighter: rouge

# Themes are encouraged to use these universal variables

# so be sure to set them if your theme uses them.

#

title : DAseq

author :

  name : Jun Zhao

  email : jun.zhao@yale.edu

  github : KlugerLab

# NOTE: Replacing this next line with your own URL

production_url : https://klugerlab.github.io/DAseq

# Tell Github to use the kramdown markdown interpreter

# (see https://help.github.com/articles/migrating-your-pages-site-from-maruku)

markdown: kramdown

# All Jekyll-Bootstrap specific configurations are namespaced into this hash

#

JB :

  version : 0.3.0

  # All links will be namespaced by BASE_PATH if defined.

  # Links in your website should always be prefixed with {{BASE_PATH}}

  # however this value will be dynamically changed depending on your deployment situation.

  #

  # CNAME (http://yourcustomdomain.com)

  #   DO NOT SET BASE_PATH

  #   (urls will be prefixed with "/" and work relatively)

  #

  # GitHub Pages (http://username.github.io)

  #   DO NOT SET BASE_PATH

  #   (urls will be prefixed with "/" and work relatively)

  #

  # GitHub Project Pages (http://username.github.io/project-name)

  #

  #   A GitHub Project site exists in the `gh-pages` branch of one of your repositories.

  #  REQUIRED! Set BASE_PATH to: http://username.github.io/project-name

  #

  # CAUTION:

  #   - When in Localhost, your site will run from root "/" regardless of BASE_PATH

  #   - Only the following values are falsy: ["", null, false]

  #   - When setting BASE_PATH it must be a valid url.

  #     This means always setting the protocol (http|https) or prefixing with "/"

  #

  # NOTE: Replace this next line with your own URL, likely with username.github.io

  BASE_PATH : https://klugerlab.github.io/DAseq

  # By default, the asset_path is automatically defined relative to BASE_PATH plus the enabled theme.

  # ex: [BASE_PATH]/assets/themes/[THEME-NAME]

  #

  # Override this by defining an absolute path to assets here.

  # ex:

  #   http://s3.amazonaws.com/yoursite/themes/watermelon

  #   /assets

  #

  # ASSET_PATH : https://kbroman.org/simple_site/assets/themes/twitter

  # These paths are to the main pages Jekyll-Bootstrap ships with.

  # Some JB helpers refer to these paths; change them here if needed.

  #

  archive_path: nil

  categories_path : nil

  tags_path : nil

  atom_path : nil

  rss_path : nil

  # Settings for comments helper

  # Set 'provider' to the comment provider you want to use.

  # Set 'provider' to false to turn commenting off globally.

  #

  comments :

    provider : false

  # Settings for analytics helper

  # Set 'provider' to the analytics provider you want to use.

  # Set 'provider' to false to turn analytics off globally.

  #

  analytics :

    provider : false

  # Settings for sharing helper.

  # Sharing is for things like tweet, plusone, like, reddit buttons etc.

  # Set 'provider' to the sharing provider you want to use.

  # Set 'provider' to false to turn sharing off globally.

  #

  sharing :

    provider : false

  # Settings for all other include helpers can be defined by creating

  # a hash with key named for the given helper. ex:

  #

  #   pages_list :

  #     provider : "custom"

  #

  # Setting any helper's provider to 'custom' will bypass the helper code

  # and include your custom code. Your custom file must be defined at:

  #   ./_includes/custom/[HELPER]

  # where [HELPER] is the name of the helper you are overriding.