Initial commit

.gitignore

@@ -0,0 +1,4 @@
+_site
+.sass-cache
+.jekyll-metadata
+*~

404.html

@@ -0,0 +1,24 @@
+---
+layout: default
+---
+
+<style type="text/css" media="screen">
+  .container {
+    margin: 10px auto;
+    max-width: 600px;
+    text-align: center;
+  }
+  h1 {
+    margin: 30px 0;
+    font-size: 4em;
+    line-height: 1;
+    letter-spacing: -1px;
+  }
+</style>
+
+<div class="container">
+  <h1>404</h1>
+
+  <p><strong>Page not found :(</strong></p>
+  <p>The requested page could not be found.</p>
+</div>

Gemfile

@@ -0,0 +1,30 @@
+source "https://rubygems.org"
+
+# Hello! This is where you manage which Jekyll version is used to run.
+# When you want to use a different version, change it below, save the
+# file and run `bundle install`. Run Jekyll with `bundle exec`, like so:
+#
+#     bundle exec jekyll serve
+#
+# This will help ensure the proper Jekyll version is running.
+# Happy Jekylling!
+gem "jekyll", "~> 3.8.5"
+
+# This is the default theme for new Jekyll sites. You may change this to anything you like.
+gem "minima", "~> 2.0"
+
+# If you want to use GitHub Pages, remove the "gem "jekyll"" above and
+# uncomment the line below. To upgrade, run `bundle update github-pages`.
+# gem "github-pages", group: :jekyll_plugins
+
+# If you have any plugins, put them here!
+group :jekyll_plugins do
+  gem "jekyll-feed", "~> 0.6"
+end
+
+# Windows does not include zoneinfo files, so bundle the tzinfo-data gem
+gem "tzinfo-data", platforms: [:mingw, :mswin, :x64_mingw, :jruby]
+
+# Performance-booster for watching directories on Windows
+gem "wdm", "~> 0.1.0" if Gem.win_platform?
+

Gemfile.lock

@@ -0,0 +1,74 @@
+GEM
+  remote: https://rubygems.org/
+  specs:
+    addressable (2.5.2)
+      public_suffix (>= 2.0.2, < 4.0)
+    colorator (1.1.0)
+    concurrent-ruby (1.1.3)
+    em-websocket (0.5.1)
+      eventmachine (>= 0.12.9)
+      http_parser.rb (~> 0.6.0)
+    eventmachine (1.2.7)
+    ffi (1.9.25)
+    forwardable-extended (2.6.0)
+    http_parser.rb (0.6.0)
+    i18n (0.9.5)
+      concurrent-ruby (~> 1.0)
+    jekyll (3.8.5)
+      addressable (~> 2.4)
+      colorator (~> 1.0)
+      em-websocket (~> 0.5)
+      i18n (~> 0.7)
+      jekyll-sass-converter (~> 1.0)
+      jekyll-watch (~> 2.0)
+      kramdown (~> 1.14)
+      liquid (~> 4.0)
+      mercenary (~> 0.3.3)
+      pathutil (~> 0.9)
+      rouge (>= 1.7, < 4)
+      safe_yaml (~> 1.0)
+    jekyll-feed (0.11.0)
+      jekyll (~> 3.3)
+    jekyll-sass-converter (1.5.2)
+      sass (~> 3.4)
+    jekyll-seo-tag (2.5.0)
+      jekyll (~> 3.3)
+    jekyll-watch (2.1.2)
+      listen (~> 3.0)
+    kramdown (1.17.0)
+    liquid (4.0.1)
+    listen (3.1.5)
+      rb-fsevent (~> 0.9, >= 0.9.4)
+      rb-inotify (~> 0.9, >= 0.9.7)
+      ruby_dep (~> 1.2)
+    mercenary (0.3.6)
+    minima (2.5.0)
+      jekyll (~> 3.5)
+      jekyll-feed (~> 0.9)
+      jekyll-seo-tag (~> 2.1)
+    pathutil (0.16.2)
+      forwardable-extended (~> 2.6)
+    public_suffix (3.0.3)
+    rb-fsevent (0.10.3)
+    rb-inotify (0.9.10)
+      ffi (>= 0.5.0, < 2)
+    rouge (3.3.0)
+    ruby_dep (1.5.0)
+    safe_yaml (1.0.4)
+    sass (3.7.2)
+      sass-listen (~> 4.0.0)
+    sass-listen (4.0.0)
+      rb-fsevent (~> 0.9, >= 0.9.4)
+      rb-inotify (~> 0.9, >= 0.9.7)
+
+PLATFORMS
+  ruby
+
+DEPENDENCIES
+  jekyll (~> 3.8.5)
+  jekyll-feed (~> 0.6)
+  minima (~> 2.0)
+  tzinfo-data
+
+BUNDLED WITH
+   1.17.1

_config.yml

@@ -0,0 +1,43 @@
+# Welcome to Jekyll!
+#
+# This config file is meant for settings that affect your whole blog, values
+# which you are expected to set up once and rarely edit after that. If you find
+# yourself editing this file very often, consider using Jekyll's data files
+# feature for the data you need to update frequently.
+#
+# For technical reasons, this file is *NOT* reloaded automatically when you use
+# 'bundle exec jekyll serve'. If you change this file, please restart the server process.
+
+# Site settings
+# These are used to personalize your new site. If you look in the HTML files,
+# you will see them accessed via {{ site.title }}, {{ site.email }}, and so on.
+# You can create any custom variable you would like, and they will be accessible
+# in the templates via {{ site.myvariable }}.
+title: Sunbeam metagenomics pipeline
+email: sunbeam-labs@freemail.com
+description: >- # this means to ignore newlines until "baseurl:"
+  Write an awesome description for your new site here. You can edit this
+  line in _config.yml. It will appear in your document head meta (for
+  Google search results) and in your feed.xml site description.
+baseurl: "" # the subpath of your site, e.g. /blog
+url: "http://sunbeam-labs.org" # the base hostname & protocol for your site, e.g. http://example.com
+twitter_username: sunbeam-labs
+github_username:  sunbeam-labs
+
+# Build settings
+markdown: kramdown
+theme: minima
+plugins:
+  - jekyll-feed
+
+# Exclude from processing.
+# The following items will not be processed, by default. Create a custom list
+# to override the default setting.
+# exclude:
+#   - Gemfile
+#   - Gemfile.lock
+#   - node_modules
+#   - vendor/bundle/
+#   - vendor/cache/
+#   - vendor/gems/
+#   - vendor/ruby/

_data/repos.yml

@@ -0,0 +1,14 @@
+- user: sunbeam-labs
+  repo: sbx_report
+  updated_at: 2018-10-31T20:15:30Z
+  watchers_count: 1
+  forks_count: 3
+  open_issues: 0
+  target: final_report
+- user: sunbeam-labs
+  repo: sbx_metaphlan
+  updated_at: 2018-10-31T20:15:30Z
+  watchers_count: 0
+  forks_count: 2
+  open_issues: 2
+  target: all_metaphlan

index.md

@@ -0,0 +1,22 @@
+---
+layout: default
+---
+
+Sunbeam is a bioinformatics analysis pipeline that supports
+reproducible analysis of shotgun metagenomics data sets. Its main
+feature is easy-to-make extensions, which allow users to specify
+additional functionality for the pipeline with only a few lines of
+code.
+
+## Extensions
+
+{% for item in site.data.repos %}
+[{{ item.repo }}](https://github.com/{{ item.user }}/{{ item.repo }})
+
+Targets: {{ item.target }}
+
+  - Last update: {{ item.updated_at }}
+  - Watchers: {{ item.watchers_count }}
+  - Open issues: {{ item.open_issues }}
+
+{% endfor %}