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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,277 @@ | ||
| GEM | ||
| remote: https://rubygems.org/ | ||
| specs: | ||
| activesupport (7.1.3.2) | ||
| base64 | ||
| bigdecimal | ||
| concurrent-ruby (~> 1.0, >= 1.0.2) | ||
| connection_pool (>= 2.2.5) | ||
| drb | ||
| i18n (>= 1.6, < 2) | ||
| minitest (>= 5.1) | ||
| mutex_m | ||
| tzinfo (~> 2.0) | ||
| addressable (2.8.6) | ||
| public_suffix (>= 2.0.2, < 6.0) | ||
| base64 (0.2.0) | ||
| bigdecimal (3.1.6) | ||
| coffee-script (2.4.1) | ||
| coffee-script-source | ||
| execjs | ||
| coffee-script-source (1.12.2) | ||
| colorator (1.1.0) | ||
| commonmarker (0.23.10) | ||
| concurrent-ruby (1.2.3) | ||
| connection_pool (2.4.1) | ||
| dnsruby (1.70.0) | ||
| simpleidn (~> 0.2.1) | ||
| drb (2.2.0) | ||
| ruby2_keywords | ||
| em-websocket (0.5.3) | ||
| eventmachine (>= 0.12.9) | ||
| http_parser.rb (~> 0) | ||
| ethon (0.16.0) | ||
| ffi (>= 1.15.0) | ||
| eventmachine (1.2.7) | ||
| execjs (2.9.1) | ||
| faraday (2.8.1) | ||
| base64 | ||
| faraday-net_http (>= 2.0, < 3.1) | ||
| ruby2_keywords (>= 0.0.4) | ||
| faraday-net_http (3.0.2) | ||
| ffi (1.16.3) | ||
| forwardable-extended (2.6.0) | ||
| gemoji (4.1.0) | ||
| github-pages (231) | ||
| github-pages-health-check (= 1.18.2) | ||
| jekyll (= 3.9.5) | ||
| jekyll-avatar (= 0.8.0) | ||
| jekyll-coffeescript (= 1.2.2) | ||
| jekyll-commonmark-ghpages (= 0.4.0) | ||
| jekyll-default-layout (= 0.1.5) | ||
| jekyll-feed (= 0.17.0) | ||
| jekyll-gist (= 1.5.0) | ||
| jekyll-github-metadata (= 2.16.1) | ||
| jekyll-include-cache (= 0.2.1) | ||
| jekyll-mentions (= 1.6.0) | ||
| jekyll-optional-front-matter (= 0.3.2) | ||
| jekyll-paginate (= 1.1.0) | ||
| jekyll-readme-index (= 0.3.0) | ||
| jekyll-redirect-from (= 0.16.0) | ||
| jekyll-relative-links (= 0.6.1) | ||
| jekyll-remote-theme (= 0.4.3) | ||
| jekyll-sass-converter (= 1.5.2) | ||
| jekyll-seo-tag (= 2.8.0) | ||
| jekyll-sitemap (= 1.4.0) | ||
| jekyll-swiss (= 1.0.0) | ||
| jekyll-theme-architect (= 0.2.0) | ||
| jekyll-theme-cayman (= 0.2.0) | ||
| jekyll-theme-dinky (= 0.2.0) | ||
| jekyll-theme-hacker (= 0.2.0) | ||
| jekyll-theme-leap-day (= 0.2.0) | ||
| jekyll-theme-merlot (= 0.2.0) | ||
| jekyll-theme-midnight (= 0.2.0) | ||
| jekyll-theme-minimal (= 0.2.0) | ||
| jekyll-theme-modernist (= 0.2.0) | ||
| jekyll-theme-primer (= 0.6.0) | ||
| jekyll-theme-slate (= 0.2.0) | ||
| jekyll-theme-tactile (= 0.2.0) | ||
| jekyll-theme-time-machine (= 0.2.0) | ||
| jekyll-titles-from-headings (= 0.5.3) | ||
| jemoji (= 0.13.0) | ||
| kramdown (= 2.4.0) | ||
| kramdown-parser-gfm (= 1.1.0) | ||
| liquid (= 4.0.4) | ||
| mercenary (~> 0.3) | ||
| minima (= 2.5.1) | ||
| nokogiri (>= 1.13.6, < 2.0) | ||
| rouge (= 3.30.0) | ||
| terminal-table (~> 1.4) | ||
| github-pages-health-check (1.18.2) | ||
| addressable (~> 2.3) | ||
| dnsruby (~> 1.60) | ||
| octokit (>= 4, < 8) | ||
| public_suffix (>= 3.0, < 6.0) | ||
| typhoeus (~> 1.3) | ||
| html-pipeline (2.14.3) | ||
| activesupport (>= 2) | ||
| nokogiri (>= 1.4) | ||
| http_parser.rb (0.8.0) | ||
| i18n (1.14.1) | ||
| concurrent-ruby (~> 1.0) | ||
| jekyll (3.9.5) | ||
| addressable (~> 2.4) | ||
| colorator (~> 1.0) | ||
| em-websocket (~> 0.5) | ||
| i18n (>= 0.7, < 2) | ||
| jekyll-sass-converter (~> 1.0) | ||
| jekyll-watch (~> 2.0) | ||
| kramdown (>= 1.17, < 3) | ||
| liquid (~> 4.0) | ||
| mercenary (~> 0.3.3) | ||
| pathutil (~> 0.9) | ||
| rouge (>= 1.7, < 4) | ||
| safe_yaml (~> 1.0) | ||
| jekyll-avatar (0.8.0) | ||
| jekyll (>= 3.0, < 5.0) | ||
| jekyll-coffeescript (1.2.2) | ||
| coffee-script (~> 2.2) | ||
| coffee-script-source (~> 1.12) | ||
| jekyll-commonmark (1.4.0) | ||
| commonmarker (~> 0.22) | ||
| jekyll-commonmark-ghpages (0.4.0) | ||
| commonmarker (~> 0.23.7) | ||
| jekyll (~> 3.9.0) | ||
| jekyll-commonmark (~> 1.4.0) | ||
| rouge (>= 2.0, < 5.0) | ||
| jekyll-default-layout (0.1.5) | ||
| jekyll (>= 3.0, < 5.0) | ||
| jekyll-feed (0.17.0) | ||
| jekyll (>= 3.7, < 5.0) | ||
| jekyll-figure (0.2.0) | ||
| jekyll-gist (1.5.0) | ||
| octokit (~> 4.2) | ||
| jekyll-github-metadata (2.16.1) | ||
| jekyll (>= 3.4, < 5.0) | ||
| octokit (>= 4, < 7, != 4.4.0) | ||
| jekyll-include-cache (0.2.1) | ||
| jekyll (>= 3.7, < 5.0) | ||
| jekyll-mentions (1.6.0) | ||
| html-pipeline (~> 2.3) | ||
| jekyll (>= 3.7, < 5.0) | ||
| jekyll-optional-front-matter (0.3.2) | ||
| jekyll (>= 3.0, < 5.0) | ||
| jekyll-paginate (1.1.0) | ||
| jekyll-pdf-embed (1.1.3) | ||
| jekyll | ||
| jekyll-readme-index (0.3.0) | ||
| jekyll (>= 3.0, < 5.0) | ||
| jekyll-redirect-from (0.16.0) | ||
| jekyll (>= 3.3, < 5.0) | ||
| jekyll-relative-links (0.6.1) | ||
| jekyll (>= 3.3, < 5.0) | ||
| jekyll-remote-theme (0.4.3) | ||
| addressable (~> 2.0) | ||
| jekyll (>= 3.5, < 5.0) | ||
| jekyll-sass-converter (>= 1.0, <= 3.0.0, != 2.0.0) | ||
| rubyzip (>= 1.3.0, < 3.0) | ||
| jekyll-sass-converter (1.5.2) | ||
| sass (~> 3.4) | ||
| jekyll-seo-tag (2.8.0) | ||
| jekyll (>= 3.8, < 5.0) | ||
| jekyll-sitemap (1.4.0) | ||
| jekyll (>= 3.7, < 5.0) | ||
| jekyll-swiss (1.0.0) | ||
| jekyll-theme-architect (0.2.0) | ||
| jekyll (> 3.5, < 5.0) | ||
| jekyll-seo-tag (~> 2.0) | ||
| jekyll-theme-cayman (0.2.0) | ||
| jekyll (> 3.5, < 5.0) | ||
| jekyll-seo-tag (~> 2.0) | ||
| jekyll-theme-dinky (0.2.0) | ||
| jekyll (> 3.5, < 5.0) | ||
| jekyll-seo-tag (~> 2.0) | ||
| jekyll-theme-hacker (0.2.0) | ||
| jekyll (> 3.5, < 5.0) | ||
| jekyll-seo-tag (~> 2.0) | ||
| jekyll-theme-leap-day (0.2.0) | ||
| jekyll (> 3.5, < 5.0) | ||
| jekyll-seo-tag (~> 2.0) | ||
| jekyll-theme-merlot (0.2.0) | ||
| jekyll (> 3.5, < 5.0) | ||
| jekyll-seo-tag (~> 2.0) | ||
| jekyll-theme-midnight (0.2.0) | ||
| jekyll (> 3.5, < 5.0) | ||
| jekyll-seo-tag (~> 2.0) | ||
| jekyll-theme-minimal (0.2.0) | ||
| jekyll (> 3.5, < 5.0) | ||
| jekyll-seo-tag (~> 2.0) | ||
| jekyll-theme-modernist (0.2.0) | ||
| jekyll (> 3.5, < 5.0) | ||
| jekyll-seo-tag (~> 2.0) | ||
| jekyll-theme-primer (0.6.0) | ||
| jekyll (> 3.5, < 5.0) | ||
| jekyll-github-metadata (~> 2.9) | ||
| jekyll-seo-tag (~> 2.0) | ||
| jekyll-theme-slate (0.2.0) | ||
| jekyll (> 3.5, < 5.0) | ||
| jekyll-seo-tag (~> 2.0) | ||
| jekyll-theme-tactile (0.2.0) | ||
| jekyll (> 3.5, < 5.0) | ||
| jekyll-seo-tag (~> 2.0) | ||
| jekyll-theme-time-machine (0.2.0) | ||
| jekyll (> 3.5, < 5.0) | ||
| jekyll-seo-tag (~> 2.0) | ||
| jekyll-titles-from-headings (0.5.3) | ||
| jekyll (>= 3.3, < 5.0) | ||
| jekyll-watch (2.2.1) | ||
| listen (~> 3.0) | ||
| jemoji (0.13.0) | ||
| gemoji (>= 3, < 5) | ||
| html-pipeline (~> 2.2) | ||
| jekyll (>= 3.0, < 5.0) | ||
| kramdown (2.4.0) | ||
| rexml | ||
| kramdown-parser-gfm (1.1.0) | ||
| kramdown (~> 2.0) | ||
| liquid (4.0.4) | ||
| listen (3.9.0) | ||
| rb-fsevent (~> 0.10, >= 0.10.3) | ||
| rb-inotify (~> 0.9, >= 0.9.10) | ||
| mercenary (0.3.6) | ||
| mini_portile2 (2.8.5) | ||
| minima (2.5.1) | ||
| jekyll (>= 3.5, < 5.0) | ||
| jekyll-feed (~> 0.9) | ||
| jekyll-seo-tag (~> 2.1) | ||
| minitest (5.22.2) | ||
| mutex_m (0.2.0) | ||
| nokogiri (1.15.5) | ||
| mini_portile2 (~> 2.8.2) | ||
| racc (~> 1.4) | ||
| octokit (4.25.1) | ||
| faraday (>= 1, < 3) | ||
| sawyer (~> 0.9) | ||
| pathutil (0.16.2) | ||
| forwardable-extended (~> 2.6) | ||
| public_suffix (5.0.4) | ||
| racc (1.7.3) | ||
| rb-fsevent (0.11.2) | ||
| rb-inotify (0.10.1) | ||
| ffi (~> 1.0) | ||
| rexml (3.2.6) | ||
| rouge (3.30.0) | ||
| ruby2_keywords (0.0.5) | ||
| rubyzip (2.3.2) | ||
| safe_yaml (1.0.5) | ||
| sass (3.7.4) | ||
| sass-listen (~> 4.0.0) | ||
| sass-listen (4.0.0) | ||
| rb-fsevent (~> 0.9, >= 0.9.4) | ||
| rb-inotify (~> 0.9, >= 0.9.7) | ||
| sawyer (0.9.2) | ||
| addressable (>= 2.3.5) | ||
| faraday (>= 0.17.3, < 3) | ||
| simpleidn (0.2.1) | ||
| unf (~> 0.1.4) | ||
| terminal-table (1.8.0) | ||
| unicode-display_width (~> 1.1, >= 1.1.1) | ||
| typhoeus (1.4.1) | ||
| ethon (>= 0.9.0) | ||
| tzinfo (2.0.6) | ||
| concurrent-ruby (~> 1.0) | ||
| unf (0.1.4) | ||
| unf_ext | ||
| unf_ext (0.0.9.1) | ||
| unicode-display_width (1.8.0) | ||
|
|
||
| PLATFORMS | ||
| ruby | ||
|
|
||
| DEPENDENCIES | ||
| github-pages | ||
| jekyll-figure | ||
| jekyll-pdf-embed | ||
|
|
||
| BUNDLED WITH | ||
| 2.1.4 |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,3 +1,10 @@ | ||
| title: Course-in-a-Box | ||
| description: An open-source project for creating online courses, built by <a href="https://www.p2pu.org">P2PU</a> | ||
| modules: ["setup", "content", "customize"] | ||
| title: Bioinformatics for Genomic Epidemiology March 2024 | ||
| description: An introductory course on Pathogen Bioinformatics for Genomic Epidemiology | ||
| modules: | ||
| - "unix-linux-introduction" | ||
| - "package-management-conda" | ||
| - "containers" | ||
| - "nextflow" | ||
| - "r-programming" | ||
| - "galaxy-introduction" | ||
| - "cholera-case-study" |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,39 @@ | ||
| # basic configuration | ||
| markdown: kramdown | ||
| permalink: /:categories/:title/ | ||
|
|
||
| # Change this tracking code with your own tracking code | ||
| ga_tracking_code: G-Z7RMVPYZ5K | ||
| # Please leave this code here for us to see how Course in a Box get used | ||
| p2pu_ga_tracking_code: UA-55722824-1 | ||
|
|
||
| # Some files we need to exclude, so Github can build the site | ||
| exclude: [Gemfile, Gemfile.lock, README.md] | ||
|
|
||
| defaults: | ||
| - | ||
| scope: | ||
| path: "modules" # an empty string here means all files in the project | ||
| values: | ||
| layout: "course_page" | ||
|
|
||
| prose: | ||
| media: img | ||
| ignore: | ||
| - /_includes | ||
| - /_layouts | ||
| - /_sass | ||
| - /fonts | ||
| - /js | ||
| - /css | ||
|
|
||
| # Set some personal styles and logo for your course | ||
| # this is a hex value http://www.w3schools.com/tags/ref_colorpicker.asp | ||
| jumbotron_color: "#348F41" | ||
| jumbotron_image: "img/bacteria.svg" | ||
| jumbotron_mask: "img/jumbotron-mask.svg" | ||
| # jumbotron_icon: "img/box-icon.png" | ||
|
|
||
| plugins: | ||
| - jekyll-figure | ||
| - jekyll-pdf-embed |
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