diff --git a/docs/Gemfile b/docs/Gemfile new file mode 100644 index 0000000..5312a4b --- /dev/null +++ b/docs/Gemfile @@ -0,0 +1,3 @@ +source 'https://rubygems.org' +gem 'jekyll' +gem 'github-pages', group: :jekyll_plugins diff --git a/docs/Gemfile.lock b/docs/Gemfile.lock new file mode 100644 index 0000000..46a78a5 --- /dev/null +++ b/docs/Gemfile.lock @@ -0,0 +1,261 @@ +GEM + remote: https://rubygems.org/ + specs: + activesupport (7.0.4.3) + concurrent-ruby (~> 1.0, >= 1.0.2) + i18n (>= 1.6, < 2) + minitest (>= 5.1) + tzinfo (~> 2.0) + addressable (2.8.1) + public_suffix (>= 2.0.2, < 6.0) + coffee-script (2.4.1) + coffee-script-source + execjs + coffee-script-source (1.11.1) + colorator (1.1.0) + commonmarker (0.23.9) + concurrent-ruby (1.2.2) + dnsruby (1.61.9) + simpleidn (~> 0.1) + 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 (2.8.1) + faraday (2.7.4) + faraday-net_http (>= 2.0, < 3.1) + ruby2_keywords (>= 0.0.4) + faraday-net_http (3.0.2) + ffi (1.15.5) + forwardable-extended (2.6.0) + gemoji (3.0.1) + github-pages (228) + github-pages-health-check (= 1.17.9) + jekyll (= 3.9.3) + jekyll-avatar (= 0.7.0) + jekyll-coffeescript (= 1.1.1) + jekyll-commonmark-ghpages (= 0.4.0) + jekyll-default-layout (= 0.1.4) + jekyll-feed (= 0.15.1) + jekyll-gist (= 1.5.0) + jekyll-github-metadata (= 2.13.0) + 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 (= 0.12.0) + kramdown (= 2.3.2) + kramdown-parser-gfm (= 1.1.0) + liquid (= 4.0.4) + mercenary (~> 0.3) + minima (= 2.5.1) + nokogiri (>= 1.13.6, < 2.0) + rouge (= 3.26.0) + terminal-table (~> 1.4) + github-pages-health-check (1.17.9) + addressable (~> 2.3) + dnsruby (~> 1.60) + octokit (~> 4.0) + public_suffix (>= 3.0, < 5.0) + typhoeus (~> 1.3) + html-pipeline (2.14.3) + activesupport (>= 2) + nokogiri (>= 1.4) + http_parser.rb (0.8.0) + i18n (1.12.0) + concurrent-ruby (~> 1.0) + jekyll (3.9.3) + 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 (0.7.0) + jekyll (>= 3.0, < 5.0) + jekyll-coffeescript (1.1.1) + coffee-script (~> 2.2) + coffee-script-source (~> 1.11.1) + 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 (0.1.4) + jekyll (~> 3.0) + jekyll-feed (0.15.1) + jekyll (>= 3.7, < 5.0) + jekyll-gist (1.5.0) + octokit (~> 4.2) + jekyll-github-metadata (2.13.0) + jekyll (>= 3.4, < 5.0) + octokit (~> 4.0, != 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-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 (0.12.0) + gemoji (~> 3.0) + html-pipeline (~> 2.2) + jekyll (>= 3.0, < 5.0) + kramdown (2.3.2) + rexml + kramdown-parser-gfm (1.1.0) + kramdown (~> 2.0) + liquid (4.0.4) + listen (3.8.0) + rb-fsevent (~> 0.10, >= 0.10.3) + rb-inotify (~> 0.9, >= 0.9.10) + mercenary (0.3.6) + mini_portile2 (2.8.1) + minima (2.5.1) + jekyll (>= 3.5, < 5.0) + jekyll-feed (~> 0.9) + jekyll-seo-tag (~> 2.1) + minitest (5.18.0) + nokogiri (1.14.3) + mini_portile2 (~> 2.8.0) + racc (~> 1.4) + octokit (4.25.1) + faraday (>= 1, < 3) + sawyer (~> 0.9) + pathutil (0.16.2) + forwardable-extended (~> 2.6) + public_suffix (4.0.7) + racc (1.6.2) + rb-fsevent (0.11.2) + rb-inotify (0.10.1) + ffi (~> 1.0) + rexml (3.2.5) + rouge (3.26.0) + 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 (1.4.0) + ethon (>= 0.9.0) + tzinfo (2.0.6) + concurrent-ruby (~> 1.0) + unf (0.1.4) + unf_ext + unf_ext (0.0.8.2) + unicode-display_width (1.8.0) + +PLATFORMS + ruby + +DEPENDENCIES + github-pages + jekyll + +BUNDLED WITH + 2.1.4 diff --git a/docs/_config.yml b/docs/_config.yml new file mode 100644 index 0000000..7616e1f --- /dev/null +++ b/docs/_config.yml @@ -0,0 +1,2 @@ +remote_theme: chrisrhymes/bulma-clean-theme +title: HIVIntact diff --git a/docs/_data/navigation.yml b/docs/_data/navigation.yml new file mode 100644 index 0000000..9adc74e --- /dev/null +++ b/docs/_data/navigation.yml @@ -0,0 +1,19 @@ +- name: Getting Started + link: /getting_started.html +- name: Admin + link: /admin.html +- name: Steps and Files + link: /steps.html + dropdown: + - name: G2P + link: /design/fastq_g2p.html + - name: Remap + link: /design/remap.html + - name: De Novo Assembly + link: /design/assembly.html + - name: Resistance + link: /design/resistance.html + - name: Genome Coverage + link: /genome_coverage.html +- name: GitHub + link: https://github.com/cfe-lab/HIVIntact diff --git a/docs/_includes/footer.html b/docs/_includes/footer.html new file mode 100644 index 0000000..93005af --- /dev/null +++ b/docs/_includes/footer.html @@ -0,0 +1,22 @@ + \ No newline at end of file