updating Gemfile, tweaking homepage

informatics-isi-edu · Nov 16, 2023 · f40b7eb · f40b7eb
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diff --git a/docs/Gemfile b/docs/Gemfile
@@ -7,12 +7,12 @@ ruby RUBY_VERSION
 gem "github-pages", group: :jekyll_plugins
 
 # If you have any plugins, put them here!
-# group :jekyll_plugins do
-#    gem "jekyll-feed"
-#    gem "jekyll-sitemap"
-#    gem "jekyll-redirect-from"
-#    gem "jekyll-seo-tag"
-# end
+ group :jekyll_plugins do
+    gem "jekyll-feed"
+    gem "jekyll-sitemap"
+    gem "jekyll-redirect-from"
+    gem "jekyll-seo-tag"
+ end
 
 # Windows and JRuby does not include zoneinfo files, so bundle the tzinfo-data gem
 # and associated library.

diff --git a/docs/Gemfile.lock b/docs/Gemfile.lock
@@ -221,12 +221,16 @@ GEM
       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 (5.14.4)
     multipart-post (2.1.1)
+    nokogiri (1.13.6)
+      mini_portile2 (~> 2.8.0)
+      racc (~> 1.4)
     nokogiri (1.13.6-x64-mingw32)
       racc (~> 1.4)
     nokogiri (1.13.6-x86_64-linux)
@@ -276,17 +280,22 @@ GEM
     zeitwerk (2.5.1)
 
 PLATFORMS
+  ruby
   x64-mingw32
   x86_64-linux
 
 DEPENDENCIES
   github-pages
+  jekyll-feed
+  jekyll-redirect-from
+  jekyll-seo-tag
+  jekyll-sitemap
   tzinfo (~> 1.2)
   tzinfo-data
   wdm (~> 0.1.1)
 
 RUBY VERSION
-   ruby 2.7.8p225
+   ruby 2.7.0p0
 
 BUNDLED WITH
    2.2.31
diff --git a/docs/_docs/index.md b/docs/_docs/index.md
@@ -1,12 +1,9 @@
 ---
 title: ATLAS-D2K User and Submitter Guide
 permalink: /docs/home/
-redirect_from:
-- /docs/index.html
-- /index.html
 ---
 
-This is the home of public documentation for the ATLAS-D2K Center. If you find anything that needs correcting or have suggestions for more documentation, please send email to:
+This is the home of public documentation for the ATLAS-D2K Center, which publishes data and resources from the [GUDMAP](https://www.atlas-d2k.org/rebuildingakidney/) and [ReBuilding A Kidney (RBK)](https://www.atlas-d2k.org/gudmap/) consortiums. If you find anything that needs correcting or have suggestions for more documentation, please send email to:
 
 - [[email protected]](mailto:[email protected])
 
@@ -19,28 +16,27 @@ This is the home of public documentation for the ATLAS-D2K Center. If you find a
 ## Exporting Data
 - [How to export data (includes how to export to a GEO-compliant file)](../exporting-data)
 
-## Submitting Data (for members of ATLAS-D2K)
+## Submitting Data
 
-For members of ATLAS-D2K to submit data, use our self-curation tools to add or edit data. **Note that [you must have the correct access](../accessing-atlas-resources) before you are able to submit any data.**
+For members of ATLAS-D2K (specifically members of GUDMAP and RBK) to submit data, use our self-curation tools to add or edit data. **Note that [you must have the correct access](../accessing-atlas-resources) before you are able to submit any data.**
 
 - **If the type of data you need to submit is not listed below**, please contact [[email protected]](mailto:[email protected]).
 - **If you are publishing a paper using ATLAS-D2K data,** it's a good idea to contact us as well to make sure you have an appropriate [Data Collection](../data-collections) for optimal citation.
 
 **To add or edit data:**
 - [Standard files and formats for submission](../standard-files-and-formats-for-submission)
+- [Imaging Data (Specimen)](../specimen-v2)
+- [Sequencing, Metabolomics, and Image Mass Cytometry Data (Study)](../submitting-sequencing-data-v3-1)
 - [Antibodies](../antibodies)
 - [Cell Lines](../cell-lines)
 - [Data Collections (esp for publications!)](../data-collections)
-- [Imaging Data/Specimen (Histology, Immunofluorescence/Immunohistochemistry, In Situ Hybridization)](../specimen-v2)
 - [Protocols](../protocols)
-- [Sequencing, Metabolomics, and Image Mass Cytometry Data](../submitting-sequencing-data-v3-1)
 - [Single Cell Visualization Files](../single-cell-visualization-files) (draft)
 - [Color Palette for Image Annotation](../color-palette-for-image-annotation)
 
 **To upload your data files in bulk:**
 - [Uploading Files via the DERIVA Client Tools (commmandline and GUI versions available)](../uploading-files-using-deriva-client-tools)
 
-
 ## Images and Videos
 - [Thumbnail creation guideline](../thumbnail-creation-guideline)
 - [Supported Video Platforms](../available-video-platforms)

diff --git a/docs/_includes/topnav.html b/docs/_includes/topnav.html
@@ -7,7 +7,7 @@
         <span class="icon-bar"></span>
         <span class="icon-bar"></span>
       </button>
-            <a class="navbar-brand" href="{{ site.baseurl }}/">
+            <a class="navbar-brand" href="{{ site.baseurl }}/docs/home/">
                  <span><img src="{{ "/assets/img/atlas-logo-inverted.png" | relative_url }}" alt="Logo"></span>
                  {%- comment -%} {{ site.title }} {%- endcomment -%}