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nesi · Feb 29, 2024 · a5af9e2 · a5af9e2
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diff --git a/README.md b/README.md
@@ -1,4 +1,4 @@
 # agdr-docs-concept
 Proof of Concept for Mkdocs based AGDR support pages.
 
-[AGDR support files example](https://nesi.github.io/agdr-docs-concept/)
+[AGDR support files example](https://nesi.github.io/agdr-docs-concept/docs/index.md)
diff --git a/docs/assets/css/my.css b/docs/assets/css/my.css
@@ -39,4 +39,6 @@
   .pillarcard:hover img {
   opacity: 1.0;
   }
-  /*end Pillar style*/
+  /*end Pillar style*/
+
+
diff --git a/docs/index.md b/docs/index.md
@@ -1,14 +1,16 @@
 # Aotearoa Genomic Data Repository
 
-[cards cols=3 (cards-services.yaml)]
+- [User Guides](user-guides/index.md)
 
-[cards cols=2 (cards-home.yaml)]
+- [Release Notes](releases/index.md)
 
-[User Guides](user-guides/index.md){ .md-button .md-button--primary }
 
-[Release Notes](releases/index.md){ .md-button .md-button--primary }
+# <mark font-family: Calibri><kbd> [ User Guides ](user-guides/index.md) </kbd></mark> &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; <mark><kbd>  [ Release Notes ](releases/index.md)<br> </kbd></mark>
 
 ## Recent activity
 
 <!--START_SECTION:activity-->
-<!--END_SECTION:activity-->
+
+<!--END_SECTION:activity-->
+
+
diff --git a/docs/releases/08Aug2023.md b/docs/releases/08Aug2023.md
@@ -59,4 +59,6 @@ Note: JupyterHub, Kibana are not used and not updated
 - https://test.agdr.org.nz/TAONGA-KAKAPO official project page now opens in a separate tab
 Removing the starting G in "GKakapo125+ genome sequencing"
 
-(Note: Repo.data.nesi.org.nz was updated on the 3rd of August with the following version differences: indexd 2022.05 and peregrine: 2022.05)
+(Note: Repo.data.nesi.org.nz was updated on the 3rd of August with the following version differences: indexd 2022.05 and peregrine: 2022.05)
+
+[back](index.md)
diff --git a/docs/releases/16Jan2024.md b/docs/releases/16Jan2024.md
@@ -52,3 +52,4 @@ Note: JupyterHub, Kibana are not used and not updated
 
 (Note: Repo.data.nesi.org.nz is not updated. We will start deprecating this deployment soon. Please use data.agdr.org.nz)
 
+[back](index.md)
diff --git a/docs/releases/16Oct2023.md b/docs/releases/16Oct2023.md
@@ -4,4 +4,6 @@
 
 - Updated text on the landing page
 
-Note: no change of versions https://gadr.zendesk.com/hc/en-gb/articles/7512059827087-data-agdr-org-nz-08-August-2023
+Note: no change of versions https://gadr.zendesk.com/hc/en-gb/articles/7512059827087-data-agdr-org-nz-08-August-2023
+
+[back](index.md)
diff --git a/docs/releases/deficiencies.md b/docs/releases/deficiencies.md
@@ -4,4 +4,6 @@
 
 - Also message": "'unaligned reads' is not one of ['Unaligned Reads']" - must be capital case
 
-- TSV cannot have any empty columns
+- TSV cannot have any empty columns
+
+[back](index.md)
diff --git a/docs/releases/index.md b/docs/releases/index.md
@@ -6,3 +6,5 @@ data.agdr.org.nz web application release notes
 - [data.agdr.org.nz 16 January 2024](16Jan2024.md)
 - [data.agdr.org.nz 16 October 2023](16Oct2023.md)
 - [data.agdr.org.nz 08 August 2023](08Aug2023.md)
+
+[back](../index.md)
diff --git a/docs/user-guides/globus.md b/docs/user-guides/globus.md
@@ -1 +1,5 @@
 # Accessing data hosted on NeSI Globus endpoint
+
+en construction
+
+[back](index.md)
diff --git a/docs/user-guides/index.md b/docs/user-guides/index.md
@@ -4,3 +4,5 @@
 - [Requesting access to data](requesting.md)
 - [Accessing data hosted on NeSI Globus endpoint](globus.md)
 - [Submission Process](submission.md)
+
+[back](../index.md)
diff --git a/docs/user-guides/navigating.md b/docs/user-guides/navigating.md
@@ -2,8 +2,10 @@
 
 The Aotearoa Genomic Data Repository landing page is available at https://data.agdr.org.nz/
 
+![Alt text](../assets/images/getstart1.png) [Title](navigating.md)
+
 <figure markdown>
-  ![Alt text](../assets/images/getstart1.png)
+    ![Alt text](../assets/images/getstart1.png)
 </figure>
 
 ## Authentication is not required
@@ -31,7 +33,7 @@ By selecting any filter element, such as a project ID, other filters and total c
 Clicking on the ‘Files’ tab enables exploration of uploaded files based on project ID, data types, and data format.
 
 <figure markdown>
-  ![Alt text](../assets/images/getstart4.png)
+  ![Alt text](/docs/assets/images/getstart4.png)
 </figure>
 
 Scroll down to see the list of files.
@@ -40,6 +42,10 @@ Scroll down to see the list of files.
   ![Alt text](../assets/images/getstart5.png)
 </figure>
 
+<img src="/docs/assets/images/getstart5.png"
+     alt="getstart5"
+     style="float: left; margin-right: 10px;" />
+
 Clicking on the project ID of a file will display more information about the associated project. 
 
 Please note although file metadata is shown, the data files are not available for download without completing the application process. Please click on the "Apply for access" link to do this.  
@@ -63,4 +69,6 @@ Relationships between nodes are represented by arrows from one node to another.
 
 - View the Data Dictionary as a table to see the name and a brief description of each node, organised by node category. Click on the name of a node to display more information about its properties.
 
-The metadata dictionary is under review and we would appreciate feedback.
+The metadata dictionary is under review and we would appreciate feedback.
+
+[back](index.md)
diff --git a/docs/user-guides/requesting.md b/docs/user-guides/requesting.md
@@ -1 +1,5 @@
 # Requesting access to data
+
+en construction
+
+[back](index.md)
diff --git a/docs/user-guides/submission.md b/docs/user-guides/submission.md
@@ -1 +1,5 @@
 # Submission Process
+
+en construction
+
+[back](index.md)
diff --git a/docs/user-guides/summary.md b/docs/user-guides/summary.md
@@ -1,5 +1,5 @@
 * [User Guides](index.md)
-* [Navigating the data repository](navigation.md)
+* [Navigating the data repository](navigating.md)
 * [Requesting access to data](requesting.md)
 * [Accessing data hosted on NeSI Globus endpoint](globus.md)
 * [Submission Process](submission.md)

diff --git a/mkdocs.yml b/mkdocs.yml
@@ -54,4 +54,4 @@ plugins:
 extra_css:
   - assets/css/neoteroi-mkdocs.css
   - assets/css/footer.css
-  # - assets/css/my.css
+  - assets/css/my.css
Original file line number	Diff line number	Diff line change
Expand Up		@@ -52,3 +52,4 @@ Note: JupyterHub, Kibana are not used and not updated

		(Note: Repo.data.nesi.org.nz is not updated. We will start deprecating this deployment soon. Please use data.agdr.org.nz)

		[back](index.md)