Lectern Documentation Update

README.md

@@ -90,7 +90,7 @@ npm start
 
 - **Robust Error Handling**: Docusaurus has excellent error catching, particularly for broken and missing links, reducing the need for manual testing.
 
-![Pro Tip](./website/docs/03-other-software/images/proTip.png "Use Overture Docs repo to search across all Overture repos")
+![Pro Tip](./website/docs/02-platform-tools/images/proTip.png "Use Overture Docs repo to search across all Overture repos")
 
 > [!TIP]  
 > The Overture Docs repo contains everything, therefore finding & tracking links and content across all our repos has never been easier.

website/community/02-funding.md

@@ -6,22 +6,22 @@ We gratefully acknowledge the financial support that has made this project possi
 
 As working group 2, we are developing a federated framework for genomic data access and analysis, specifically building an enhanced Overture data submission system to facilitate the ingestion, validation, and tracking of clinical and molecular data into the PCGL platform.
 
-  - **Project Title:** Pan-Canadian Genome Library (PCGL)
-  - **Funding Period:** 2023-2028
+- **Project Title:** [Pan-Canadian Genome Library (PCGL)](https://genomelibrary.ca/)
+- **Funding Period:** 2023-2028
 
 ### National Cancer Institute at the US National Institutes of Health
 
 Under this grant we are making the Overture platform more accessible by breaking down barriers to adoption, integrating existing analysis tools and adding federated search functionality between distributed Overture instances using standardized data governance frameworks ([GA4GH](https://www.ga4gh.org/)).
 
-  - **Grant Number:** #U24CA253529
-  - **Funding Period:** 2021-2026
+- **Grant Number:** #U24CA253529
+- **Funding Period:** 2021-2026
 
-### Canadian COVID-19 Genomic Data Infrastructure 
+### Canadian COVID-19 Genomic Data Infrastructure
 
 The [VirusSeq Data Portal](https://virusseq-dataportal.ca/) demonstrates Overture's successful expansion beyond oncology data management. This funding facilitated the platform's adaptation to support viral genomic data, while enabling the development, deployment, and ongoing maintenance of Canada's central SARS-CoV-2 sequence repository.
 
-  - **Project Title:** VirusSeq Data Portal
-  - **Funding Period:** 2020-2024
+- **Project Title:** VirusSeq Data Portal
+- **Funding Period:** 2020-2024
 
 ### The Government of Ontario
 
@@ -37,4 +37,4 @@ We also thank the following organizations for their contributions:
 
 For more information about our funding or to discuss potential collaborations, please email us at contact@overture.bio.
 
-**Last updated:** 11-19-24
+**Last updated:** 11-19-24

website/docs/00-getting-started.mdx

@@ -18,13 +18,13 @@ Our documentation is the definitive resource for the Overture project. Here you'
   {
     type: 'link',
     label: 'Other Software',
-    href: '/docs/other-software/',
+    href: '/docs/platform-tools/',
     description: 'Software that complements and supports Overture.'
   },
   {
     type: 'link',
     label: 'Standards',
-    href: '/docs/standards/',
+    href: '/docs/documentation-standards/',
     description: 'The formal basis of our Overture documentation and developement practices.'
   },
 

website/docs/01-core-software/00-Lectern

@@ -0,0 +1 @@
+../../../submodules/lectern/docs/

website/docs/01-core-software/01-core-software.mdx

@@ -1,6 +1,6 @@
 # Core Software
 
-![Core Software](./images/core-software.webp 'Core Software')
+![Core Software](./images/core-software.webp "Core Software")
 
 :::info
 Overture is a genomics data platform that combines front and back-end services. Stage handles navigation, while Arranger enables data search. Authentication runs through Keycloak/Ego, Song manages metadata, Score handles S3 file transfers, and Maestro indexes to Elasticsearch for Arranger's search functionality. Together, these components enable efficient genomics data management.
@@ -10,46 +10,44 @@ Overture is a genomics data platform that combines front and back-end services.
 
 Our core software documentation is organized as follows:
 
-   ```
-   .
-   └── /Service/
-      ├── /Overview
-      ├── /Setup
-      └── /Usage
-   ```
+```
+.
+└── /Service/
+   ├── /Overview
+   ├── /Setup
+   └── /Usage
+```
 
 ### Overview
 
-The Overview section for each service typically includes:
-    - High-level overview of the service
-    - System architecture diagram and explanation
-    - Key features and capabilities
-    - Repository structure
-    - Links to relevant GitHub repositories or additional resources
+The Overview section for each service typically includes: - High-level overview of the service - System architecture diagram and explanation - Key features and capabilities - Repository structure - Links to relevant GitHub repositories or additional resources
 
-### Setup 
+### Setup
 
 The Setup section runs you through the process of getting each service setup in a development environment. We offer guidance for the following Overture development configurations:
 
-
 <Tabs>
   <TabItem value="platform" label="Platform" default>
-  ![Platform](../03-other-software/images/platform.svg 'Overture Platform')
+    ![Platform](../02-platform-tools/images/platform.svg 'Overture Platform')
   </TabItem>
   <TabItem value="songDev" label="SongDev">
-     ![Song Dev](../03-other-software/images/songDev.svg 'Song Dev Environment')
+    ![Song Dev](../02-platform-tools/images/songDev.svg 'Song Dev Environment')
   </TabItem>
   <TabItem value="scoreDev" label="ScoreDev">
-     ![Score Dev](../03-other-software/images/scoreDev.svg 'Score Dev Environment')
+    ![Score Dev](../02-platform-tools/images/scoreDev.svg 'Score Dev
+    Environment')
   </TabItem>
   <TabItem value="maestroDev" label="MaestroDev">
-     ![Maestro Dev](../03-other-software/images/maestroDev.svg 'Maestro Dev Environment')
+    ![Maestro Dev](../02-platform-tools/images/maestroDev.svg 'Maestro Dev
+    Environment')
   </TabItem>
   <TabItem value="arrangerDev" label="ArrangerDev">
-     ![Arranger Dev](../03-other-software/images/arrangerDev.svg 'Arranger Dev Environment')
+    ![Arranger Dev](../02-platform-tools/images/arrangerDev.svg 'Arranger Dev
+    Environment')
   </TabItem>
   <TabItem value="stageDev" label="StageDev">
-    ![Stage Dev](../03-other-software/images/stageDev.svg 'Stage Dev Environment')
+    ![Stage Dev](../02-platform-tools/images/stageDev.svg 'Stage Dev
+    Environment')
   </TabItem>
 </Tabs>
 
@@ -60,6 +58,7 @@ For newcomers to Overture, we recommend starting with our Platform Quickstart an
 ### Usage
 
 The Usage section provides detailed information on how to effectively use each service, including:
+
 - Interacting with the API
 - Common use cases and best practices
 - Troubleshooting and FAQs
@@ -69,5 +68,3 @@ The Usage section provides detailed information on how to effectively use each s
 ### Contents
 
 <DocCardList />
-
-

website/docs/03-other-software/03-Other-Software.mdx → website/docs/02-platform-tools/02-platform-tools.mdx

@@ -1,7 +1,5 @@
-# Other Software
+# Platfrom Tools
 
 This section provides information on supplemental software that, while not directly integrated into the Overture platform, is part of the broader Overture project. Although primarily used for internal purposes, feel free to explore the documentation for these tools that support our open-source initiative.
 
-
-
-<DocCardList />
+<DocCardList />