bob changes to get quarto working on my laptop

_quarto.yml

@@ -39,12 +39,13 @@ website:
       - section: "Data"
         contents:
           - website_docs/data_description.qmd
-          - text: "The data-DAG (TODO)"
+          #- text: "The data-DAG (TODO)"
       - section: "Tool landscaping"
         contents:
           - text: "The landscaping matrix"
             file: website_docs/tool_landscaping.qmd
-          - text: "Installing via the plasmogenepi.r-universe (TODO)"
+          - text: "Installing via the plasmogenepi.r-universe"
+            file: website_docs/R_universe.qmd
       - section: "Tutorials"
         contents:
           - text: "**Overview of all tutorials**"
@@ -177,15 +178,21 @@ website:
               file: tutorials/THEREALMcCOIL/RMCL_analysis.Rmd
       - section: "Software standards"
         contents:
+          - website_docs/software_standards.qmd
           - text: "Overview by tool"
             file: website_docs/tools_to_standards.qmd
-          - text: "How do I get my tool on PGEforge? (TODO)"
-      - section: "Events and meetings"
+      - section: "Analysis workflows"
         contents:
+          - website_docs/workflows.qmd
+      - section: "How to contribute"
+        contents:
+          - website_docs/how_to_contribute.qmd
+          - section: "Events and meetings"
+            contents:
             - text: "RADISH23 Hackathon"
               file: website_docs/radish23.qmd
-      - href: website_docs/contributors.qmd
-        text: "Contributors"
+          - href: website_docs/contributors.qmd
+            text: "Contributors"
 
 format:
   html:

index.qmd

@@ -1,8 +1,12 @@
 ---
 title: "PGEforge"
-subtitle: "Your resource hub for *Plasmodium* genomic analysis"
+subtitle: "Resources for enhancing **P**lasmodium **G**enomic **E**pidemiology analysis"
 ---
 
+<div class="custom-title">
+Your resource hub for <br> *Plasmodium* genomic analysis
+</div>
+
 ## Welcome
 
 PGEforge is a community-driven platform designed to simplify *Plasmodium* genomic data analysis. The process of analyzing genomic data often involves various software tools with different formats, user interfaces, and levels of accessibility. These differences can create barriers, especially for those without strong computational skills.
@@ -12,11 +16,11 @@ PGEforge aims to overcome these challenges by providing clear tutorials, streaml
 ## How to use this site
 The site is organized to help you efficiently access and utilize our resources. Here’s an overview of what you’ll find in each section:
 
--	[Data](website_docs/tutorials_overview.qmd): Access a curated selection of datasets commonly used in genomic analysis. These datasets help you familiarize yourself with standard data formats and are used consistently across our tutorials, ensuring easy comparison of tools.
+-	[Data](website_docs/data_description.qmd): Access a curated selection of datasets commonly used in genomic analysis. These datasets help you familiarize yourself with standard data formats and are used consistently across our tutorials, ensuring easy comparison of tools.
 -	[Tool Landscaping](website_docs/tool_landscaping.qmd): Discover a wide range of analysis tools, complete with basic information on their functions, where to find them, and whether we offer tutorials for them. We also introduce the “PlasmoGenEpi R-universe,” a website that simplifies tool installation.
 -	[Tutorials](website_docs/tutorials_overview.qmd): Explore comprehensive guides covering the entire process of installing software, formatting data, running basic functions, and interpreting outputs. These tutorials are designed to make complex tasks straightforward and accessible.
 -	[Software Standards](website_docs/tools_to_standards.qmd): Learn about our objective software standards aimed at guiding developers towards best practices and creating user-friendly tools.
--	Workflows: Understand how different tools can be integrated to address common questions in malaria genomic epidemiology. This section outlines typical workflows and maps tools to various analytical steps.
--	How to Contribute: Find out how you can contribute to this community-driven resource. We welcome input from all areas of the research community to continuously improve and expand our platform.
+-	[Analysis Workflows](website_docs/workflows.qmd): Understand how different tools can be integrated to address common questions in malaria genomic epidemiology. This section outlines typical workflows and maps tools to various analytical steps.
+-	[How to Contribute](website_docs/how_to_contribute.qmd): Find out how you can contribute to this community-driven resource. We welcome input from all areas of the research community to continuously improve and expand our platform.
 
 

tutorials/moire/moire_analysis_cache/html/__packages

@@ -1,10 +1,3 @@
-base
-methods
-datasets
-utils
-grDevices
-graphics
-stats
 kableExtra
 tidyverse
 ggplot2
@@ -18,3 +11,4 @@ forcats
 lubridate
 here
 vcfR
+PGEhammer

website_docs/R_universe.qmd

@@ -0,0 +1,8 @@
+---
+title: "Installing via the plasmogenepi.r-universe"
+format: html
+---
+# Overview
+
+PGEforge hosts simulated and empirical datasets of:
+

website_docs/how_to_contribute.qmd

@@ -0,0 +1,8 @@
+---
+title: "Add your tool to the list"
+format: html
+---
+# Overview
+
+PGEforge hosts simulated and empirical datasets of:
+

website_docs/software_standards.qmd

@@ -0,0 +1,8 @@
+---
+title: "Evaluation framework"
+format: html
+---
+# Overview
+
+PGEforge hosts simulated and empirical datasets of:
+

website_docs/styles.scss

@@ -13,4 +13,11 @@ a{
     border-bottom: 1px solid $hover-color;
   }
 
+}
+
+.custom-title {
+    color: #34495E;
+    text-align: center;
+    font-weight: bold;
+    font-size: 48px; /* Adjust the size as needed */
 }