workaround till issue r-lib/pkgdown#2821 is addressed

bastienchassagnol · Nov 29, 2024 · 0b4dd29 · 0b4dd29
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diff --git a/_pkgdown.yml b/_pkgdown.yml
@@ -31,4 +31,11 @@ articles:
 # development:
 #   mode: auto
 
+# till quarto is not supported properly
+external-articles:
+- name: download
+  title: Browse and download Biobases.
+  description: Compare disticnt approaches to fetch data from Biomodels, ERA and SRA ftps and gene annotation databases.
+  href: https://github.com/bastienchassagnol/DrosophiliaDeconv/tree/main/inst/html/download.html
+
 
diff --git a/inst/html/download.html b/inst/html/download.html
diff --git a/inst/www/.gitignore b/inst/www/.gitignore
@@ -0,0 +1 @@
+/.quarto/
diff --git a/vignettes/download.qmd → inst/www/download.qmd b/vignettes/download.qmd → inst/www/download.qmd
@@ -1,14 +1,19 @@
 ---
 title: "Browse and download Biobases"
-vignette: >
-  %\VignetteIndexEntry{Analyse bulk RNASeq experiences}
-  %\VignetteEngine{quarto::html}
-  %\VignetteEncoding{UTF-8}
-bibliography: references.bib
-knitr:
-  opts_chunk:
-    collapse: true
-    comment: '#>'
+# Global metadata
+author: "Bastien CHASSAGNOL and Savandara BESSE"
+date: last-modified
+bibliography: ../../vignettes/references.bib
+
+# General format for each html page
+format:
+  html:
+    theme: cosmo
+    toc: true
+    toc-depth: 3
+    toc-expand: 2
+    self-contained: true
+    embed-resources: true
 ---
 
 # Protocol to download and retrieve metadata to build reference datasets

diff --git a/inst/www/img/E-MTAB-10519-ERR-correspondance.png b/inst/www/img/E-MTAB-10519-ERR-correspondance.png
diff --git a/inst/www/img/FlyBase_Profile_Search.png b/inst/www/img/FlyBase_Profile_Search.png
diff --git a/inst/www/img/FlyBase_cell_lines.png b/inst/www/img/FlyBase_cell_lines.png
diff --git a/inst/www/img/FlyBase_tissues.png b/inst/www/img/FlyBase_tissues.png
diff --git a/inst/www/img/ena_structure.jpg b/inst/www/img/ena_structure.jpg
diff --git a/inst/www/img/fly_cell_atlas_datasets.png b/inst/www/img/fly_cell_atlas_datasets.png
diff --git a/inst/www/img/fly_cell_atlas_preprocessing.png b/inst/www/img/fly_cell_atlas_preprocessing.png
diff --git a/inst/www/img/sra_databases.png b/inst/www/img/sra_databases.png
diff --git a/inst/www/img/sra_pipeline.png b/inst/www/img/sra_pipeline.png
diff --git a/inst/www/img/sra_structure.png b/inst/www/img/sra_structure.png
diff --git a/vignettes/DrosophiliaDeconv.Rmd b/vignettes/DrosophiliaDeconv.Rmd
@@ -0,0 +1,14 @@
+---
+title: "How to reproduce results?"
+output: rmarkdown::html_vignette
+vignette: >
+  %\VignetteIndexEntry{How to reproduce results?}
+  %\VignetteEngine{knitr::rmarkdown}
+  %\VignetteEncoding{UTF-8}
+knitr:
+  opts_chunk:
+    collapse: true
+    comment: '#>'
+---
+
+Let's get started with basics.
diff --git a/vignettes/DrosophiliaDeconv.qmd b/vignettes/DrosophiliaDeconv.qmd
diff --git a/vignettes/preprocess_bulkRNASeq.qmd → vignettes/preprocess_bulkRNASeq.Rmd b/vignettes/preprocess_bulkRNASeq.qmd → vignettes/preprocess_bulkRNASeq.Rmd
@@ -1,13 +1,11 @@
 ---
 title: "Analyse bulk RNASeq experiences"
+output: rmarkdown::html_vignette
+bibliography: references.bib
 vignette: >
   %\VignetteIndexEntry{Analyse bulk RNASeq experiences}
-  %\VignetteEngine{quarto::html}
+  %\VignetteEngine{knitr::rmarkdown}
   %\VignetteEncoding{UTF-8}
-knitr:
-  opts_chunk:
-    collapse: true
-    comment: '#>'
 ---
 
 # Key steps for bulk RNASeq analysis

diff --git a/vignettes/preprocess_scRNASeq.qmd → vignettes/preprocess_scRNASeq.Rmd b/vignettes/preprocess_scRNASeq.qmd → vignettes/preprocess_scRNASeq.Rmd
@@ -1,8 +1,10 @@
 ---
 title: "Analyse single cell RNASeq experiences"
+output: rmarkdown::html_vignette
+bibliography: references.bib
 vignette: >
   %\VignetteIndexEntry{Analyse single cell RNASeq experiences}
-  %\VignetteEngine{quarto::html}
+  %\VignetteEngine{knitr::rmarkdown}
   %\VignetteEncoding{UTF-8}
 knitr:
   opts_chunk: