Get gitpod working!

Author: jfy133

.gitpod.Dockerfile

@@ -1,6 +1,9 @@
 FROM gitpod/workspace-full
 
 RUN brew install R
-RUN wget https://github.com/quarto-dev/quarto-cli/releases/download/v1.0.36/quarto-1.0.36-linux-amd64.deb
+RUN wget https://github.com/quarto-dev/quarto-cli/releases/download/v1.3.361/quarto-1.3.361-linux-amd64.deb
 RUN sudo dpkg -i quarto*
 RUN rm *.deb
+RUN Rscript -e 'install.packages("rmarkdown", repos="https://cloud.r-project.org")'
+RUN Rscript -e 'install.packages("languageserver", repos="https://cloud.r-project.org")'
+RUN sudo apt install -y librsvg2-bin

.gitpod.yml

@@ -4,8 +4,9 @@ image:
   # List the start up tasks. Learn more https://www.gitpod.io/docs/config-start-tasks/
 tasks:
   - name: quarto
-    # init: echo 'init script' # runs during prebuild
-    command: quarto preview
+    init: |
+      quarto install tinytex
+    command: quarto preview /workspace/intro-to-ancient-metagenomics-book --render all --no-browser --no-watch-inputs
 
 # List the ports to expose. Learn more https://www.gitpod.io/docs/config-ports/
 ports:
@@ -14,9 +15,6 @@ ports:
 
 vscode:
   extensions:
-    - [email protected]:z5vr1v1bfS++U/aHLSXQ6Q==
     - quarto.quarto
- 
-# init/before start steps?   
-#      quarto check
-#      quarto install tinytex
+    - REditorSupport.r
+

docs/Introduction-to-Ancient-Metagenomics.pdf

@@ -2,126 +2,126 @@
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     <loc>https://spaam-community.github.io/intro-to-ancient-metagenomics-book/index.html</loc>
-    <lastmod>2023-06-05T13:32:24.043Z</lastmod>
+    <lastmod>2023-06-12T10:36:17.189Z</lastmod>
   </url>
   <url>
     <loc>https://spaam-community.github.io/intro-to-ancient-metagenomics-book/authors.html</loc>
-    <lastmod>2023-06-05T13:32:24.047Z</lastmod>
+    <lastmod>2023-06-12T10:36:17.205Z</lastmod>
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     <loc>https://spaam-community.github.io/intro-to-ancient-metagenomics-book/acknowledgements.html</loc>
-    <lastmod>2023-06-05T13:32:24.055Z</lastmod>
+    <lastmod>2023-06-12T10:36:17.209Z</lastmod>
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-    <lastmod>2023-06-05T13:32:24.067Z</lastmod>
+    <lastmod>2023-06-12T10:36:17.221Z</lastmod>
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     <loc>https://spaam-community.github.io/intro-to-ancient-metagenomics-book/section-theory.html</loc>
-    <lastmod>2023-06-05T13:32:24.075Z</lastmod>
+    <lastmod>2023-06-12T10:36:17.229Z</lastmod>
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     <loc>https://spaam-community.github.io/intro-to-ancient-metagenomics-book/introduction-to-ngs-sequencing.html</loc>
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   <url>
     <loc>https://spaam-community.github.io/intro-to-ancient-metagenomics-book/introduction-to-ancient-dna.html</loc>
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+    <lastmod>2023-06-12T10:36:17.245Z</lastmod>
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     <loc>https://spaam-community.github.io/intro-to-ancient-metagenomics-book/introduction-to-metagenomics.html</loc>
-    <lastmod>2023-06-05T13:32:24.095Z</lastmod>
+    <lastmod>2023-06-12T10:36:17.253Z</lastmod>
   </url>
   <url>
     <loc>https://spaam-community.github.io/intro-to-ancient-metagenomics-book/introduction-to-microbial-genomics.html</loc>
-    <lastmod>2023-06-05T13:32:24.103Z</lastmod>
+    <lastmod>2023-06-12T10:36:17.257Z</lastmod>
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   <url>
     <loc>https://spaam-community.github.io/intro-to-ancient-metagenomics-book/introduction-to-evolutionary-biology.html</loc>
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+    <lastmod>2023-06-12T10:36:17.265Z</lastmod>
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   <url>
     <loc>https://spaam-community.github.io/intro-to-ancient-metagenomics-book/section-useful-skills.html</loc>
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+    <lastmod>2023-06-12T10:36:17.269Z</lastmod>
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   <url>
     <loc>https://spaam-community.github.io/intro-to-ancient-metagenomics-book/bare-bones-bash.html</loc>
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+    <lastmod>2023-06-12T10:36:17.281Z</lastmod>
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+    <lastmod>2023-06-12T10:36:17.329Z</lastmod>
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   <url>
     <loc>https://spaam-community.github.io/intro-to-ancient-metagenomics-book/introduction-to-python.html</loc>
-    <lastmod>2023-06-05T13:32:24.247Z</lastmod>
+    <lastmod>2023-06-12T10:36:17.401Z</lastmod>
   </url>
   <url>
     <loc>https://spaam-community.github.io/intro-to-ancient-metagenomics-book/introduction-to-git.html</loc>
-    <lastmod>2023-06-05T13:32:24.255Z</lastmod>
+    <lastmod>2023-06-12T10:36:17.413Z</lastmod>
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-    <lastmod>2023-06-05T13:32:24.523Z</lastmod>
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 </urlset>