Add section on how to run the notebooks

.gitignore

@@ -9,4 +9,6 @@ chapters/zilinois_lung_with_celltypist/
 *.tiledb
 *_cache
 *_files
-tutorials/cache/*``
+tutorials/cache/*``
+cache/
+.ipynb_checkpoints

README.md

@@ -9,14 +9,14 @@ To get started locally, follow these steps:
 - Install [quarto-cli](https://quarto.org/docs/get-started/).
 - Install the necessary packages listed in [requirements.txt](./requirements.txt) and [rpackages.R](rpackages.R).
 
-```shell
+```sh
 pip install -r requirements.txt
 Rscript rpackages.R
 ```
 
 - Run quarto preview to view the HTML version of the site.
 
-```shell
+```sh
 qurto preview
 ```
 

_quarto.yml

@@ -18,6 +18,7 @@ website:
     logo: ./assets/logo.png
     contents:
       - index.qmd
+      - howto.qmd
       - section: "Tutorials"
         contents:
           - tutorials/genomic_ranges.qmd
@@ -30,46 +31,9 @@ website:
     center: 
       - text: "(c) Jayaram Kancherla & Aaron Lun."
 
-  # navbar:
-  #   left:
-  #     - href: index.qmd
-  #       text: Home
-  #     - tutorials/annotate_cell_types.qmd
-  #     - tutorials/sessioninfo
-
-# book:
-#   title: "Bioc2024: Interoperability between R and Python using BiocPy"
-#   author: "[Jayaram Kancherla](mailto:[email protected])"
-#   contributor: "[Aaron Lun](mailto:[email protected])"
-#   favicon: ./assets/short.png
-#   site-url: https://biocpy.github.io/tutorial
-#   date: "5/31/2024"
-#   search: true
-#   repo-url: https://github.com/BiocPy/tutorial
-#   repo-actions: [issue]
-#   # downloads: [pdf, epub]
-#   sharing: [twitter]
-#   twitter-card: true
-#   cover-image: ./assets/full.png
-#   page-footer:
-#     center: 
-#       - text: "(c) BiocPy core contributors"
-#         # href: chapters/summary.qmd
-#   sidebar:
-#     style: docked
-#     background: light
-#   chapters:
-#     - index.qmd
-#     - tutorials/annotate_cell_types.qmd
-#     - tutorials/sessioninfo.qmd
-#     # - chapters/references.qmd
-
 format:
   html:
     theme: sandstone
     number-sections: false
     code-link: true
-    toc: true
-  # pdf:
-  #   keep-tex: true
-  #   documentclass: scrreprt
+    toc: true

howto.qmd

@@ -0,0 +1,39 @@
+# How to run the notebooks
+
+## Option 1: Run notebooks locally
+
+If you want to run locally, please clone the repository and install the python packages used for the workshop.
+
+```sh
+git clone https://github.com/BiocPy/BiocWorkshop2024
+cd BiocWorkshop2024
+
+# Assuming python is available
+# You are free to use mamba, conda or virtualenv's
+pip install -r requirements.txt
+
+# Start the jupyter server
+jupyter lab
+```
+
+Then checkout the [notebook](https://github.com/BiocPy/BiocWorkshop2024/tree/master/notebook) directory that contain Jupyter notebooks.
+
+## Option 2: Using Google colab
+
+To open the session in Google colab
+
+1. Open [Google colab](https://colab.research.google.com/) in a new tab.
+2. On the page, It should open up a dialog to "Open notebook" as shown in the screenshot below. If not, go to file -> Open Notebook from the menu in the top left.
+3. Choose Github and enter the repository url for the workshop: `https://github.com/BiocPy/BiocWorkshop2024`. This will automatically find the python notebooks available in the repository.
+
+![](./assets/colab_session.png)
+
+4. Choose the open icon to explore this notebook
+
+![](./assets/colab_open_notebook.png)
+
+:::{.callout-important}
+This process does not download the [RDS file](https://github.com/BiocPy/BiocWorkshop2024/tree/master/notebook) available in the repository. Folks might have to manually download this to their colab sessions.
+:::
+
+and thats it!

index.qmd

@@ -18,7 +18,6 @@ on [GitHub](https://github.com/BiocPy).
 
 ![](./assets/workshop.png)
 
-
 ### Core contributors
 
 - [Jayaram Kancherla](https://github.com/jkanche)
@@ -33,4 +32,4 @@ We are looking for more contributions from the community to improve our packages
 
 ## Developer notes
 
-This is a reproducible Quarto book with reusable snippets. To learn more about Quarto books visit <https://quarto.org/docs/books>. Check out [sessioninfo](./tutorials/sessioninfo.qmd) for more information.
+This is a reproducible Quarto book with reusable snippets. Check out [sessioninfo](./tutorials/sessioninfo.qmd) for packages installed during the build.

tutorials/genomic_ranges.qmd

@@ -25,7 +25,7 @@ Let's start by installing the required packages for R and Python.
 
 You can install the Python packages using pip:
 
-```bash
+```sh
 pip install -U biocutils genomicranges rds2py numpy pandas geniml
 ```