diff --git a/.gitignore b/.gitignore index 324eab1..a5d65e8 100644 --- a/.gitignore +++ b/.gitignore @@ -9,4 +9,6 @@ chapters/zilinois_lung_with_celltypist/ *.tiledb *_cache *_files -tutorials/cache/*`` \ No newline at end of file +tutorials/cache/*`` +cache/ +.ipynb_checkpoints \ No newline at end of file diff --git a/README.md b/README.md index ec4d43f..c3a42ea 100644 --- a/README.md +++ b/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 ``` diff --git a/_quarto.yml b/_quarto.yml index 4ce5d5c..87bda12 100644 --- a/_quarto.yml +++ b/_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:jayaram.kancherla@gmail.com)" -# contributor: "[Aaron Lun](mailto:infinite.monkeys.with.keys@gmail.com)" -# 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 \ No newline at end of file + toc: true \ No newline at end of file diff --git a/assets/colab_open_notebook.png b/assets/colab_open_notebook.png new file mode 100644 index 0000000..913553c Binary files /dev/null and b/assets/colab_open_notebook.png differ diff --git a/assets/colab_session.png b/assets/colab_session.png new file mode 100644 index 0000000..f77f44a Binary files /dev/null and b/assets/colab_session.png differ diff --git a/howto.qmd b/howto.qmd new file mode 100644 index 0000000..8ee7659 --- /dev/null +++ b/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! \ No newline at end of file diff --git a/index.qmd b/index.qmd index c01ef94..4020a8c 100644 --- a/index.qmd +++ b/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 . Check out [sessioninfo](./tutorials/sessioninfo.qmd) for more information. \ No newline at end of file +This is a reproducible Quarto book with reusable snippets. Check out [sessioninfo](./tutorials/sessioninfo.qmd) for packages installed during the build. \ No newline at end of file diff --git a/notebook/genomic_ranges.ipynb b/notebook/genomic_ranges.ipynb index 3de0524..b14264e 100644 --- a/notebook/genomic_ranges.ipynb +++ b/notebook/genomic_ranges.ipynb @@ -41,175 +41,28 @@ ] }, { - "cell_type": "code", - "execution_count": 22, + "cell_type": "markdown", "metadata": { "scrolled": true }, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "Requirement already satisfied: biocutils in /Users/kancherj/miniforge3/lib/python3.10/site-packages (0.1.5)\n", - "Requirement already satisfied: genomicranges in /Users/kancherj/miniforge3/lib/python3.10/site-packages (0.4.28)\n", - "Requirement already satisfied: rds2py in /Users/kancherj/miniforge3/lib/python3.10/site-packages (0.4.4)\n", - "Requirement already satisfied: numpy in /Users/kancherj/miniforge3/lib/python3.10/site-packages (1.26.4)\n", - "Collecting numpy\n", - " Using cached numpy-2.0.0-cp310-cp310-macosx_14_0_arm64.whl.metadata (60 kB)\n", - 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] - } - ], "source": [ "!pip install -U biocutils genomicranges rds2py numpy pandas geniml" ] }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "If you are using Google colab, you may not have access to the RDS file used, in this tutorial. Change the block below from markdown to code and run the chunk." + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "!wget https://raw.githubusercontent.com/BiocPy/BiocWorkshop2024/master/notebook/hg38_exons_by_tx.rds" + ] + }, { "cell_type": "markdown", "metadata": {}, diff --git a/tutorials/genomic_ranges.qmd b/tutorials/genomic_ranges.qmd index b26090d..9be7102 100644 --- a/tutorials/genomic_ranges.qmd +++ b/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 ```