diff --git a/assets/biocworkshop_jupyter.png b/assets/biocworkshop_jupyter.png new file mode 100644 index 0000000..884101e Binary files /dev/null and b/assets/biocworkshop_jupyter.png differ diff --git a/assets/biocworkshop_open_session.png b/assets/biocworkshop_open_session.png new file mode 100644 index 0000000..5f34f79 Binary files /dev/null and b/assets/biocworkshop_open_session.png differ diff --git a/assets/biocworkshop_run_tool.png b/assets/biocworkshop_run_tool.png new file mode 100644 index 0000000..96748bb Binary files /dev/null and b/assets/biocworkshop_run_tool.png differ diff --git a/assets/biocworkshop_select_rjupyter.png b/assets/biocworkshop_select_rjupyter.png new file mode 100644 index 0000000..9e5ba17 Binary files /dev/null and b/assets/biocworkshop_select_rjupyter.png differ diff --git a/howto.qmd b/howto.qmd index 3f6ca08..899f579 100644 --- a/howto.qmd +++ b/howto.qmd @@ -1,22 +1,27 @@ # How to run the notebooks -## Option 1: Run notebooks locally +## Option 1. Using BiocWorkshop (Preferred) -If you want to run locally, please clone the repository and install the python packages used for the workshop. +If you are attending the workshop at Bioconductor: -```sh -git clone https://github.com/BiocPy/BiocWorkshop2024 -cd BiocWorkshop2024 +1. Open [BiocWorkshops](https://workshop.bioconductor.org/) in a new tab. +2. Select "R/Bioconductor Jupyter Workshop" as shown in the screenshot. -# Assuming python is available -# You are free to use mamba, conda or virtualenv's -pip install -r requirements.txt +![](./assets/biocworkshop_select_rjupyter.png) -# Start the jupyter server -jupyter lab -``` +3. Click the "Run the tool". + +![](./assets/biocworkshop_run_tool.png) + +4. Click on "Interactive Tools" in the left sidebar to check on the status of the session. Once the session is ready, click on the "BiocPy" to open the Jupyter notebook. -Then checkout the [notebook](https://github.com/BiocPy/BiocWorkshop2024/tree/master/notebook) directory that contain Jupyter notebooks. +![](./assets/biocworkshop_open_session.png) + +5. You should be able to see the BiocWorkshop repository cloned into the session. + +![](./assets/biocworkshop_jupyter.png) + +---- ## Option 2: Using Google Colab @@ -35,4 +40,24 @@ To open the session in Google Colab: :::{.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 Google Colab sessions. -::: \ No newline at end of file +::: + +---- + +## Option 3: 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. \ No newline at end of file