Merge pull request #4 from elixir-europe-training/1-developing-practical-1

1 developing practical 1

Author: rasools

.gitignore

@@ -1,2 +1,6 @@
 /.quarto/
 .Rproj.user
+
+# Ignore all directories named "data"
+data/
+*/data/

day_1/practical_1/Dockerfile

@@ -0,0 +1,44 @@
+FROM jupyter/minimal-notebook:latest
+LABEL org.opencontainers.image.source=https://github.com/scilifelabdatacentre/serve-images
+
+ARG SERVE_BRANCH=develop
+WORKDIR /home/jovyan
+
+COPY requirements.txt /tmp
+COPY imaging_based_data_analysis_env.yml /tmp
+COPY lab /home/jovyan/lab
+COPY start-script.sh /usr/local/bin/start-script.sh
+
+USER root
+RUN apt-get update && apt-get install curl -y --no-install-recommends && \
+    apt-get clean && rm -rf /var/lib/apt/lists/*
+
+RUN pip install --no-cache-dir -r /tmp/requirements.txt
+
+RUN conda install -n base -c conda-forge mamba
+
+RUN mamba env create -f /tmp/imaging_based_data_analysis_env.yml && conda clean --all --yes
+
+RUN echo "conda activate imaging_based_data_analysis_env" >> /etc/profile.d/conda.sh
+
+RUN /opt/conda/envs/imaging_based_data_analysis_env/bin/pip install ipykernel && \
+    /opt/conda/envs/imaging_based_data_analysis_env/bin/python -m ipykernel install --name imaging_based_data_analysis_env --display-name "Python (imaging_based_data_analysis_env)"
+
+RUN chown -R jovyan:users /opt/conda /home/jovyan/.cache /home/jovyan/lab && \
+    chmod -R a+rwx /home/jovyan/lab && \
+    chmod +x /usr/local/bin/start-script.sh
+
+USER jovyan
+
+# Set default conda environment
+ENV PATH=/opt/conda/envs/imaging_based_data_analysis_env/bin:$PATH
+
+# Disable Jupyter token authentication
+RUN jupyter notebook --generate-config && \
+    echo "c.NotebookApp.token = ''" >> /home/jovyan/.jupyter/jupyter_notebook_config.py && \
+    echo "c.NotebookApp.password = ''" >> /home/jovyan/.jupyter/jupyter_notebook_config.py && \
+    echo "c.NotebookApp.ip = '0.0.0.0'" >> /home/jovyan/.jupyter/jupyter_notebook_config.py && \
+    echo "c.NotebookApp.open_browser = False" >> /home/jovyan/.jupyter/jupyter_notebook_config.py
+
+# Set the startup script as the entrypoint
+ENTRYPOINT ["/usr/local/bin/start-script.sh"]

day_1/practical_1/imaging_based_data_analysis_env.yml

@@ -0,0 +1,17 @@
+name: imaging_based_data_analysis_env
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - python=3.9
+  - scanpy
+  - squidpy
+  - pandas
+  - scipy
+  - scikit-learn
+  - matplotlib
+  - seaborn
+  - ipykernel
+  - jupyterlab
+  - pip

day_1/practical_1/lab/imaging_based_data_analysis.ipynb

@@ -0,0 +1,33 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# Practical 1: Imaging-Based Data Analysis with Xenium (Mouse Brain, Cancer)\n",
+    "### Author: Rasool Saghaleyni"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Import necessary libraries\n",
+    "import scanpy as sc\n",
+    "import squidpy as sq\n",
+    "import matplotlib.pyplot as plt\n",
+    "import numpy as np\n",
+    "import pandas as pd"
+   ]
+  }
+ ],
+ "metadata": {
+  "language_info": {
+   "name": "python"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}

day_1/practical_1/requirements.txt

@@ -0,0 +1,3 @@
+mlflow==2.8.1
+boto3==1.28.50 
+minio==7.1.16

day_1/practical_1/start-script.sh

@@ -0,0 +1,5 @@
+#!/bin/bash
+# Activate the conda environment
+source /opt/conda/bin/activate imaging_based_data_analysis_env
+# Start the Jupyter Notebook server
+exec jupyter notebook --allow-root --notebook-dir=/home/jovyan/lab