From 85a6cb892c993a2b0cff403917d1d44104e4f17f Mon Sep 17 00:00:00 2001 From: MahiRaj22 Date: Fri, 20 Feb 2026 15:56:28 +0530 Subject: [PATCH 1/2] docs: fix step numbering in README --- README.md | 150 ++++++++++++++++++++++-------------------------------- 1 file changed, 62 insertions(+), 88 deletions(-) diff --git a/README.md b/README.md index 3b995b66..871b9cf0 100644 --- a/README.md +++ b/README.md @@ -1,6 +1,6 @@ -# OpenMS streamlit template +# OpenMS streamlit template + -[![Open Template!](https://static.streamlit.io/badges/streamlit_badge_black_white.svg)](https://abi-services.cs.uni-tuebingen.de/streamlit-template/) This repository contains a template app for OpenMS workflows in a web application using the **streamlit** framework. It serves as a foundation for apps ranging from simple workflows with **pyOpenMS** to complex workflows utilizing **OpenMS TOPP tools** with parallel execution. It includes solutions for handling user data and parameters in workspaces as well as deployment with docker-compose. @@ -16,34 +16,32 @@ This repository contains a template app for OpenMS workflows in a web applicatio ## 🔗 Try the Online Demo -Explore the hosted version here: 👉 [Live App](https://abi-services.cs.uni-tuebingen.de/streamlit-template/) +Explore the hosted version here: 👉 [Live App](https://abi-services.cs.uni-tuebingen.de/streamlit-template/) ## 💻 Run Locally To run the app locally: 1. **Clone the repository** - ```bash - git clone https://github.com/OpenMS/streamlit-template.git - cd streamlit-template - ``` + ```bash + git clone https://github.com/OpenMS/streamlit-template.git + cd streamlit-template + ``` 2. **Install dependencies** - - Make sure you can run ```pip``` commands. - - Install all dependencies with: - ```bash - pip install -r requirements.txt - ``` - -4. **Launch the app** - ```bash - streamlit run app.py - ``` + Make sure you can run `pip` commands. + Install all dependencies with: + ```bash + pip install -r requirements.txt -> ⚠️ Note: The local version offers limited functionality. Features that depend on OpenMS TOPP tools are only available out of the box in the Docker setup. For the local version [OpenMS Command Line Tools](https://openms.readthedocs.io/en/latest/about/installation.html) must be installed separately. + ``` +3. **Launch the app** + ```bash + streamlit run app.py + ``` + +> ⚠️ Note: The local version offers limited functionality. Features that depend on OpenMS TOPP tools are only available out of the box in the Docker setup. For the local version [OpenMS Command Line Tools](https://openms.readthedocs.io/en/latest/about/installation.html) must be installed separately. ## 🐳 Build with Docker @@ -51,70 +49,49 @@ This repository contains two Dockerfiles. 1. `Dockerfile`: This Dockerfile builds all dependencies for the app including Python packages and the OpenMS TOPP tools. Recommended for more complex workflows where you want to use the OpenMS TOPP tools for instance with the **TOPP Workflow Framework**. 2. `Dockerfile_simple`: This Dockerfile builds only the Python packages. Recommended for simple apps using pyOpenMS only. - -1. **Install Docker** - - Install Docker from the [official Docker installation guide](https://docs.docker.com/engine/install/) - -
- Click to expand - - ```bash - # Remove older Docker versions (if any) - for pkg in docker.io docker-doc docker-compose docker-compose-v2 podman-docker containerd runc; do sudo apt-get remove -y $pkg; done - ``` - -
- -2. **Test Docker** - - Verify that Docker is working. - ```bash - docker run hello-world - ``` - When running this command, you should see a hello world message from Docker. - -3. **Clone the repository** - ```bash - git clone https://github.com/OpenMS/streamlit-template.git - cd streamlit-template - ``` - -4. **Specify GitHub token (to download Windows executables).** - - Create a temporary `.env` file with your Github token. - - It should contain only one line: - `GITHUB_TOKEN=` - - ℹ️ **Note:** This step is not strictly required, but skipping it will remove the option to download executables from the WebApp. - -3. **Build & Launch the App** - - To build and start the containers. - From the project root directory: - - ```bash - docker-compose up -d --build - ``` - At the end, you should see this: - ``` - [+] Running 2/2 - ✔ openms-streamlit-template Built - ✔ Container openms-streamlit-template Started - ``` - - To make sure server started successfully, run `docker compose ps`. You should see `Up` status: - ``` - CONTAINER ID IMAGE COMMAND CREATED STATUS PORTS NAMES - 4abe0603e521 openms_streamlit_template "/app/entrypoint.sh …" 7 minutes ago Up 7 minutes 0.0.0.0:8501->8501/tcp, :::8501->8501/tcp openms-streamlit-template - ``` - - To map the port to default streamlit port `8501` and launch. - - ``` - docker run -p 8505:8501 openms_streamlit_template - ``` +3. **Install Docker** + Install Docker from the [official Docker installation guide](https://docs.docker.com/engine/install/) + ```bash + # Remove older Docker versions (if any) + for pkg in docker.io docker-doc docker-compose docker-compose-v2 podman-docker containerd runc; do sudo apt-get remove -y $pkg; done + ``` +4. **Test Docker** + Verify that Docker is working. + ```bash + docker run hello-world + ``` + When running this command, you should see a hello world message from Docker. +5. **Clone the repository** + ```bash + git clone https://github.com/OpenMS/streamlit-template.git + cd streamlit-template + ``` +6. **Specify GitHub token (to download Windows executables).** + Create a temporary `.env` file with your Github token. + It should contain only one line: `GITHUB_TOKEN=` + ℹ️ **Note:** This step is not strictly required, but skipping it will remove the option to download executables from the WebApp. +7. **Build & Launch the App** + To build and start the containers. From the project root directory: + ```bash + docker-compose up -d --build + ``` + At the end, you should see this: + ``` + [+] Running 2/2 + ✔ openms-streamlit-template Built + ✔ Container openms-streamlit-template Started + ``` + To make sure server started successfully, run `docker compose ps`. You should see `Up` status: + ``` + CONTAINER ID IMAGE COMMAND CREATED STATUS PORTS NAMES + 4abe0603e521 openms_streamlit_template "/app/entrypoint.sh …" 7 minutes ago Up 7 minutes 0.0.0.0:8501->8501/tcp, :::8501->8501/tcp openms-streamlit-template + + ``` + To map the port to default streamlit port `8501` and launch. + ``` + docker run -p 8505:8501 openms_streamlit_template + + ``` ## Documentation @@ -122,13 +99,10 @@ Documentation for **users** and **developers** is included as pages in [this tem ## Citation -Please cite: -Müller, T. D., Siraj, A., et al. OpenMS WebApps: Building User-Friendly Solutions for MS Analysis. Journal of Proteome Research (2025). [https://doi.org/10.1021/acs.jproteome.4c00872](https://doi.org/10.1021/acs.jproteome.4c00872) +Please cite: Müller, T. D., Siraj, A., et al. OpenMS WebApps: Building User-Friendly Solutions for MS Analysis. Journal of Proteome Research (2025). [https://doi.org/10.1021/acs.jproteome.4c00872](https://doi.org/10.1021/acs.jproteome.4c00872) ## References - Pfeuffer, J., Bielow, C., Wein, S. et al. OpenMS 3 enables reproducible analysis of large-scale mass spectrometry data. Nat Methods 21, 365–367 (2024). [https://doi.org/10.1038/s41592-024-02197-7](https://doi.org/10.1038/s41592-024-02197-7) - - Röst HL, Schmitt U, Aebersold R, Malmström L. pyOpenMS: a Python-based interface to the OpenMS mass-spectrometry algorithm library. Proteomics. 2014 Jan;14(1):74-7. [https://doi.org/10.1002/pmic.201300246](https://doi.org/10.1002/pmic.201300246). PMID: [24420968](https://pubmed.ncbi.nlm.nih.gov/24420968/). - From ee903cdb9965fc3eb1e0fcecd67c1077fc255295 Mon Sep 17 00:00:00 2001 From: MahiRaj22 Date: Fri, 20 Feb 2026 16:07:20 +0530 Subject: [PATCH 2/2] docs: refine step numbering fix in README --- README.md | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/README.md b/README.md index 871b9cf0..ecb6f297 100644 --- a/README.md +++ b/README.md @@ -51,20 +51,25 @@ This repository contains two Dockerfiles. 2. `Dockerfile_simple`: This Dockerfile builds only the Python packages. Recommended for simple apps using pyOpenMS only. 3. **Install Docker** Install Docker from the [official Docker installation guide](https://docs.docker.com/engine/install/) +
Click to expand ```bash # Remove older Docker versions (if any) for pkg in docker.io docker-doc docker-compose docker-compose-v2 podman-docker containerd runc; do sudo apt-get remove -y $pkg; done + ``` +
4. **Test Docker** Verify that Docker is working. ```bash docker run hello-world + ``` When running this command, you should see a hello world message from Docker. 5. **Clone the repository** ```bash git clone https://github.com/OpenMS/streamlit-template.git cd streamlit-template + ``` 6. **Specify GitHub token (to download Windows executables).** Create a temporary `.env` file with your Github token. @@ -74,12 +79,14 @@ This repository contains two Dockerfiles. To build and start the containers. From the project root directory: ```bash docker-compose up -d --build + ``` At the end, you should see this: ``` [+] Running 2/2 ✔ openms-streamlit-template Built ✔ Container openms-streamlit-template Started + ``` To make sure server started successfully, run `docker compose ps`. You should see `Up` status: ```