Add OS, hardware and software version requirements

Author: menoldmt

README.md

@@ -1,12 +1,26 @@
 # Olink® PEA Analysis Workflow
 
-**AnalyzeOlink** provides a configurable framework for analyzing Olink® Proximity Extension Assay (PEA) data, focusing on differential abundance testing and downstream validation. Supported statistical methods include Type III ANCOVA and linear mixed-effects models (via the `afex` package), t-tests and Wilcoxon tests (paired and unpaired), as well as Kruskal–Wallis and Friedman tests.
-
-The package includes nine R Markdown analysis reports that cover key workflow components: assumption checks for ANOVA and LMER models, leave-one-out sensitivity analyses for model terms and sample-level robustness, ELISA validation, non-parametric covariate effects, and NPX correlations with metadata variables.
-
-An annotations module integrates Human Protein Atlas (HPA) metadata, including tissue- and cell-type–specific expression profiles and Tau specificity scores. These annotations can be used to color downstream visualizations such as volcano plots and estimate-vs-estimate plots.
-
-Each phase of the analysis is implemented as an `.Rmd` report and can be coordinated by a [Snakemake](https://snakemake.readthedocs.io/en/stable/) pipeline. The central `.Rds` outputs are created by:
+**AnalyzeOlink** provides a configurable report-based framework for analyzing
+Olink® Proximity Extension Assay (PEA) data, focusing on differential abundance
+testing and downstream validation. Supported statistical methods include Type
+III ANCOVA and linear mixed-effects models (via the `afex` package), t-tests
+and Wilcoxon tests (paired and unpaired), as well as Kruskal–Wallis and
+Friedman tests.
+
+The package includes nine R Markdown analysis reports that cover key workflow
+components: assumption checks for ANOVA and LMER models, leave-one-out
+sensitivity analyses for model terms and sample-level robustness, ELISA
+validation, non-parametric covariate effects, and NPX correlations with
+metadata variables.
+
+An annotations module integrates Human Protein Atlas (HPA) metadata, including
+tissue- and cell-type–specific expression profiles and Tau specificity scores.
+These annotations can be used to color interactive downstream visualizations
+such as volcano plots and estimate-vs-estimate plots.
+
+Each phase of the analysis is implemented as an `.Rmd` report and can be
+coordinated by a [Snakemake](https://snakemake.readthedocs.io/en/stable/)
+pipeline. The central `.Rds` outputs are created by:
 
 - `differential_expression.Rmd`: Outputs the PEA `.Rds` required by all `_pea.Rmd` scripts.
 - `elisa.Rmd`: Outputs the ELISA `.Rds` required by all `_elisa.Rmd` scripts.
@@ -36,41 +50,63 @@ Each phase of the analysis is implemented as an `.Rmd` report and can be coordin
 
 ## Quickstart using Test Data on Linux
 
-### 1. Create the Conda environment
+### 1. Clone the GitHub repository
+
+```bash
+git clone git@github.com:NICHD-BSPC/AnalyzeOlink.git
+```
+
+### 2. Create the Conda environment
 
 ```bash
 cd environment/
 conda env create -p ./env --file env.yaml -y
 ```
 
-### 2. Activate the environment
+### 3. Activate the environment
 
 ```bash
 conda activate ./env
 ```
 
-### 3. Generate test data
+### 4. Generate test data
 
 ```bash
 # From repo root
 cd ../
 Rscript data/test_data.R
 ```
 
-### 4. Run the pipeline
+### 5. Run the pipeline
 
 ```bash
 cd snakemake
 snakemake -j 8
 ```
 
-### 5. View results
+### 6. View results
 
 Open the `.html` reports generated in the `rmds/` directory in a web browser. Each report links to its exported tables and figures.
 
 ---
 
-## User Configuration
+## Resource Requirements and Runtime
+
+- **Installation time:** < 3 minutes to clone the repo, build the Conda environment, and create the test data.
+- **Workflow runtime (test data):** < 3 minutes to run the Snakefile.
+- **Hardware requirements:**
+  - ≥ 2 GB RAM
+  - ≥ 2 CPU cores
+
+## Tested Platforms
+
+- **Operating system:** Linux (Ubuntu LTS; tested on GitHub Actions `ubuntu-latest` runners, as of December 2025: Ubuntu 24.04)
+- **Conda distribution:** Miniforge3 (GitHub Actions latest Miniforge3 release, as of December 2025)
+- **Conda version:** 25.11.1
+
+---
+
+## User Configuration (for your projects data)
 
 To run the workflow on your own PEA/ELISA data, you must configure the pipeline in two locations.
 
@@ -108,12 +144,22 @@ The `.html` reports in `rmds/` provide clickable links to these outputs.
 
 ---
 
-## Dependencies
+## Dependencies and Package Versions
 
-All package dependencies are managed via Conda in `environment/env.yaml`. Use the same environment to run both Snakemake and the `.Rmd` scripts (if running them outside of Snakemake).
+All package dependencies are managed via Conda in `environment/env.yaml`. Use
+the same environment to run both Snakemake and the `.Rmd` scripts (if running
+them outside of Snakemake). See the Conda specification file at
+`environment/env.yaml` for exact package versions and dependency resolution.
 
 ---
 
 ## Support
 
 For questions or issues, please reach out to the [NICHD Bioinformatics and Scientific Programming Core](https://www.nichd.nih.gov/about/org/dir/other-facilities/cores/bioinformatics).
+
+---
+
+## License
+
+This project is licensed under the **GNU General Public License v3.0 (GPL-3.0)**.
+See the [LICENSE](LICENSE) file for full terms.