Package installation

PACKAGE_INSTALLATION_GUIDE.md

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+# Pre-installing Packages in Workbench Apps
+
+Users often want specific packages pre-installed in their apps to avoid running `pip install` or `install.packages()` every time. This guide shows two simple approaches.
+
+---
+
+## Approach 1: Natural Language with Claude (Easiest!)
+
+Just ask Claude what you need, and it will help you install packages:
+
+**Examples:**
+- "I need ggplot2"
+- "Set me up for machine learning"
+- "I want tools for genomics analysis"
+- "Install deep learning packages"
+
+Claude understands natural language and will either:
+- Generate an installation command for you to run
+- Pre-configure your app with the packages
+
+**Supported domains:**
+- Machine Learning, Deep Learning, NLP
+- Data Visualization, Dashboards  
+- Bioinformatics, Genomics, Single-cell
+- BigQuery/GCP, Statistics, Time Series
+- And more...
+
+---
+
+## Approach 2: Pre-install with common-packages Feature
+
+Use the built-in `common-packages` feature in your `.devcontainer.json`:
+
+```json
+{
+  "features": {
+    "ghcr.io/verily-src/workbench-app-devcontainers/common-packages": {
+      "pythonPackages": "tensorflow scikit-learn pandas numpy matplotlib",
+      "rPackages": "Seurat,DESeq2,ggplot2,tidyverse"
+    }
+  }
+}
+```
+
+**Python packages:** Space-separated  
+**R packages:** Comma-separated (NO SPACES)
+
+**When to use this:**
+- You know exactly which packages you need
+- You want packages available immediately at app startup
+- You're creating a new app
+
+See [`features/src/common-packages/README.md`](features/src/common-packages/README.md) for details.
+
+---
+
+## Complete Examples
+
+### Example 1: Jupyter with Machine Learning Packages
+
+**With Claude:**
+Just say: "Create a Jupyter app for machine learning"
+
+**Manual configuration:**
+```json
+{
+  "name": "Jupyter - Machine Learning",
+  "features": {
+    "ghcr.io/verily-src/workbench-app-devcontainers/common-packages": {
+      "pythonPackages": "scikit-learn xgboost tensorflow torch pandas numpy matplotlib"
+    }
+  }
+}
+```
+
+### Example 2: R Analysis for Genomics
+
+**With Claude:**
+Just say: "I need R packages for genomics analysis"
+
+**Manual configuration:**
+```json
+{
+  "name": "R Analysis - Genomics",
+  "features": {
+    "ghcr.io/verily-src/workbench-app-devcontainers/common-packages": {
+      "rPackages": "Seurat,DESeq2,GenomicRanges,tidyverse,ggplot2"
+    }
+  }
+}
+```
+
+### Example 3: On-Demand Installation (Already in Jupyter)
+
+If you're already working and realize you need more packages:
+
+**Ask Claude:** "I need plotly for visualization"
+
+**Claude will show you:**
+```python
+!pip install plotly
+```
+
+Or for R:
+```python
+%%R
+install.packages("plotly")
+```
+
+---
+
+## Comparison
+
+| Approach | When Available | Requires Rebuild | Natural Language |
+|----------|---------------|------------------|------------------|
+| **Ask Claude** | On-demand or pre-build | No (on-demand) / Yes (pre-build) | ✅ Yes |
+| **common-packages feature** | At app startup | Yes | ❌ No |
+
+**Best practice:** 
+- Use `common-packages` for packages you know you'll need
+- Ask Claude when you discover new needs while working
+
+---
+
+## Common Package Lists
+
+### Python
+
+**Data Science:** pandas, numpy, scipy, matplotlib, seaborn  
+**Machine Learning:** scikit-learn, xgboost, lightgbm  
+**Deep Learning:** tensorflow, torch, transformers, keras  
+**NLP:** transformers, spacy, nltk, gensim  
+**Bioinformatics:** biopython, scanpy, anndata  
+**BigQuery:** google-cloud-bigquery, google-cloud-storage, db-dtypes  
+**Visualization:** matplotlib, seaborn, plotly, dash, streamlit
+
+### R
+
+**Core Data Science:** tidyverse, dplyr, tidyr, readr, ggplot2  
+**Visualization:** ggplot2, plotly, shiny, shinydashboard  
+**Machine Learning:** caret, randomForest, xgboost  
+**Bioinformatics:** Seurat, DESeq2, edgeR, limma  
+**Genomics:** GenomicRanges, AnnotationDbi, biomaRt  
+**BigQuery:** bigrquery, googleCloudStorageR
+
+---
+
+## FAQ
+
+### Q: How do I install packages I discover I need while working?
+
+**A:** Just ask Claude! Say "I need <package>" or "I need tools for <task>", and Claude will generate the installation command for you.
+
+### Q: Can I use both Python and R packages?
+
+**A:** Yes! Just specify both:
+```json
+{
+  "pythonPackages": "pandas numpy",
+  "rPackages": "ggplot2,tidyverse"
+}
+```
+
+### Q: What if I need a package that's not in the common lists?
+
+**A:** Just ask Claude or add it explicitly to the `pythonPackages` or `rPackages` field. For example:
+- "I need the 'polars' package"
+- Or add: `"pythonPackages": "polars duckdb"`
+
+### Q: How do I install Bioconductor packages?
+
+**A:** Ask Claude "I need Bioconductor packages for RNA-seq", or use:
+```json
+{
+  "rPackages": "BiocManager,DESeq2,edgeR,limma"
+}
+```
+
+The `common-packages` feature automatically handles Bioconductor installation.
+
+---
+
+## Summary
+
+**Easiest way:** Ask Claude in natural language  
+**For known needs:** Use `common-packages` feature in `.devcontainer.json`  
+**Both work together:** Pre-install common packages, ask Claude for additional ones
+
+No more manual `pip install` or `install.packages()` every time! 🎉

features/src/common-packages/README.md

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+# Pre-install Packages Feature
+
+Pre-install your Python and R packages so you don't have to run `pip install` or `install.packages()` every time you create an app.
+
+## Usage
+
+Just list the packages you want in your `.devcontainer.json`:
+
+```json
+{
+  "features": {
+    "ghcr.io/verily-src/workbench-app-devcontainers/common-packages": {
+      "pythonPackages": "pandas numpy scikit-learn matplotlib",
+      "rPackages": "tidyverse,ggplot2,dplyr,plotly,shiny"
+    }
+  }
+}
+```
+
+That's it! Packages will be pre-installed when the app is built.
+
+## Examples
+
+### R Analysis with 15 packages
+
+```json
+{
+  "features": {
+    "ghcr.io/verily-src/workbench-app-devcontainers/common-packages": {
+      "rPackages": "tidyverse,ggplot2,dplyr,tidyr,readr,plotly,shiny,DT,data.table,caret,randomForest,bigrquery,googleCloudStorageR,arrow,lubridate"
+    }
+  }
+}
+```
+
+### Jupyter with Python packages
+
+```json
+{
+  "features": {
+    "ghcr.io/verily-src/workbench-app-devcontainers/common-packages": {
+      "pythonPackages": "pandas numpy matplotlib seaborn scikit-learn google-cloud-bigquery google-cloud-storage"
+    }
+  }
+}
+```
+
+### Both Python and R
+
+```json
+{
+  "features": {
+    "ghcr.io/verily-src/workbench-app-devcontainers/common-packages": {
+      "pythonPackages": "pandas numpy",
+      "rPackages": "ggplot2,dplyr"
+    }
+  }
+}
+```
+
+## Format
+
+- **Python packages:** Space-separated (e.g., `"pandas numpy scikit-learn"`)
+- **R packages:** Comma-separated (e.g., `"tidyverse,ggplot2,dplyr"`)
+
+## How It Works
+
+- Packages install during container build (one-time)
+- Apps launch instantly with packages ready
+- Users can still install more packages at runtime if needed
+- Much simpler than creating custom app configs
+
+## Performance
+
+- **First build:** Takes time to install packages
+- **Every app after:** Instant - packages already there
+- **vs. manual install every time:** Saves 5-10 minutes per app launch

features/src/common-packages/devcontainer-feature.json

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+{
+  "id": "common-packages",
+  "version": "1.0.0",
+  "name": "Pre-install Packages",
+  "description": "Pre-install Python and R packages so users don't have to run pip install or install.packages() every time",
+  "documentationURL": "https://github.com/verily-src/workbench-app-devcontainers/tree/main/features/src/common-packages",
+  "options": {
+    "pythonPackages": {
+      "type": "string",
+      "default": "",
+      "description": "Python packages to install (space-separated, e.g., 'pandas numpy scikit-learn')"
+    },
+    "rPackages": {
+      "type": "string",
+      "default": "",
+      "description": "R packages to install (comma-separated, e.g., 'tidyverse,ggplot2,dplyr')"
+    }
+  }
+}

features/src/common-packages/install.sh

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+#!/bin/bash
+set -e
+
+echo "Installing user-specified packages..."
+
+# Install Python packages
+if [ -n "${PYTHONPACKAGES}" ] && command -v pip &> /dev/null; then
+    echo "Installing Python packages: ${PYTHONPACKAGES}"
+    pip install --no-cache-dir ${PYTHONPACKAGES}
+fi
+
+# Install R packages
+if [ -n "${RPACKAGES}" ] && command -v R &> /dev/null; then
+    echo "Installing R packages: ${RPACKAGES}"
+    R --quiet -e "install.packages(strsplit('${RPACKAGES}', ',')[[1]], repos='https://cran.rstudio.com/', quiet=TRUE)"
+fi
+
+echo "Package installation complete!"