bioenv

• 2025.1.12
• tak1217

Reusable Docker-based environments for reproducible bioinformatics analysis.

This repository provides curated Docker environments for bioinformatics workflows, designed to be shared across projects and machines (Windows + WSL2, macOS, Linux servers).

The goal is:

• Reproducibility
• Portability
• Separation of environment and project code
• Easy interactive use (Jupyter, bash, R, Python)

---

Repository structure

├── README.md
└── env
    ├── dev
    │   ├── Dockerfile
    │   └── environment.yml
    └── rnaseq

Each subdirectory under env/ represents an independent environment that can be built into its own Docker image.

---

Environments

bio-dev (currently available)

Purpose
Exploratory analysis and development environment for laptops and workstations.

Typical use cases:

• Interactive data analysis (Python / R)
• Visualization (matplotlib, seaborn, plotly, ggplot2)
• Jupyter notebooks
• Light bioinformatics processing (QC, file manipulation)
• Writing reusable scripts across projects

Included software

Python stack:

• numpy, pandas, scipy
• matplotlib, seaborn, plotly
• scikit-learn, statsmodels
• tqdm, joblib, pyyaml
• openpyxl, xlrd, nbconvert, pandoc
• ipython, ipykernel
• biopython

R stack:

• r-base (4.3)
• tidyverse
• data.table
• patchwork
• r-essentials

Bioinformatics tools:

• samtools, bcftools, htslib
• bedtools
• seqkit
• fastqc, multiqc

Utilities:

• git, curl, wget, unzip, pigz, parallel, tree

---

Build

From the repository root:

docker build -t bio-dev:step2 -f env/dev/Dockerfile env/dev

---

Basic usage

Run an interactive shell:

docker run --rm -it bio-dev:step2

The container starts with the work environment activated:

(work) mambauser@container:/work$ python --version
Python 3.11.14

---

Using with a project directory

Assume a project structure like:

TR001/
├── Data/
├── Scripts/
└── Work/

From inside the project root:

docker run --rm -it \
  -v "$PWD":/work \
  -w /work \
  -p 8888:8888 \
  bio-dev:step2

Inside the container:

ls
# Data/ Scripts/ Work/ ...

This keeps:

• Project code/data → in project repository
• Environment → managed centrally in bioenv

---

JupyterLab

Inside the container:

jupyter lab --ip=0.0.0.0 --no-browser --allow-root

Then open the displayed URL in your browser.

---

Design principles

• Environment separation

  • Environments live in this repository
  • Project-specific code lives in each project repository

• Reproducibility

  • All packages are declared in environment.yml
  • Images can be versioned via Docker tags (e.g. step2, later v0.1.0)

• Portability

  • Same environment usable across:

    • Windows + WSL2
    • macOS (Apple Silicon)
    • Linux servers

• Modularity

  • Separate images for different purposes:

    • dev (exploration, visualization, development)
    • rnaseq (planned: heavy pipelines like STAR/RSEM/Salmon)
    • scrna (planned: Seurat-based analysis)

---

Versioning policy

Currently using experimental tags during development:

bio-dev:step1
bio-dev:step2

Planned transition to stable versioning:

bio-dev:v0.1.0
bio-dev:v0.2.0
bio-dev:v1.0.0

Git tags and Docker image tags will be aligned for reproducibility.

---

Planned environments

• env/rnaseq/

  • STAR, RSEM, Salmon
  • samtools, bedtools, multiqc
  • Possibly Nextflow pipelines

• env/scrna/

  • R + Seurat
  • Single-cell analysis workflows

---

License

This repository is currently intended for personal / internal research use. Add a LICENSE file if you plan to publish or share externally.