quick-dna

Repository to setup OakVar and DNA-seq modules quicker

Setup

This repository uses micromamba to manage dependencies.

Note: While Anaconda can also be used, micromamba is recommended as it's faster and more lightweight.

System Compatibility

• Fully tested on Linux
• Should work on MacOS and Windows
• Windows users have two options:
  1. Recommended: Install WSL2 with Ubuntu 24.04 and follow Linux instructions
  2. Use native Windows (commands will differ)

Installation Steps

1. Install micromamba:

"${SHELL}" <(curl -L micro.mamba.pm/install.sh)

2. Install dependencies:

micromamba create -f environment.yaml

Alternative: If using Anaconda:

conda env create -f environment.yaml

3. Install OakVar modules:

Full installation (includes all just-dna-seq modules):

micromamba activate quick-dna
ov system setup -f setup.yaml

Note: The dbsnp module is large and may take significant time to download.

Minimal installation:

micromamba activate quick-dna
ov setup

Note: You'll need to create a free account (email + password) on the OakVar store.

Usage

Start the OakVar GUI:

ov gui --multiuser --port 8000

Then access the interface at http://localhost:8000

Documentation

• OakVar Documentation
• Just-DNA-Seq Documentation

Module Development

• Module Development Guide
• Sample input file available at: data/longevity_snps_1000genom.vcf

Learn More

Read our research paper: "Just-DNA-Seq, open-source personal genomics platform: longevity science for everyone"