oakvar-longevity

Oakvar-Longevity is a module of OakVar which annotates user genome with longevity associated gene variants using the longevitymap annotator, and provides longevity PRS, variants, drugs and major risks(oncorisk) reports with longevity-combinedreporter.

The repository contains:

• postaggregators:

  just_longevitymap - postagregator for longevity report in oakvar

  just_prs - postagregato for polygenic risk scores

  just_cancer and just_coronary- postagregator for major health risks

• reporters:

  longevity2reporter - outputs prs, longevity report, major risks report (contains cancer and coronary arthery diseases)

• webviewerwidgets:

  wglongevitymap - widget for presenting a detailed view for longevity annotator

• other folders for preprocessing information for development purposes

• environment.yaml file for conda environment

Setting up

First, git clone the repository and activate submodules:

git clone --recurse-submodules [email protected]:dna-seq/oakvar-longevity.git

Then, activate the environment. We provide environment.yaml that allows setting up the project quickly with Conda or Micromamba. Here we describe instructions to install with micromamba, however conda/anaconda installation is the same. You can either do it from bash or with graphical user interface of you IDE. First, install micromamba, then run:

micromamba create --file environment.yaml
micromamba activate oakvar-longevity

After installation OakVar will be available with ov command and you can install the modules with:

ov module install path_to_the_module

Then, you are ready to use. Note: as the project contains submodules if changes happeneed inside any of them you can keep submodules updated with:

git submodule update --recursive --remote

Documentation

You can learn how to install and use modules from this repository from Just-DNA-Seq Documentation

You can join our discord if you want to discuss the project or if you encountered any issue.