opencravat-longevity

Repository for longevity annotators for opencravat.

The repository contains:

• annotators:

  longevitymap - for longevity related information, original data from https://genomics.senescence.info

  prs - for polygenic risk scores

• reporters:

  longevity_combinedreporter - outputs prs, longevity report, cancer report

• 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

Install conda environment

Annotation modules and dvc are included in the conda environment that goes with the project. The environment can be setup either with Anaconda or micromamba (superior version of conda). Here is installation instruction for micromamba:

wget -qO- https://micromamba.snakepit.net/api/micromamba/linux-64/latest | tar -xvj bin/micromamba

We can use ./micromamba shell init ... to initialize a shell (.bashrc) and a new root environment in ~/micromamba:

./bin/micromamba shell init -s bash -p ~/micromamba
source ~/.bashrc

To create a micromamba environment use:

micromamba create -f environment.yaml
micromamba activate opencravat-longevity

The instructions above are provided for Linux and MacOS (note: in MacOS you have to install wget). For Windows you can either install Linux Subsystem or use Windows version of anaconda.

Installing moduals

First, read the tutorial about opencravat and locate the path to the modules directory:

oc config md

Change to the module folder, for example:

oc config md .

Then activate github update script to download moduals to moduals path:

python gh_update.py --path YOUR_PATH

Run opencravat:

oc gui