Singularity containers for GWAS and post-GWAS analysis

This repository is used to develop and document singularity containers with various software and analytical tools for GWAS and post-GWAS analysis.

Getting started

For new users we recommend to go over introductory instructions in docs/hello.md, which explain the basic usage of singularity containers, using a minimalistic example (singularity container with plink binary).

If you would like to contribute to developing these containers, please see docs/contributing.md.

For a tutorial on GWAS with synthetic data, see docs/gwas.md.

Prerequisites (to running tutorials):

• download containers shared on the Google Drive.
• download comorment_ref.tar.gz file from the above Google Drive folder, extract it with tar -xzvf comorment_ref.tar.gz command, and create an environmental variable COMORMENT_REF pointing to the folder containing extracted comorment_ref.tar.gz data. If you want to see the content of comorment_ref.tar.gz without downloading and extracting, you may take a quick look here. This is a private repository, and you need to get access. Please contact Oleksandr and Bayram by e-mail and send us your github user name. If you don't have it, create one here.
• create an empty folder called data, for storing the results and intermediate files produced by running containers. (most instructinos mount this folder like this: -B data:/data).

Description of available containers:

• hello - a hello-world introductory container
• gwas - basic tools for gwas (plink, plink2, prsice, BoltLMM)
• python3 - python3 packages distributed via miniconda. This package also contains jupyter notebook.
• ldsc - LD score regression
• matlab - container allowing to run pre-compiled MATLAB software. This container also has OCTAVE installed.
• R - contaienr for R analysis (installed by native R package manager)

All containers have a shared layer of common utilities (wget, gzip, etc).

Feedback

If you face any issues, or if you need additional software, please let us know by creating an issue.