The list of all tools is provided in the pages describing each container listed below. For a comprehensive understanding of the installation of tools within each container, please confer the build files in the /docker directory.
This software is organized into the following containers:
- hello.sif - a simple container for demo purpose, allowing to experiment with singularity features
- gwas.sif - multiple tools (released as binaries/executables) for imputation and GWAS analysis
- python3.sif - python3 environment with pre-installed modules and tools
- r.sif - R 4.0.5 environment with rareGWAMA, GenomicSEM, TwoSampleMR and GSMR packages installed (plus some standard R packages)
All containers have a common set of linux tools like gzip, tar, parallel, etc.
Please open an issue if you'd like to add more of such basic tools, or if you would like to update some software to a newer version.
To improve interoperability between different tools we developed the following data format specification:
These format specifications are applicable to various scripts, released in this repository, including
- gwas.py - pipeline for GWAS analysis
- LDpred2 - command-line wrapper around LDpred2
- pgs_toolkit - pipeline for PGS analysis