https://github.com/biona001/ghostbasilwrap

https://github.com/biona001/ghostbasilwrap

Last synced: 4 days ago
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• Host: GitHub
• URL: https://github.com/biona001/ghostbasilwrap
• Owner: biona001
• Created: 2023-08-25T19:45:42.000Z (about 1 year ago)
• Default Branch: main
• Last Pushed: 2023-08-27T21:52:01.000Z (about 1 year ago)
• Last Synced: 2024-10-12T14:53:34.427Z (about 1 month ago)
• Language: Jupyter Notebook
• Size: 4.88 KB
• Stars: 0
• Watchers: 1
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md

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README

        
# ghostbasilwrap

This repo contains experimental code to call C++ from Julia. 

+ The intention is to create Julia wrapper for [ghostbasil's C++ routine](https://github.com/JamesYang007/ghostbasil) (currently not publically available) to be used in `GhostKnockoffGWAS.jl`. 

+ Ultimately, we want to make [GhostKnockoffGWAS.jl](https://github.com/biona001/GhostKnockoffGWAS) package entirely self-contained within Julia, so we can create binaries and Apps for easy usage. That is, we need to be able to install `ghostbasil` and use it directly within Julia. 

## Roadmap to creating an App for `GhostKnockoffGWAS.jl`

1. Create Julia wrappers for ghostbasil's C++ routine

    + High priority functions: `BlockMatrix`, `BlockGroupGhostMatrix`, `ghostbasil` (these are being used in `GhostKnockoffGWAS.jl`)

    + Mid priority functions: `quad_form` (this was previously used but not anymore)

    + Low priority functions: everything else

2. Use [BinaryBuilder.jl](https://github.com/JuliaPackaging/BinaryBuilder.jl) to create a `jll` package (e.g. `ghostbasil_jll.jl`) that enables usage of ghostbasil functions in Julia directly (this will require ghostbasil to be publically available)

3. Host this `jll` on [Yggdrasil](https://github.com/JuliaPackaging/Yggdrasil)

4. Use [PackageCompiler.jl](https://github.com/JuliaLang/PackageCompiler.jl) to bundle all source code (maybe also pre-computed knockoff statistics) into an [App](https://julialang.github.io/PackageCompiler.jl/stable/apps.html) which can be used by potentially users for re-analysis of GWAS summary statistics data. 

## Compiler/software versions

This was tested on Sherlock with 

+ `cmake/3.11.1`

+ `gcc/12.1.0`

+ `julia/1.8.4`