RbowtieCuda

[FranckRICHARD01]

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[bioc-issue-bot]

Hi @FranckRICHARD01

Thanks for submitting your package. We are taking a quick
look at it and you will hear back from us soon.

The DESCRIPTION file for this package is:

Package: RbowtieCuda
Type: Package
Title: An R Wrapper for nvBowtie and nvBWT, a rewritten version of Bowtie2 for cuda
Version: 0.99.0
Date: 2024-12-01
Authors@R: 
        c(person(given = "Jacopo", family = "Pantaleoni", role = c("aut"), 
  email = "[email protected]"),
        person(given = "Nuno", family = "Subtil", role = c("aut"), 
  email = "[email protected]"),
        person(given = "Samuel", family = "Simon-Sanchez", role = c("aut"), 
  email = "[email protected]"),
        person(given = "Franck", family = "RICHARD", role = c("aut","cre"), 
  email = "[email protected]"))
Description: This package provides an R wrapper for the popular Bowtie2 sequencing read aligner,
 optimized to run on NVIDIA graphics cards. It includes wrapper functions that enable both genome 
 indexing and alignment to the generated indexes, ensuring high performance and ease of use within the R environment.
License: BSD_3_clause + file LICENSE
Depends: R (>= 4.4.0), SummarizedExperiment
Encoding: UTF-8
Suggests: 
    knitr,
    testthat (>= 3.0.0),
    rmarkdown,
    RUnit,
    BiocGenerics
SystemRequirements: C++17, GNU make, CUDA Toolkit (<= 12.4), MSVC, libthrust-dev, libcub-dev, gcc (< 14.0)
Archs: x64
RoxygenNote: 7.3.2
biocViews: Sequencing, Alignment, Preprocessing, Coverage
VignetteBuilder: knitr
Config/testthat/edition: 3
NeedsCompilation: yes
Author: c(Jacopo Pantaleoni [aut],
  Nuno Subtil  [aut],
  Samuel Simon Sanchez [aut],
  Franck RICHARD [aut, cre])
BugReports: https://github.com/FranckRICHARD01/RbowtieCuda/issues 
URL: https://github.com/FranckRICHARD01/RbowtieCuda, https://belacqua-labo.ovh/bioinformatic/RbowtieCuda

[hpages]

Hi @FranckRICHARD01,

Thanks for this submission.

Please move the installation_cuda*.sh scripts to inst/scripts/. Unfortunately our Linux and Windows builders (nebbiolo1 and palomino7) don't have NVIDIA GPUs. How can we handle this? Can CUDA be used on non NVIDIA GPUs? Do we need to install some kind of generic CUDA-compatible drivers for that? Of course, this kind of workaround will have poor performance but at least it would allow RbowtieCuda to "work" on our builders.

Also I suppose that the package is not supported on macOS right?

Thanks,
H.

[FranckRICHARD01]

Hi hpages!

Okay for the scripts. I'll move them.
No, unfortunately, you need a Nvidia graphics card to run a program made with Cuda.
There is still no universal driver to simulate Cuda.
I could compile executables for Linux and Windows, but I have no idea how to run the program on your builders.
Am I the first to propose a Cuda-compatible program under bioconductor?
I don't have a Mac myself and Apple refuses to accept Nvidia cards in its desktops...

Franck