** Additional Installation Instructions **


__________________ Ubuntu 22.04 and more _________________

To compile nvBowtie, it is essential to install the CUDA development suite. You can find many pages explaining how to 
install cuda on your linux distribution. If you're using Ubuntu 24.04 or higher, you can also use the installation_cuda.sh 
script located in the 'inst/scripts' directory.
This script will erase all traces of drivers and older versions of cuda before you start. This can be useful if you are 
unable to install cuda correctly after several attempts.
In addition, this script also offers to install the default version of your distribution, or to install the latest version (12.8) 
if you're having problems with the older version. Use the default version first.


An additional script, called check_requirements.sh, verifies your installation and determines if everything went smoothly.

The default architecture supported by nvBowtie is Pascal (sm_60). However, you can modify this parameter
by editing src/nvbio/CMakefile.txt. Ensure that the selected architecture is compatible with the
installed version of the CUDA software suite. Refer to the compatibility guide for NVIDIA cards here:
(https://arnon.dk/matching-sm-architectures-arch-and-gencode-for-various-nvidia-cards). 

It is also necessary to install the thrust and cub libraries by typing in a terminal :
sudo apt install libthrust-dev libcub-dev

_____________________ Windows __________________

** Cuda installation on Windows **

You must have a developer account on the NVidia website (https://developer.nvidia.com).
If you don’t already have one, you will need to create an account.

Next, download the CUDA Toolkit 11.8, which is available here:

https://developer.nvidia.com/cuda-11-8-0-download-archive?target_os=Windows&target_arch=x86_64

For detailed instructions on installing CUDA on Windows, refer to this guide:
 
https://docs.nvidia.com/cuda/cuda-installation-guide-microsoft-windows/index.html

Note that RbowtieCuda is compatible with Cuda versions >= 10.

** Installing RTools on Windows **

RTools must also be installed on Windows. You can download it here:

https://cran.r-project.org/bin/windows/Rtools/

** Installing Build Tools for Visual Studio 2022 **

The Visual Studio Build Tools are required and can be downloaded here:

https://visualstudio.microsoft.com/en/downloads/

** Note: Compilation on Windows **

The package compilation process on Windows can be lengthy (up to 15 minutes).