NEAT (https://github.com/ncsa/neat) is essentially a simple program, since attempts to add some of the data packages from Python met with memory issues, time issues and more. As such, it required us to code NEAT in a way that would potentially translate well to a systems-level language such as C++ or Rust. Because of the desire to multi-thread NEAT, and the helpful way rust builds both thread parallelization and thread safety into their code, it is an appealing option to recreate NEAT and hopefully gain some speed and parallelization.
We will be taking an iterative approach, partly out of necessity as we learn the complexities of Rust.
Check this branch for updates or submit a request to contribute code directly. There won't be any solid tasks yet until we're further along in development.
Download the executable in the release (current version 0.1.0).
./rusty-neat -h
displays help
./rusty-neat
rusty-neat on the default file (data/H1N1.fa). Only works from the repo level dir, run from anywhere else, you will need to specify the input reference file. The file is expected to be in FASTA format:
>Contig_name: other_info
AAAAAAAAAA
>Contig_name2: other_info2
GGGGGGGGGG
Use the help menu to see the available options and leave an issue if you find something bad happening. This data is not currently considered usable for anything requiring real rigor, but this is the first iteration toward a final product.
To compile and run rusty-neat yourself, you will need the Rust environment (https://www.rust-lang.org/tools/install), with cargo. You will also need git installed for your operating system. You will then need to git clone and cd into the repo directory. From your home directory in Linux the process might look something like:
~/$ git clone [email protected]/ncsa/rusty-neat.git
~/$ cd rusty-neat
~/rusty-neat/$
For Windows and Mac users, you can use a GUI or some similar command line method, but you'll figure it out (Post help requests in the Issues tab).
Once in the repo, you can build the program either in debug (default) or release mode. The main difference is how much info it gives you if there is an error.
~/rusty-neat/$ cargo build --release
If you prefer to run the package directly without using the binary, you can also use
~/rusty-neat/$ cargo run
Rust will download any required packages. Compiling Rust code is the slowest part of the process. The final binary will be built and the program run immediately after in the second case. To run the program manually, from the repo main dir, run
~/rusty-neat/$ ./target/debug/rusty-neat