diff --git a/README.md b/README.md index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..01273e918a730bd5ece5535195c9d39c50a1ba2c 100644 --- a/README.md +++ b/README.md @@ -0,0 +1,61 @@ +# SW-Actors: Smith--Waterman with Actors + +SW-Actors uses the Actor Model to perform parallelized sequence alignment with [Smith–Waterman algorithm](https://icbi.i-med.ac.at/courses/bioinformatics_ex_2021/7265238.pdf) across DNA, RNA, or protein sequence pairs. This approach enhances scalability and efficiency for sequence alignment, optimizing computational resources for large datasets. SW-Actors is implemented using the [C++ Actor Framework](https://github.com/actor-framework/actor-framework). + +## Documentation +This guide will cover the essentials for compiling and running SW-Actors. For further details or to report any issues, feel free to open an issue in this repository. + +## Compiling SW-Actors + +### Dependencies +SW-Actors has dependency on the [C++ Actor Framework](https://github.com/actor-framework/actor-framework), specifically the [1.0.1 +release](https://github.com/actor-framework/actor-framework/archive/refs/tags/1.0.1.tar.gz). + +The following steps can be used to install the C++ Actor Framework on a Linux system: +```bash +wget https://github.com/actor-framework/actor-framework/archive/refs/tags/0.18.6.tar.gz +tar -xzf 1.0.1.tar.gz +cd actor-framework-1.0.1/ +./configure --prefix=/path/to/install +cd build +make # [-j] for parallel build +make install # [use root privileges if necessary] +``` + +### Steps To Compile +To compile SW-Actors: + +1. Clone the repository: + + ``` + git clone https://git.cs.usask.ca/numerical_simulations_lab/actors/papers/sw-actors + cd SW-Actors + ``` + +2. Modify the paths in the `Makefile` to match your CAF installation path. + +3. Run: + +``` +make +``` + + +## Running SUMMA-Actors +After compilation, SW-Actors can be executed using the job.sh script. Modify job.sh to match your system’s configurations, such as paths, resources, and any specific environment modules you may need. + +For basic use, run: +``` +bash job.sh +``` + +## Credits +The implementation of SW-Actors builds on the foundation provided by the [Smith–Waterman algorithm](https://icbi.i-med.ac.at/courses/bioinformatics_ex_2021/7265238.pdf) and the [C++ Actor Framework](https://github.com/actor-framework/actor-framework). We credit the original creators of the C++ Actor Framework which allowed us to implement the actor model into SUMMA-Actors. Links to their research work can be found below. + + * Charousset, D., Schmidt, T. C., Hiesgen, R., Wählisch, M., 2013: Native actors: + a scalable software platform for distributed, heterogeneous environments. _AGERE!_, + [doi:10.1145/2541329.2541336](http://dx.doi.org/10.1145/2541329.2541336). + + * Charousset, D., Schmidt, T. C., Hiesgen, R., 2016: Revisiting actor programming in + C++. _Computer Languages, Systems & Structures_, [doi:10.1016/j.cl.2016.01.002](http:// + dx.doi.org/10.1016/j.cl.2016.01.002) \ No newline at end of file