This repo hosts scripts and data for Handika and Esselstyn (In review).

• Fish Shell
• Git
• GH CLI (optional)
• R
• RStudio

gh repo clone hhandika/segul-bench

Or using git:

git clone https://github.com/hhandika/segul-bench

The scripts are written in FISH SHELL. The latest revision of the manuscript only conducted automatic benchmarks on Linux. The GUI benchmark was done manually and inputted later into the automatic benchmark results.

Follow the link in the manuscript to download the data. The data is not included in this repository.

Create a alignments directory in the root of the repository. Then, move the data to the alignments directory.

cd segul-bench

mkdir alignments

We recommend copying the scripts to the same PATH environment of your Linux machine. The scripts are optimized for FISH SHELL. The scripts files are named based on the type of analysis and data type.

cp scripts/linux/* [PATH-ENV]

Then, run the scripts in the directory where the data is located.

For example, to run concatenation benchmark for DNA data:

concat_bench_openSUSE.sh

Running multiple scripts at once:

concat_bench_openSUSE.sh && concat_bench_AA_openSUSE.sh

The latest version of the manuscript uses the data in data/ms_rev2. The data was parsed using bench-parser. The result is saved as data/data_ms_rev2.csv. You can use the data to reproduce the analysis in the manuscript. The scripts should work on any operating system where R and RStudio are installed. We use RMarkdown to write the main R scripts.

1. Open segul-bench.Rproj in RStudio.

2. Open R/benchmark.Rmd in RStudio.

3. Run the script.