From cf104c859d7e9f76e83c6c7d932944f3a3573f74 Mon Sep 17 00:00:00 2001 From: Harrison Date: Fri, 28 Apr 2023 14:29:34 -0500 Subject: [PATCH] Added some more help to 'README.md' --- README.md | 17 ++++++++++++++++- 1 file changed, 16 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index 4c86ff0..7e878f7 100644 --- a/README.md +++ b/README.md @@ -2,7 +2,7 @@ # BMLSA -A Basic multi local sequence alignment tool using the Biopython implementation of the Smith-Waterman alignment algorithm. +A Basic multi local sequence alignment tool using the Biopython implementation of the Smith-Waterman alignment algorithm. May be used as a python library, or as a full command line interface. ## Features @@ -13,6 +13,21 @@ A Basic multi local sequence alignment tool using the Biopython implementation o - Automatically align with all sequences in reference FASTA - All produced output is human readable! + ## Install via `pip` + +Just run `pip install --index-url https://git.reslate.systems/api/packages/ydeng/pypi/simple/ bmlsa` in a console that is capable of running `pip`! + +## CLI Demo from Git Repo + +Resources have been provided in this package for CI purposes, but you may use them to try out the program yourself! + +1. Install the program +2. clone this repository +3. Change into the cloned repository directory +4. Run `bmlsa -I id -S sequence -B BLASTp tests/resources/SARS_CoV-2_genes.csv tests/resources/NC_045512_coding.fasta ./output/` + +The results will show up in a `output` folder (which will be generated if it doesn't exist). Use `bmlsa -h` to see what each part of the above command does! + ## More Information For all live downloadable artifacts, build statuses, unit test results, and documentation, check out the continuous integration page for the [master branch](https://ci.reslate.systems/job/ydeng/job/bmlsa/job/master/) ([development branch](https://ci.reslate.systems/job/ydeng/job/bmlsa/job/develop/)). \ No newline at end of file