From 714702dfab743c83fef32b112ad6ccb8c6454b04 Mon Sep 17 00:00:00 2001 From: Vijini Mallawaarachchi Date: Wed, 24 Apr 2024 15:03:24 +0930 Subject: [PATCH] DOC: Update README --- README.md | 12 ++++++++++-- 1 file changed, 10 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index 58d3b28..968df41 100644 --- a/README.md +++ b/README.md @@ -12,6 +12,7 @@ [![Anaconda-Server Badge](https://anaconda.org/bioconda/metacoag/badges/downloads.svg)](https://anaconda.org/bioconda/metacoag) [![CI](https://github.com/metagentools/MetaCoAG/actions/workflows/testing_python.yml/badge.svg)](https://github.com/metagentools/MetaCoAG/actions/workflows/testing_python.yml) +[![Coverage Status](https://coveralls.io/repos/github/metagentools/MetaCoAG/badge.svg?branch=develop)](https://coveralls.io/github/metagentools/MetaCoAG?branch=develop) ![GitHub](https://img.shields.io/github/license/Vini2/MetaCoAG) [![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black) [![CodeQL](https://github.com/metagentools/MetaCoAG/actions/workflows/codeql.yml/badge.svg)](https://github.com/metagentools/MetaCoAG/actions/workflows/codeql.yml) @@ -93,14 +94,21 @@ You can run the following command to install MetaCoAG using `pip`. Make sure you pip install . ``` -**Note:** If you use pip to setup MetaCoAG for development, you will have to install [FragGeneScan](https://sourceforge.net/projects/fraggenescan/) and [HMMER](http://hmmer.org/) manually and add them to your system path. +### Using `flit` +You can run the following command to install MetaCoAG using `flit`. Make sure you are in the MetaCoAG folder. + +``` +flit install +``` + +**Note:** If you use pip or flit to setup MetaCoAG for development, you will have to install [FragGeneScan](https://sourceforge.net/projects/fraggenescan/) and [HMMER](http://hmmer.org/) manually and add them to your system path. ### Test the setup After setting up, run the following command to ensure that metacoag is working. ``` -metacoag -h +metacoag --help ``` ## Example Usage