Update README.md

Author: DaanJansen94

README.md

@@ -13,25 +13,63 @@ Virasign has been validated to classify the diversity of human pathogens well. H
 
 ## Installation
 
-### 1. Create Conda Environment with Required Tools
+### Prerequisites
+First, install conda if you haven't already:
+```bash
+wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
+bash Miniconda3-latest-Linux-x86_64.sh
+```
 
-Create a new conda environment with all required tools:
+Then, ensure you have the required channels:
+```bash
+conda config --add channels defaults
+conda config --add channels bioconda
+conda config --add channels conda-forge
+```
 
+### Option 1: Using Conda (Recommended)
+Install [virasign via Conda](https://anaconda.org/bioconda/virasign):
 ```bash
-conda create -n virasign python=3.9 -y
+conda create -n virasign -c bioconda virasign -y
 conda activate virasign
-conda install -c bioconda -c conda-forge minimap2=2.24 seqtk=1.3 curl=7.88 samtools=1.17 mmseqs2=15.6f452 -y
 ```
 
-### 2. Install Virasign
+### Option 2: From Source Code
+1. Create and activate a new conda environment:
+   ```bash
+   conda create -n virasign python=3.9 -y
+   conda activate virasign
+   conda install -c bioconda -c conda-forge minimap2=2.24 seqtk=1.3 curl=7.88 samtools=1.17 mmseqs2=15.6f452 -y
+   ```
+
+2. Install virasign:
+   ```bash
+   git clone https://github.com/DaanJansen94/virasign.git  
+   cd virasign
+   pip install .
+   ```
+
+3. Re-installation (when updates are available):
+   ```bash
+   conda activate virasign  # Make sure you're in the right environment
+   cd virasign
+   git pull  # Get the latest updates from GitHub
+   pip uninstall virasign
+   pip install .
+   ```
+   Note: Any time you modify the code or pull updates from GitHub, you need to reinstall the package using these commands for the changes to take effect.
+
+## Usage
 
+First, make sure your conda environment is activated:
 ```bash
-git clone https://github.com/DaanJansen94/virasign.git
-cd virasign
-pip install .
+conda activate virasign
 ```
 
-## Usage
+To see all available options:
+```bash
+virasign --help
+```
 
 ### Basic Usage