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add install from source instructions
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yangchen2 committed Jan 20, 2024
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Expand Up @@ -13,6 +13,8 @@ Importantly, Qadabra focuses on both FDR corrected p-values *and* [feature ranks
Please note this software is currently a work in progress. Your patience is appreciated as we continue to develop and enhance its features. Please leave an issue on GitHub should you run into any errors.

## Installation

### Option 1: Pip install from [PyPI](https://pypi.org/project/qadabra/0.3.0a1/)
```
pip install qadabra
```
Expand All @@ -26,12 +28,31 @@ Qadabra requires the following dependencies:
* cython
* iow

Check out the [tutorial](tutorial.md) for more in-depth instructions on installation.


### Option 2: Install from source (this GitHub repository)
Prerequisites

Before you begin, ensure you have Git and the necessary build tools installed on your system.

Clone the Repository
```
git clone https://github.com/biocore/qadabra.git
```

Navigate to repo root directory where the `setup.py` file is located and then install QADABRA in editable mode
```
cd qadabra
pip install -e .
```

## Usage

### 1. Creating the workflow directory

Qadabra can be used on multiple datasets at once.
First, we want to create the workflow directory to perfrom differential abundance with all methods:
First, we want to create the workflow directory to perform differential abundance with all methods:

```
qadabra create-workflow --workflow-dest <directory_name>
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