[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.4003825.svg)](https://doi.org/10.5281/zenodo.4003825) [![PyPI version](https://badge.fury.io/py/amdirt.svg)](https://pypi.org/project/amdirt) [![Documentation Status](https://readthedocs.org/projects/amdirt/badge/?version=dev)](https://amdirt.readthedocs.io/en/dev/?badge=dev) [![amdirt-CI](https://github.com/SPAAM-community/amdirt/actions/workflows/ci_test.yml/badge.svg)](https://github.com/SPAAM-community/amdirt/actions/workflows/ci_test.yml)

  <picture>
    <img alt="amdirt Logo" src="https://raw.githubusercontent.com/SPAAM-community/amdirt/master/assets/logo_rectangular_transparent.png">
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**amdirt**: [**A**ncient**M**etagenome**Dir**](https://github.com/SPAAM-community/ancientmetagenomedir) **T**oolkit

amdirt is a toolkit for interacting with the AncientMetagenomeDir metadata repository of ancient metagenomic samples and ancient microbial genomes.

This tool provides ways to explore and download sequencing data for ancient microbial and environmental (meta)genomes, automatically prepare input samplesheets for a range of bioinformatic processing pipelines, and to validate AncientMetagenomeDir submissions.

For documentation on using the tool, please see [How Tos](https://amdirt.readthedocs.io/en/latest/how_to/index.html), [Tutorials](https://amdirt.readthedocs.io/en/latest/tutorials/index.html) and/or [Quick Reference](https://amdirt.readthedocs.io/en/latest/reference.html).

## Install

amdirt has been tested on different Unix systems (macOS and Ubuntu) using Intel and AMD chips. If you suspect that amdirt isn't working properly because you use a different hardware/OS, please open an [issue on GitHub](https://github.com/SPAAM-community/amdirt/issues).

### 1. With [pip](https://pip.pypa.io/en/stable/getting-started/)

```bash
pip install amdirt
```

### 2. With conda

Installing amdirt in a dedicated [conda](https://docs.conda.io/projects/miniconda/en/latest/index.html) environment

```bash
conda create -n amdirt -c bioconda amdirt #install amdirt in a dedicated conda environment
conda activate amdirt # activate the conda environment
# use amdirt
conda deactivate amdirt # deactivate the conda environment
```

### The latest development version, directly from GitHub

```bash
pip install --upgrade --force-reinstall git+https://github.com/SPAAM-community/amdirt.git@dev
```

### The latest development version, with local changes

- Fork amdirt on GitHub
- Clone your fork `git clone [your-amdirt-fork]`
- Checkout the `dev` branch `git switch dev`
- Create the conda environment `conda env create -f environment.yml`
- Activate the environment `conda activate amdirt`
- Install amdirt in development mode `pip install -e .`
  - In some cases you may need to force update streamlit with `pip install --upgrade steamlit`

To locally render documentation:

- `conda activate amdirt`
- Install additional requirements `cd docs && pip install -r requirements.txt`
- Build the HTML `make html`
- Open the `build/html/README.html` file in your browser

## Cite

amdirt has been published in F1000 with the following _DOI_: [10.12688/f1000research.134798.2](https://doi.org/10.12688/f1000research.134798.2).  

You can cite amdirt like so:

```
Borry M, Forsythe A, Andrades Valtueña A et al. Facilitating accessible, rapid, and appropriate processing of ancient metagenomic data with amdirt. F1000Research 2024, 12:926
```

A bibtex file is also available here: [amdirt.bib](amdirt.bib)


## More information

For more information, please see the amdirt Documentation

- Stable: [amdirt.readthedocs.io/en/latest/](https://amdirt.readthedocs.io/en/latest/)
- Development version: [amdirt.readthedocs.io/en/dev/](https://amdirt.readthedocs.io/en/dev/)