amdirt: AncientMetagenomeDir Toolkit
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, Tutorials and/or Quick Reference.
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.
1. With pip
pip install amdirt
Installing amdirt in a dedicated conda environment
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
pip install --upgrade --force-reinstall git+https://github.com/SPAAM-community/amdirt.git@dev
- Fork amdirt on GitHub
- Clone your fork
git clone [your-amdirt-fork]
- Checkout the
dev
branchgit 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
- In some cases you may need to force update streamlit with
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
amdirt has been published in F1000 with the following DOI: 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
For more information, please see the amdirt Documentation
- Stable: amdirt.readthedocs.io/en/latest/
- Development version: amdirt.readthedocs.io/en/dev/