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.
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.
1. With pip
pip install amdirt
2. With conda
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
The latest development version, directly from GitHub
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
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
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.
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
More information
For more information, please see the AMDirT Documentation
Stable: amdirt.readthedocs.io/en/latest/
Development version: amdirt.readthedocs.io/en/dev/