DOI PyPI version Documentation Status AMDirT-CI
AMDirT
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 validate AncientMetagenomeDir submissions, explore and download sequencing data for ancient microbial and environmental (meta)genomes, and automatically prepare input samplesheets for a range of bioinformatic processing pipelines.
For documentation on using the tool, please see How Tos, Tutorials and/or Quick Reference.
Install
Before we release AMDirt on (bio)Conda, please follow the instructions below.
1. With pip
…upon release of v 1.4
2. With conda
…upon release of v 1.4
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
More information
For more information, please see the AMDirT Documentation
Stable: amdirt.readthedocs.io/en/latest/
Development version: amdirt.readthedocs.io/en/dev/