amdirt 1.4

AMDirT: AncientMetagenomeDir Toolkit

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 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

More information

For more information, please see the AMDirT Documentation

• Stable: amdirt.readthedocs.io/en/latest/
• Development version: amdirt.readthedocs.io/en/dev/