Scripts and infrastructure for "Stable states in an unstable landscape: microbial resistance at the front line of climate change"

This is the public-facing version of the private repository https://github.com/emerge-bii/temporal_paper, which was originally copied on 2025-05-30 @ 12:59 EDT, retaining all the original contents except for the exclusion of data files with sharing restrictions (those paths are listed in this repository's .gitignore).

The following people contributed to the original code:

• Samuel Aroney
• Hannah Holland-Moritz
• Dylan Cronin
• Suzanne Hodgkins
• Derek Smith
• Benjamin Woodcroft
• Sarah Bagby

Setup

Create conda environment

git clone git@github.com:emerge-bii/temporal_paper.git
cd temporal_paper
./install_dependencies.sh
conda activate temporal_paper_vX

If you require packages not installed in the above environment, add them to temporal_paper.yml and update the version number.

Prepare data

Download from Zenodo at doi:10.5281/zenodo.13901514 and doi:10.5281/zenodo.20536110. Create symlinks in data to the location of these files in your system.

1. Emerge_MAGs_v1 #No longer an explicit requirement, although needed for the fasta files
2. SingleM_otu_tables_v4
3. EMERGE_distillate_v9
4. DRAM_distillate_v2
5. Manual_methanogen_calls_v1
6. DRAM_annotations_v4
7. Emerge_metaTs_v5
8. Emerge_metaTs_processed_v6
9. AA_frequencies_v1

Example:

cd data
ln -s <path/to/Emerge_MAGs_v1> Emerge_MAGs_v1

Large files or folders should also be added here and to .gitignore.

Create your analysis file

Source setup.R for all inputs.

Output results from your analysis into results folder

Separate analysis subfolders for each type.

Cazyme Scraper

If you plan to use the cazyme scraper, it will need to run in it's own conda environment. Instructions for installation of this environment and use of the script can be found in the cazyme_scraper repository.

Citation

Stable states in an unstable landscape: microbial resistance at the front line of climate change. Dylan R. Cronin, Hannah Holland-Moritz, Derek A. Smith, Samuel T. N. Aroney, Suzanne B. Hodgkins, Mikayla Borton, Yueh-Fen Li, Ahmed Zayed, Kieran Healy, Andreas Persson, IsoGenie Field & Analytic Teams 2010-2017, EMERGE Institute Coordinators, Malak M. Tfaily, Patrick Crill, Carmody K. McCalley, Kelly Wrighton, Ruth K. Varner, Gene W. Tyson, Ben J. Woodcroft, Sarah C. Bagby, Jessica Ernakovich, Virginia I. Rich. bioRxiv 2025.02.07.636677; doi: https://doi.org/10.1101/2025.02.07.636677.