This repository contains files and scripts to generate analysis and figures in AMPSphere manuscript:
Computational exploration of the global microbiome for antibiotic discovery Célio Dias Santos-Júnior, Marcelo Der Torossian Torres, Yiqian Duan, Álvaro Rodríguez del Río, Thomas S.B. Schmidt, Hui Chong, Anthony Fullam, Michael Kuhn, Chengkai Zhu, Amy Houseman, Jelena Somborski, Anna Vines, Xing-Ming Zhao, Peer Bork, Jaime Huerta-Cepas, Cesar de la Fuente-Nunez, Luis Pedro Coelho bioRxiv 2023.08.31.555663; doi: https://doi.org/10.1101/2023.08.31.555663
The folder General_Scripts contains scripts needed to regenerate the AMPSphere resource from the
raw data. To have more info, follow the link.
The folder Manuscript_Analysis contains files needed to run the analysis and tests in the AMPSphere paper,
for more information, go to its README.md.
To install the conda environment needed to run these scritps, you can use conda:
$ conda env create -f environment.yml -n ampsphere_manuscript
$ conda activate ampsphere_manuscriptThese scripts rely on a series of pre-computed files and core resources that are necessary to the proper functioning. Download them from Zenodo, to this folder and then do following commands:
$ tar -xf data_folder.tar
$ tar -xf docs.tar
$ rm -rf data_folder.tar docs.tar