Published May 26, 2023 | Version 1.3.0
Software Open

PhyloNext Pipeline - Docker and Singularity Image Archives

Creators

  • 1. Institute of Ecology and Earth Sciences, University of Tartu, Estonia
  • 2. Natural History Museum, University of Tartu, Estonia
  • 3. Earth and Sustainability Science Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, Australia
  • 4. Global Biodiversity Information Facility, Copenhagen, Denmark
  • 5. School of Natural Sciences, University of California, Merced, USA
  • 6. Department of Ecology & Evolutionary Biology, University of Kansas, Lawrence, USA

Description

PhyloNext is a pipeline for phylogenetic diversity analysis of GBIF-mediated data.

Source code at GitHub: https://github.com/vmikk/PhyloNext

User documentation: https://phylonext.github.io/

 

This repository contains Docker and Singularity image archives of the PhyloNext pipeline, which facilitate the use and reproducibility of computational phylogenetics and biodiversity analyses. The images encapsulate all the software dependencies used by PhyloNext, compartmentalized into three distinct containers:

  1. rarrow: This container integrates the statistical programming language R and Apache Arrow. This combination provides a powerful set of tools for data analysis and manipulation in PhyloNext, utilizing Arrow's columnar format for efficient data analytics operations.

  2. biodiverse: The biodiverse container comprises Biodiverse, a tool for the spatial analysis of diversity (Laffan et al., 2010, DOI:10.1111/j.1600-0587.2010.06237.x; https://github.com/shawnlaffan/biodiverse/), and Perl, a high-level, general-purpose, interpreted, dynamic programming language. Biodiverse, powered by Perl, allows users to analyze spatial patterns of diversity using indices based on taxon, phylogenetic, trait and matrix-based (e.g. genetic, distance) variations.

  3. opentree: The opentree container integrates the Open Tree of Life (OToL) resource, a comprehensive, dynamic and digitally-available tree of life by synthesizing published phylogenetic trees, and Python, a widely used high-level programming language. This enables PhyloNext to incorporate and manipulate phylogenetic data from OpenTree using Python's vast suite of libraries and tools.

Docker and Singularity definition files used to create containers are available at:

https://github.com/vmikk/PhyloNext/tree/main/containerfiles

https://github.com/vmikk/biodiverse-docker

All images are hosted on

 

Files

Files (3.7 GB)

Name Size Download all
md5:bb30952a1a6a6e6b0ae0056474d68456
848.3 MB Download
md5:a24e828b472be35a3d7d7c55ab10a1db
368.8 MB Download
md5:cad44863ab68aeb2e655aebd65410ae3
761.5 MB Download
md5:91d1196eea5ac5f9a2edb6f80fb8ec41
667.0 MB Download
md5:6cc45653bd4bd73f9cda73dd1a037151
343.3 MB Download
md5:1f83ffe2a03ea08935627e1c9defcfd1
731.8 MB Download