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

Docker and Singularity images to run Biodiverse software
https://github.com/vmikk/biodiverse-docker

biodiversity docker endemism phylogenetic-diversity singularity

Last synced: 4 months ago
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Docker and Singularity images to run Biodiverse software

• Host: GitHub
• URL: https://github.com/vmikk/biodiverse-docker
• Owner: vmikk
• License: mit
• Created: 2022-01-27T13:15:11.000Z (over 3 years ago)
• Default Branch: main
• Last Pushed: 2025-01-22T07:52:59.000Z (4 months ago)
• Last Synced: 2025-01-22T08:33:23.506Z (4 months ago)
• Topics: biodiversity, docker, endemism, phylogenetic-diversity, singularity
• Language: Perl
• Homepage:
• Size: 32.2 KB
• Stars: 0
• Watchers: 4
• Forks: 1
• Open Issues: 1
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
# Biodiverse

[![GitHub license](https://img.shields.io/github/license/vmikk/biodiverse-docker)](https://github.com/vmikk/biodiverse-docker/blob/main/LICENSE)

[![Hosted_DockerHub](https://img.shields.io/badge/Hosted-DockerHub-blue)](https://hub.docker.com/r/vmikk/biodiverse)

[![Hosted_SingularityLibrary](https://img.shields.io/badge/Hosted-SingularityLibrary-blue)](https://cloud.sylabs.io/library/vmiks/gbif/biodiverse)

This repository contains definition files the [Biodiverse](https://shawnlaffan.github.io/biodiverse/) (Laffan et al., 2010) containers.

# Docker image

To build the [Docker](https://www.docker.com/) image with Biodiverse run:

```

docker build --tag biodiverse --file Dockerfile_NoPerlbrew . 

```

The `Dockerfile_NoPerlbrew` should be present in the current directory.

A ready-to-use image is available at [Docker Hub](https://hub.docker.com/r/vmikk/biodiverse) and can be downloaded with:

```

docker pull vmikk/biodiverse:1.5.0

```

# Singularity image

To build the [Singularity](https://sylabs.io/singularity/) image with Biodiverse run:

```

sudo singularity build Biodiverse.sif SingularityDef_NoPerlbrew.def

```

The `SingularityDef_NoPerlbrew.def` should be present in the current directory.

A ready-to-use image is available at the [Singularity Library](https://cloud.sylabs.io/library/vmiks/gbif/biodiverse) and can be downloaded with:

```

singularity pull --arch amd64 library://vmiks/gbif/biodiverse:1-5-0

```

# Citation

Laffan SW, Lubarsky E, Rosauer DF (2010) Biodiverse, a tool for the spatial analysis of biological and related diversity. Ecography, 33: 643-647. [DOI: 10.1111/j.1600-0587.2010.06237.x](https://onlinelibrary.wiley.com/doi/10.1111/j.1600-0587.2010.06237.x)