https://github.com/jbris/beast2-docker
Docker and Apptainer setup for the BEAST 2 software
https://github.com/jbris/beast2-docker
apptainer bayesian bayesian-inference bayesian-statistics beast beast2 compartmental-model compartmental-modeling compartmental-models docker docker-compose evolutionary-models phylodynamics phylogenetic-trees phylogenetics phylogenomics phylogeography
Last synced: about 1 month ago
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Docker and Apptainer setup for the BEAST 2 software
- Host: GitHub
- URL: https://github.com/jbris/beast2-docker
- Owner: JBris
- License: apache-2.0
- Created: 2024-12-31T09:26:22.000Z (5 months ago)
- Default Branch: main
- Last Pushed: 2025-01-09T21:22:09.000Z (5 months ago)
- Last Synced: 2025-04-30T17:07:17.941Z (about 1 month ago)
- Topics: apptainer, bayesian, bayesian-inference, bayesian-statistics, beast, beast2, compartmental-model, compartmental-modeling, compartmental-models, docker, docker-compose, evolutionary-models, phylodynamics, phylogenetic-trees, phylogenetics, phylogenomics, phylogeography
- Language: R
- Homepage:
- Size: 679 KB
- Stars: 1
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# BEAST 2 Docker and Apptainer
Docker and Apptainer setup for the BEAST 2 software
# Table of contents
- [BEAST 2 Docker and Apptainer](#beast-2-docker-and-apptainer)
- [Table of contents](#table-of-contents)
- [Docker](#docker)
- [Apptainer](#apptainer)
# Docker
Pull the Docker image:
```
./workspace/scripts/pull.sh
```
Run BEAST2:
```
cd workspace
./scripts/run.sh examples/testRNA.xml
```
Run BEAST2 with BEAGLE:
```
cd workspace
./scripts/run.sh -beagle -beagle_SSE -beagle_CPU -threads 4 examples/testRNA.xml
```
# Apptainer
Build the Apptainer image:
```
./workspace/scripts/apptainer_build.sh
```
Run BEAST2:
```
./beast2.sif workspace/examples/testRNA.xml
```
Run BEAST2 with BEAGLE:
```
./beast2.sif -beagle -beagle_SSE -beagle_CPU -threads 4 workspace/examples/testRNA.xml
```