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Dockerfile for phylogenetics in R
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For most users you first want to install docker. Then you want to do the following commands:

docker pull bomeara/phydocker

Then in a command window or within docker:

docker run -v ~/Desktop:/data -p 8787:8787 bomeara/phydocker

Then you can go to http://localhost:8787 to run it; log in as rstudio with password rstudio. Replace ~/Desktop with the full path to the folder where you have files (i.e., /Users/jsmith/Documents/Chapter1). You can keep it ~/Desktop, it'll then have your desktop present as the /data directory in Docker (i.e., in R, you can do save(ape::rcoal(10), file="/data/random.tre") and it'll save a random tree to your desktop. When you're done, you can kill the process with control+C.

If you want to run on the command line instead (i.e., from inside Terminal on a Mac) you can do

docker run -it -v ~/Desktop:/data bomeara/phydocker /bin/bash

You can then use programs like treePL and phlawd without having to go through installation. exit command when done.

For building this from scratch (not most users)

docker build -t bomeara/phydocker .

Or if you want to not use the cached images:

docker build --no-cache -t bomeara/phydocker .

To push to docker hub

docker push bomeara/phydocker

However, it is currently set to automatically build with pushes to github.

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