bomeara / phydocker

Dockerfile for phylogenetics in R

phydocker

This will let you run R in your browser (using Rstudio) with phylogenetics packages installed already; you can also connect directly to run command line phylogenetics tools. These are all installed and configured to work. All of this is free.

You will need to install docker.

Then in a command window (i.e., using a terminal program (on a Mac, in /Applications/Utilities/Terminal.app):

docker run -v ~/Desktop:/data -e PASSWORD=mypassword -p 8787:8787 bomeara/phydocker

Then you can go to http://localhost:8787 in your web browser to run it; log in as rstudio with password mypassword (and you could replace mypassword with another string). 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.

Advanced

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 raxmlHPC-SSE, treePL, and phlawd without having to go through installation. exit command when done.

Building

For building this from scratch (not most users)

docker build -t bomeara/phydocker .

Or if you want to not use the cached images (the --squash will make compressed images, but requires experimental docker):

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

To push to docker hub

docker push bomeara/phydocker

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