bomeara/phydocker repository overview

⁠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 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.