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
~/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.