Trouble starting Docker instance with data persistence

[jembrown]

@reid-wagner I was following the instructions that we currently have in the user guide for running Docker instances locally, but I could not successfully set up a version with data persistence. It seemed to start fine at the command line, but couldn't be accessed through a browser. The version without data persistence worked great.

In trying to run with data persistence, I also had to work through an initial issue where the directory for local storage had to be added to a list of directories under "Resources", then "File Sharing" in Docker Desktop. We should probably add some information about this to the user guide.

[reid-wagner]

Hi @jembrown,

Short answer:

Using a volume with these steps listed below may be easier, so I suggest giving that a try.

1. docker volume create cloudforest-volume
2. docker run -d -p 8080:80 --name cloudforest --mount source=cloudforest-volume,target=/export/ -e "GALAXY_DESTINATIONS_DEFAULT=local_no_container" -e "GALAXY_SLOTS=2" cloudforestphylogenomics/cloudforest_galaxy:latest

Long answer:

I also had some trouble starting it this way. First, it took about 20 minutes in total for the startup scripts from docker-galaxy-stable to copy all of the necessary files to the host, so it may just be that this hadn't finished running on your system yet.

But I also encountered an issue where I had to actually start the container twice for this copy operation to finish successfully, due to an exception in file copying code.

I may suggest that we actually switch to using volumes instead of bind mounts. The current documentation focuses on bind mounts so that users don't need to manage volumes. But I'm not sure at this point in the project that volumes are much more difficult, plus they are simpler in other ways, and ideally all of this could be abstracted out.

This is also much faster than the bind mount. I will update the documentation with directions for volumes, but keep the documentation for bind mounts in case users are interested. I'll also include your note about Docker Desktop, which wasn't actually an issue for me - are you using MacOS?

[jembrown]

Thanks, your commands worked for me. Using the volumes approach, where are the data stored locally?

Yep, I'm using MacOS.

[reid-wagner]

The data would be in ~/Library/Containers/com.docker.docker/Data/vms/0/data/Docker.raw or Docker.qcow, which is the disk image for the VM on which Docker Desktop runs.

This is different from Linux where the files would be stored directly on the filesystem at the path specified by docker inspect cloudforest-volume | grep mountpoint. Instead they're store at this path within the VM.

Aside from accessing the data from the running CloudForest container, it's also possible to get a shell in the VM.