The provided DOCKERFILE in this repository was used to run most of the anlayses (unless stated otherwise).
Below we provide a short description on how we used docker containers with charliecloud.
You have to have docker installed on your system and the docker service/daemon needs to be running.
Here is an example how you could build a container (we provide the path to the dockerfile via '-f <./path/to/file>' and a nice name via '-t '):
docker build -f DOCKERFILE -t exported_image .
Don't forget the . at the end of the command, otherwise docker will complain.
NOTE: Avoid putting large files in the directory from which you start the build. Docker will send all files in the workding directory to the build context which can take a long while. Therefore, also export your images to a different directory outside of the current one.
NOTE: Tested on a Windows 10 machine with WLS, the above command had to be called twice in order to successfully build the container, the first call resulted in an error.
If you want to use the container in a charliecloud cluster environment, you have to package it as an charliecloud-readable container. To achieve this, you can call the following commands:
id=$(docker create DOCKERFILE)
docker exported_image $id > exported_image.tar
gzip -c exported_image.tar > exported_image.tar.gz
The resulting tar.gz file can then be transferred to a server and run via charliecloud.
The above commands can also be combined to make it more straight forward to use:
docker export $(docker create DOCKERFILE) | gzip -c > exported_image.tar.gz