mount s3 bucket to /tmp in docker container, AWS batch

[BJWiley233]

Hi,

I am getting zero help from the slack community. I would like to know how I can get a scratch s3 bucket mounted to the /tmp directory for cellranger because they were ignorant enough to only send scratch data to the /tmp directory and not setup the ability to send it to any directory the user wants, i.e. the "working directory" such as -work-dir s3://wiley-data/scratch. The fusion documentation only indicates that the s3 bucket is the working directory. Maybe there is a way to mount the current directory to the docker /tmp folder for instance with -v .:/tmp?

Brian

[BJWiley233]

Testing maybe if this would work in the config in addition to -work-dir s3://wiley-data/scratch

docker {
    enabled = true
    temp = '.'
}

[BJWiley233]

#SuperClap!!!!!! 😄 👏
this works I believe:

docker {
    enabled = true
    temp = "\$PWD"
}

EDIT: this only worked one time. Can't get it to work again.

[BJWiley233]

trying with the nvme storage option of the additional EBS on my host also gives error:

Caused by:
  Task failed to start - CannotStartContainerError: Error response from daemon: failed to create shim task: OCI runtime create failed: runc create failed: unable to start container process: error during container init: error mounting "/dev/nvme1n1" to rootfs at "/tmp": mount /dev

adding process.scratch = false makes the job stuck in "Runnable" but never "Running" status.