stxue1

It looks like the config file does not work for toil-cwl-runner. I think configargparse has an issue with `nargs=argparse.REMAINDER`. It looks like if another `nargs`/`append` action is in the mix,...

Lon will probably be the one who would work on this, though it will be a while before this is added to the sprint. We don't have many internal people...

Latest versions of Singularity always attempt to mount with FUSE before sandboxing. Maybe updating Singularity in the Dockerfile is all that is needed. One downside is that old Docker images...

For future reference: As of now, for Kubernetes, [I don't think this is possible.](https://github.com/kubernetes/kubernetes/issues/7890) The only two options I have seen are to use a third party plugin (which runs...

There's currently some code in [issues/4807-unprivileged-fuse](https://github.com/DataBiosphere/toil/tree/issues/4807-unprivileged-fuse) that gives toil-wdl-runner the ability to use FUSE in an unprivileged context if it's available. The way it detects that FUSE can be used...

`--privileged` might need to be enabled. `CAP_SYS_ADMIN` results in a weird permission error: ``` ERROR [U=0,P=596] apply_privileges() Requesting capability set 0x000001ffffffffff while permitted capability set is 0x00000000a82c25ff ``` I assume...

I was able to avoid loop devices by mounting `/dev/fuse` instead of `/lib/modules`, but getting FUSE to work in an unprivileged cluster is likely impossible for now #4807

This should be fixed by #4700

I think I changed the `setup.py` file [some time ago](https://github.com/DataBiosphere/toil/pull/4646) to [properly use importlib](https://github.com/DataBiosphere/toil/blob/3815a2e2b713a5f659050e1e6956dc2569e883a3/setup.py#L155-L157), but left the comment even though it doesn't seem to apply anymore. With the ported code...

Closes #4903