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higlass / higlass-docker

Builds a docker container wrapping higlass-server and higlass-client in nginx
MIT License
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Docker higlass-container fails to start if userns-remap is in use #175

Open bmcnally-uw opened 2 years ago

bmcnally-uw commented 2 years ago

Hi,

We have "userns-remap": "docker" set in our /etc/docker/daemon.json to prevent Docker apps from running as root. Doing this causes the higlass-container Docker container to fail to start:

[root@higlass ~]# docker run --detach \
>            --publish 8989:80 \
>            --volume ~/hg-data:/data/higlass/hg-data \
>            --volume ~/hg-tmp:/data/higlass/hg-tmp \
>            --name higlass-container \
>          higlass/higlass-docker:v0.6.1
fc5b14d74f514f02598cfce87e06a86895e13e922feb384d8761c45f0fcc1273
/usr/bin/docker-current: Error response from daemon: oci runtime error: container_linux.go:235: starting container process caused "container init exited prematurely".

It's not clear what the image/container is trying to do, but it's a bit concerning that this appears to need to be run as root at the moment.

pkerpedjiev commented 2 years ago

TBH, I'm not sure I fully understand what the "userns-rempa": "docker" setting does. Here's the Dockerfile if you're curious what the container actually does. Might be worthwhile to look at the logs in ~/hg-data/log and ~/hg-tmp to see if it complains about anything.

bmcnally-uw commented 2 years ago

I'll take a look at the Dockerfile, but the userns-remap option directs the entire Docker stack to run as some user than root, so docker in our case. This means that something the docker run... is doing is failing because it's not running as root.