I was trying to run the WDL file on locally by the dockstore
command[1]. Because it's an easy way to check a WDL file rather than uploading it to the Dockstore site. Right now I couldn't find the dockstore
command with the Podman[2][3], I installed Docker as a compromised way. But I remember I was struggled with the official docker installation because it conflicts with the podman's libraries. So, an easy way is Fedora's RPM package moby-engine
.
$ sudo dnf install moby-engine $ rpm -q moby-engine moby-engine-20.10.17-5.fc36.x86_64
Then add my user to the docker group.
$ sudo usermod -a -G docker jaruga $ cat /etc/group | grep docker docker:x:975:jaruga
Then run the newgrp docker
or restart the OS. The document [4] helped me to find the steps.
$ id uid=1000(jaruga) gid=1000(jaruga) groups=1000(jaruga),10(wheel),135(mock),1001(plugdev) context=unconfined_u:unconfined_r:unconfined_t:s0-s0:c0.c1023 $ newgrp docker $ id uid=1000(jaruga) gid=975(docker) groups=975(docker),10(wheel),135(mock),1000(jaruga),1001(plugdev) context=unconfined_u:unconfined_r:unconfined_t:s0-s0:c0.c1023
Then start docker deamon.
$ systemctl status docker $ sudo systemctl start docker
Then I could run the command below. This command works when the connection to the server works.
$ docker version Client: Version: 20.10.17 API version: 1.41 Go version: go1.18.4 Git commit: aa7e414 Built: Tue Jul 19 21:40:23 2022 OS/Arch: linux/amd64 Context: default Experimental: true Server: Engine: Version: 20.10.17 API version: 1.41 (minimum version 1.12) Go version: go1.18.4 Git commit: f756502 Built: Tue Jul 19 21:40:23 2022 OS/Arch: linux/amd64 Experimental: false containerd: Version: 1.6.8 GitCommit: runc: Version: 1.1.3 GitCommit: docker-init: Version: 0.19.0 GitCommit: $ echo $? 0
References
- [1] https://github.com/dockstore/dockstore-cli
- [2] https://discuss.dockstore.org/t/dockstore-cli-support-podman-alternatrive-docker-or-workaround/5849/2
- [3] https://github.com/dockstore/dockstore/issues/5119
- [4] https://stackoverflow.com/questions/47854463/docker-got-permission-denied-while-trying-to-connect-to-the-docker-daemon-socke