Error: docker not installed

[nebfield]

Hello,

I tried following the instructions on Linux to install and run Monet:

[ben@asclepius ben]$ monet --input=ad.tsv --method=K1 --container=docker --output=ad
ERROR: you specified --container=docker, but docker is not installed
Please visit https://www.docker.com

Docker is installed 😢 for example

[ben@asclepius ben]$ docker run hello-world

Hello from Docker!
This message shows that your installation appears to be working correctly.

To generate this message, Docker took the following steps:
 1. The Docker client contacted the Docker daemon.
 2. The Docker daemon pulled the "hello-world" image from the Docker Hub.
    (amd64)
 3. The Docker daemon created a new container from that image which runs the
    executable that produces the output you are currently reading.
 4. The Docker daemon streamed that output to the Docker client, which sent it
    to your terminal.

To try something more ambitious, you can run an Ubuntu container with:
 $ docker run -it ubuntu bash

Share images, automate workflows, and more with a free Docker ID:
 https://hub.docker.com/

For more examples and ideas, visit:
 https://docs.docker.com/get-started/

Additional info:

[ben@asclepius ben]$ docker info
Client:
 Context:    default
 Debug Mode: false
 Plugins:
  app: Docker App (Docker Inc., v0.9.1-beta3)
  buildx: Build with BuildKit (Docker Inc., v0.5.1-docker)

Server:
 Containers: 80
  Running: 1
  Paused: 0
  Stopped: 79
 Images: 189
 Server Version: 20.10.3
 Storage Driver: overlay2
  Backing Filesystem: xfs
  Supports d_type: true
  Native Overlay Diff: true
 Logging Driver: json-file
 Cgroup Driver: cgroupfs
 Cgroup Version: 1
 Plugins:
  Volume: local
  Network: bridge host ipvlan macvlan null overlay
  Log: awslogs fluentd gcplogs gelf journald json-file local logentries splunk syslog
 Swarm: inactive
 Runtimes: io.containerd.runtime.v1.linux runc io.containerd.runc.v2
 Default Runtime: runc
 Init Binary: docker-init
 containerd version: 269548fa27e0089a8b8278fc4fc781d7f65a939b
 runc version: ff819c7e9184c13b7c2607fe6c30ae19403a7aff
 init version: de40ad0
 Security Options:
  seccomp
   Profile: default
 Kernel Version: 3.10.0-1160.15.2.el7.x86_64
 Operating System: CentOS Linux 7 (Core)
 OSType: linux
 Architecture: x86_64
 CPUs: 64
 Total Memory: 314.1GiB
 Name: asclepius.host.ulster.ac.uk
 ID: R2C3:ULD6:PDYV:NEZ4:Y5QL:42XG:RRRQ:EQPV:VE4A:HXII:UGD4:JLLY
 Docker Root Dir: /data/services/docker
 Debug Mode: false
 Registry: https://index.docker.io/v1/
 Labels:
 Experimental: false
 Insecure Registries:
  127.0.0.0/8
 Live Restore Enabled: false

Thanks, Ben

[nebfield]

Also having the same problem on OSX:

e16000474@CESSL2601 MONET % docker info
Client:
 Context:    default
 Debug Mode: false
 Plugins:
  app: Docker App (Docker Inc., v0.9.1-beta3)
  buildx: Build with BuildKit (Docker Inc., v0.5.1-docker)
  scan: Docker Scan (Docker Inc., v0.5.0)

Server:
 Containers: 28
  Running: 0
  Paused: 0
  Stopped: 28
 Images: 107
 Server Version: 20.10.2
 Storage Driver: overlay2
  Backing Filesystem: extfs
  Supports d_type: true
  Native Overlay Diff: true
 Logging Driver: json-file
 Cgroup Driver: cgroupfs
 Cgroup Version: 1
 Plugins:
  Volume: local
  Network: bridge host ipvlan macvlan null overlay
  Log: awslogs fluentd gcplogs gelf journald json-file local logentries splunk syslog
 Swarm: inactive
 Runtimes: runc io.containerd.runc.v2 io.containerd.runtime.v1.linux
 Default Runtime: runc
 Init Binary: docker-init
 containerd version: 269548fa27e0089a8b8278fc4fc781d7f65a939b
 runc version: ff819c7e9184c13b7c2607fe6c30ae19403a7aff
 init version: de40ad0
 Security Options:
  seccomp
   Profile: default
 Kernel Version: 4.19.121-linuxkit
 Operating System: Docker Desktop
 OSType: linux
 Architecture: x86_64
 CPUs: 2
 Total Memory: 7.779GiB
 Name: docker-desktop
 ID: D4RR:4M5V:2TR4:IB7O:W42P:VV7U:7VUJ:OLLL:7MQ4:WFK2:KR5G:FCLZ
 Docker Root Dir: /var/lib/docker
 Debug Mode: true
  File Descriptors: 40
  Goroutines: 44
  System Time: 2021-02-17T14:43:27.335277707Z
  EventsListeners: 3
 HTTP Proxy: gateway.docker.internal:3128
 HTTPS Proxy: gateway.docker.internal:3129
 Registry: https://index.docker.io/v1/
 Labels:
 Experimental: false
 Insecure Registries:
  127.0.0.0/8
 Live Restore Enabled: false

[mattiat]

Dear nebfield, thank you for reporting this bug. Sorry for the wait, I recently defended my PhD thesis. I have pushed a fix. https://github.com/BergmannLab/MONET/commit/3810e67ac5a0706678e4c2306261d4d7a0701a83

Please, pull then just run .install again (you will be asked to overwrite the current installation). Let me know if it works. I tested on Ubuntu 20.04 (all three MONET methods) Cheers, Mattia

[nebfield]

Thanks for your help 😀 Everything works OK now. I hope your defence went well!