Jun Aruga's Blog

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Install yEd, the Graph Editor on Fedora 36.

Info-tech

I installed yEd, the Graph Editor[1] on Fedora 36 on my Framework Laptop. I wrote about the yEd a little bit in the past on my blog.[2]

This yEd is helpful for thinking clearly. I have used the yEd to think with the Theory of Constraints (TOC) - thinking process - "Current Reality Tree", "Future Reality Tree" and "Evaporating cloud".[3] For the TOC - thinking process, I wrote a blog article in the past.[4]

How to download and install

Go to the download page: https://www.yworks.com/products/yed/download#download and download, then in the case of Linux, I downloaded the "yEd-3.22_with-JRE15_64-bit_setup.sh".

Run the installer by bash yEd-3.22_with-JRE15_64-bit_setup.sh. Then the GUI installer starts.

In the page: "Select directory for symlinks", the "/usr/local/bin" was selected by default. I changed it to the "/home/jaruga/.local/bin", as I wanted to install it to the /home/jaruga/.local.

After finishing the installation, I saw the yEd app is installed in /home/jaruga/yEd. And the symbolic link is linked there. It's not convenient especially to know the installed app's version and to install multiple versions.

  • yEd app: /home/jaruga/yEd
  • Symbolic link: /home/jaruga/.local/bin/yEd -> /home/jaruga/yEd/yEd

So, I changed the directory and the symbolic link manually below. The alias alias yed='yEd' is convenient.

  • yEd app: /home/jaruga/.local/yEd-3.22
  • Symbolic link: /home/jaruga/.local/bin/yEd -> /home/jaruga/.local/yEd-3.22/yEd

How to start

$ yEd &

References

Use Docker on Fedora 36

Info-tech Bio-tech

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