Jun Aruga's Blog

Output, activities, memo and etc.

Info-tech

Install yEd, the Graph Editor on Fedora 36.

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 (…

Use Docker on Fedora 36

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 …

Using Quay.io

This article is a memo on how to use Quay.io[1] and how to change the login from the original Quay ID/password to Red Hat SSO (Single Sign On). Change how to log in from Quay ID/Password to Red Hat SSO Now the Quay only encourages Red Hat …

Format USB drive on Fedora

This blog is a note on how to format a USB drive on Fedora Linux 36. I have Framework Laptop, and I have a 256 GB expansion card. So, I formatted the USB disk to use on Fedora Linux 36. Even when it is not formatted, you can see the device…

Install Freeplane on Fedora 36

Freeplane is a mindmap app mentioned before [1]. $ sudo dnf install java-17-openjdk I did put the extracted directory into the directory below. /home/jaruga/.local/freeplane-1.10.3 And I did set a symbolic link $ pwd /home/jaruga/.local/bi…

i3: Customize keyboard layout on X based window manager

This blog is to summarize the outcome of communication[1] in the xkeyboard-config project through my pull request. Thanks for the help! On Wayland-based window managers such as Sway, people can customize keyboard layout freely under their …

Install Google Chrome on Fedora 35

Tomorrow I will attend a virtual conference. But the live stream's caption feature is only available on Google Chrome using the Live Caption feature. So, I installed Google Chrome to Fedora 35 on my Framework Laptop. I referred this site […

Highligher, marker plugins on Firefox

When reading papers on web browser, saved text highlight is useful to read, memorize and see it again. I saw someone using Super Simple Highlighter plugin on Brave browser, maybe that is Chrome based. When tested the plugin on Brave, it wa…

Framework Laptop: Install Skype/Slack on Fedora 35

Skype Install Skype [1] seeing the document [2] on Fedora project. $ wget https://repo.skype.com/rpm/stable/skype-stable.repo $ sudo mv skype-stable.repo /etc/yum.repos.d/ $ sudo dnf install skypeforlinux $ skypeforlinux & Slack Install Sl…

Framework Laptop: How to run concole when GDM is not starting

This article is about a solution when GDM is not start. Here is a thread I created for this topic: https://ask.fedoraproject.org/t/the-best-practice-when-facing-gdm-not-starting/20789 When I will face GDM not starting next time, Select dif…

Framework Laptop: Login from console without GDM

On the previous article https://junaruga.hatenablog.com/entry/2022/03/23/100747, I wrote there might be issue in GDM on my Fedora. I think not using GDM in the login process is a possible way to prevent this situation essentially. On my Fe…

Framework Laptop: GDM (the GNOME Display Manager) failed to start on the kernel 5.15.18?

Maybe it was 20th February. When launching the Fedora 35 with the kernel kernel-5.15.18-200.fc35.x86_64 on Framework Laptop, there was a page only showing gray color. Maybe the ID, password GUI page failed to start. However today when open…

Fedora: setup packager tools

Install packager tools to do packaging on Fedora, seeing https://docs.fedoraproject.org/en-US/package-maintainers/Installing_Packager_Tools/. Install the following packages. $ sudo dnf install fedora-packager fedora-review SSH keys The typ…

Sway, i3: Set up Japanese input with fcitx5.

In the past, I did set up Japanese input by fcitx. As a reference, here are the blog pages. However I noticed there is fcitx5 that is successor version of fcitx. It looks the UI is better. According to the ArchWiki fcitx5, fcitx5-mozc is "…

Setup and use Alacritty on Fedora

I am trying to use Sway window manager on Fedora, stopping the i3 window manager. Here is a Sway installation guide on Fedora. And after installing the Sway, I see the terminal emulator Alacritty is used as the window manager's default ter…

Upgrade Fedora 34 to 35

I referred How to Upgrade Fedora 34 to Fedora 35? - #7 by marcedwin - Ask Fedora. Here are the steps. $ sudo dnf upgrade --refresh $ sudo dnf install dnf-plugin-system-upgrade $ sudo dnf system-upgrade download --releasever=35 --allowerasi…

Fedora 35: Enable WiFi

I replaced wifi antenna cables on my Framework Laptopo as I broke those. I followed the Antena Replacement Guide. Fortunately it was succeeded. Now the Wifi works on Fedora 35 on my Framework Laptop. After replacing the Wifi cables, the Wi…

Fedora 35: Show GRUB 2 menu

After installing Fedora 35 on my Framework Laptop, I noticed the GRUB 2 menu is hidden on boot. Seeing a Ask Fedora page, the change looks since Fedora 2X. Anyway, here are the current setting related to GRUB 2. $ cat /etc/default/grub GRU…

BioHackathon Europe

I joined the BioHackathon Europe in Barcelona. That's a hacking event, co-working event related to biology. This time it's to select one project from 37 projects (There are 38 projects on the page, but the "Single Cell Multi-Omics Analysis…

Miniconda, Bioconda on Fedora and Galaxy

This page is the memo about installing miniconda (conda command) on Fedora Linux. I referred the document [1]. I wanted to install a bioconda package. Because I wanted to build a Galaxy tool using Planemo [2]. The tutorial is using biocond…

libinput and related tools

Recently I see customizing the libinput is useful to use input devices such as keyboard, trackpad (touchpad), trackpoind and mouse effectively on Linux. Here are the useful documents. https://wayland.freedesktop.org/libinput/doc/latest/ ht…

i3: Mouse emulation on keyboard

When I was looking at the ZSA's customizable keyboard: Plank EZ page - mouse emulation the keyboard on the firmware (hardware level), I was inspired. Maybe it's possible to emulate the mouse on the keyboard on the software level? The way 1…

i3: Setup bluetooth keyboard

I did set up my bluetooth keyboard by the company Golodtouch by command line on the i3 window manager on Fedora 34. Here are the list I checked to do it. I referred the [1][2][3]. Check the bluetooth service. $ systemctl status bluetooth C…

i3: Set up Japanese input environment - kkc

Seeing https://wiki.archlinux.org/title/Localization/Japanese, the project Anthy is actually dead project. So, I changed the Japanese input from fcitx-anthy to fcitx-kkc. $ sudo dnf remove fcitx-anthy $ sudo dnf install fcitx-kkc

i3: Touch-pad: natural scrolling and lock

Natural scrolling The natural scrolling is like double finger swipe like Mac OSX. As a default of i3 config, the double finger swipe scrolling is opposite direction. To enable it, add the following file, and restart the X. $ sudo vi /etc/X…

How to use "git bisect".

I used git bisect command related to this issue on the Ruby project. The situation is that the some tests in test/ruby/test_jit.rb fail on the v2_7_4 tag, but pass on v2_7_3 tag on the ruby/ruby repository. So, here is steps to find which …

Freeplane: A better compatible FreeMind alternative

While a mind map tool "FreeMind"'s development has not been updated for a long time and I see some bugs there, I can see the Freeplane is a better compatible FreeMind software on Mac and Linux now. You can open a .mm file created by FreeMi…

How to debug C code in Ruby (ruby/ruby).

This article is to debug the C source code running a specific unit test in Ruby itself (ruby/ruby). First you can set your preferred compiler flags like this. Build $ autoconf $ optflags=-O0 debugflags="-g3 -ggdb3 -gdwarf-4" \ ./configure …

i3: Set up Czech input environment 3

Last time I shared the top of Czech input environment here. I see the Czech UCW keyborad is the best choice so far. $ vi .config/i3/config ... exec --no-startup-id "setxkbmap -layout us,cz -variant ,ucw -option grp:caps_switch" ... $ setxk…

i3: Set up Czech input environment 2

I wrote the article to set up Czech keyboard input environment. junaruga.hatenablog.com This time I would share what I improved for the topic, as I heard the info from my colleagues. Thanks! The key command is setxkbmap (= Set X keyboard m…