Progress log

Initial

  1. Installed ubuntu 24.04 all default
  2. installed vim, neofetch, curl, git, qrencode
  3. connected with github

NAS connection

sudo apt install cifs-utils
sudo apt install nfs-common

Gnome Tweaks

sudo apt-get install gnome-tweaks

Installing fonts

sudo apt install ttf-mscorefonts-installer
sudo fc-cache -f -v

Install windows compatibility layer

link to resources

  1. Get your VERSION_CODENAME
cat /etc/os-release
  1. Add the wine repository
sudo mkdir -pm755 /etc/apt/keyrings
wget -O - https://dl.winehq.org/wine-builds/winehq.key | sudo gpg --dearmor -o /etc/apt/keyrings/winehq-archive.key -
  1. Add the sources files for “noble”
sudo wget -NP /etc/apt/sources.list.d/ https://dl.winehq.org/wine-builds/ubuntu/dists/noble/winehq-noble.sources
  1. Update
sudo apt update
  1. Install stable version
sudo apt install --install-recommends winehq-stable

install total commander to test the wine is working

is working

install zen software using wine to see if it is working

testing it with ZENblack_2011SP4_2012… threw a couple of errors did not work, trying to do it with the official lite version looks it works, waiting for some confirmation password saved in mozzilla browser

Installing deb packages

sudo dpkg -i /path/to/package.deb

Academic tools

Install Zotero

There is a package instead of the tarball, trying to use this

curl -sL https://raw.githubusercontent.com/retorquere/zotero-deb/master/install.sh | sudo bash
sudo apt update
sudo apt install zotero

This worked, not sure wha

Install Fiji

link to the download, downloaded the stable version for linux placed it in Document/Programs/ tried to make an icon on a desktop, not sure it works

Create a desktop entry file to make the application launchable from the desktop. Use a text editor to create a file named fiji.desktop in the ~/.local/share/applications/ directory with the following content:

[Desktop Entry]
Name=Fiji
Type=Application
Exec=~/Fiji.app/ImageJ-linux64
Icon=~/Fiji.app/images/icon.png
Categories=Science;ImageTools;
Terminal=false

Save the file and ensure it is executable by running chmod +x ~/.local/share/applications/fiji.desktop.
 After creating the desktop entry,

Install Cell Profiler

Official page of cell profiler project link Is installed through the wine compatibility layer

  1. Download the windows 10/11 version
  2. Double click and go through installation
  3. Requires confirmation of some other download stuff
  4. To start it from terminal, find where it is located: /home/<user>/.wine/drive_c/Program\ Files/CellProfiler/CellProfiler.exe
  5. Set alias in your ~/.bashrc alias cellprofiler="wine /home/<user>/.wine/drive_c/Program\ Files/CellProfiler/CellProfiler.exe"

Works

To make a clicable icon this is suggested by chatGPT

[Desktop Entry]
Name=CellProfiler (Wine)
Comment=Cell image analysis via Wine
Exec=wine "/home/vld/.wine/drive_c/Program Files/CellProfiler/CellProfiler.exe"
Icon=wine
Terminal=false
Type=Application
Categories=Science;

Miniconda installation for bioinformatics

mkdir -p ~/miniconda3
wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O ~/miniconda3/miniconda.sh
bash ~/miniconda3/miniconda.scd ~h -b -u -p ~/miniconda3
rm ~/miniconda3/miniconda.sh
conda init --all --dry-run

Example of installing some tools to search for domains

# after checnking the modifications
source ~/miniconda3/bin/activate
conda create -n domainsearch python=3.11
conda activate domainsearch
conda install -c bioconda seqkit
conda install -c bioconda interproscan
conda install -c bioconda blast

Virtual environments

Virtual environments venv

sudo apt install python3-venv -y
sudo apt install python3-venv -y

is working

make a dedicated folder for venvs

mkdir -p ~/.venvs

csvkit in venv

Install it

move to .venvs

python3 -m venv csvenv
source csvenv/bin/activate
csvenv\Scripts\activate
pip install csvkit

check it is working

csvcut --help

get in and out of it

source /home/vld/.venvs/csvenv/bin/activate

deactivate

make a wrapper for it to work in its enviroment

mkdir -p ~/.local/bin

Add following to .bashrc

export PATH="$HOME/.local/bin:$PATH"

Create the wrapper in ~/.local/bin

for cmd in csvclean csvcut csvformat csvgrep csvjoin csvjson csvlook csvpy csvsort csvstack csvstat; do
    cat << EOF > ~/.local/bin/$cmd
#!/bicat n/bash
/home/vld/.venvs/csvenv/bin/$cmd "\$@"
EOF
    chmod +x ~/.local/bin/$cmd
done

Test it works

csvcut --help

works

App stores

flatpak

link to the article

sudo apt install flatpak -y
flatpak remote-add --if-not-exists flathub https://flathub.org/repo/flathub.flatpakrepo

Internet

Web-browser brave

curl -fsS https://dl.brave.com/install.sh | sh

worked immediately, installed zotero connector and vimium

Whatsapp

worked through the whatsdesk via snap store, but stopped working on 8/1/2026 link to article

Note: Is missing fonts, when trying to attach or download documents displays just squares instead of letters

Whatsie

Recomended on ubuntufree.com

sudo snap install whatsie

Telegram app

got it from brave ai recommended the ppa repository installation as the snap installation image has a limited usability

sudo add-apt-repository ppa:atareao/telegram
sudo apt update
sudo apt install telegram

Works

E-obcanka

Using a smart card reader AK-CR-03BKV2

link to the website describing installation

CHeck if the usb device is recognized

lsusb

should list something with a smart reader

Install the necessary pacakges

sudo apt update
sudo apt install pcscd pcsc-tools libccid

Was necessary to run

sudo apt --fix-broken install

Start the service

sudo systemctl enable pcscd

Install the downloaded deb package

navigate to the downloads folder

sudo dpkg -i eObcanka.deb

Works

When it did not work again:

If it does not work, check if the drivers are installed

dpkg -l | grep pcscd

Then uninstall eobcanka and install the tools, then reinstall the package FInd the name of the package

sudo dpkg -l | grep -i eobcanka

sudo dpkg -P eobcanka

sudo apt install pcscd pcsc-tools

sudo dpkg -i eObcanka.deb

Check the daemon is running

sudo systemctl restart/status pcscd

NOw it works

MUNI and FNUSA compatibility

Install eduVPN for muni access

curl --proto '=https' --tlsv1.2 https://docs.eduvpn.org/client/linux/install.sh -O
bash ./install.sh

Is working

Install openVPN for FNUSA

sudo apt-get install network-manager-openvpn-gnome

works

Access the shared folder on the CELLIM server

Check reachability first

ping -c 2 <server-ip-or-name> # check reachability

make a mount point

sudo mkdir -p /mnt/odeon

Connect using manual typig a password

sudo mount -t cifs //<server>/<share> /mnt/winshare -o username=<user>,password='<pass>',vers=3.0

Next steps: make a script to log in without exposing the password in the script

Flash drives not mounting

Quite often the flash drive will not mount automatically
If it is a ntfs filesystem, can be fixed (also other ones, but have just this one problematic)

Identify all the devices/disks

sudo lsblk -f

gives you the sda1, sdb1 or whatever with the filesystem type

Try to mount manually

sudo mounte -t ntfs /dev/sda1 /media/

Run the ntfsfixer

sudo ntfsfix /dev/sda1

Mount again

sudo mounte -t ntfs /dev/sda1 /media/

Audio and video

ffmpeg

Essential tool for command line video conversions, cutting speeding up etc.
Is not by default

sudo apt install ffmpeg

OBS

Tool for recording and streaming video

sudo add-apt-repository ppa:obsproject/obs-studio -y
sudo apt update
sudo apt install obs-studio -y

OBS launches but does not run Error log

19:55:50.493: >>> new qsv encoder
19:55:50.493: [qsv encoder: 'simple_video_recording'] settings:
19:55:50.493: 	codec:          H.264
19:55:50.493: 	rate_control:   ICQ
19:55:50.493: 	ICQ Quality:    23
19:55:50.493: 	target_usage:   TU4
19:55:50.493: 	profile:        high
19:55:50.493: 	keyint:         0
19:55:50.493: 	latency:        normal
19:55:50.493: 	b-frames:       3
19:55:50.493: 	fps_num:        60
19:55:50.493: 	fps_den:        1
19:55:50.493: 	width:          1920
19:55:50.493: 	height:         1080
19:55:50.493: [qsv encoder: 'simple_video_recording'] debug info:
19:55:50.495: Failed to initialize MFX
19:55:50.495: [qsv encoder: 'msdk_impl'] Specified object/item/sync point not found. (MFX_ERR_NOT_FOUND)
19:55:50.495: [qsv encoder: 'simple_video_recording'] qsv failed to load
19:55:50.495: 	major:          1
19:55:50.495: 	minor:          0
19:56:02.591: [pipewire] Stream 0x566f1b19d7f0 state: "paused" (error: none)
19:56:04.612: >>> new qsv encoder
19:56:04.613: [qsv encoder: 'simple_video_recording'] settings:
19:56:04.613: 	codec:          H.264
19:56:04.613: 	rate_control:   ICQ
19:56:04.613: 	ICQ Quality:    23
19:56:04.613: 	target_usage:   TU4
19:56:04.613: 	profile:        high
19:56:04.613: 	keyint:         0
19:56:04.613: 	latency:        normal
19:56:04.613: 	b-frames:       3
19:56:04.613: 	fps_num:        60
19:56:04.613: 	fps_den:        1
19:56:04.613: 	width:          1920
19:56:04.613: 	height:         1080
19:56:04.613: [qsv encoder: 'simple_video_recording'] debug info:
19:56:04.614: Failed to initialize MFX
19:56:04.614: [qsv encoder: 'msdk_impl'] Specified object/item/sync point not found. (MFX_ERR_NOT_FOUND)
19:56:04.614: [qsv encoder: 'simple_video_recording'] qsv failed to load
19:56:04.614: 	major:          1
19:56:04.614: 	minor:          0

sudo apt update
sudo apt install intel-media-va-driver-non-free i965-va-driver
sudo apt install libmfx1 libmfx-dev
sudo apt install vainfo
sudo apt update
sudo apt install intel-media-va-driver-non-free i965-va-driver mesa-utils vainfo

need to add intel repository

sudo rm /etc/apt/sources.list.d/intel-gpu-jammy.list
sudo apt update
sudo mkdir -p /etc/apt/keyrings
curl -fsSL https://raw.githubusercontent.com/intel/intel-linux-graphics/master/keys/intel-linux-graphics.gpg | \
  sudo gpg --dearmor -o /etc/apt/keyrings/intel-linux-graphics.gpg

echo "deb [arch=amd64 signed-by=/etc/apt/keyrings/intel-linux-graphics.gpg] \
https://repositories.intel.com/graphics/ubuntu jammy unified" | \
sudo tee /etc/apt/sources.list.d/intel-graphics.list

sudo apt update
sudo apt install intel-opencl-icd intel-level-zero-gpu level-zero intel-media-va-driver-non-free libmfx1 libmfx-tools

Looks the QSV does not work, need to use the VAAPI This checks if the encoding is there

/opt/intel/oneapi/level-zero/bin/ze_info | head -n 20
vainfo | grep -E "H264|HEVC"

start OBS with the proper setting

export LIBVA_DRIVER_NAME=iHD
export MFX_LOAD_PLUGIN=hw
obs

CHange the encoding in:
File-> Settings -> Output -> Advanced -> recording ->encoder
This setting works, but the microphone quality is very poor probably needs better drivers

Networking tools

Find ip address and other devices on network

sudo apt install net-tools -y
sudo apt install nmap -y
  1. to get your connections ip a
  2. to get the other devices nmap -nm -v <ip-address>/24

Use a VPN like stuff to connect remotely

tailscale:
link

The oneliner does not work for the install, need to scroll down copy codelines from the ubuntu noble

Setup the remote desktop

On the remote machine

gsettings set org.gnome.desktop.remote-desktop.rdp enable true

# set credentials
grdctl rdp set-credentials username password

# start the service
systemctl --user enable --now gnome-remote-desktop

On the local machine

Steps:
Open Remmina
New connection → Protocol: RDP
Server: use the Tailscale IP (e.g. 100.x.x.x)
Enter credentials

Working with documents and images

Libre suite (like office)

Installed by default but the default fonts are really ugly

Install the czech language packs for libre office

sudo apt update -y
sudo apt install language-pack-cs language-pack-gnome-cs -y
sudo apt install hunspell-cs hyphen-cs mythes-cs libreoffice-l10n-cs -y

After installing works, but needs to set a new input device in keyboards, add the czech one and change to it (Win+space).
Had some issues with delete not working but closing and opening libre office worked.

Using Microsoft office fonts in Libre office suite

  • Find the fonts on internet or your computer in C:\Windows\Fonts
  • Copy the files (.tff) into the Downloads folder
sudo mkdir -p /usr/local/share/fonts/
sudo cp *.ttf *.otf /usr/local/share/fonts/
sudo fc-cache -f -v

this will install the fonts for the libre office (and others?) programs
Note: this may not work unless each font has its own folder(see below for example)

Did not find the aptos font, so downloaded from internet and did following:

sudo mkdir -p /usr/local/share/fonts/aptos
sudo cp *.ttf *.otf /usr/local/share/fonts/aptos/
sudo fc-cache -f -v

Afterwards it works

Pandoc

Tool to convert between different formats of documents

sudo apt install pandoc
sudo apt install texlive-latex-recommended texlive-latex-extra texlive-fonts-recommended texlive-xetex

For some strange reason failed to set it in the ~/.config/pandoc/pandoc.yaml file, so for each conversion need to run:

pandoc --pdf-engine <in> <out>

magick

Tool to manipulate images, create panels etc.
already installed, still in 6th version, is okey(?)

Computer interaction

I need to swap some keys to make the computer better usable from keyboard only:

Get rid of the preset key combinations which would be in conflict

Open Settings → Keyboard → Keyboard Shortcuts

Look for Window Menu

Remove or change the shortcut

INstall keyd

Keyd should enable me to make changes to configuration, runs as a service, is not available in the official ubuntu repository

sudo add-apt-repository ppa:keyd-team/ppa
sudo apt update
sudo apt install keyd

Edit the configuraiton file:

sudo nano /etc/keyd/default.conf

[ids]
*

[main]
capslock = esc
esc = capslock
leftalt = layer(alt_layer)

[alt_layer]
space = enter
q = S-grave
semicolon = backspace

this setting creates a new layer after pressing alt, where space is interpreted as an backspace.
the simple leftatl+space=backspace in main section does not work (tested)

sudo systemctl restart keyd

Swapping esc and capslock

gsettings set org.gnome.desktop.input-sources xkb-options "['caps:swapescape']"

Websites

To be able to create static hugo website

Install go-lang

sudo apt-get install golang

install hugo

First need to check which version is required for papermod, the ubuntu one may be too old The version needed for PaperMod theeme is >=v0.112.4 (26/12/2025) link

which hugo # tells you if installed

if not installed:

hugo

outputs the options, which could be installed, apt version (0.123.7-ubuntu0.3) is older then recomended on hugo website , so better to install the snap version: 0.0152.2

sudo snap install hugo

Copying files etc

File manager

 sudo apt install doublecmd-qt
  • works
  • looks really ugly but changing the fonts and making the icons smaller works somehow
  • Added the treeview on the left side, super useful
  • changed the default editor to vim

Clipboard

sudo apt install wl-clipboard

to use it redirect the SOUT into wl-clipboard

pwd | wl-copy

This puts the current directory path into clipboard Would be great to give it a better alias

Motivation

I would like to switch to linux in order to make several improvments in quality of my work

  • Better searching for files (the default windows experience with search is terrible, search in terminal is both much faster and detailed)
  • Working with video from the command line
  • Web content creation using the hugo
  • Backups
  • Bioinformatics (working with virtual environments and docker containers for R)
  • Own bash scripts

Linux distribution

I decided to use Ubuntu 24.04 as it is the most common distribution so it should be the easiest to get help from the internet and also make it easier for other people to adopt the same system. However I am aware I will need to run the microsoft office suite (I like the desktop version) and some other software which may not work through the compatibility layer, so I would like to have the virtual machine with a windows inside linux. This could fail through the inability to share and work on presentations, present at conferences and inability to connect to online meetings without hitches.

Resources

Installing windows 11 in virtual machine Hopefully, most likely obsolote, winboat seems to solve this problem 

sudo apt install virtualbox virtualbox-guest-additions-iso virtualbox-ext-pack

Installation works, now need to get the windows ISO

Additional installed programmes

General linux

  • vim
  • neofetch
  • curl
  • venv
  • git
  • okular
  • openVPN
  • eduVPN
  • samba
  • tailscale
  • borg
  • hugo
  • go-lang
  • ffmpeg
  • pandoc
  • magick
  • fzf
  • scp
  • rsync
  • vlc

Remaping keys keyd

git clone https://github.com/rvaiya/keyd
cd keyd
make && sudo make install
sudo systemctl enable --now keyd

Biology should run under linux

  • R
  • R Studio
  • ImageJ
  • Cell Profiler
  • csvkit
  • zotero

Windows applications running through the compatibility layer

  • GraphPad
  • FlowJo

Windows applications running through a virtual machine with windows

  • Microsoft Powerpoint
  • Microsoft Excel
  • Microsoft Word
  • Zen from ZEISS

Working with containers

  • Distrobox

Applications running in containers from distrobox(?)

  • R for bioinformatic (conductor)
  • R studio
  • brave
  • OBS
  • Audacity
  • yt-dlp

Things which need to be working

Printing

Using the local NAS

Email client

Video-conferencing

Audio

Had a bad sound quality when recording, got fixed by

  • reducing the microphone input to 30%
  • adding a filtering out module

This was initially done using commands from terminal, to reduce mic gain, recording sound and replaying it:

arecord -f cd test.wav
aplay test.wav
alsamixer # this enables changing the mic gain

Then i tried easyeffects, did not really work
Settled on using the pipe-wire modules running as a service(??)

[Unit]
Description=Microphone noise and echo cancel fix
After=pipewire.service pipewire-pulse.service wireplumber.service

[Service]
Type=oneshot
ExecStart=/bin/bash -c 'sleep 8 && pactl unload-module module-echo-cancel 2>/dev/null; pactl load-module module-echo-cancel aec_method=webrtc source_name=mic_clean sink_master=alsa_output.pci-0000_00_1f.3.analog-stereo use_master_format=1 && pactl set-default-source mic_clean && pactl set-default-sink alsa_output.pci-0000_00_1f.3.analog-stereo && pactl set-source-volume alsa_input.pci-0000_00_1f.3.analog-stereo 30%'

[Install]
WantedBy=default.target

into:

nano ~/.config/systemd/user/micfix.service

needs enabeling and starting the service

sudo systemctl enable micfix.service
sudo systemctl start micfix.service

Works well, works with obs and works for videoconferencing too

- Microsoft Teams

runs well with Teams for linux snap installed

Google meet

runs well from the browser

  • Zoom

Important fuckup lesson installing qcad from .run file

  1. Downloaded the qcad installer from the website

  2. Run it using sudo bash qcad...run

  3. Lost all icons and terminal

  4. needed to start terminal with Ctrl+Alt+F3

  5. By switching between terminal and gnome desktop Alt+F2 installed the icons again

This is the file I run in the terminal

#!/bin/bash

sudo update-mime-database /usr/share/mime
sudo gtk-update-icon-cache -f /usr/share/icons/hicolor
sudo update-desktop-database

NOTE:
Never run installation file with .run with sudo privileges and check if it exists in a repository native to ubuntu

System Backups

Installed timeshift, not used yet

Timeshift

Is installed set to back up bi-weekly

List snapshots

sudo timeshift --list

See configuration

cat /etc/timeshift/timeshift.json

Restore previous snapshot

sudo timeshift --restore

prompted to select the backup with a date, and reinstalling grub, selected 0, not the second, which is a partition, not the disk
Worked well

Installed preload to speed loading of applications

installed tldr

Wineboat to run windows in a container

should be better than running windows in VM link

Set the dns to google, cloudflare to speed up internet

ipv4 and ipv6 for cat75 hotspot

Installation script