Linux Mint

This is a brief introduction how to get started with Linux Mint for data science and academic research.

To see your current version of Mint, use in the terminal:

cat /etc/os-release

Programming Tools

Install R

Install R via the terminal:

sudo apt update

sudo apt-get install r-base

You can test R by simply:

R

install.packages("ggplot2")

q()

Install Rstudio

get the name of the last Ubuntu/Debian Rstudio version at https://rstudio.com/products/rstudio/download/#download Do a right-click, copy file location.

wget https://download1.rstudio.org/desktop/bionic/amd64/rstudio-1.3.1093-amd64.deb

If needed to install gdebi:

sudo apt install gdebi

Then install the deb-file:

sudo gdebi rstudio-1.3.959-amd64.deb

The R-file here installs all basic needed packages. You can open and run it in Rstudio. In case of errors, you can use:

apt install r-cran-stringi

And if this results in errors, then try:

sudo apt purge -y r-base r-base-core r-base-dev

sudo apt install -y r-base r-base-core r-base-dev

! For Mint you will need following for installing devtools:

sudo apt install libxml2-dev

sudo apt install libssl-dev

sudo apt install libcurl4-openssl-dev

Install pyCharm

For pyCharm, do not use the Software Manager, as this version is often outdated. Use the jetBrains website instead, and preferrably install via the tar.

Go to your download location and then use the recommended installation location according to the filesystem hierarchy standard (FHS). --> is /opt. To install PyCharm into this directory, enter the following command:

sudo tar xzf pycharm-*.tar.gz -C /opt/

Switch to the bin subdirectory with the terminal.

cd /opt/pycharm-*/bin

Run pyCharm from this directory.

sh pycharm.sh

After a graphical configuration setup, you get the standard IDE. If an error occured because the Python interpreter could not be installed, then do:

• Configure Python interpreter
• Add interpreter
• System interpreter
• Select the latest Python version
• OK

You'll notice none of the frequent packages are installed (try import numpy). First install pip in the terminal:

sudo apt update

sudo apt install python3-pip python3-pip

Then install the package in the terminal:

pip3 install numpy

Other useful packages to install are:

• numpy
• pandas
• matplotlib
• bs4

You can now see the package installed in pyCharm Go to File > Settings > Project > Python interpreter

To add a desktop shortcut:

• Desktop > RM > New Launcher
• Command > Browse > go to /opt/pycharm*/bin/pycharm.sh
• Command: type sh before the path
• Fill in Name, Comment, Picture as you like
• Say Yes to add to Menu as well.

In these settings, the shortcut for executing one line of code can be set as well: File > Settings > Keymap > Other > Execute selection --> set to Ctrl+Enter or ²

Installing additional packages can now also be done in the terminal in pyCharm.

For your information: The alternative install of pyCharm via snap is no longer supported from Mint 20 onwards. Yes, there is a workaround and this gives away admin privileges to snap.

Resource Management Tools

Install Smartgit

SmartGit is a version control management software. The flatpack version has the most readable interface.

sudo apt-get install gdebi

wget https://www.syntevo.com/downloads/smartgit/smartgit-20_2_2.deb

sudo gdebi smartgit-20_2_2.deb

You need to install git as well:

sudo apt-get install git

sudo add-apt-repository ppa:git-core/ppa

sudo apt update; apt install git

Alternatively, via tar.gz bundle...

First, unpack the downloaded file into a directory of your choice (don't unpack over an existing installation!):

tar xzf <smartgit*.tar.gz>

start SmartGit: invoke

bin/smartgit.sh

create SmartGit menu item: invoke

bin/add-menuitem.sh

remove SmartGit menu item: invoke

bin/remove-menuitem.sh

SmartGit authentication:

Edit - Preferences - Hosting Providers. On your Hosting Providers, click add. Select hosting (Github), click Generate API Token automatically opens browser and generates token then copy go back to your SmartGit then paste the token and finally click add and OK.

(OR Install Gitkraken)

Gitkraken is an alternative for smartgit. It can be installed via the software manager or via:

wget https://release.gitkraken.com/linux/gitkraken-amd64.tar.gz

sudo tar -xvzf gitkraken-amd64.tar.g

(Repair broken packages)

Not all goes perfect the first time, so in case something brakes down:

sudo apt update --fix-missing

sudo apt install -f

Datebase Tools

Install DBeaver

DBeaver is a database explorer, which visualises all accessible tables via the database scheme. It also enables easy querying of different sources. Supports MySQL, MariaDB, SQLite, Oracle, DB2, SQL Server, Sybase, MS Access, Teradata, Firebird and Derby.

First update the linux:

sudo apt update

sudo apt upgrade

DBeaver requires java:

To check the current version:

java --version

To install Java:

sudo add-apt-repository ppa:linuxuprising/java

sudo apt install oracle-java12-installer

Install DBeaver now:

sudo apt update && sudo apt install dbeaver-ce

Test DBeaver:

sudo apt install mariadb-server

sudo mysql -u root -p

CREATE DATABASE dbeaver;

GRANT ALL PRIVILEGES ON dbeaver.* TO 'dbeaveruser'@'localhost' IDENTIFIED BY 'dbeaverpss';

FLUSH PRIVILEGES;

exit;

Help with System issues

Ethernet card

To see all cards:

lshw -C network

To see if your card is up:

inxi -Fxxxz

You'll see the logical name e.g. eno1. To activate your card:

sudo ifconfig eno1 up

or as a selection:

lspci -nn|grep Ethernet

To restart network manager:

sudo service network-manager restart

or

sudo systemctl restart NetworkManager.service

or

sudo nmcli networking off

sudo nmcli networking on

or

sudo ifdown -a && sudo ifup -a

or graphically with

nmtui

Put driver together with kernel

Download the driver from https://downloadcenter.intel.com/download/15817, currently 3.2.4.2 (as shown in lshw -C above)

make install in the src folder

rmmod e1000e

modprobe e1000e

and to make the new driver survive a reboot update-initramfs -u

Belgium eID

Copy link from website https://eid.belgium.be/en/linux-eid-software-installation

Then execute:

wget https://eid.belgium.be/sites/default/files/software/eid-archive_2020.2_all_2.deb

Then check the PGP key and install

Update via:

sudo apt-get update

sudo apt-get install eid-mw eid-viewer

Remote access

To install TeamViewer on a 64 bit system:

wget https://download.teamviewer.com/download/linux/teamviewer_amd64.deb

sudo dpkg -i teamviewer_amd64.deb

If you have errors, try first:

sudo apt-get install -f

To run:

teamviewer

Community

https://community.linuxmint.com/software

Fast terminal commands

Search files

FIND

find

-iname <file*>

find

-name <file*>

LOCATE

Update search DB:

sudo updatedb

Info on DB:

locate -S

basic search:

locate <part_file_name>

lower and uppercase search:

locate -i <filename*>

Exactly meeting the name:

locate -r /findfile$

Count number of hits:

locate -c <part_file_name>

Open a file (with default program) via terminal

Use tab for autocomplete

xdg-open

Terminal variables

fl = $(locate "keyword1keyword2*")

echo "$fl"

xdg-open $fl

Update

You can set updates to install automatically in the update manager, but if you are solving a problem, these commands can help to start with:

sudo apt update

sudo apt upgrade

Productivity Tools

Create pop-up message with a timer in terminal

sleep 15m; zenity --question --text "Time to go!"; echo $?

GIT in terminal

sudo apt-get install git

f.lux

Latest version: https://github.com/xflux-gui/fluxgui Install instructions:

sudo apt-get install python3-pexpect python3-distutils gir1.2-appindicator3-0.1 gir1.2-gtk-3.0

Download fluxgui, install system wide

cd /tmp

git clone "https://github.com/xflux-gui/fluxgui.git"

cd fluxgui

./download-xflux.py

sudo ./setup.py install --record installed.txt

Run flux

fluxgui

yEd Graph Editor

Download on https://www.yworks.com/products/yed/download#download

Change permissions of the .sh file before installing it:

chmod +x yEd-3.17.2_64-bit_setup.sh

./yEd-3.17.2_64-bit_setup.sh

AutoKey GTK

Google Translate

Install NodeJS:

curl -sL https://deb.nodesource.com/setup_14.x | sudo -E bash -

sudo apt-get install -y nodejs

Install Yarn

curl -sS https://dl.yarnpkg.com/debian/pubkey.gpg | sudo apt-key add -

echo "deb https://dl.yarnpkg.com/debian/ stable main" | sudo tee /etc/apt/sources.list.d/yarn.list

sudo apt-get update

sudo apt-get install yarn

Install DeepL Translator CLI

yarn global add deepl-translator-cli

deepl --version oi

deepl translate -t 'DE' 'How do you do?'

echo 'How do you do?' | deepl translate -t 'DE'

deepl detect 'Wie geht es Ihnen?'

deepl -h

deepl translate -h

deepl detect -h

Printer

When CUPS is giving problems:

sudo systemctl stop cups-browsed

sudo systemctl disable cups-browsed

Download driver from https://www.dell.com/support/home/en-us/drivers/driversdetails?driverid=074w2&oscode=1204a&productcode=dell-e525w-printer

unzip Printer_E525w_Driver_Dell_A00_Linux.zip

sudo apt install ./dell-color-mfp-e525w_1.0-28_all.deb