ProgrammingNotes/linux_setup_again.md at main · kbroman/ProgrammingNotes

Linux setup

I got a new linux laptop, an Oryx Pro from System76. This document describes what I did when setting it up.

(I later purchased a System76 Galago Pro; I made some changes to the instructions below, the second time around.)

(I later purchased a System76 Darter Pro (darp8); I made further changes.)

(I later purchased a newer System76 Darter Pro (darp11).)

I had them install their Pop!_OS which is basically Ubuntu but with some re-configured sessions and different choices of included apps.

Log in for the first time, creating a new account
- Set up including ability to connect google account.
- That also had an option for Microsoft Exchange, so I briefly tried to connect to the UW-Madison Office 365, but it didn't work immediately so I moved on.
- Settings: Natural scrolling for mouse and trackpad; move dock to left side and hide it
Connect to the internet (wired)
- Plugged in a cable and it just worked.
Opened firefox and logged in

Software update

sudo apt update
sudo apt list --upgradable
sudo apt upgrade

Install emacs and mg
```
sudo apt install emacs mg
```

*6. Connect to the internet (wifi), using eduroam

See https://kb.wisc.edu/helpdesk/page.php?id=25020
Eduroam Configuration Assistance Tool, which gives a python script to download

Get UW-Madison VPN working

Now using GlobalProtect, instructions at https://kb.wisc.edu/helpdesk/page.php?id=105971
- Download and extract PanGPLinux-[version].tgz from https://www.net.wisc.edu/vpn/clients/
- This gives a GlobalProtext_UI_deb-[version].deb file, to install via sudo dpkg -i GlobalProtect_UI_deb-*.deb.
- Use globalprotect launch-ui
- Use NetID and password; use [username]_1 for static IP.
- type 1 to have it push a DUO verification to your phone
- the download page wasn't working, so copied over from other computer; it asked for VPN address, which is uwmadison.vpn.wisc.edu (now using smph.vpn.wisc.edu, but won't take [username]_1 just [username])
ssh keys + connect to github
- created new ssh key
- used ssh-keygen -t ed25519
- installed xclip with sudo apt install xclip
- pasted to clipboard with xclip -sel clip < ~/.ssh/id_rsa.pub
- At github, settings -> ssh and gpg keys -> New SSH key
- Tested it out by cloning git clone git@github.com:kbroman/ProgrammingNotes
- Also add the key to bitbucket
- Trying to commit change to the repository, was reminded to set up git:
```
git config --global user.email "kbroman@gmail.com"
git config --global user.name "Karl Broman"
git config --global core.editor "mg"
git config --global core.excludesfile "/home/kbroman/.gitignore_global"
```
Install R

Install a bunch of linux stuff

sudo apt install xauth xorg libx11-dev openbox
sudo apt install libglu1-mesa-dev libfreetype6-dev
sudo apt install libtiff-dev libfftw3-dev
sudo apt install gfortran-9 libgdal-dev libproj-dev
sudo apt install libcurl4-openssl-dev libssl-dev
sudo apt install libxml2-dev libssh2-1-dev

Set up secure apt

sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9

Add the following line to /etc/apt/sources.list

deb https://cloud.r-project.org/bin/linux/ubuntu/ jammy-cran40/

Install R

sudo apt update
sudo apt install software-properties-common
sudo apt update
sudo apt install r-base r-recommended

Copy over .Rprofile and .Renviron; both needed a bit of editing
Need r-cran-sqlite?
For checking configure scripts in packages, needed sudo apt install devscripts (would get a warning otherwise)
Install some packages: tidyverse, broman, qtl, qtlcharts, qtl2, devtools
For the imager package, I got an error about X11. I ended up installing a bunch more ubuntu things. Some of these may not be necessary; was looking at what was needed for the rgl package.
In some cases, R CMD check needs checkbashisms, which is installed with devscripts:
```
sudo apt install devscripts
```
R CMD check also needed tidy, installation instructions at https://www.html-tidy.org/documentation/#building-tidy

This also required cmake:
```
sudo apt install cmake

git clone git@github.com:htacg/tidy.html5.git
cd tidy-html5/build/cmake
cmake ../..
make
sudo make install
```

Install ess and other emacs modes (mostly cloned from GitHub; all placed in ~/.emacs.d) and edit ~/.emacs file.
- ess
- magit (and dependencies dash, with-editor, magit-popup, ghub, git-modes)
- dracula-theme
- my own fork of polymode
- arduino-mode
- markdown-mode
- d-mode
- adoc-mode (for asciidoc)
- coffee-mode
- inf-ruby
- emacs-pry (another interactive ruby)
I also wanted html-helper-mode, but I've not gotten it working yet.
Install LaTeX (texlive)
- I just did plain sudo apt install texlive-full
- It hung up part-way through; got it to continue by pressing return multiple times
Install DropBox via Pop_Shop, but there are two choices and you want the one that says "Sync your files..." rather than "Access your files..."
Install SimpleNote (Pop_Shop has old version so get amd64 deb file from github)
Install Zoom via Pop_Shop
Changed hostname by editing the files /etc/hostname and /etc/hosts
- replace popos or whatever with what you want, single line in /etc/hostname and on the line with 128.0.1.1 in /etc/hosts
Connect to printer
- When I got home and connected to my home wifi, it automatically detected and added our printer. And it just worked: opened a PDF in evince and was able to print a couple of pages double-sided and in color.
Install Google Chrome
- Download from https://www.google.com/chrome/browser/desktop/index.html
- Install with sudo dpkg -i google-chrome-*.deb
- Needed libappindicator1
- Used sudo apt --fix-broken install
Connect a USB stick
- Plug into USB port and it shows up in /media/kbroman
- Before removing, use umount /media/kbroman/[drive name]
- Create a shortcut
```
ln -s /media/kbroman/BROMAN ~/Key
```
Install RStudio
- Download Ubuntu 22 .deb file from https://www.rstudio.com/products/rstudio/download
- sudo dpkg -i rstudio*.deb
- error re libjpeg62
- sudo apt install libjpeg62
- Needed to zoom in to the greatest extent or all of the dialogs were tiny
- Needed to change CRAN mirror (in Tools -> global options -> packages) away from rstudio to something with https to avoid the warning at startup

Link to pandoc and quarto that shipped with RStudio (see https://github.com/rstudio/rmarkdown/blob/main/PANDOC.md)

sudo ln -s /usr/lib/rstudio/resources/app/bin/quarto/bin/tools/x86_64/pandoc /usr/local/bin/
sudo ln -s /usr/lib/rstudio/resources/app/bin/quarto/bin/quarto /usr/local/bin/

Okular pdf reader
- sudo apt install okular
- Installs a ton of dependencies
- Make it the default app for PDFs:
  - Open folder and right click on a PDF
  - Select Properties and then the "Open With" tab
  - Choose okular and click "Set default"
- Previously got a bunch of warnings, so used this:
```
sudo apt install breeze-icon-theme elementary-icon-theme
```
- Also tried sudo apt install oxygen-icon-theme
Additional packages
```
sudo apt install gnome-tweaks
```

Create a start script that acts like open on a Mac, as a little shell script that just calls xdg-open repeatedly for each command-line argument. Placed this in ~/.local/bin

#!/bin/bash
# loop over command-line arguments and open each with xdg-open

for file in "$@"
do
    xdg-open "$file" >& /dev/null  # ">& /dev/null" to suppress all warnings
done

Get terminal to open at startup
- Super key and type "Startup"
- Click "Add"; for the command, use "gnome-terminal"
- To start at a particular size and position, use like
```
gnome-terminal --geometry=960x990+0+0
```
Testing webcam
- Look at https://help.ubuntu.com/community/Webcam
- Install cheese (it's like "photobooth" on Mac)
```
sudo apt install cheese
cheese
```
Download moneydance
- Available for linux as well as Mac :)
- Downloaded .deb file; right click and "open" in chrome when it was done downloading, and it opened Eddy, a debian package installer.
Color picker gpick, and image viewer gthumb
```
sudo apt install gpick gthumb
```
Copy stuff into .bashrc
Install some more packages with sudo apt install
- enscript (for making PS files from text files, rotated or 2 column)
- gv (ghostview, for viewing PS files)
- ubuntu-restricted-extras (allows reading DVDs etc)

Install Inconsolata font

sudo apt install fonts-inconsolata
sudo fc-cache -fv

Install a bunch more programs
- vlc (video player)
- calibre (organizes ebooks)
Install espanso (much better than autokey); customizations in ~/.config/espanso/match/base.yml
```
sudo apt install libnotify-bin
sudo apt install snapd
sudo snap install espanso --classic
espanso start
```
copy over stuff from ~/.config/espanso
Install npm and coffeescript
- sudo apt install npm
- sudo npm install -g coffeescript
- sudo npm install -g yarn
Also gistup:
- sudo npm install -g gistup
Also some others
- sudo npm install -g babel-core uglify-js uglifycss
Install ruby (not sure whether I really need this)
- sudo apt install ruby-dev (gives version 3.0.2p107; close enough?)

Install java

sudo apt update
sudo apt install default-jre default-jdk

Test that it's working:

java -version
javac -version

Install Minecraft; see https://minecraft.net/en-us/download/
- Download Minecraft.deb and install with sudo dpkg -i Minecraft.deb.
Install 1Password (needed gnupg2); download from https://1password.com/downloads/linux/
```
sudo dpkg -i 1password-latest
sudo apt install --fix-broken
```
More stuff via sudo apt install
- pdftk (pdf tools) [now it suggests pdftk-java instead)
- tried installing pdfnup but it seems it's included with texlive; actually no longer included in texlive. got it from https://github.com/rrthomas/pdfjam-extras
- handbrake (for ripping DVDs)
- clementine (music app)
- libnotify-bin (enables you to create desktop notifications with notify-send; so in R you could do like system('notify-send "R is done!"'))
- trash-cli (move files to "trash" via the command line (trash in place of rm)
Stuff I left for future:
- rclone (like rsync for cloud storage)
- filezilla (ftp client)
- pinta (like MS paint)
- gimp (like photoshop)
- inkscape (like illustrator)
- k3b (for burning CDs)
Gnome extensions
- (Can install, uninstall, and configure extensions within browser)
- Clipboard indicator (gives clipboard history)
- OpenWeather
- emoji selector (also did sudo apt install fonts-emojione)
- gtile (tile windows with a grid)
  - select window you want to resize
  - use Super-Enter (on number key pad) to open gtile
  - click one corner position and then the other on the grid
  - esc to exit
  - also use Super-Alt-[keypad numbers]
  - Disabled the "pop shell" extension (with Tile Windows); disabled it in the extensions app. Actually had to re-enable it, as when disabled, the super key stopped working
- Refresh wifi connections (adds a refresh button to the wifi connection dialog)
- AppIndicator used by dropbox, and seems to help ensure that all apps (including globalprotect) are shown in the menubar)
- Audio Output Switcher/
- system-monitor (also needed sudo apt install gir1.2-gtop-2.0, and to log out and back in again)
Install Slack from Pop_Shop Also Discord.
Set up backups
- Install Deja Dup via "Pop Shop"
- Used command-line program gnome-disks to change to name of my extra hard drive. (Select the drive, click the gears, choose "Edit Filesystem...")
- Set up Deja Dup for a daily backup of my home folder, ignoring the Downloads folder.
- Ignore the folders ~/Dropbox and ~/VirtualBox VMs and ~/ISOs
- selected to backup to local folder, and to the backup drive and a folder I created there
- need to edit /etc/fstab to get the disk to auto-mount
  - Use "Disks" app to find partition address like /dev/nvme1n1p1
  - edit /etc/fstab with a line like
```
/dev/nvme1n1p1  /media/kbroman/Broster3Backup  auto  nosuid,nodev,nofail,x-gvfs-show  0  0
```
- also setup backup with duplicati using two external drives (transfer settings to the new machine); copied over configuration from ~/.config/Duplicati/ (2.5 GB)
Copy over music
- Used rsync; issue of having spaces in paths, but can do like this (note the backslashes and quotes):
```
rsync -a "fig.local:Music/iTunes/iTunes\ Music/They\ Might\ Be\ Giants" .
```
Was looking at finding a better linux terminal, but I think the standard gnome terminal will be fine for me.
- Can open a new terminal in an additional tab with ctrl-shift-T
- Switch between tabs with ctrl-PgUp and ctrl-PgDn
- Alt-1, Alt-2, etc., to switch to a particular tab (by number, up to 9; Alt-0 for tab 10)
- See all keyboard shortcuts by going to Edit -> Preferences -> Shortcuts
Install gitg, a git GUI similar to gitx (which is Mac only)
```
sudo apt install gitg
```
Tunnelbear VPN
- sudo apt install network-manager-openvpn-gnome
- mkdir ~/.tunnelbear_config
- Grab config files and unzip to the above .tunnelbear_config directory
- Open Network settings; click plus sign by VPN and choose "Import from file"; find directory created above and select the file for the desired country. Add email address and tunnelbear password. Click "Add".
- To start/stop: turn on/off VPN in network settings via status bar in top-right of display
- To test:
  - check your IP
  - check for DNS leaks with "Extended test" at dnsleaktest.com
kmag useful for simulating color blindness: sudo apt install kmag
- It's a screen magnification tool; in menubar View → Color, you can choose different versions of colorblindness.
Regarding battery life, see this system76 article which recommends:
```
sudo apt install powertop
sudo powertop -c
sudo powertop --help=report
sudo powertop --auto-tune
sudo powertop --html=report.html
```
- Previously there was discussion of tlp but now they say it's not compatible with system76-power.
- The article also points to the tool intel_gpu_top for monitoring the integrated intel graphics. Install with
```
sudo apt install intel-gpu-tools
```
- Can check battery health with upower -d.
- Control charging thresholds with system76-power.
```
system76-power charge-thresholds 20 52
```
Made a keyboard shortcut to open toodledo.com in a web browser:
- open Settings -> Keyboard
- Scroll to the bottom of the Keyboard Shortcuts and click the +
- Create a new shortcut (I used ctrl-alt-T) with the command firefox https://toodledo.com/tasks/index.php
- Additional shortcuts:
  - navigation: move window one monitor to left/right, move window one workspace up/down, using shift+super+arrow
  - ctrl-alt-p for interactive screenshot. (screenshots saved to ~/Pictures/Screenshots)
  - super-c for calculator
No longer installing Anaconda because they changed their license.
- Just going to use the built-in python3
Installed Julia with sudo apt install julia but it had a lot of problems. So installed followed the official instructions:
```
curl -fsSL https://install.julialang.org | sh
```
This put julia in ~/.juliaup/bin/julia.

*55. Installed Jupyter

  ```
  sudo apt install jupyter
  ```

- ran R and installed `IRkernel` package and then
  `IRkernel::installspec()`

  then when running `jupyter notebook`, can click "New" and the
  options are both "Python 3" and "R"

- ran `julia` and installed IJulia to enable use in jupyter
  notebooks

  ```
  using Pkg
  Pkg.add("IJulia")
  ```

  then when running `jupyter notebook`, can click "New" and the
  options should include "Python 3", "R", and "Julia1.11.7"

Mouse acceleration (also want touchpad acceleration, but there doesn't seem to be a setting for it):

gsettings list-keys org.gnome.desktop.peripherals.mouse
gsettings list-keys org.gnome.desktop.peripherals.touchpad
sudo gsettings get org.gnome.desktop.peripherals.mouse accel-profile
sudo gsettings set org.gnome.desktop.peripherals.mouse accel-profile 'adaptive'

Can also change these settings with the gnome tweaks gui.

Setup playback of dvds

sudo apt install libdvd-pkg
sudo dpkg-reconfigure libdvd-pkg

neofetch provides system info at the command-line

Install ccache and use for compiling R

sudo apt install ccache

In ~/.R/Makevars:

CC=ccache gcc
CXX=ccache g++
CFLAGS=-DNDEBUG -fpic -g -O2 -fstack-protector-strong -D_FORTIFY_SOURCE=2
CXXFLAGS=-fpic -g -O2 -fstack-protector-strong -D_FORTIFY_SOURCE=2

Set up yubikeys as in yubikeys.md
Install speedtest with sudo apt install speedtest-cli

Install some packages for Libre Office

 sudo apt-get install default-jre libreoffice-java-common

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