linux_refresh.md

Linux refresh

My galago pro laptop froze so I did a hard reboot but it wouldn't get passed the decryption of the drive.

So I used a [live disk] of Pop!_OS 20.04 and "refreshed" the OS.

• insert USB stick with OS installed
• turn on while pressing F1
• choose firmware
• choose boot
• choose the USB
• then select to decrypt the drive and enter password
• then refresh the OS

This all worked fine, booted up normally, and all my personal stuff was still there, but all programs are gone, so I did the following slow reinstall

1. Update and upgrade

   sudo apt update
   sudo apt upgrade

2. Edit /etc/hostname and /etc/hosts

   • replace popos with what I want.
   • In /etc/hostname, it's just the one word
   • In /etc/hosts, it's on the line with 128.0.1.1

3. emacs

   sudo apt install emacs

4. R

   sudo apt install [whole bunch of libraries]
   sudo apt install libudunits2-dev libmagick++-dev
   sudo apt install qpdf
   sudo apt install libgit2-dev
   sudo apt install devscripts
   sudo apt-key [blah blah blah]
   sudo apt install r-base r-recommended

5. LaTeX

   sudo apt install texlive-full

6. node

   sudo apt install npm
   sudo npm install -g coffeescript yarn gistup babel-core uglify-js uglifycss

7. ruby

   sudo apt install ruby-dev
   sudo gem update

8. dropbox, from https://dropbox.com/install-linux

   sudo dpkg -i dropbox_2020.03.04_amd64.deb

9. simplenote, from https://simplenote.com

   sudo dpkg -i Simplenote-linux-1.17.0-amd64.deb
   sudo apt --fix-broken install

10. wanted to install libgnome2-bin for gnome-open, but it's no longer available. can instead use xdg-open which was already installed. I have a shell script start that loops over command-line arguments to open multiple files

11. gnome tweaks

    sudo apt install gnome-tweak-tool

12. bunch of stuff

    sudo apt install cheese gpick enscript gv ubuntu-restricted-extras
    sudo apt install vlc calibre handbrake gitg mg neofetch
    sudo apt install pdftk imagemagick trash-cli clementine
    sudo apt install ccache openssh-server htop

13. libnotify (desktop notifications with notify-send)

    sudo apt install libnotify-bin

    Could do like system('notify-send "R is done!"') in R

14. inconsolata font

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

15. espanso (much better than autokey); customizations in ~/.config/espanso/default.yml

    sudo apt install libnotify-bin
    sudo apt install snapd
    sudo snap install espanso --classic
    espanso start

16. playback of DVDs

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

17. LibreOffice

    sudo apt install libreoffice
    sudo apt install okular

18. moneydance

    sudo dpkg -i moneydance_linux_amd64.deb

19. Chrome

    sudo dpkg -i google-chrome-stable_current_amd64.deb
    sudo apt --fix-broken install

20. RStudio (check file download with sha256sum)

    sudo apt install libclang-dev
    sudo dpkg -i rstudio-1.3.959-amd64.deb

21. Set up backups

    • Install Deja Dup via "Pop Shop"

    • Folders to save: "Home (kbroman)"

    • Folders to ignore: Downloads, Dropbox, ISOs, and ~/VirtualBox VMs.

    • Storage Location: Local Folder, /media/kbroman/Broster2Backup/kbroman_backup

    • Needed to enter decryption password for Deja Dup (see keepassxc)

    • complaint about "broster2" vs "broster2.localdomain", but it seemed to work

    • Also want to have the drive mounted automatically. I found this post at techrepublic helpful.

      • sudo fdisk -l to find the drive

      • sudo blkid to get the UUID for the drive

      • add line to /etc/fstab

        UUID=[blah blah] /media/kbroman/Broster2Backup auto nosuid,nodev,nofail,x-gvfs-show 0 0
        

      • verify fstab with sudo mount -a

22. Tunnelbear

    • sudo apt install network-manager-openvpn-gnome
    • previous configuration files were already there, but needed to make use of them
    • Open Network settings; click plus sign by VPN and choose "Import from file"
    • needed to right-click and show hidden files, then navigated to .tunnelbear_config/openvpn and selected a file and clicked "Add"
    • need to open config and add tunnelbear email and password under "identify" tab

23. Globalprotect vpn

• 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

24. Zoom

    • Download .deb file from https://zoom.us/download
    • sudo dpkg -i zoom_amd64.deb
    • Needed to install libegl1-mesa, libgl1-mesa-glx, libxcb-xtest0; accomplished with sudo apt --fix-broken install
    • decided to remove those with sudo apt remove zoom and sudo apt autoremove and then install via "pop shop", but then needed to edit ~/.config/zoomus.conf to have autoScale=false (otherwise, text in the GUI was super small, for example chat was nearly unreadable)

25. Julia

    • downloaded the .tar.gz file with "generic linux binaries", from https://julialang.org/downloads/

    • extracted into /usr/local/

    • created symbolic link to /usr/local/src/julia-1.5.3/bin/julia in /usr/local/bin

    • 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 are both "Python3" and "Julia1.1.1"

26. Gnome extensions

    • audio switcher 40 by albertomosconi
    • clipboard indicator by Tudmotu
    • emoji selector by Maestroschan
    • gTile by scherepanov
    • OpenWeather by jens
    • system-monitor by Cerin

    For audio switcher, said it was not compatible with latest version of gnome, but was able to install via its github repository, and it seems to work fine. Cloned the repository into ~/.local/share/gnome-shell/extensions/audio-switcher@AndresCidoncha and then restarted gnome-shell and it showed up. Actually, I needed to edit metadata.json to include "42" among the `"shell-version".

    The same is true for system-monitor and emoji selector; can manually install them by downloading/installing from github and then editing the metadata.json file

27. Gnome extensions: for system-monitor, needed:

    sudo apt install gir1.2-gtop-2.0 gir1.2-nm-1.0 gir1.2-clutter-1.0

    As above for audio switcher 40, had to do a bit more work to install this, since it's not been updated for Gnome 42.

    • Downloaded zip file from GitHub.
    • extracted, entered directory, and typed make install
    • went to its directory in ~/.local/share/gnome-shell/extensions/... and edited the metadata.json file to include "42" as one of the values for "shell-version".

    In the preferences, deselected "Display icon" and selected "show tooltip", "move the clock", and "disply in the middle".

    De-selected "Display" in the "Net" tab, and de-selected "Show text" in the "Cpu" and "Memory" tabs.

28. Ability to connect to USB drive attached to a router

    sudo apt install smbclient exfat-fuse exfat-utils

    Add to [global] section of /etc/samba/smb.conf:

    client min protocol = CORE
    

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to do:

• virtual box?
• eduroam
• java
• Minecraft

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No need

• Conda was installed in ~/.anaconda3 so still there and working
• pandoc was installed with conda