ProgrammingNotes/linux_setup.md at master · eikemq/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 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.
Connect to the internet (wired)
- Plugged in a cable and it just worked.
Opened firefox and logged in
Connected to Office365
- Settings → Online accounts
- Microsoft Exchange → Add
- email = (my biostat account)
- custom: username = (my vanilla UW account, with @wisc.edu)
- custom: server = outlook.office365.com
- Use only for mail (deselect contacts and calendar)

Software update

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

Install emacs
```
sudo apt install emacs25
```
Connect to the internet (wifi), using eduroam
- Followed the instructions at https://kb.wisc.edu/page.php?id=22075
Get UW-Madison VPN working

Now using GlobalProtect, instructions at https://kb.wisc.edu/helpdesk/page.php?id=85193
- Download and extract PanGPLinux-*.tgz from https://www.net.wisc.edu/vpn/clients/.
- This gives a GlobalProtext_*.deb file, to install via sudo dpkg -i GlobalProtect_*.deb.
- First time, use globalprotect connect --portal uwmadison.vpn.wisc.edu
- Then use globalprotect connect and globalprotect disconnect.
- Use NetID and password; use [username]_1 for static IP.
ssh keys + connect to github
- created new ssh key
- 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 "emacs"
git config --global core.excludesfile "/home/kbroman/.gitignore_global"
```
Copy over stuff from my desktop
- Attached USB drive that I'd copied stuff to
- Showed up in `/media/kbroman/[drive name]
- Used rsync -a to copy stuff over
- Got a bunch of errors like "send_files failed ... Permission denied (13)"
  - No errors if I use sudo rsync
  - But then ls -l shows that the owner and group are odd for the offensive files.
  - So followed with sudo chown kbroman -R [blah]
  - Also sudo chgrp kbroman -R [blah]
  - (seems like I'm doing it wrong, but so be it)
- Afterwards, I used sudo umount /media/kbroman/KarlBkStuff (I think I maybe didn't need the "sudo".)
Set up mail in Geary
- First tried setting up gmail; authentication didn't work
- Needed to create an App-specific password; see https://support.google.com/accounts/answer/185833
- Added the UW-Madison Office365 account too:
  - "Geary" in menu bar -> Accounts -> plus sign
  - Service -> Other
  - Settings as at https://kb.wisc.edu/page.php?id=28427
- Also added my iCloud account, following instructions at https://support.apple.com/en-in/HT202304, including need to get an app-specific password at https://appleid.apple.com/account/manage
- To control default font in messages, create a file ~/.config/geary/user-message.css, for example with:
```
body {
    font-family: Inconsolata;
    font-size: 150%
}
```
Install R

See instructions at digitalocean

sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9
sudo add-apt-repository ppa:marutter/rrutter3.5
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
Also copy over .rpushpullet.json
Needed sudo apt install libcurl4-openssl-dev libssl-dev libxml2-dev libssh2-1-dev r-cran-sqlite
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.
```
sudo apt install xauth xorg libx11-dev openbox
sudo apt install libglu1-mesa-dev libfreetype6-dev
sudo apt install libtiff-dev fftw3 libfftw3-dev
sudo apt install gfortran-7
```

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
Install DropBox
- Download .deb file from https://www.dropbox.com/install-linux
- Use sudo dpkg -i dropbox_2015.10.28_amd64.deb
Install SimpleNote
- Download .deb file from https://simplenote.com
- Need dependency: sudo apt install pango1.0-0
- sudo dpkg -i Simplenote-*.deb
Install Skype
- Download .deb file from https://www.skype.com/en/get-skype/
- Need some dependencies: sudo apt install gconf-service libgconf-2-4
- Install with sudo dpkg -i skypeforlinux-64.deb
- Skype was starting automatically on restarting the computer; had to de-select an option in the settings
- FIX ME: shows up really small when screen is in high-def mode
- Camera was not working initially, but when studying it, learned about cheese (like Mac photobooth; see more below) and it worked fine. So opened skype again and found the camera was working. Not sure what changed.
- Fn-F10 toggles the camera on and off; so maybe it was off and got toggled back on?
Changed hostname by editing the files /etc/hostname and /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]
Install RStudio
- Download Ubuntu 16.04+ .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 that shipped with RStudio (see https://github.com/rstudio/rmarkdown/blob/master/PANDOC.md)

sudo ln -s /usr/lib/rstudio/bin/pandoc/pandoc /usr/local/bin
sudo ln -s /usr/lib/rstudio/bin/pandoc/pandoc-citeproc /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"

Was getting a bunch of warnings. Got some of them to go away with:

sudo apt install breeze-icon-theme elementary-icon-theme

But some remaining warnings:

Invalid Type= "Scaleable" line for icon theme:  "/usr/share/icons/pop-os-branding/round-logos/16/"
Invalid Type= "Scaleable" line for icon theme:  "/usr/share/icons/pop-os-branding/round-logos/22/"
Invalid Type= "Scaleable" line for icon theme:  "/usr/share/icons/pop-os-branding/round-logos/24/"
Invalid Type= "Scaleable" line for icon theme:  "/usr/share/icons/pop-os-branding/round-logos/32/"
Invalid Type= "Scaleable" line for icon theme:  "/usr/share/icons/pop-os-branding/round-logos/48/"
Invalid Type= "Scaleable" line for icon theme:  "/usr/share/icons/pop-os-branding/round-logos/64/"
Invalid Context= "stock" line for icon theme:  "/usr/share/icons/ubuntu-mono-dark/stock/16/"
Invalid Context= "stock" line for icon theme:  "/usr/share/icons/ubuntu-mono-dark/stock/22/"
Invalid Context= "stock" line for icon theme:  "/usr/share/icons/ubuntu-mono-dark/stock/24/"
Invalid Context= "stock" line for icon theme:  "/usr/share/icons/ubuntu-mono-dark/stock/32/"
Invalid Context= "stock" line for icon theme:  "/usr/share/icons/ubuntu-mono-dark/stock/48/"
Invalid Context= "stock" line for icon theme:  "/usr/share/icons/ubuntu-mono-dark/stock/64/"
Invalid Context= "stock" line for icon theme:  "/usr/share/icons/ubuntu-mono-dark/stock/128/"
Icon theme "Mint-X" not found.

Tried also sudo apt install oxygen-icon-theme
Tried installing mint themes

Additional packages
- libgnome2-bin (for gnome-open which acts like open on a Mac)
- gnome-tweak-tool
Create a start script that acts like open on a Mac, as a little shell script that just calls gnome-open repeatedly for each command-line argument. Placed this in ~/.local/bin
```
#!/bin/bash

for file in "$@"
do
    gnome-open "$file"
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 117x57+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
```
sudo apt install gpick
```
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 programms
- vlc (video player)
- calibre (organizes ebooks)
- digikam (organizing photos)
- autokey-gtk (desktop automation)
Autokey had some wrinkles on my new system, running Pop OS 18.10. Added a ppa for autokey:
```
sudo add-apt-repository ppa:sporkwitch/autokey
```
This worked fine on Pop OS 18.04, but on Pop OS 18.10, you need to go in and edit the record, replacing cosmic (nominally for 18.10) with bionic (for 18.04). There was a file in /etc/apt/sources.list.d named sporkwitch-ubuntu-autokey-cosmic.list; changed the cosmic in its name and contents to bionic and after that all was well.
Install npm and coffeescript
- sudo apt install npm
- sudo npm install --global coffeescript
Also gistup:
- sudo npm install -g gistup
Install ruby (not sure whether I really need this)
- sudo apt install ruby-dev (gives version 2.3.3; close enough?)
Install python-dev (not sure whether I really need this)
- sudo apt install python-dev python3-dev
Install peek (screen recording)
```
sudo apt install peek
```

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 keepassXC
```
sudo apt install keepassxc
```
(this took me a while because I kept typing keypassxc rather than keepassxc)
Mount exFAT drive connect to a router
- Install smbclient and exFAT stuff
```
sudo apt install smbclient exfat-fuse exfat-utils
```
- List volumes
```
smbclient -L //192.168.0.3
```
- Mount the drive...was trying the following:
```
sudo mount -t cifs -o username=kbroman //192.168.0.3/volume10/ /media/kbroman
```
  but got an error like one of these two:
```
mount error(115): Operation now in progress
mount error(112): Host is down
```
- However, I was able to connect using the GUI file browser. Clicked "Other locations" and then typed smb://192.168.0.3
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)
- pinta (like MS paint)
- handbrake (for ripping DVDs)
- gimp (like photoshop)
- inkscape (like illustrator)
- shutter (image capture) [no longer available]
- k3b (for burning CDs)
- banshee (music app)
- rclone (like rsync for cloud storage)
- filezilla (ftp client)
- 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)
Gnome extensions
- (Can install, uninstall, and configure extensions within browser)
- Clipboard indicator (gives clipboard history)
- OpenWeather
- Audio Switcher
- system-monitor (also needed sudo apt install gir1.2-gtop-2.0, and to log out and back in again)
- 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
- hide activities button
- Refresh wifi connections (adds a refresh button to the wifi connection dialog)
- Media player indicator
- log out button
Install Slack
- Downloaded .deb file; opened it from Chrome to install.
Install Corebird, twitter client
- Just used Pop shop (the software installer for Pop!_OS
Installed WINE and PlayOnLinux in the same way as Slack and Corebird. Seems like if I use PlayOnLinux, I don't really need to have installed WINE. And it seems that Office365 (Office 2016) can't be installed with either at this point, so I don't really have any use for these.
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
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" .
```
- In banshee: Tools -> Rescan Music Library
- .m4a files seem to work just as well as .mp3
autokey is great, but after a day or so it seems to start using up 100% of a CPU. In short term, seems like I could just use a cron job to re-start it every evening.

So I made a shell script with
```
pkill autokey
sleep 10
autokey-gtk >& /dev/null &
```
I then used crontab -e to add to my crontab file:
```
0 2 * * * /bin/bash [path_to_shell_script]
```
VirtualBox and Windows + Office365 See https://www.extremetech.com/computing/198427-how-to-install-windows-10-in-a-virtual-machine
- Download Windows 10 from https://www.microsoft.com/en-us/software-download/windows10ISO
- Download VirtualBox from https://www.virtualbox.org/wiki/Downloads
  - Add to /etc/apt/sources.list
  - Register Oracle public keys
  - sudo apt install virtualbox-5.2
  - sudo apt install dkms
- Start virtualbox, create new Windows10 machine, adjust memory, disk size, connect to the windows ISO, and adjust display stuff
- Then start the virtual machine to install windows10. I said I had no product key, chose Windows 10 Home edition, and said something like fresh install
- The thing was deathly slow. Searched for solutions and found this: http://blog.jdpfu.com/2012/09/14/solution-for-slow-ubuntu-in-virtualbox
  - Followed these instructions, except for Network when I tried "Bridged" I didn't get a network connection so I switched back to the default "NAT" and that worked
  - Gave the machine 150 GB harddrive (dynamically sized) and 8192 MB RAM. And went for 2 CPUs
  - Once windows was up and running, and changed the VM display to "scaled" and then within windows I changed the screen resolution to 1600x1200. Seems to work better.
- Within Windows, installed Office365 (by going to office365.com and then logging in with my NetID from UW-Madison), R, Rtools, RStudio, and a bunch of R packages (devtools + tidyverse first)
- Need to install "Guest additions". While the virtual box is running, you need the VirtualBox tool bar to be showing (it won't if you're using a "scaled" window, it seems). In the "Devices" menu there's an option to "insert guest additions CD". Then within windows, click on the CD and install the software.
- Having installed the guest additions, you can share a linux folder with windows. First create a folder in your home directory that you will share. Then in VirtualBox settings, go to "Shared Folders" and right-click on "Machine Folders" and select "Add shared folder" and enter the path to the folder.
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
```
Installed Thunderbird because Geary seems simplistic. Also installed the Lightning calendar add-on (sandwich button -> Add ons -> Get add ons -> search for lightning). Also installed the add on "Provider for google calendar".

For read-only access to a google calendar, use ICS. Go to the calendar's settings; the iCal URL is the ICS URL.

For access to Apple Calendar, go to icloud and get the url for a particular calendar, then in thunderbird, under calendars, right-click and select "New calendar" and then "On network"; then give it a name and paste in the location.

(Note: for iphone/ipad access to shared google calendars, go to https://calendar.google.com/calendar/iphoneselect. Also note: work calendar is at https://outlook.office365.com/calendar/.)
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
To try to avoid continual (but irregular) login problems, we switched from gdm3 to lightdm as the "display manager". See the lightDM wiki.
```
sudo apt install lightdm
sudo dpkg-reconfigure lightdm
```
It asks you to choose between gdm3 and lightdm; choose lightdm.

At login, there's a startup sound that I don't like. Mute the speaker on that screen; that setting seems to persist between logins.

I also don't like the background; especially the grid of dots.

I edited /usr/share/glib-2.0/schemas/com.canonical.unity-greeter.gschema.xml to change "draw-grid" to false and to change background to /usr/share/backgrounds/yosemite....jpg (a file I'd copied there from ~/Pictures/Wallpapers. Then ran sudo glib-compile-schemas /usr/share/glib-2.0/schemas/
OpenRefine
- Download .tar.gz file from http://openrefine.org/download.html
- Extract and move to `~/.local/
- Create a shell script, as ~/.local/bin/refine`, containing:
```
#!/bin/bash

cd /home/kbroman/.local/openrefine-2.8
./refine
```

DB Browser for SQLite

Download .tar.gz file from https://sqlitebrowser.org/
Extract and change into directory

Need to install a bunch of stuff:

sudo apt install cmake
sudo apt install qt5-default qttools5-dev qttools5-dev-tools
sudo apt install libsqlite3-dev libantlr-dev libqscintilla2-qt5-dev

build and install
```
cmake .
make
sudo make install
```

kmag useful for simulating color blindness: sudo apt install kmag

Regarding battery life, see this system76 article which recommends:

sudo apt install tlp tlp-rdw --no-install-recommends
sudo tlp-stat

sudo apt install powertop
sudo powertop -c
sudo powertop --help=report
sudo powertop --auto-tune

Configure tlp by editing /etc/default/tlp.

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
I installed Anaconda by downloading the .sh script from its web site and running bash Anaconda-*.sh. I chose to install it in ~/.anaconda3 and had it modify my .bashrc file.
Installed Julia with sudo apt install julia but this gave version 1.0.1 which seems really old (current is 1.1 and long-term support release is 1.0.3). So I instead
- downloaded the .tar.gz file with "generic linux binaries", from https://julialang.org/downloads/
- extracted into /usr/local/src
- created symbolic link to /usr/local/src/julia-1.1.0/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"

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.

Installed the mini-emacs application, mg via
```
sudo apt install mg
```
Made it the default for git commit messages by editing ~/.gitconfig. More than sufficient for that, and way faster to start up.

Setup playback of dvds

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

Install ccache and use for compiling R
- sudo apt install ccache
- In ~/.R:
Additional possible gnome extensions:
- Places status indicator
- Pomodoro timer

Stuff that didn't work:

Set up Apple magic mouse via bluetooth settings
- It came up with a weird name; I had to go back to Mac and pair it and then rename it and then back to pair again with the linux laptop
- Scrolling speed was deathly slow. Followed instructions at https://askubuntu.com/a/262730. In particular, I used:
```
options hid_magicmouse scroll-speed=60 scroll-acceleration=2
```
- FIX ME: want scrolling to go in the opposite direction
- FIX ME: after restarting and messing with the trackpad (not sure what I did), the mouse stopped working.
Try to get Apple Magic Trackpad working
- Looking at Touchégg
```
git clone git://github.com/JoseExposito/touchegg.git
sudo apt-get build-dep touchegg
qmake
make
sudo make install
```
- FIX ME: At present, it's not working
- Removed Touchégg with sudo make uninstall

Problems

I hade some gnome extensions that weren't working but that I couldn't delete. Followed these instructions:

Look in ~/.local/share/gnome-shell/extensions and also /usr/share/gnome-shell/extensions
Delete the directories for extensions you want to get rid of
Reload gnome-shell by pressing ALT+F2, typing r, and pressing ENTER.

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