Linux notes

This is a nice lightweight environment once you have adjusted the shortcuts to be more familiar. In addition to the Control Center, there is mate-tweak which provides a GUI for additional customisation.

• See these notes on how to set up a University of Melbourne Researcher Desktop.

1. Create a Linux Researcher Desktop via the Research Computing Portal and make a note of the IP address of the server.
2. Add the host to your SSH configuration, ~/.ssh/config, using the example below. SSH into the server with ssh <hostalias>.
3. Run sudo apt update and sudo apt upgrade and install the following packages: htop screen tree.
4. Install Miniconda using the instructions on the Anaconda website. My conda notes might be useful at this point. (Basically, this is running their shell script then running the initialisation command.)
5. Configure your file manager to connect to the server. For GNOME files you can ask it to connect to sftp://hostalias. In ~/.bashrc add prompt configuration below.

Host myDemoHost
        Hostname vm-XXX-XX-XXX-XX.desktop.cloud.unimelb.edu.au
        User azarebski

In this example XXX-XX-XXX-XX is the IP address of the host.

PS1='${debian_chroot:+($debian_chroot)}\[\033[01;32m\]\h\[\033[00m\]:\[\033[01;34m\]\W\[\033[00m\]\[\033[1;31m\](Hostalias)\[\033[0m\]\$ '

There is a GUI called Dconf Editor which makes editing your configuration much easier than editing files.

The do-release-upgrade command can be used to run an update. First run do-release-upgrade -c to check if there is an available upgrade. When asking to upgrade you might get an error message saying that there are packages that need to be upgraded first. Comments on the internet make this sound scary, but when I encountered this I just needed to remove an old program I didn't need which refused to upgrade and then everything worked fine.

To zip the directory foo into a file called foo.zip run the following

zip -r foo.zip foo

To unpack a zipped up tarball use the following

tar -zxvf foobar.tar.gz

LibreOffice Draw is surprisingly good for editing and annotating PDFs!

pdftk is a great tool for working with the pages of a PDF. The man page has some useful examples.

To install the Monaco font there is a useful stackexchange post linking to a script. For the Source Code Pro font, I have a script in my dotfiles repository. If the method above does not work, you can download the TTF file into ~/.fonts/ and then run sudo fc-cache -fv and it should work after that.

You can download all of the TFF files and then drag them into the Font Viewer application that comes with Ubuntu. Then there is a button to click which should install the font.

According to Wikipedia "[t]he Filesystem Hierarchy Standard (FHS) is a reference describing the conventions used for the layout of a UNIX system." The standard is maintained by the Linux foundation and the main directories to know about are is well documented. If you are unsure of where something should be located, this would be a good place to go for guidance.

A file can be read from, r, written to, w, or executed, x. The permission to carry out these actions is specified for the owner of the file, members of the group, and other users. For example, rwxr-x--- means the owner has read write and execute, other group members can read and execute and others cannot read, write or execute. The chmod functions is used to change the permissions.

chmod 750 foo.sh  # makes foo.sh rwxr-x---

The screen program helps you manage long-running tasks, it is particularly helpful if you need to be able to disconnect from the task and come back later without interrupting the program in the mean time.

• Start a session with screen.
  • use screen -S <session_id> to name a session
• Detach from a session with C-a d.
• Kill a session with C-a k.
• Get help on available keybindings with C-a ?.
• screen -ls lists sessions.
• Re-attach to a session with screen -r (screen -r <session_id> if there is ambiguity.)

To run the VPN GUI in Ubuntu

/opt/cisco/anyconnect/bin/vpnui

Then you need to connect to vpn.ox.ac.uk with the zool[0-9]{4} username.

This information is available from Settings > Network and then click on the button (cog) next to the wired connection.

Alternatively, you can use ifconfig at the command line which will print out a bunch of network information and you should be able to spot a sensible IP address among it.

Here is an example of a script I used to copy files from my desktop at work to my laptop.

LOCAL_DIR=out/result-v2
REMOTE_DIR=/home/aez/projects/example/$LOCAL_DIR
REMOTE_HOST=zool

scp $REMOTE_HOST:$REMOTE_DIR/*{html,png} $LOCAL_DIR/

Note that this makes use of the zool alias from above.

ln -s /path/to/file /path/to/symlink

Note that these paths need to be full paths otherwise the file wont get found.

grep [OPTION]... PATTERNS [FILE]...

The package inotify-tools provides the inotifywait command which will run a command after an event relating to a file occurs.

The xrandr command allows you to specify the configuration of the monitor/s. There is a GUI for xranrd called arandr which may substantially simplify the process of configuring the monitor. Once you have a configuration you are happy with, you can use arandr to write it to file. By default these configurations will be stored in the ~/.screenlayout directory.

When I first installed Ubuntu, the windows were all far too small. Running xrandr -s 1440x900 was much more suitable for a 14 inch laptop. Update: all of a sudden the display on my second monitor went strange. I tried use xrandr to set the display to 1440x900 but it didn't appear as one of the options. The solution was to run the following command.

$ cvt 1440 900
# 1440x900 59.89 Hz (CVT 1.30MA) hsync: 55.93 kHz; pclk: 106.50 MHz
Modeline "1440x900_60.00"  106.50  1440 1528 1672 1904  900 903 909 934 -hsync +vsync

The output of this is then what you are meant to use to fix the display by running the following

$ xrandr --newmode "1440x900_60.00"  106.50  1440 1528 1672 1904  900 903 909 934 -hsync +vsync
$ xrandr --addmode DP-1 "1440x900_60.00"
$ xrandr -s 1440x900

They say for this to persist, you need to add those lines to a file at /etc/profile.d/external_monitor_resolution.sh but I haven't tried this yet.

The caps lock key is solid real-estate but is wildly underutilised, and control is more useful than alt a lot of the time. Adding the following to a file called Xmodmap and then run it with xmodmap <path/to/Xmodmap>. It will switch escape and caps lock and the right alt key will become another control key.

clear lock
keycode 9 = Caps_Lock
keycode 66 = Escape

remove Control = Control_R
remove Mod1 = Alt_R
keycode 105 = Alt_R
keycode 108 = Control_R
add Control = Control_R
add Mod1 = Alt_R

Use nmcli device wifi list to get a list of all the available wifi networks. Note the SSID of the network you want to connect to.

nmcli device wifi connect <SSID> password <password>

The following will print, in human readable form, the size of all sub-directories of foobar recursively up to 2 levels deep.

du -h --max-depth=2 foobar

Although, unless you are limited to a terminal, something like disk usage analyzer GUI is a much better solution.

The Disk Usage Analyzer provides an interactive tree map of disk usage which makes it easy to find large files on your machine.

The htop command provides an interactive process viewer. Make sure that you keep the F6 and F9 keys unbound if you want to use this because they are used to sort the processes and kill them respectively. When killing processes, you probably want to use signal number 9.

Definitely want to use this with colour!

tree -C <filepath>

Be careful though, if you use this without thinking you can get a ridiculous amount of material printed out. There is a command line option for ignoring particular directories.

The rsync utility provides a way to synchronise the files from one place to another. There is a useful introduction to rsync here (and a simpler one here.) Commands will look like the following:

rsync [OPTIONS] SRC DEST

My use case for this is keeping the same set of PDFs on multiple machines. The following command will make a copy of all the files on zool in the library to my local library.

rsync --verbose --progress --stats --compress --rsh=/usr/bin/ssh \
      --recursive --times --perms --links \
      zool:/home/aez/Documents/library/* /home/aez/Documents/library/

Here we have used zool which is a host described in ~/.ssh/config . I have a script to synchronise my libraries across machines.

To avoid confusion between the .bashrc and .bash_profile you can just add the following to .bash_profile and then you'll have the same script evaluated regardless.

if [ -f $HOME/.bashrc ]; then
    source $HOME/.bashrc
fi

By default, tab completion is case sensitive, to fix this add the following line to the file /etc/inputrc.

set completion-ignore-case on

If you find that audio comes out stuttered, try restarting Bluetooth with the following command:

sudo service bluetooth restart

You may have to repeat this process a few times, but it seems to work eventually. Alternatively, you may need to add the following line to /etc/modprobe.d/alsa-base.conf before restarting the service for this to work:

options snd-hda-intel model=generic

The program Gpick displays the hexcode of the pixel under the cursor.

To open nautilus without the desktop fuss use nautilus --no-desktop

1. Open Software & Updates.
2. Navigate to the Other Software tab.
3. Select and Remove the desired PPAs.

Note that the <path/to.deb> needs to actually be a path, e.g. ./foo.deb not foo.deb.

sudo apt install <path/to.deb>

This is a new way to distribute packages: download the file, make the file exectuble, and run it. Done! If you are concerned about what the program might do, there are sandboxes available, for example Firejail. Inkscape is available as an appimage.

There are instructions on how to install this program here. Use youtube-dl --help to get help on usage.

To run comands conditional upon the presence or absence of a directory, consider the following example

if [ -d "foobar" ]; then
    echo "There is a directory called foobar"
    exit 0
fi

if [ ! -d "foobar" ]; then
    echo "Could not find directory: foobar"
    exit 1
fi

As an example, here is a simple shell script

#!/bin/sh
# demo.sh
echo "foo: $2"
echo "bar: $1"

Running it we get the following

$ ./demo.sh hello world
foo: world
bar: hello

Here is a silly little example of how to loop over an explicity list of strings.

for month in jan feb mar;
do
    cat foo-$month.csv
done

Alternatively, one can construct the list programmatically for example with for x in * which would be used to iterate over all files in the current directory or for x in $* which would iterate over all the command line arguments.

Here is another example of iterating over some integers and print 1, 2, 3 to standard out.

for ix in `seq 1 3`;
do
    echo $ix
done

The following helps you to quickly download a bunch of crosswords and compile them into a single PDF. We use the sleep command to be kind to the Guardian servers.

for i in $(seq 1140 1165)
do
    sleep 2                     # be nice!
    google-chrome --headless --disable-gpu --print-to-pdf https://www.theguardian.com/crosswords/quiptic/$i/print
    mv output.pdf quiptic-$i.pdf
done

echo "==========================================================="
echo ""
echo "Guardian - Quiptics"
echo "-------------------"
echo ""
echo "Use the following command to compile the quiptics into a"
echo "single pdf after you have removed any broken ones by hand:"
echo ""
echo "pdftk quiptic-* cat output quiptics.pdf"
echo ""
echo "==========================================================="