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Settings_Linux

Useful bash scripts and settings for managing a Linux server

Other programs installed after upgrade to Ubuntu 18.04 LTS for chalkboard

Last Update 2018-12-14 by Adam Lu

Installed git (already done)
```
  sudo apt-get install git
```
Installed the modified VI editor:
```
  sudo apt-get install vim
```
Installed plugins for gedit:
```
  sudo apt-get install gedit-plugins
```
Changed the default editor to vim-basic with the command
```
  select-editor
```
Installed lightdm:
```
  sudo apt-get install lightdm
```
Changed default display manager from gdm3 to lightdm (gdm3 is super slow on chalkboard)
Installed trash-cli:
```
  sudo apt-get install trash-cli
```
Installed htop:
```
  sudo apt-get install htop
```
Installed atop:
```
  sudo apt-get install atop
```

Installed the XFCE desktop

  sudo apt-get install xfce4
  sudo apt-get install xfce4-goodies

Installed the MATE desktop environment:
```
  sudo apt-get install mate
```
Installed GNOME panel:
```
  sudo apt-get install gnome-panel
```
Installed VNC Server:
```
  sudo apt-get install vnc4server
```

Installed X2Go Server

  sudo apt-add-repository ppa:x2go/stable
  sudo apt-get update
  sudo apt-get install x2goserver
  sudo apt-get install x2goserver-xsession

Installed ntp (Network Time Protocol):
```
  sudo apt-get install ntp
```
Installed curl:
```
  sudo apt-get install curl
```

Installed system-config-samba:

  sudo apt-get install system-config-samba
  sudo touch /etc/libuser.conf

Installed rename:
```
  sudo apt-get install rename
```
Installed ncdu:
```
  sudo apt-get install ncdu
```
Installed symlinks:
```
  sudo apt-get install symlinks
```
Installed inotify-tools (for inotifywait):
```
  sudo apt-get install inotify-tools
```
Installed the synaptic package manager:
```
  sudo apt-get install synaptic
```
Installed at (for at and atq):
```
  sudo apt-get install at
```

Installed png libraries per these instructions:

  sudo apt-get install libpng-dev
  sudo apt-get install zlib1g-dev

Installed pdftk with the script pdftk_installer.sh taken from this thread
```
  sudo bash pdftk_installer.sh
```

Installed mailutils for the mail command:

  sudo apt-get install mailutils

Used the domain name “chalkboard.com”

One must use the mail command this way:

  # Get the server name
  serverName=$(hostname)
    
  # Get the user name
  userName=$(whoami)
    
  # Send mail
  mail -r "${userName}@${serverName}.com" 'markbeen@virginia.edu'

Installed make
```
  sudo apt-get install make
```
Installed the GNU C Compiler
```
  sudo apt-get install gcc
```
Installed the GNU C++ library:
```
  sudo apt-get install g++
```

Installed the new curses library

  sudo apt-get install libncurses5-dev
  sudo apt-get install libncurses5-dbg
  sudo apt-get install ncurses-doc
  sudo apt-get install ncurses-examples
  sudo apt-get install libncursesw5-dev
  sudo apt-get install libncursesw5-dbg

Installed Anaconda 5.2.0 per instructions here.
Installed Matlab R2018a per instructions here, then set it up per instructions here.
Installed ImageJ (Fiji):
1. First, download zip file and extract the Fiji.app directory
2. Move the directory to /opt and change permissions recursively to 775
3. Copy the .desktop file with the custom command setup_desktopfiles.sh
4. Copy the icon file (TODO)

Installed MATLAB Compiler Runtime version R2015b (9.0):

Downloaded the zip file and extracted the installation directory.
Change to the installation directory and apply the command:
```
sudo ./install
```

Appended these two lines to the file /etc/bash.bashrc:

export MCR_ROOT="/usr/local/MATLAB/MATLAB_Runtime/v90"
export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:/usr/local/MATLAB/MATLAB_Runtime/v90/runtime/glnxa64:/usr/local/MATLAB/MATLAB_Runtime/v90/bin/glnxa64:/usr/local/MATLAB/MATLAB_Runtime/v90/sys/os/glnxa64"

Installed NEURON 7.5 per instructions here.
Installed s3cmd:
```
sudo apt-get install s3cmd
```
Then configured S3 key access with
```
s3cmd --configure
```
The access keys are saved in /media/adamX/Settings_AWS/Account_Info_beenhakkerlab.txt on fishfish
Installed HUGO:
```
  sudo apt-get install hugo
```
Installed catdoc (programs for converting Microsoft documents such as xls2csv):
```
  sudo apt-get install catdoc
```
Installed xlsx2csv:
```
  sudo apt-get install xlsx2csv
```

Installed VLC player:

  sudo apt-get install vlc browser-plugin-vlc

Installed ffmpeg
```
  sudo apt-get install ffmpeg
```

Installed gstreamer1.0-plugins-bad

  sudo apt-get install gstreamer1.0-plugins-bad