Other programs installed after upgrade to Ubuntu 18.04 LTS for fishfish

Last Updated 2020-01-06 by Adam Lu

Installed git

  sudo apt-get install git
  git config --global core.editor "vim"

Installed the modified VI editor:
```
  sudo apt-get install vim
```
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 displayed nonsensical words)
Installed trash-cli:
```
  sudo apt-get install trash-cli
```
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 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 Matlab R2018a, then followed instructions in Settings_Matlab/Setting_Matlab_Notes.md

  sudo apt-get install matlab-support
  cp -p /usr/share/applications/matlab.desktop /home/adam/Desktop

Installed pdftk. First tried this command, but didn’t work anymore:
```
  sudo apt-get install pdftk
```
Thereafter, downloaded the script from this thread and installed it successfully
Installed ImageJ (Fiji), then setup desktop files
Installed mailutils for the mail command:
```
  sudo apt-get install mailutils
```
Used the domain name “fishfish.tools”

Some outputs:

Postfix (main.cf) is now set up with a default configuration. If you need to make changes, edit /etc/postfix/main.cf (and others) as needed. To view Postfix configuration values, see postconf(1).

After modifying main.cf, be sure to run ‘service postfix reload’.

However, the e-mails are still sent with the domain name “fishfish” by default

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}.tools" 'markbeen@virginia.edu'
```
Installed ntp (Network Time Protocol):
```
  sudo apt-get install ntp
```
Installed ntpdate:
```
  sudo apt-get install ntpdate
```
Installed Anaconda 5.2.0 per instructions in Settings_Anaconda/Installation_instructions.md

Installed png libraries per these instructions:

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

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

Installed system-config-samba:

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

Installed curl:
```
  sudo apt-get install curl
```
Installed NEURON 7.5. First downloaded the .deb package from this site, then applied the command:
```
  sudo dpkg -i nrn-7.5.x86_64.deb
```
Installed make (needed for NEURON’s nrnivmodl to work):
```
  sudo apt-get install make
```
Installed the GNU C Compiler (needed for NEURON’s nrnivmodl to work):
```
  sudo apt-get install gcc
```

Installed the new curses library (needed for NEURON’s nrnivmodl to work):

  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 rename:
```
  sudo apt-get install rename
```
Installed htop:
```
  sudo apt-get install htop
```
Installed atop:
```
  sudo apt-get install atop
```
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 plugins for gedit:
```
  sudo apt-get install gedit-plugins
```
Installed GNOME panel:
```
  sudo apt-get install gnome-panel
```
Installed the GNU C++ library:
```
  sudo apt-get install g++
```

Installed the NVIDIA drivers per these instructions:

  # Installed the wrong NVIDIA drivers, then purged them
  sudo apt-get install nvidia-340
  sudo apt-get install nvidia-driver-390
  sudo apt-get install nvidia-utils-390
  sudo apt-get purge nvidia*
    
  # Update the repository for graphics drivers
  sudo add-apt-repository ppa:graphics-drivers/ppa
  sudo apt-get update
  sudo apt-get install nvidia-390

Restarted the server, then applied this command to verify the driver is loaded (see these instructions):

  nvidia-smi
  nvidia-settings

The second command yielded:

ERROR: Unable to load info from any available system

Re-installed NVIDIA driver 396.24 per these instructions:
```
  # Purged the old versions
  sudo apt-get purge nvidia*
    
  # Install the latest driver
  sudo apt-get install nvidia-driver-396
```
Restarted the server, then applied this command to verify the driver is loaded (see these instructions):

Updated NVIDIA drivers. Based on these instructions, only these lines should have been necessary:

  # Add the graphics drivers repository
  sudo add-apt-repository ppa:graphics-drivers/ppa

  # Update all apt repositories
  sudo apt update

  # Identify the graphic card model
  ubuntu-drivers devices

Installed mesa-utils (for glxinfo):
```
  sudo apt-get install mesa-utils
```
Installed Hugo:
```
  sudo apt-get install hugo
```
Installed Pandoc:
```
  sudo apt-get install pandoc
```
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

Installed npm
```
  sudo apt-get install npm
```
Installed gitk
```
  sudo apt-get install gitk
```

Settings_Linux

Useful bash scripts and settings for managing a Linux server

Other programs installed after upgrade to Ubuntu 18.04 LTS for fishfish