ksferguson/Ubuntu Post Install Setup.txt

## Ubuntu Post Install Setup.txt
#TODO - convert this into an installation script to help quickly setup the machine post installation


0. Time in Windows gets corrupted when dual boot with Ubuntu. (Note needed on 18.04 LTS)
  First adjust hardware time in BIOS to UTC time
  Windows will automatically recognise it and will display appropriate local time
  For Ubuntu, update /etc/default/rcS and change line with UTC=no to UTC=yes, indicating that BOIS time is UTC.
  Reboot - and check both systems.
0. Open Disks, and edit mount options for C and D drives. Remove check box for Mount at Startup and Show in user interface. Also disable Automatic mount.
0. To speed up ubuntu Updates select the best Server.
System Settings -> Software & Updates -> Download from -> Select best server

1. VIM and add alias
sudo apt install vim
edit .bashrc and add line alias vi=vim


1. Install Codecs and Flash Plugin
   sudo apt-get install ubuntu-restricted-extras
2. Ubuntu tweak -   For 18.04 the command is sudo apt install gnome-tweak-tool . No additional repo needs to be added. Install ubuntu-tweak for Ubuntu before 18.04
  sudo add-apt-repository ppa:tualatrix/ppa
  sudo apt-get update
  sudo apt-get install ubuntu-tweak

  - Using gnome-tweaks tool is disable Animations from the Appreance tab. This make workspace switching a snap
  - Also in the worksoace tab i disable dynamic workspaces. Keep them to three vertical.

3. Sensors
  sudo apt-get install lm-sensors
  sudo apt-get install psensor
  psensor configuration. start psensor manually for the first time using the command `psensor`.
  - Go to Pferences
    - In Interface Tab, ensure Enable Menu checkbox is selected. This displays the sensor icon in the top menu bar for easy access.
    -	In start up all three checkboxes are selected, ensure launch session at startup is selected.
    - In Providers tab ensure GPU information is being obtained using NVCtrl (Nvidia)
    - Note - psensor is messing with audio resulting in clackling sound. It happens as the refresh interval of psensors is 2 seconds. I increased it to 60 seconda.
  - Go to Sensor Preferences from the meu of the icon in the main menu
  	- For each of GPU, CPU and the 2 processor fans, i select them from the left side and then for each go to the Application Indicator tab and enable display of the sensor in the label. This will show the sensor value in the menu - which can be quickly used to see oif GPU is ON (will have a temperature value) or OFF (in which case the temperature value will be 1)
4. Git
	apt-cache policy git  -- compare the candidate version `Candidate: 1:2.17.1-1ubuntu0.1 for example` and check the version after the 1:. Compare that with the lates on git website and it not much difference, go ahead and install. If the version is far behind then check the apt repository ppa:git-core/ppa

  sudo apt-get install git
5. GitKraken (though it does not need Git mentioned above) ## not installing going ahead as need to get confortable with git on command line
Deb from https://www.gitkraken.com/download and then use Ubuntu Software Center to install
6. Virtual Box
	add to /etc/apt/sources.list
      sudo -i
      echo 'deb [arch=amd64] https://download.virtualbox.org/virtualbox/debian bionic contrib' >> /etc/apt/sources/list
      exit
The add the keys
  wget -q https://www.virtualbox.org/download/oracle_vbox_2016.asc -O- | sudo apt-key add -
  wget -q https://www.virtualbox.org/download/oracle_vbox.asc -O- | sudo apt-key add -
Then
  sudo apt-get update
  udo apt-get install virtualbox-5.2
7. Vagrant - download the deb file and proceed installing with software manager

7.1 Dcoker
  sudo apt-get install apt-transport-https ca-certificates curl software-properties-common
  curl -fsSL https://download.docker.com/linux/ubuntu/gpg | sudo apt-key add -
  sudo add-apt-repository "deb [arch=amd64] https://download.docker.com/linux/ubuntu $(lsb_release -cs) stable"
  sudo apt-get update
  sudo apt-get install docker-ce

  Add user to docker group our you will get permission denied error when executing docker commands
  sudo usermod -a -G docker $USER

  Need to logout and login for this to take effect

  Once done, using Ubuntu Software install Docker Integration Gnome Shell Extension .. https://extensions.gnome.org/extension/1065/docker-status/. This can also be installed from Ubuntu Software Center.

7.2 nvidia-docker.

  curl -s -L https://nvidia.github.io/nvidia-docker/gpgkey | sudo apt-key add -
  distribution=$(. /etc/os-release;echo $ID$VERSION_ID)
  curl -s -L https://nvidia.github.io/nvidia-docker/$distribution/nvidia-docker.list | sudo tee /etc/apt/sources.list.d/nvidia-docker.list
  sudo apt-get update

  sudo apt-get install nvidia-docker2
  sudo pkill -SIGHUP dockerd


8. NodeJS
  Install as from here https://nodejs.org/en/download/package-manager/#debian-and-ubuntu-based-linux-distributions
  curl -sL https://deb.nodesource.com/setup_10.x | sudo -E bash -
  sudo apt-get install -y build-essential gcc g++ make
  sudo apt-get install -y nodejs


  Optional  ##not installed
  ## To install the Yarn package manager, run:
     curl -sL https://dl.yarnpkg.com/debian/pubkey.gpg | sudo apt-key add -
     echo "deb https://dl.yarnpkg.com/debian/ stable main" | sudo tee /etc/apt/sources.list.d/yarn.list
     sudo apt-get update && sudo apt-get install yarn

8.1 Disable touchpad when external mouse is connected to the system
	sudo add-apt-repository ppa:atareao/atareao
    sudo apt-get update
    sudo apt-get install touchpad-indicator

    Then configure as described at http://www.linuxandubuntu.com/home/how-to-disable-touchpad-while-writing-article-or-documentation-in-ubuntulinux-mint-or-derivatives-linux

8.2 In case the keyboard backlight turns off very quickly then try the procedure at http://www.dell.com/support/article/us/en/04/sln308123/how-to-configure-the-keyboard-backlight-time-out-interval-in-ubuntu-linux?lang=en


9. Gitbook cli ## Note installed. No longer using. Moved to Lepton
  sudo npm install -g gitbook-cli

9.1 Lepton
	Moved to Lepton as the note taking application.
    Download the x86_64.AppImage file from Github releases https://github.com/hackjutsu/Lepton/releases
    Copy the AppImage file to /opt/Lepton
    chmod u+x that AppImage file
    ./run that AppImage file

	Create a desktop file as below .local/share/applications/lepton.desktop. Ensure the lepton.ico file is copied to /opt

[Desktop Entry]
Comment=lepton
Terminal=false
Name=Lepton
Exec=/opt/lepton/Lepton-1.6.2-x86_64.AppImage
Type=Application
Icon=/opt/lepton/lepton.png

Refer - https://github.com/AppImage/AppImageKit/wiki/Extracting-AppImages to understand how to extract icons


10. Ruby + gems
  sudo apt-get install autoconf bison build-essential libssl-dev libyaml-dev libreadline-dev zlib1g-dev libncurses5-dev libffi-dev libgdbm5 libgdbm-dev
  sudo apt-get install ruby-full                      # as entioned at https://www.ruby-lang.org/en/documentation/installation/#apt


  ## old sudo apt-add-repository ppa:brightbox/ruby-ng
  ## old sudo apt-get update
  ## old sudo apt-get install ruby2.3 ruby2.3-dev
11. Jekyll

  Ruby GEMS should not be installed asd root

echo '# Install Ruby Gems to ~/gems' >> ~/.bashrc
echo 'export GEM_HOME=$HOME/gems' >> ~/.bashrc
echo 'export PATH=$PATH:$HOME/gems/bin' >> ~/.bashrc
source ~/.bashrc
gem install jekyll
gem install jekyll-sitemap jekyll-gist jekyll-paginate

12. R
# We will install Microsoft R open instead of the CRAN R

# sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E084DAB9
# Add the below lines in /etc/apt/sources.list
# R studio
# deb http://cran.stat.ucla.edu/bin/linux/ubuntu trusty/
#sudo apt-get update
#sudo apt-get install r-base
#sudo apt-get install r-base-dev

Follow instructions at https://mran.microsoft.com/documents/rro/installation#revorinst-lin
* Download latest version of MRAN from https://mran.microsoft.com/download
* Untar the file downloaded, cd to microsoft-r-open
* sudo ./install.sh

Gettig segfault when starting R - issue https://github.com/Microsoft/microsoft-r-open/issues/34
Verified `apt list --installed` that libpng is installed `libpng16-16/bionic,now 1.6.34-1 amd64 [installed]`
```
hemen@hemen-Inspiron-7559:/usr/lib/x86_64-linux-gnu$ ls -l *png*
lrwxrwxrwx 1 root root     19 May 24 01:13 libpng16.so.16 -> libpng16.so.16.34.0
-rw-r--r-- 1 root root 202672 Sep 29  2017 libpng16.so.16.34.0
hemen@hemen-Inspiron-7559:/usr/lib/x86_64-linux-gnu$ sudo ln -s libpng16.so.16.34.0 libpng12.so.0
[sudo] password for hemen:
hemen@hemen-Inspiron-7559:/usr/lib/x86_64-linux-gnu$ ls -l *png*
lrwxrwxrwx 1 root root     19 Jul  1 09:22 libpng12.so.0 -> libpng16.so.16.34.0
lrwxrwxrwx 1 root root     19 May 24 01:13 libpng16.so.16 -> libpng16.so.16.34.0
-rw-r--r-- 1 root root 202672 Sep 29  2017 libpng16.so.16.34.0
hemen@hemen-Inspiron-7559:/usr/lib/x86_64-linux-gnu$
```


12. rstudio
  Download the Ubuntu deb file from https://www.rstudio.com/products/rstudio/download/#download and install

13. Touchpad-indicator
  sudo add-apt-repository ppa:atareao/atareao
  sudo apt-get update
  sudo apt-get install touchpad-indicator

14. Restricted Extras - various media formats - https://en.wikipedia.org/wiki/Ubuntu-restricted-extras
  sudo apt-get install ubuntu-restricted-extras

15. Oracle JDK 8 (Ref - https://help.ubuntu.com/community/Java, http://www.webupd8.org/2012/09/install-oracle-java-8-in-ubuntu-via-ppa.html)
  # sudo add-apt-repository ppa:webupd8team/java
  # sudo apt-get update
  # sudo apt-get install oracle-java8-installer
  # sudo apt-get install oracle-java8-set-default

  Transitioning to OpenJDK - https://medium.com/codefx-weekly/no-free-java-lts-version-b850192745fb
  Need to understand till when is OpenJDK 8 will be supported. For now going to install it from Ubuntu apt (easier to remove)
  openjdk-11-jdk currently points to openjdk-10

  Keep an eye on https://adoptopenjdk.net/installation.html#x64_linux

  ```
  hemen@hemen-Inspiron-7559:~$ apt-cache policy openjdk-11-jdk
openjdk-11-jdk:
  Installed: (none)
  Candidate: 10.0.1+10-3ubuntu1
  Version table:
     10.0.1+10-3ubuntu1 500
        500 http://us.archive.ubuntu.com/ubuntu bionic/main amd64 Packages

hemen@hemen-Inspiron-7559:~$ apt-cache policy openjdk-8-jdk
openjdk-8-jdk:
  Installed: (none)
  Candidate: 8u171-b11-0ubuntu0.18.04.1
  Version table:
     8u171-b11-0ubuntu0.18.04.1 500
        500 http://us.archive.ubuntu.com/ubuntu bionic-updates/universe amd64 Packages
        500 http://security.ubuntu.com/ubuntu bionic-security/universe amd64 Packages
     8u162-b12-1 500
        500 http://us.archive.ubuntu.com/ubuntu bionic/universe amd64 Packages
hemen@hemen-Inspiron-7559:~$

sudo apt install openjdk-8-jdk

  ```

16. Gnu Octave  ## Not installed as not needed for now.
  sudo add-apt-repository ppa:octave/stable
  sudo apt-get update
  sudo apt-get install octave

17.0 vim keybindings

add following to ~/.vimrc

noremap ; l
noremap l k
noremap k j
noremap j h


17.1 VSCode
Reference - https://code.visualstudio.com/docs/setup/linux#_installation
But search for VSCODE in Ubuntu Software Center in install from there. It has the latest version and supports upgrade using apt


17.2 - Installed Kodi - Not installed
  sudo add-apt-repository ppa:team-xbmc/ppa
  sudo apt-get update
  sudp apt-get installl kodi


18. P4Merge and git configuration # DID not install for now. Can be installed later.
  Copy p4v.tgz to /opt and cd to /opt
  sudo mv p4v* p4v
  Ensure /opt/p4v/bin is in $PATH. if not then update ~/.bashrc for the same.
  Add the below to ~/.gitconfig
-----------------------------------------
[merge]
    keepBackup = false;
    tool = p4merge
[mergetool]
    prompt = false
[mergetool "p4merge"]
    cmd = p4merge "$BASE" "$LOCAL" "$REMOTE" "$MERGED"
    keepTemporaries = false
    trustExitCode = false
    keepBackup = false
[diff]
    tool = p4merge
[difftool]
    prompt = false
[difftool "p4merge"]
    cmd = p4merge "$LOCAL" "$REMOTE"
    keepTemporaries = false
    trustExitCode = false
    keepBackup = false
--------------------------------------------


19. DO NOT install i8kutils - I have noticed it interfering with the normal fan control and the machine starts heating up. Things went back to normal when it removed i8kutils.


# Instead of this I went on to install anaconda3, I removed the changes to bashrc, but kept the
# pip and virtualenv installed

# For Python never have alias for python or pip in the .bashrc. On a system it is critical to have python map to python2 and python3 map to python 3
```hemen@hemen-Inspiron-7559:~$ ls -l /usr/bin/pyth*
lrwxrwxrwx 1 root root       9 Apr 16 07:31 /usr/bin/python -> python2.7
lrwxrwxrwx 1 root root       9 Apr 16 07:31 /usr/bin/python2 -> python2.7
-rwxr-xr-x 1 root root 3633560 Apr 15 14:51 /usr/bin/python2.7
lrwxrwxrwx 1 root root       9 May 24 01:13 /usr/bin/python3 -> python3.6
-rwxr-xr-x 1 root root 4576440 Mar 31 22:46 /usr/bin/python3.6
-rwxr-xr-x 1 root root 4576440 Mar 31 22:46 /usr/bin/python3.6m
lrwxrwxrwx 1 root root      10 May 24 01:13 /usr/bin/python3m -> python3.6m
hemen@hemen-Inspiron-7559:~$
```
However we will always use anaconda

  20. Install Python pip # not installed
    sudo apt-get install python3-pip
    sudo easy_install3 pip
    sudo pip install virtualenv
    sudo pip install virtualenvwrapper

    vi ~/.bashrc and add the following lines

    # Setup python virtualenv variables. Source the command file
    export WORKON_HOME="$HOME/.virtualenvs"
    export PROJECT_HOME="$HOME/Workspace"
    export VIRTUALENVWRAPPER_PYTHON=/usr/bin/python3
    export VIRTUALENVWRAPPER_VIRTUALENV=/usr/local/bin/virtualenv
    source /usr/local/bin/virtualenvwrapper.sh

30. Install Anaconda
  sudo su -
  addgroup --system datascience
  adduser --system --ingroup datascience --disabled-login --no-create-home anaconda
  usermod -a -G datascience hemen

  Verify users 'hemen' and 'anaconda' using the id command. Both should have 'datascience' as a group.

  mkdir /opt/anaconda3 && chown anaconda:datascience /opt/anaconda3
  chmod g+w /opt/anaconda3
  exit (to get back to hemen)

  # One needs to logout and log in again for adding hemen to datascience to persist


  ./Anaconda3-4.2.0-Linux-x86_64.sh -u -p /opt/anaconda3

  # Edit .bashrc, once it is update by Anaconda installer.
  # ensure that $PATH, preceeds Anaconda bin

  export PATH="$PATH:/opt/anaconda3/bin"

  ## So system python installations on /usr/bin are kept as is. Moreover Anaconda bin comes later than /usr/bin in $PATH, so system is intact.
  ```hemen@hemen-Inspiron-7559:~$ ls -l /usr/bin/pyth*
lrwxrwxrwx 1 root root       9 Apr 16 07:31 /usr/bin/python -> python2.7
lrwxrwxrwx 1 root root       9 Apr 16 07:31 /usr/bin/python2 -> python2.7
-rwxr-xr-x 1 root root 3633560 Apr 15 14:51 /usr/bin/python2.7
lrwxrwxrwx 1 root root       9 May 24 01:13 /usr/bin/python3 -> python3.6
-rwxr-xr-x 1 root root 4576440 Mar 31 22:46 /usr/bin/python3.6
-rwxr-xr-x 1 root root 4576440 Mar 31 22:46 /usr/bin/python3.6m
lrwxrwxrwx 1 root root      10 May 24 01:13 /usr/bin/python3m -> python3.6m
hemen@hemen-Inspiron-7559:~$ ls -l  /opt/anaconda3/bin/pyth*
lrwxrwxrwx 1 hemen hemen       9 Jul  1 11:43 /opt/anaconda3/bin/python -> python3.6
lrwxrwxrwx 1 hemen hemen       9 Jul  1 11:43 /opt/anaconda3/bin/python3 -> python3.6
-rwxr-xr-x 1 hemen hemen 3752088 Jul  1 11:43 /opt/anaconda3/bin/python3.6
lrwxrwxrwx 1 hemen hemen      17 Jul  1 11:43 /opt/anaconda3/bin/python3.6-config -> python3.6m-config
lrwxrwxrwx 1 hemen hemen       9 Jul  1 11:43 /opt/anaconda3/bin/python3.6m -> python3.6
-rwxr-xr-x 1 hemen hemen    3419 Jul  1 11:43 /opt/anaconda3/bin/python3.6m-config
lrwxrwxrwx 1 hemen hemen      17 Jul  1 11:43 /opt/anaconda3/bin/python3-config -> python3.6m-config
hemen@hemen-Inspiron-7559:~$ echo $PATH
/home/hemen/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/opt/p4v/bin:/usr/local/cuda/bin:/opt/miniconda3/bin:/home/hemen/bin:/home/hemen/gems/bin:/opt/anaconda3/bin
hemen@hemen-Inspiron-7559:~$
```

## i use anaconda python using a conda environment only - for any python development...


  # Python dependency will be handled by the conda environment we create

  # Creating an environemnt for data science
  conda create --name datascience python=3.5
  source activate datascience
  which python        # should use the one in /opt/anaconda
  python --version    # should be one from continuoum analytics
  conda list

  # installing sloth dependencies and sloth  # did not install check other options https://en.wikipedia.org/wiki/List_of_manual_image_annotation_tools
  conda install pyqt=4.11.4
  conda install scikit-image=0.11.3
  pip install git+https://github.com/cvhciKIT/sloth.git
  which sloth
	sloth

   source deactivate datascience
  # Now check python and we are back to the original system python

  # Create an environment for kodi development
  conda create --name kodidev python=2.7 beautifulsoup4
  source activate kodidev
  pip install kodiswift
  conda list
  source deactivate kodidev

31. Stellarium # did not install

sudo add-apt-repository ppa:stellarium/stellarium-releases
sudo apt-get update
sudo apt-get install


33. web-ext for Firefox and Chrome web extension development
# https://nodejs.org/en/blog/npm/npm-1-0-global-vs-local-installation/ ... since web-ext is a command used aon the shell we install it globally
sudo npm install --global web-ext

34. Xtreme Download Manager ## Not installed, why do i need this ?
   sudo add-apt-repository ppa:noobslab/apps
   sudo apt-get update
   sudo apt-get install xdman-downloader

35 . IntelliJ IDEA and python plugin

* Downlaod Communit edition without the JDK sudo snap lfrom https://www.jetbrains.com/idea/download/index.html#section=linux
* We will use snap for IntelliJ. sudo snap list shows VSCODE is also installed on the system as a snap

```
Tried, but this was giving 503 error so going with standard approach
$ sudo snap install intellij-idea-community --classic

Once IntelliJ is working, download JB SDK Bintray Downloader plugin. Restart
Once restarted, press Ctrl+Shift+A to open the uinversal command paletter and searc for `Get JB SDK....` and using that download the latest 64 bit version on the JDK.
NOTE - Esnure you download the JDK that ends with linux_64.tar.gz, there is a 32 bit version too and download it will cause the IDE to crash
Once restart again press Ctrl + Shit + A and then search Switch Boot JRE --- and seslect the downloaded JDK. If not found it will be in ~/.Idea<version>/config/jdk directory.
Once IDEA will restart...not fonts will render properly

```
* Downloaded tar.gz without JDK from https://www.jetbrains.com/idea/download/index.html#section=linux
* cd ~/Downloads; sudo tar xzf ideaIC-2018.1.5-no-jdk.tar.gz -C /opt/
* cd /opt/idea-IC-181.5281.24/bin
* sudo chown -R /opt/idea-IC-181.5281.24
* ./idea.sh

For vim emulation in IDA Editor, create a file ~/.ideavimrc with contents source ~/.vimrc. It will source in vim keybindings and other settings and apply in the terminal.

36. Tig - ncurses based Git GIU client
Installing as per https://jonas.github.io/tig/INSTALL.html
* Get latest tar.gz from https://github.com/jonas/tig/releases/.
	#TODO - convert this into an installation script to help quickly setup the machine post installation


	0. Time in Windows gets corrupted when dual boot with Ubuntu. (Note needed on 18.04 LTS)
	First adjust hardware time in BIOS to UTC time
	Windows will automatically recognise it and will display appropriate local time
	For Ubuntu, update /etc/default/rcS and change line with UTC=no to UTC=yes, indicating that BOIS time is UTC.
	Reboot - and check both systems.
	0. Open Disks, and edit mount options for C and D drives. Remove check box for Mount at Startup and Show in user interface. Also disable Automatic mount.
	0. To speed up ubuntu Updates select the best Server.
	System Settings -> Software & Updates -> Download from -> Select best server

	1. VIM and add alias
	sudo apt install vim
	edit .bashrc and add line alias vi=vim


	1. Install Codecs and Flash Plugin
	sudo apt-get install ubuntu-restricted-extras
	2. Ubuntu tweak - For 18.04 the command is sudo apt install gnome-tweak-tool . No additional repo needs to be added. Install ubuntu-tweak for Ubuntu before 18.04
	sudo add-apt-repository ppa:tualatrix/ppa
	sudo apt-get update
	sudo apt-get install ubuntu-tweak

	- Using gnome-tweaks tool is disable Animations from the Appreance tab. This make workspace switching a snap
	- Also in the worksoace tab i disable dynamic workspaces. Keep them to three vertical.

	3. Sensors
	sudo apt-get install lm-sensors
	sudo apt-get install psensor
	psensor configuration. start psensor manually for the first time using the command `psensor`.
	- Go to Pferences
	- In Interface Tab, ensure Enable Menu checkbox is selected. This displays the sensor icon in the top menu bar for easy access.
	- In start up all three checkboxes are selected, ensure launch session at startup is selected.
	- In Providers tab ensure GPU information is being obtained using NVCtrl (Nvidia)
	- Note - psensor is messing with audio resulting in clackling sound. It happens as the refresh interval of psensors is 2 seconds. I increased it to 60 seconda.
	- Go to Sensor Preferences from the meu of the icon in the main menu
	- For each of GPU, CPU and the 2 processor fans, i select them from the left side and then for each go to the Application Indicator tab and enable display of the sensor in the label. This will show the sensor value in the menu - which can be quickly used to see oif GPU is ON (will have a temperature value) or OFF (in which case the temperature value will be 1)
	4. Git
	apt-cache policy git -- compare the candidate version `Candidate: 1:2.17.1-1ubuntu0.1 for example` and check the version after the 1:. Compare that with the lates on git website and it not much difference, go ahead and install. If the version is far behind then check the apt repository ppa:git-core/ppa

	sudo apt-get install git
	5. GitKraken (though it does not need Git mentioned above) ## not installing going ahead as need to get confortable with git on command line
	Deb from https://www.gitkraken.com/download and then use Ubuntu Software Center to install
	6. Virtual Box
	add to /etc/apt/sources.list
	sudo -i
	echo 'deb [arch=amd64] https://download.virtualbox.org/virtualbox/debian bionic contrib' >> /etc/apt/sources/list
	exit
	The add the keys
	wget -q https://www.virtualbox.org/download/oracle_vbox_2016.asc -O- \| sudo apt-key add -
	wget -q https://www.virtualbox.org/download/oracle_vbox.asc -O- \| sudo apt-key add -
	Then
	sudo apt-get update
	udo apt-get install virtualbox-5.2
	7. Vagrant - download the deb file and proceed installing with software manager

	7.1 Dcoker
	sudo apt-get install apt-transport-https ca-certificates curl software-properties-common
	curl -fsSL https://download.docker.com/linux/ubuntu/gpg \| sudo apt-key add -
	sudo add-apt-repository "deb [arch=amd64] https://download.docker.com/linux/ubuntu $(lsb_release -cs) stable"
	sudo apt-get update
	sudo apt-get install docker-ce

	Add user to docker group our you will get permission denied error when executing docker commands
	sudo usermod -a -G docker $USER

	Need to logout and login for this to take effect

	Once done, using Ubuntu Software install Docker Integration Gnome Shell Extension .. https://extensions.gnome.org/extension/1065/docker-status/. This can also be installed from Ubuntu Software Center.

	7.2 nvidia-docker.

	curl -s -L https://nvidia.github.io/nvidia-docker/gpgkey \| sudo apt-key add -
	distribution=$(. /etc/os-release;echo $ID$VERSION_ID)
	curl -s -L https://nvidia.github.io/nvidia-docker/$distribution/nvidia-docker.list \| sudo tee /etc/apt/sources.list.d/nvidia-docker.list
	sudo apt-get update

	sudo apt-get install nvidia-docker2
	sudo pkill -SIGHUP dockerd


	8. NodeJS
	Install as from here https://nodejs.org/en/download/package-manager/#debian-and-ubuntu-based-linux-distributions
	curl -sL https://deb.nodesource.com/setup_10.x \| sudo -E bash -
	sudo apt-get install -y build-essential gcc g++ make
	sudo apt-get install -y nodejs


	Optional ##not installed
	## To install the Yarn package manager, run:
	curl -sL https://dl.yarnpkg.com/debian/pubkey.gpg \| sudo apt-key add -
	echo "deb https://dl.yarnpkg.com/debian/ stable main" \| sudo tee /etc/apt/sources.list.d/yarn.list
	sudo apt-get update && sudo apt-get install yarn

	8.1 Disable touchpad when external mouse is connected to the system
	sudo add-apt-repository ppa:atareao/atareao
	sudo apt-get update
	sudo apt-get install touchpad-indicator

	Then configure as described at http://www.linuxandubuntu.com/home/how-to-disable-touchpad-while-writing-article-or-documentation-in-ubuntulinux-mint-or-derivatives-linux

	8.2 In case the keyboard backlight turns off very quickly then try the procedure at http://www.dell.com/support/article/us/en/04/sln308123/how-to-configure-the-keyboard-backlight-time-out-interval-in-ubuntu-linux?lang=en


	9. Gitbook cli ## Note installed. No longer using. Moved to Lepton
	sudo npm install -g gitbook-cli

	9.1 Lepton
	Moved to Lepton as the note taking application.
	Download the x86_64.AppImage file from Github releases https://github.com/hackjutsu/Lepton/releases
	Copy the AppImage file to /opt/Lepton
	chmod u+x that AppImage file
	./run that AppImage file

	Create a desktop file as below .local/share/applications/lepton.desktop. Ensure the lepton.ico file is copied to /opt

	[Desktop Entry]
	Comment=lepton
	Terminal=false
	Name=Lepton
	Exec=/opt/lepton/Lepton-1.6.2-x86_64.AppImage
	Type=Application
	Icon=/opt/lepton/lepton.png

	Refer - https://github.com/AppImage/AppImageKit/wiki/Extracting-AppImages to understand how to extract icons




	10. Ruby + gems
	sudo apt-get install autoconf bison build-essential libssl-dev libyaml-dev libreadline-dev zlib1g-dev libncurses5-dev libffi-dev libgdbm5 libgdbm-dev
	sudo apt-get install ruby-full # as entioned at https://www.ruby-lang.org/en/documentation/installation/#apt


	## old sudo apt-add-repository ppa:brightbox/ruby-ng
	## old sudo apt-get update
	## old sudo apt-get install ruby2.3 ruby2.3-dev
	11. Jekyll

	Ruby GEMS should not be installed asd root

	echo '# Install Ruby Gems to ~/gems' >> ~/.bashrc
	echo 'export GEM_HOME=$HOME/gems' >> ~/.bashrc
	echo 'export PATH=$PATH:$HOME/gems/bin' >> ~/.bashrc
	source ~/.bashrc
	gem install jekyll
	gem install jekyll-sitemap jekyll-gist jekyll-paginate

	12. R
	# We will install Microsoft R open instead of the CRAN R

	# sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E084DAB9
	# Add the below lines in /etc/apt/sources.list
	# R studio
	# deb http://cran.stat.ucla.edu/bin/linux/ubuntu trusty/
	#sudo apt-get update
	#sudo apt-get install r-base
	#sudo apt-get install r-base-dev

	Follow instructions at https://mran.microsoft.com/documents/rro/installation#revorinst-lin
	* Download latest version of MRAN from https://mran.microsoft.com/download
	* Untar the file downloaded, cd to microsoft-r-open
	* sudo ./install.sh

	Gettig segfault when starting R - issue https://github.com/Microsoft/microsoft-r-open/issues/34
	Verified `apt list --installed` that libpng is installed `libpng16-16/bionic,now 1.6.34-1 amd64 [installed]`
	```
	hemen@hemen-Inspiron-7559:/usr/lib/x86_64-linux-gnu$ ls -l png
	lrwxrwxrwx 1 root root 19 May 24 01:13 libpng16.so.16 -> libpng16.so.16.34.0
	-rw-r--r-- 1 root root 202672 Sep 29 2017 libpng16.so.16.34.0
	hemen@hemen-Inspiron-7559:/usr/lib/x86_64-linux-gnu$ sudo ln -s libpng16.so.16.34.0 libpng12.so.0
	[sudo] password for hemen:
	hemen@hemen-Inspiron-7559:/usr/lib/x86_64-linux-gnu$ ls -l png
	lrwxrwxrwx 1 root root 19 Jul 1 09:22 libpng12.so.0 -> libpng16.so.16.34.0
	lrwxrwxrwx 1 root root 19 May 24 01:13 libpng16.so.16 -> libpng16.so.16.34.0
	-rw-r--r-- 1 root root 202672 Sep 29 2017 libpng16.so.16.34.0
	hemen@hemen-Inspiron-7559:/usr/lib/x86_64-linux-gnu$
	```


	12. rstudio
	Download the Ubuntu deb file from https://www.rstudio.com/products/rstudio/download/#download and install

	13. Touchpad-indicator
	sudo add-apt-repository ppa:atareao/atareao
	sudo apt-get update
	sudo apt-get install touchpad-indicator

	14. Restricted Extras - various media formats - https://en.wikipedia.org/wiki/Ubuntu-restricted-extras
	sudo apt-get install ubuntu-restricted-extras

	15. Oracle JDK 8 (Ref - https://help.ubuntu.com/community/Java, http://www.webupd8.org/2012/09/install-oracle-java-8-in-ubuntu-via-ppa.html)
	# sudo add-apt-repository ppa:webupd8team/java
	# sudo apt-get update
	# sudo apt-get install oracle-java8-installer
	# sudo apt-get install oracle-java8-set-default

	Transitioning to OpenJDK - https://medium.com/codefx-weekly/no-free-java-lts-version-b850192745fb
	Need to understand till when is OpenJDK 8 will be supported. For now going to install it from Ubuntu apt (easier to remove)
	openjdk-11-jdk currently points to openjdk-10

	Keep an eye on https://adoptopenjdk.net/installation.html#x64_linux

	```
	hemen@hemen-Inspiron-7559:~$ apt-cache policy openjdk-11-jdk
	openjdk-11-jdk:
	Installed: (none)
	Candidate: 10.0.1+10-3ubuntu1
	Version table:
	10.0.1+10-3ubuntu1 500
	500 http://us.archive.ubuntu.com/ubuntu bionic/main amd64 Packages

	hemen@hemen-Inspiron-7559:~$ apt-cache policy openjdk-8-jdk
	openjdk-8-jdk:
	Installed: (none)
	Candidate: 8u171-b11-0ubuntu0.18.04.1
	Version table:
	8u171-b11-0ubuntu0.18.04.1 500
	500 http://us.archive.ubuntu.com/ubuntu bionic-updates/universe amd64 Packages
	500 http://security.ubuntu.com/ubuntu bionic-security/universe amd64 Packages
	8u162-b12-1 500
	500 http://us.archive.ubuntu.com/ubuntu bionic/universe amd64 Packages
	hemen@hemen-Inspiron-7559:~$

	sudo apt install openjdk-8-jdk

	```

	16. Gnu Octave ## Not installed as not needed for now.
	sudo add-apt-repository ppa:octave/stable
	sudo apt-get update
	sudo apt-get install octave

	17.0 vim keybindings

	add following to ~/.vimrc

	noremap ; l
	noremap l k
	noremap k j
	noremap j h


	17.1 VSCode
	Reference - https://code.visualstudio.com/docs/setup/linux#_installation
	But search for VSCODE in Ubuntu Software Center in install from there. It has the latest version and supports upgrade using apt


	17.2 - Installed Kodi - Not installed
	sudo add-apt-repository ppa:team-xbmc/ppa
	sudo apt-get update
	sudp apt-get installl kodi


	18. P4Merge and git configuration # DID not install for now. Can be installed later.
	Copy p4v.tgz to /opt and cd to /opt
	sudo mv p4v* p4v
	Ensure /opt/p4v/bin is in $PATH. if not then update ~/.bashrc for the same.
	Add the below to ~/.gitconfig
	-----------------------------------------
	[merge]
	keepBackup = false;
	tool = p4merge
	[mergetool]
	prompt = false
	[mergetool "p4merge"]
	cmd = p4merge "$BASE" "$LOCAL" "$REMOTE" "$MERGED"
	keepTemporaries = false
	trustExitCode = false
	keepBackup = false
	[diff]
	tool = p4merge
	[difftool]
	prompt = false
	[difftool "p4merge"]
	cmd = p4merge "$LOCAL" "$REMOTE"
	keepTemporaries = false
	trustExitCode = false
	keepBackup = false
	--------------------------------------------


	19. DO NOT install i8kutils - I have noticed it interfering with the normal fan control and the machine starts heating up. Things went back to normal when it removed i8kutils.


	# Instead of this I went on to install anaconda3, I removed the changes to bashrc, but kept the
	# pip and virtualenv installed

	# For Python never have alias for python or pip in the .bashrc. On a system it is critical to have python map to python2 and python3 map to python 3
	```hemen@hemen-Inspiron-7559:~$ ls -l /usr/bin/pyth*
	lrwxrwxrwx 1 root root 9 Apr 16 07:31 /usr/bin/python -> python2.7
	lrwxrwxrwx 1 root root 9 Apr 16 07:31 /usr/bin/python2 -> python2.7
	-rwxr-xr-x 1 root root 3633560 Apr 15 14:51 /usr/bin/python2.7
	lrwxrwxrwx 1 root root 9 May 24 01:13 /usr/bin/python3 -> python3.6
	-rwxr-xr-x 1 root root 4576440 Mar 31 22:46 /usr/bin/python3.6
	-rwxr-xr-x 1 root root 4576440 Mar 31 22:46 /usr/bin/python3.6m
	lrwxrwxrwx 1 root root 10 May 24 01:13 /usr/bin/python3m -> python3.6m
	hemen@hemen-Inspiron-7559:~$
	```
	However we will always use anaconda

	20. Install Python pip # not installed
	sudo apt-get install python3-pip
	sudo easy_install3 pip
	sudo pip install virtualenv
	sudo pip install virtualenvwrapper

	vi ~/.bashrc and add the following lines

	# Setup python virtualenv variables. Source the command file
	export WORKON_HOME="$HOME/.virtualenvs"
	export PROJECT_HOME="$HOME/Workspace"
	export VIRTUALENVWRAPPER_PYTHON=/usr/bin/python3
	export VIRTUALENVWRAPPER_VIRTUALENV=/usr/local/bin/virtualenv
	source /usr/local/bin/virtualenvwrapper.sh

	30. Install Anaconda
	sudo su -
	addgroup --system datascience
	adduser --system --ingroup datascience --disabled-login --no-create-home anaconda
	usermod -a -G datascience hemen

	Verify users 'hemen' and 'anaconda' using the id command. Both should have 'datascience' as a group.

	mkdir /opt/anaconda3 && chown anaconda:datascience /opt/anaconda3
	chmod g+w /opt/anaconda3
	exit (to get back to hemen)

	# One needs to logout and log in again for adding hemen to datascience to persist


	./Anaconda3-4.2.0-Linux-x86_64.sh -u -p /opt/anaconda3

	# Edit .bashrc, once it is update by Anaconda installer.
	# ensure that $PATH, preceeds Anaconda bin

	export PATH="$PATH:/opt/anaconda3/bin"

	## So system python installations on /usr/bin are kept as is. Moreover Anaconda bin comes later than /usr/bin in $PATH, so system is intact.
	```hemen@hemen-Inspiron-7559:~$ ls -l /usr/bin/pyth*
	lrwxrwxrwx 1 root root 9 Apr 16 07:31 /usr/bin/python -> python2.7
	lrwxrwxrwx 1 root root 9 Apr 16 07:31 /usr/bin/python2 -> python2.7
	-rwxr-xr-x 1 root root 3633560 Apr 15 14:51 /usr/bin/python2.7
	lrwxrwxrwx 1 root root 9 May 24 01:13 /usr/bin/python3 -> python3.6
	-rwxr-xr-x 1 root root 4576440 Mar 31 22:46 /usr/bin/python3.6
	-rwxr-xr-x 1 root root 4576440 Mar 31 22:46 /usr/bin/python3.6m
	lrwxrwxrwx 1 root root 10 May 24 01:13 /usr/bin/python3m -> python3.6m
	hemen@hemen-Inspiron-7559:~$ ls -l /opt/anaconda3/bin/pyth*
	lrwxrwxrwx 1 hemen hemen 9 Jul 1 11:43 /opt/anaconda3/bin/python -> python3.6
	lrwxrwxrwx 1 hemen hemen 9 Jul 1 11:43 /opt/anaconda3/bin/python3 -> python3.6
	-rwxr-xr-x 1 hemen hemen 3752088 Jul 1 11:43 /opt/anaconda3/bin/python3.6
	lrwxrwxrwx 1 hemen hemen 17 Jul 1 11:43 /opt/anaconda3/bin/python3.6-config -> python3.6m-config
	lrwxrwxrwx 1 hemen hemen 9 Jul 1 11:43 /opt/anaconda3/bin/python3.6m -> python3.6
	-rwxr-xr-x 1 hemen hemen 3419 Jul 1 11:43 /opt/anaconda3/bin/python3.6m-config
	lrwxrwxrwx 1 hemen hemen 17 Jul 1 11:43 /opt/anaconda3/bin/python3-config -> python3.6m-config
	hemen@hemen-Inspiron-7559:~$ echo $PATH
	/home/hemen/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/opt/p4v/bin:/usr/local/cuda/bin:/opt/miniconda3/bin:/home/hemen/bin:/home/hemen/gems/bin:/opt/anaconda3/bin
	hemen@hemen-Inspiron-7559:~$
	```

	## i use anaconda python using a conda environment only - for any python development...


	# Python dependency will be handled by the conda environment we create

	# Creating an environemnt for data science
	conda create --name datascience python=3.5
	source activate datascience
	which python # should use the one in /opt/anaconda
	python --version # should be one from continuoum analytics
	conda list

	# installing sloth dependencies and sloth # did not install check other options https://en.wikipedia.org/wiki/List_of_manual_image_annotation_tools
	conda install pyqt=4.11.4
	conda install scikit-image=0.11.3
	pip install git+https://github.com/cvhciKIT/sloth.git
	which sloth
	sloth

	source deactivate datascience
	# Now check python and we are back to the original system python

	# Create an environment for kodi development
	conda create --name kodidev python=2.7 beautifulsoup4
	source activate kodidev
	pip install kodiswift
	conda list
	source deactivate kodidev

	31. Stellarium # did not install

	sudo add-apt-repository ppa:stellarium/stellarium-releases
	sudo apt-get update
	sudo apt-get install


	33. web-ext for Firefox and Chrome web extension development
	# https://nodejs.org/en/blog/npm/npm-1-0-global-vs-local-installation/ ... since web-ext is a command used aon the shell we install it globally
	sudo npm install --global web-ext

	34. Xtreme Download Manager ## Not installed, why do i need this ?
	sudo add-apt-repository ppa:noobslab/apps
	sudo apt-get update
	sudo apt-get install xdman-downloader

	35 . IntelliJ IDEA and python plugin

	* Downlaod Communit edition without the JDK sudo snap lfrom https://www.jetbrains.com/idea/download/index.html#section=linux
	* We will use snap for IntelliJ. sudo snap list shows VSCODE is also installed on the system as a snap

	```
	Tried, but this was giving 503 error so going with standard approach
	$ sudo snap install intellij-idea-community --classic

	Once IntelliJ is working, download JB SDK Bintray Downloader plugin. Restart
	Once restarted, press Ctrl+Shift+A to open the uinversal command paletter and searc for `Get JB SDK....` and using that download the latest 64 bit version on the JDK.
	NOTE - Esnure you download the JDK that ends with linux_64.tar.gz, there is a 32 bit version too and download it will cause the IDE to crash
	Once restart again press Ctrl + Shit + A and then search Switch Boot JRE --- and seslect the downloaded JDK. If not found it will be in ~/.Idea<version>/config/jdk directory.
	Once IDEA will restart...not fonts will render properly

	```
	* Downloaded tar.gz without JDK from https://www.jetbrains.com/idea/download/index.html#section=linux
	* cd ~/Downloads; sudo tar xzf ideaIC-2018.1.5-no-jdk.tar.gz -C /opt/
	* cd /opt/idea-IC-181.5281.24/bin
	* sudo chown -R /opt/idea-IC-181.5281.24
	* ./idea.sh

	For vim emulation in IDA Editor, create a file ~/.ideavimrc with contents source ~/.vimrc. It will source in vim keybindings and other settings and apply in the terminal.

	36. Tig - ncurses based Git GIU client
	Installing as per https://jonas.github.io/tig/INSTALL.html
	* Get latest tar.gz from https://github.com/jonas/tig/releases/.