How to install common lab software on ubuntu

1. Open a terminal. Make sure you have permission to install as a root by typing in the command line:

   sudo ls
   

   You will be asked for your password and if you get no error, then you are ready to work as a root.

2. Install git for version control:

   sudo apt install git
   

3. Download Rasi's configuration files from Github and symbolically link them by following these instructions.

4. Install vim for text editing:

   sudo apt install vim 
   

5. Add the emacs Ubuntu package repository to your system and install the latest version of emacs. See here for more instructions on installing emacs.

   sudo add-apt-repository ppa:ubuntu-elisp/ppa
   sudo apt update
   sudo apt install emacs-snapshot
   

6. Set up password-less authentication to Github:

   sudo apt install libsecret-1-dev
   cd /usr/share/doc/git/contrib/credential/libsecret/
   sudo make
   git config --global credential.helper /usr/share/doc/git/contrib/credential/libsecret/git-credential-libsecret
   

   After you do the above, you should be able to login once to Github and not have to enter your credentials again.

7. Download and install conda for installing python and R packages inside virtual environments. When it asks for the path to install, I usually put it inside my ~/lib folder instead of my home folder.

   cd ~/lib
   wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
   sh Miniconda3-latest-Linux-x86_64.sh 
   conda activate base
   

8. Install autojump for navigation. It will ask you to copy-paste a line into your ~/.bashrc. Do this by replacing the corresponding similar lines from Heungwon's version of ~/.bashrc.

   cd ~/git/
   git clone git://github.com/wting/autojump.git
   cd autojump/
   ./install.py 
   

   9. Install RStudio for data analysis from http://www.rstudio.com/products/rstudio/download/.

9. Add the libreoffice Ubuntu package repository to your system and install the latest version of libreoffice for spreadsheet and word editor:

   sudo add-apt-repository ppa:libreoffice/ppa
   sudo apt update
   sudo apt install libreoffice
   

10. Add the inkscape Ubuntu package repository to your system and install the latest version of inkscape for drawing vector graphics:

    sudo add-apt-repository ppa:inkscape.dev/stable
    sudo apt update
    sudo apt-get install inkscape
    

11. Install ssh packages for remote connections. Then make sure your ssh configuration file is symbolically linked as described here.

    sudo apt install openssh-server
    sudo apt install sshfs
    

12. Set up password-less authentication to the Hutch server rhino:

    # Accept all defaults
    ssh-keygen -t rsa
    # Create directory for config on rhino
    ssh rhino3 mkdir -p .ssh
    # Send your public key to rhino
    cat .ssh/id_rsa.pub | ssh rhino3 'cat >> .ssh/authorized_keys'
    

13. Install google-chrome web browser:

    wget https://dl.google.com/linux/direct/google-chrome-stable_current_amd64.deb
    sudo dpkg -i google-chrome-stable_current_amd64.de
    

14. I also install useful applications such as imagej (Images), zotero (Bibliography), gnome-tweak-tool (Desktop customization), okular (PDF annotation), slack (Team communication), texlive (Latex and PDF creation).