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After installing Ubuntu

  • Get google-chrome
  • Get dropbox
  • Install some stuff:
sudo apt-get install zsh git-core python3-pip radiotray clementine vlc vim-gnome i3 tig hplip-gui xclip curl transmission-cli transmission-daemon transmission-common mutt unattended-upgrades libncurses-dev python-dev build-essential cmake libiw-dev xbacklight libfreetype6-dev xautolock latexmk gummi texlive-lang-spanish meld xdec dh-autoreconf

ssh-keygen -t rsa -b 4096 -C "[email protected]"
[enter]
[enter]
[passphrase]
eval "$(ssh-agent -s)"
ssh-add ~/.ssh/id_rsa
xclip -sel clip < ~/.ssh/id_rsa.pub

sh -c "$(curl -fsSL https://raw.github.com/robbyrussell/oh-my-zsh/master/tools/install.sh)"

  • remove Ubuntu default home directories
rmdir Desktop Documents Downloads Music Pictures Public Templates Videos
mkdir ~/software
  • Install Vundle
  mkdir ~/repos
  cd ~/repos
  git clone https://github.com/VundleVim/Vundle.vim.git ~/.vim/bundle/Vundle.vim
  • Clone the dotfiles:
cs ~/repos
git clone [email protected]:jmberros/dotfiles.git
cd ~/repos/dotfiles
cp .vimrc .i3pystatus.py .zshrc ~/
  • Install i3 WM
sudo echo "deb http://debian.sur5r.net/i3/ $(lsb_release -c -s) universe" >> /etc/apt/sources.list
sudo apt-get update
sudo apt-get --allow-unauthenticated install sur5r-keyring
sudo apt-get update
sudo apt-get install i3
  • Get rid of Nautilus desktop. (If this doesn't work, install dconf-tools and maybe libdconf1 and change that option manually from the dconf-editor.)

gsettings set org.gnome.desktop.background show-desktop-icons false

  • Git aliases and config
git config --global user.email "[email protected]"
git config --global user.name "Juan Manuel Berros"
git config --global alias.co checkout
git config --global alias.ci commit
git config --global alias.st status
git config --global alias.br branch
git config --global alias.hist 'log --pretty=format:"%h %ad | %s%d [%an]" --graph --date=short'
git config --global alias.type 'cat-file -t'
git config --global alias.dump 'cat-file -p'
  • Git merge config:
[merge]
    tool = mymeld
[mergetool "mymeld"]
    cmd = meld --diff $BASE $LOCAL --diff $BASE $REMOTE --diff $LOCAL $MERGED $REMOTE
  • Shit for i3pystatus:
sudo apt-get install python3.5-dev
pip3 install psutil i3pystatus netifaces colour basiciw pyvcf
cp ~/repos/dotfiles/.i3pystatus.laptop.py ~

Reiniciar y loguearse en i3:

  • After default creation of ~/.i3/config, copy i3's config file: cp ~/repos/dotfiles/.i3.config ~/.i3/config

  • ((in case it's not in i3 config: setxkbmap -option caps:swapescape))

  • Choose (2) here to get dmenu with a reasonable font: sudo update-alternatives --config dmenu

  • Enable reboot and shutdown from i3:

sudo visudo
# Add this line to the file:
juan     ALL = NOPASSWD: /sbin/reboot, /sbin/shutdown, /sbin/poweroff
  • Renew Fonts
cp -R ~/repos/dotfiles/.fonts ~/
fc-cache -f -v
  • Copy vim themes

cp -r ~/repos/dotfiles/vim_colors ~/.vim/colors

  • Install Vim Plugins

vim +PluginInstall +qall

YouCompleteMe plugin probably needs to be compiled. Go to its directory and run ./install.sh

  • Copy fstab to automount HDDs. Use sudo fdisk -l or sudo blkid in case you need UUIDs:
sudo nano /etc/fstab
/dev/sdb1   /media/500gb    auto    auto,users  0 0
/dev/sdc3   /media/600gb    auto    auto,users    0 0
  • Fonts for airline/powerline:
git clone [email protected]:powerline/fonts.git
./install.sh

And set your gnome-terminal profile to use Ubuntu mono for Powerline 12 and gray on black with a lighter gray.

  • Bajarse Anaconda e instalar Jupyter y R.
conda install jupyter numpy pandas biopython matplotlib scipy ternary lxml html5lib beautifulsoup4
  • IPython startup:
ipython profile create
vi ~/.ipython/profile_default/ipython_config.py
# ^ Add / uncomment stuff (pending)

  • Transmission setup: sudo vi /etc/transmission-daemon/settings.json y copiarle lo que haya en ~/repos/dotfiles/settings.json ( es posible que desde transgui tengas que cambiar a mano los directorios de dl, /media/600gb/transmission-daemon/{in}complete )

    sudo service transmission-daemon start

  • Instalar ruby para los cronjobs:

git clone https://github.com/rbenv/rbenv.git ~/.rbenv
echo 'export PATH="$HOME/.rbenv/bin:$PATH"' >> ~/.zshrc
echo 'eval "$(rbenv init -)"' >> ~/.zshrc
git clone https://github.com/rbenv/ruby-build.git ~/.rbenv/plugins/ruby-build
git clone git://github.com/jf/rbenv-gemset.git $HOME/.rbenv/plugins/rbenv-gemset

sudo apt-get install libssl-dev libreadline-dev zlib1g-dev
rbenv install -l  # Check for the last stable ruby
rbenv install <version>
rbenv local <version>
rbenv rehash
ruby --version
rbenv-gemset (ver online)
gem install nokogiri pony colorize actionview pry

  • Look for .smpt_credentials in your mail archive and save it to ~/.smtp_credentials

  • Set up the cronjobs! crontab -e y copiar lo que haya en ~/repos/dotfiles/crontab

  • Get your scripts from github:

cd ~/repos
git clone [email protected]:jmberros/last-episode.git

sudo add-apt-repository ppa:kilian/f.lux
sudo apt-get update
sudo apt-get install fluxgui
xflux -l -34.60 -g -58.38
  • Set unattended-upgrades:
sudo dpkg-reconfigure unattended-upgrades
sudo vi /etc/apt/apt.conf.d/50unattended-upgrades
# Add "Google\, Inc.:stable"; to Allowed-Origins
# Uncomment updates in Allowed-Origins
# Uncomment the 'Mail root' line
sudo vi /etc/apt/apt.conf.d/20auto-upgrades
# Add these lines:
# Though I'm not quite sure if these go in the file 10periodic instead
APT::Periodic::Update-Package-Lists "1";
APT::Periodic::Unattended-Upgrade "1";
APT::Periodic::Download-Upgradeable-Packages "1";
APT::Periodic::AutocleanInterval "7";
APT::Periodic::Verbose "1";
  • Some bioinformatics shit:
    • download and install VCFtools, SAMtools, and tabix.
    • for tabix, run make after extracting and copy the executable to /usr/bin; for the rest, ./configure, make, sudo make install
pip install git+https://github.com/jamescasbon/PyVCF
pip install sklearn ftputil humanize ipdb pep8 pyyaml ipdb lxml
pip install git+https://github.com/marcharper/python-ternary.git
  • Jupyter custom themes:
cp ~/repos/dotfiles/_dot_jupyter/custom/* ~/.jupyter/custom
  • To pair the Varmilo keyboard (After pluggin the Bluetooth dongle!), follow the instructions here.
sudo add-apt-repository ppa:vidplace7/bluez5
sudo apt-get update
sudo apt-get install bluez bluetooth
  • Make sure the Varmilo Keyboard is turned on: Fn + Insert
  • Then start bluetoothctl for an interactive prompt. Try with these commands:
  • power on, agent on (or agent KeyboardOnly?), pairable on, scan on
  • The scan on command should show you the MAC address for the keyboard! Use that MAC address (autocomplete with TAB works, don't type the whole thing) in this command: pair MAC, wait for the pairing to be successful (it should print a Passkey on screen, type that number with the keyboard and hit ENTER!!)
  • Once the pairing is successfull, try connect MAC.
  • I needed to reboot the computer and then the keyboard was paired.
  • Watch out for auto-turn off of the thing, make sure it's on while pairing/connecting.

I couldn't get a passkey to be displayed on my second attemp on this, so I first connected to the thing from the GUI bluetooth-wizard, selecting "Set up new device", choosing the keyboard, and then "Do not pair" and without passkey. This would connect it without pairing it. I later did a GUI-based pairing with the keys icon (though this could be done using bluetoothctl # pair <MAC> too.) The result was a non-functional pairing though ....

I have no idea how I got it to display a passkey on the other run! Blueman does display a PASSKEY when I connect the keyboard in beleriand ....

I did got the message via Ubuntu notification ONLY when using the regular Unity session / WM, not i3.

While you do stuff on the GUI, keep an eye on bluetoothctl to check what happens.

  • Command to backup beleriand's music dir (run from arrakis!):
nice -n 19 ionice -c3 rsync [email protected]:/media/600gb/music/ ~/ -avhz --delete

  • Remove zsh theme ls alias in ~/.oh-my-zsh/lib/theme-and-appearance.zsh.

  • To remap keys in the Lenovo laptop (HOME, END, PAGE DOWN|UP), I used this https://radu.cotescu.com/remapping-keys-in-ubuntu-14.04/. Edit the file and change the keys and their mappings, it's intuitive enough to figure it out along the way:

sudo vi /usr/share/X11/xkb/symbols/pc

Biotools

  • java
  • haploview (agregar alias al zshrc)
  • vcftools
  • samtools
  • bedtools
  • Gatk (agregar alias al zshrc)
  • Python con jupyter via conda
  • fastq-mcf (ea-utils)
  • picard tools