cwonrails / dotfiles-3

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 xbacklight libfreetype6-dev xautolock latexmk gummi texlive-lang-spanish meld xdec dh-autoreconf keychain

• Set ssh-keys to clone repos: https://help.github.com/articles/generating-ssh-keys/

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

• Paste the copied key here: https://github.com/settings/ssh

• Oh my zsh!

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

i3pystatus:

sudo apt-get install libdbus-1-dev libdbus-glib-1-dev libiw-dev 
pip install psutil i3pystatus netifaces colour basiciw dbus-python
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.

Python

• Bajarse Anaconda e instalar Jupyter y R.

conda install jupyter numpy pandas biopython matplotlib scipy ternary lxml html5lib beautifulsoup4
pip install html5lib q

• IPython startup:

ipython profile create
vi ~/.ipython/profile_default/ipython_config.py
# ^ Add / uncomment stuff (pending)

Ruby

DigitalOcean guide is perfect

MySQL

DigitalOcean guide is great

Then log in with the root account whose password you set up during install, and create a juan user:

> CREATE USER 'juan'@'localhost' IDENTIFIED BY 'password';
> GRANT ALL PRIVILEGES ON * . * TO 'juan'@'localhost';

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

• Add these lines to sudo vi /etc/apt/apt.conf.d/20auto-upgrades:

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";

Stuff for @beleriand

• 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

• 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

• Bajar soulseek y copiar el ejecutable a /usr/bin/soulseek

• f.lux para atonar el monitor al momento del día: https://justgetflux.com/ y correr

sudo add-apt-repository ppa:kilian/f.lux
sudo apt-get update
sudo apt-get install fluxgui
xflux -l -34.60 -g -58.38

Bioinformatics:

sudo apt-get install bioperl libbz2-dev liblzma-dev

Install:

• Samtools + Bcftools + HTSLib
• GATK
• PicardTools
• MultiQC
• cutadapt (pip install cutadapt)
• SnpEff + SnpSift
• VEP

Etc.

• 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