things-to-set-up.txt

## Install from repos
sudo apt-get update
sudo apt-get dist-upgrade
# Fortran compiler
sudo apt-get install gfortran
# Curl
sudo apt-get install curl
# Pip for python (package manager) ## If this doesn't work just dl the file linked from the pip website
wget https://bitbucket.org/pypa/setuptools/raw/bootstrap/ez_setup.py -O - | sudo python2.7
curl --silent --show-error --retry 5 https://raw.github.com/pypa/pip/master/contrib/get-pip.py | sudo python2.7
cmake
sudo apt-get install apt-file ## then do sudo apt-file update and use as apt-file search filename
swig
libatlas libzmq-dev libsuitesparse-dev
# Things for ipython (install from apt-get)
python-nose python-tornado sphinx-common libsphinxbase-dev python-sphinx python-jinja2

emacs (aim for v25 at least)
git
vim ## Needed this as for some reason the in-built vi/vim produced ABCD for arrow-keys
mplayer
imagemagick

## better to dl R from CRAN repo using the Ubuntu deb file
## Build from source ## Or can consider downloading Ubuntu .deb from CRAN repo
R ## ./configure  --enable-R-shlib
## Depends: libxt-dev, libboost-dev, libx11-dev, libreadline-dev, g++, libc++-dev OR maybe libcppunit-dev, libgtk2.0-dev, mesa-common-dev, libpq-dev libcurl4-openssl-dev, libglu1-mesa-dev, libxml2-dev
## then R> install.packages(c("ggplot2","plyr","formatR", "deSolve", "shiny", "devtools", "knitr", "dplyr","reshape2","ggvis"), dependencies=TRUE)
## will cover a lot of good packages

## Install TeXLive
Download tar file
tar -xzf install-tl-unx.tar.gz
cd into directory
sudo ./install-tl  -> type i 
add to $PATH
check with echo $PATH in new terminal, or source ~/.bashrc in current terminal

## Things to install with pip
ipython, virtualenv

## Things to install in emacs
rainbow-mode, rainbow-delimeters, tabbar, adaptive-wrap, hlinum, highlight-indentation

## Things to change
Make terminal profile
Install Monaco-Linux.ttf and MonacoB2-Bold.otf
Play with .bashrc, .vimrc, .emacs

## Chinese keyboards
Install fcitx and many other similarly prefixed packages including: m17n, googlepinyin, wubi.
May need to uninstall ibus as well. Initially also install language packs in keyboard settings and possibly look into input method (didn't appear to help Linux Mint 19.1). Restarting with fcitx selected there and all these keyboards that are available can be selected in the fcitx configuration preferences.
CTRL+Shift+SPACE to see the options (CTRL+SPACE to switch between current and previous keyboards)

## To restore a Linux live USB
Restoring your USB key to its original state using Linux:

A. First we need to delete the old partitions that remain on the USB key.

Open a terminal and type sudo su
Type fdisk -l and note your USB drive letter.
Type fdisk /dev/sdx (replacing x with your drive letter)
Type d to proceed to delete a partition
Type 1 to select the 1st partition and press enter
Type d to proceed to delete another partition (fdisk should automatically select the second partition)
B. Next we need to create the new partition.

Type n to make a new partition
Type p to make this partition primary and press enter
Type 1 to make this the first partition and then press enter
Press enter to accept the default first cylinder
Press enter again to accept the default last cylinder
Type w to write the new partition information to the USB key
Type umount /dev/sdx1 (replacing x with your drive letter)
C. The last step is to create the fat filesystem.

Type mkfs.vfat -F 32 /dev/sdx1 (replacing x with your USB key drive letter)
That's it, you should now have a restored USB key with a single fat 32 partition that can be read from any computer.
##################
##################

## Cinnamon spices to install
http://cinnamon-spices.linuxmint.com/applets/view/116
## this makes a workspace grid. Put dl'ed unzipped folder in ~/.local/share/cinnamon/applets then restart cinnamon (alt-f2 and type r) go to setting -> applets & right click 'workspace grid 2D' add to panel. Right click in panel and select 'configure...' to alter # of workspaces.

## Set up ssh 
ssh-keygen -t rsa
ssh-add ~/.ssh/id_rsa
ssh-add -l
cat ~/.ssh/id_rsa.pub (put this in bitbucket)

## Sudo without password
sudo visudo
add a line that looks like <username> ALL=NOPASSWD: ALL at the bottom of file

## To get 2nd work screen right size run this
xrandr --output VGA1 --mode 1680x1050

## Command in vi to search for pattern (article{lettersDigits)and then lowercase the thing captured
:%s/article{\([A-Z][a-z]*[0-9]*\)/\L&/c
## Need to learn this: match globally year the do the sub
:g/year/s/$/}/
## Can do like this to delete all lines matching pattern
:g/pattern (put /d at the end to see lines to be deleted)

## If you don't want your history saved you can do
export HISTFILE=/dev/null

## Downsampling images with ImageMagick
convert ~/Desktop/OSR.jpg -resize 25% OSR-low.jpg ## Input (final quality) output
convert jacaranda.jpg -resize 50% jacaranda-low.jpg
convert IMG_4755.JPG -resize 45% rosette-low.jpg
convert IMG_4797.JPG -resize 45% mainStem-low.jpg 
convert IMG_4793.JPG -resize 45% brancing-low.jpg 
convert -density 300 loops.pdf[5] -quality 100 ~/Dropbox/CV/postdocCVs/Fellowships/network.png

## convert from jpeg to pdf
convert IMG_4434.JPG proofOfWorkContract.pdf
convert -rotate 90 *.JPG formPDU1pages1-4.pdf

## Firefox extensions
Adblock Plus
ColorfulTabs
colorPicker
ReloadEvery
Hide Caption Titlebar Plus
Classic Theme Restorer (Customize UI)

## Firefox allow backspace to go back
open an about:config tab
Set "browser.backspace_action" to 0
Set browser.search.showOneOffButtons to false ## Restore old search style bar
Set browser.showQuitWarning to true ## kinda obvious, dunno why it's not default...!!!