setup.txt

# homebrew (http://brew.sh)
/usr/bin/ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"

# get emacs
brew tap railwaycat/emacsmacport
brew cask install emacs-mac

# git
git config --global user.name [NAME]
git config --global user.email [EMAIL]

# hub (https://hub.github.com)
brew install hub

# create ssh key for github (https://help.github.com/articles/generating-a-new-ssh-key-and-adding-it-to-the-ssh-agent/)
ssh-keygen -t rsa -b 4096 -C [EMAIL]
eval "$(ssh-agent -s)"
ssh-add ~/.ssh/id_rsa
pbcopy < ~/.ssh/id_rsa.pub
## then add ssh key to github in the browser interface

# create remote repository on github with hub
hub create [NAME]

# r
brew tap homebrew/science
brew install r
## to make sure that r use the same locales as the system (to avoid it resorting to C) the locales
## need to be set in .bashrc and "imported" into emacs using exec-path-from-shell

# ghostscript, to get doc-view in emacs, among other things, to work
brew install ghostscript

# ess
## first you need wget
brew install wget --with-libressl
## then get ess
cd ~/Downloads
wget http://ess.r-project.org/downloads/ess/ess-16.10.tgz
tar -zxvf ess-16.10.tgz
## then change DESTDIR to DESTDIR=/usr/local/opt/emacs-mac
sudo make install

# install MacTeX
brew cask install mactex
## for some reason this did not work this time, so you might want to dowload from http://www.tug.org/mactex/mactex-download.html

# AUCTeX (https://www.gnu.org/software/auctex/), may require /Library/TeX/texbin (where MacTeX is)to be added to PATH
brew install homebrew/tex/auctex

# poppler, to get pdf-tools to work
brew install poppler automake

# pandoc, for conversion between file formats
brew install pandoc

# gimp
brew install gimp

# scribus
brew install Caskroom/cask/scribus

# adobe reader
brew install Caskroom/cask/adobe-reader

# libssh2, to get R devtools to work
brew install libssh2

# pip, to get csvkit among other stuff
sudo easy_install pip

# csvkit
sudo -H pip install csvkit --ignore-installed six
## the ignore-installed stuff is needed because of apple/pip related issues, see https://github.com/pypa/pip/issues/3165

# xlsx2csv, https://github.com/dilshod/xlsx2csv
sudo easy_install xlsx2csv

# texinfo, to get texi2dvi to work
brew install texinfo

# spotify
brew cask install spotify

# getnonfreefonts
wget -q http://tug.org/fonts/getnonfreefonts/install-getnonfreefonts
sudo texlua ./install-getnonfreefonts
sudo getnonfreefonts-sys -a

# GNU awk
brew link gmp
brew install gawk

# antiword
brew install antiword

# ImageMagick
brew install ImageMagick

# PDFtk
wget https://www.pdflabs.com/tools/pdftk-the-pdf-toolkit/pdftk_server-2.02-mac_osx-10.11-setup.pkg
sudo installer -pkg pdftk_server-2.02-mac_osx-10.11-setup.pkg -target /

# JAGS
wget https://sourceforge.net/projects/mcmc-jags/files/JAGS/4.x/Mac%20OS%20X/JAGS-4.2.0.dmg
sudo hdiutil attach JAGS-4.2.0.dmg
sudo installer -package /Volumes/JAGS-4.2.0/JAGS-4.2.0.mpkg -target /
sudo hdiutil detach /Volumes/JAGS-4.2.0

# mount webdav
cd ~/
mount_webdav -is https://owncloud.ki.se/remote.php/webdav/ owncloud/

# mysql (if still on mac https://www.macminivault.com/install-mysql-on-macos-sierra/)
brew install mysql
brew services start mysql

# if homebrew does not work because of ownership issues (e.g. dir not writeable) try
sudo chown -R martin:admin /usr/local/bin

# get msmtp
brew install msmtp --with-macosx-keyring
# put .msmtprc in ~/