Various configuration files
Shell VimL Python Ruby Clojure R Smarty
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background_tasks Move push_dotfiles script Feb 13, 2014
bin Add scripts to record current status May 23, 2016
data Update list of homebrew installs May 6, 2016
dircolors-solarized @ 82342cd Latest version of solarized dircolors Jun 26, 2012
docker Docker image for CLI to jira Aug 14, 2015
examples Add guardfile example Aug 28, 2013
irssi Irrsi configuration files Jan 26, 2011
jgi_bin Added script to generate show metagenome report Apr 8, 2014
jira_bin Create jira comment message in current dir Dec 28, 2014
launchd_agents Add scripts to record current status May 23, 2016
lein Update clojure profiles plugin list Mar 23, 2016
login_scripts Change permissions for cache dir Aug 12, 2011
mutt Auto sign replies in mutt Aug 14, 2015
script_system Use stow to install system files Jun 5, 2015
shell_settings Using docker-machine to set environment variables Oct 1, 2015
solarized @ e40cd41 Update solarized module Aug 17, 2015
status_bar Merge branch 'master' of Feb 13, 2014
vim Reformat text before editting mail Apr 2, 2015
zsh-git @ 715ba48 Add zsh-git submodule Aug 23, 2011
.gitignore Ignore netwhist Apr 2, 2015
.gitmodules Remove unused irbfiles Feb 4, 2014 Update README with install instructions Aug 3, 2015
Rprofile Specify default cran mirror Sep 23, 2013
aspell.conf aspell configuration Dec 2, 2008
aspell.en.pws Update dictionary May 6, 2016
bashrc Add bashrc Oct 1, 2015
gemrc Update sources for gemrc Oct 23, 2011
gitconfig Don't sign off on gitcommits Oct 1, 2015
gitignore Ignore python files Oct 24, 2013
inputrc More fixes for the bell Sep 19, 2011
lbdbrc Little brother database configuration file Dec 3, 2010
mailcap Add pdf viewer to mailcap May 20, 2012
msmtprc Update location for certificates for msmtp Jun 1, 2015
muttrc Move compose to separate file Apr 2, 2015
notmuch-config Add notmuch config Jul 22, 2014
octaverc Configure octave Oct 25, 2011 Offline imap configuration Nov 29, 2010
offlineimaprc Update certificates for offlineimap May 28, 2015
r_packages Add dplyr to common R packages Apr 28, 2014
rspec Rspec command line options Dec 30, 2010 Use stow to install system files Jun 5, 2015
tmux.conf Use absolute path of reattache to namespace script Oct 1, 2015
urlview Add urlview command Dec 3, 2010
vimrc Vim ignore python egg files Oct 1, 2015
wgetrc Update location in wget Feb 12, 2014
zshrc Reorganise shell paths Dec 10, 2014


Run the following command in the root of the dotfiles directory to pull required submodules

git submodule init
git submodule update

Run the following command to install all additional tools and apps


Install vim plugins

vim +PluginInstall +qall


Run the following command to link all the dotfiles into your home directory.

ls ~/.dotfiles | xargs -I '{}' ln -s ~/.dotfiles/{} ~/.{}

Also softlink colors schemes

ln -s ~/.dircolors-solarized/dircolors.256dark ~/.dir_colors


I use tmux as my shell. After installation with as above, edit /etc/shells to include the line:


Then run the following command

chsh -s /usr/local/bin/tmux


Reset caps lock to be ctrl, System Preferences > Keyboard > Modifier Keys. I find this a bit better than reaching for the actual control key with my small finger.


Iterm2 has better all round support for colours, tmux and accessing the the clipboard. This is installed using Caskroom in the section above.

  • Set "Allow clipboard access to terminal apps"
  • Profiles > Terminal > "Silence bell"
  • Profiles > Colors and click the drop down menu and select import. Select the file: 'solarized/iterm2-colors-solarized/Solarized Dark.terminal.' You may need to copy this file to the desktop first if you can access in in the file chooser box.
  • Set font to inconsolate-dz size 14


Download and install mactex -


Add required passwords to keychain. Then use security to fetch them in the environment. E.g. email password and github.token

Offline imap

Create maildb directories e.g.

mkdir -p ~/.maildb/michaelbarton ~/.maildb/jgi

Set up certificates files:

ruby -ropenssl -e "p OpenSSL::X509::DEFAULT_CERT_FILE"


mkdir ~/.mutt
ln -s ~/.dotfiles/solarized/mutt-colors-solarized/mutt-colors-solarized-dark-256.muttrc ~/.mutt/colors