Bioinformatics flavoured Mojave

gistfile1.sh

# Resilio, Dropbox, JupyterLab, Firefox, Sublime, Atom, Zotero, VPNs,
# Slack, Bitwarden, Office, Sketch, Typora
# Brew, Miniconda, Jupyterlab, RStudio, Docker
# Install custom jupyterlab envs https://ipython.readthedocs.io/en/latest/install/kernel_install.html#kernels-for-different-environments
# Create /opt/ and /opt/bin, place nextflow inside latter.
# Put toggle-able symlinks to brewed GCC inside here, prepend to path in .bashrc (`gcc_links_on`, `gcc_links_off`)
# Nextflow
# .ssh
# Generate keys
# Create /opt and opt/bin, add to path
# Copy dotfiles
# BitTorrent Sync .ignoreList
# Finder window layout, default directory, dock and displays config, show file extensions
# Keyboard repeat rate, mouse shortcuts
# Terminal.app config
# Add Google and Exchange accounts
# Time Machine
# Printing
# Menubar... TM, keychain lock
# Mail.app signatures
# SSH key generation... Don't use vulnerable primes
# Network drive mounting
# .bashrc .bash_profile .shh .gitconfig
# Scriptlets dir shortcuts
# Sublime Text config... Open in new window
# RStudio config
# Recreate conda envs

# -- Git --
git config --global user.name "Bede Constantinides"
git config --global user.email "[email protected]"

# -- XCode -- 
# Install XCode from app store
sudo xcodebuild -license

# -- Homebrew --
ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"
brew update && brew upgrade
brew doctor

# -- Fundamentals --
brew install python python3 pypy3 pandoc
brew install coreutils cmake open-mpisqlite gnu-tar gnu-sed wget watch parallel pigz rsync

brew install gcc # takes half an hour - defer
brew install cmake
brew install Caskroom/cask/java
# Quartz (Be careful of Tcl/Tk irritating brew!), Tablet, Sanger SeqTools

# -- Conda --
https://conda.io/miniconda.html

# -- Dotfiles --
curl https://raw.githubusercontent.com/bede/conf/master/.bashrc > ~/.bashrc
curl https://raw.githubusercontent.com/bede/conf/master/.inputrc > ~/.inputrc
curl https://raw.githubusercontent.com/bede/conf/master/.bash_profile > ~/.bash_profile
curl https://raw.githubusercontent.com/bede/conf/master/.gitconfig > ~/.gitconfig
curl https://raw.githubusercontent.com/bede/conf/master/config > ~/.ssh/config

# -- Python --
python3 -c "import plotly; plotly.tools.set_credentials_file(username='DemoAccount', api_key='DemoPassword')"

# -- Data analysis --
pip3 install plotly pandoc jupyterlab
brew install r jq spark
# R, RStudio, Anaconda

# -- Bioinformatics --
brew install htslib simplesam tictax kindel
# Tablet, Sanger SeqTools, Bandage