Preparing a crouton chroot environment for productivity.

prep-crouton.sh

#!/bin/sh

# sudo visudo
# matsen ALL = (root) NOPASSWD: /usr/local/bin/xiwi,/usr/bin/evince,/usr/bin/inkscape


set -e
set -o

sudo hostnamectl set-hostname flyx

sudo add-apt-repository ppa:neovim-ppa/unstable
sudo apt-get update
sudo apt-get upgrade -y

while read LINE
do
   echo LINE
done<<STARTHERE
STARTHERE

sudo apt-get install -y \
    autojump \
    automake \
    biber \
    cmake \
    cgdb \
    curl \
    doxygen \
    evince \
    fonts-mono \
    git \
    htop \
    imagemagick \
    info \
    inkscape \
    inotify-tools \
    keychain \
    language-pack-en \
    libxml2-dev \
    libalgorithm-diff-perl \
    neovim \
    pandoc \
    pdftk \
    poppler-utils \
    python-pip \
    python3-pip \
    scons \
    silversearcher-ag \
    software-properties-common \
    texlive-bibtex-extra \
    texlive-fonts-recommended \
    texlive-fonts-extra \
    texlive-latex-extra \
    texlive-science \
    tmux \
    tree \
    vim-gtk \
    xvfb \
    zsh

ssh-keygen
cat ~/.ssh/id_rsa.pub
echo "Upload key to github..."
read

# libcurl4-openssl-dev
# libgsl0-dev
# libsqlite3-dev
# ocaml
# rlwrap
# parallel


# pathogen!
mkdir -p ~/.vim/autoload ~/.vim/bundle && \
curl -LSso ~/.vim/autoload/pathogen.vim https://tpo.pe/pathogen.vim
cd ~/.vim/bundle
while read PKG
do
    git clone git://github.com/$PKG
done <<PATHOGENLIST
altercation/vim-colors-solarized
rking/ag.vim
ervandew/supertab
junegunn/fzf.vim
kenkov/openurl.vim
kien/ctrlp.vim
mattn/gist-vim
mattn/webapi-vim
msanders/snipmate.vim
scrooloose/syntastic
sjl/tslime.vim
tpope/vim-endwise
tpope/vim-fugitive
tpope/vim-git
tpope/vim-markdown
tpope/vim-surround
tpope/vim-vinegar
Valloric/YouCompleteMe
vim-pandoc/vim-pandoc
PATHOGENLIST

# install python packages
pip3 install --user \
    alnvu \
    biopython \
    csvkit \
    dendropy \
    flake8 \
    jupyter \
    lxml \
    neovim \
    nestly \
    pandas \
    pybtex \
    PyPDF2 \
    requests-oauthlib \
    scons \
    seaborn \
    seqmagick \
    sphinx \
    virtualenv \
    twisted \
    git+https://github.com/astraw/svg_stack.git


# In case of jekyll
sudo apt-get install ruby ruby-dev make gcc nodejs
sudo gem install jekyll --no-rdoc --no-ri


# set up various dotfiles, etc
cd ~
chsh matsen -s `which zsh`
git config --global github.user matsen
git clone git@github.com:matsen/etc.git
cd ~/etc/
git submodule init
git submodule update
./symlink_it.sh

# set up packages that need it
cd ~/.vim/bundle/YouCompleteMe
git submodule update --init --recursive
./install.py --clang-completer

# final tidying
sudo apt-get autoremove -y
hash -r
cd