Script for installing all of the software that I use.

from_scratch.sh

#!/bin/sh

set -e
set -o

sudo apt-get update
sudo apt-get upgrade -y

sudo apt-get install -y \
    autojump \
    build-essential \
    curl \
    git \
    guake \
    htop \
    imagemagick \
    inkscape \
    pandoc \
    python-dev \
    python-pip \
    rdesktop \
    rlwrap \
    scons \
    shutter \
    seaview \
    sshfs \
    tmux \
    tree \
    vim-gtk \
    zsh

# camlp4-extra
# cmake
# doxygen
# gimp
# graphviz
# inotify-tools
# libavcodec-extra-53
# libavconv-tools
# libcurl4-openssl-dev
# libgsl0-dev
# libbpp-core-dev 
# libbpp-phyl-dev
# libbpp-seq-dev 
# libsqlite3-dev
# ocaml
# osdclock
# parallel
# pstoedit
# sound-juicer
# texlive-latex-extra
# texlive-fonts-recommended
# ubuntu-restricted-extras
# xdot


# pathogen!
mkdir -p ~/.vim ~/.vim/tmp ~/.vim/autoload ~/.vim/bundle; \
curl -Sso ~/.vim/autoload/pathogen.vim \
    https://raw.github.com/tpope/vim-pathogen/master/autoload/pathogen.vim
cd ~/.vim/bundle
while read PKG
do
    git clone git://github.com/$PKG
done <<PATHOGENLIST
altercation/vim-colors-solarized
ervandew/supertab
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
vim-pandoc/vim-pandoc
PATHOGENLIST

# install python packages
sudo pip install \
    biopython \
    csvkit \
    dendropy \
    pybtex \
    seqmagick

# alnvu
# biopython
# csvkit
# DendroPy
# ete2
# flake8
# lxml
# jupyter
# nestly
# networkx
# notebook
# pandas
# pep8
# pybtex
# PyPDF2
# PyYAML
# requests
# requests-oauthlib
# scikit-learn
# seaborn
# seqmagick
# Sphinx
# taxtastic
# twisted
# virtualenv



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

# set up various dotfiles, etc
cd ~
chsh matsen -s `which zsh`
git config --global github.user matsen
git clone [email protected]:matsen/etc.git
cd ~/etc/
./symlink_it.sh
~/etc/bin/get_fonts.sh

# get all of my git repos
mkdir ~/re
~/etc/bin/full_git_pull
cd ~/etc
git submodule init
git submodule update

# remove Ubuntu rubbish
cd
rm -rf Desktop Documents Music Public Pictures Templates Videos
rm -f examples.desktop

exit 0

# opam
mkdir -p ~/local/src/
git clone git://github.com/OCamlPro/opam.git ~/local/src/opam
cd ~/local/src/opam
./configure
make
sudo make install
opam init
opam update
opam repo add pplacer-deps http://matsen.github.com/pplacer-opam-repository
opam update pplacer-deps
cd ~/re/pplacer
eval `opam config env`
cat opam-requirements.txt | xargs opam install -y
make

# beagle
cd ~/local/src
sudo apt-get install -y subversion autoconf libtool
svn checkout http://beagle-lib.googlecode.com/svn/trunk/ beagle-lib
cd beagle-lib
./autogen.sh
sudo ./configure --prefix=/usr/local/
sudo make install

sudo apt-get autoremove -y
hash -r
cd
ln -s /home/matsen/Copy/mobilehome/copyhome/wind.txt ~/wind