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01_provision_ubuntu.sh
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#!/bin/bash
# 01_vagrant_provision_ubuntu.sh
# shell script for provisioning vagrant box running ubuntu 16.04
# also, could be the basis for provisioning an AWS image, or simply for getting all the necessary software
# for this great adventure up and running on your own computer
# Jamie Collins, Armbrust Lab, University of Washington; [email protected]
# *** assumes this shell script is present on the remote computer (not your local machine)
# to do this, use scp or, better yet, clone GitHub repo containing all the scripts directly to the remote
# type at shell prompt: git clone https://github.com/jamesrco/NWPac_amplicon NWPac_amplicon
# *** if using AWS: will assume we've allowed SSH traffic in the security group we used to set up our machine image
# to run this script, type at shell prompt: source ./01_vagrant_provision_ubuntu.sh
# ----------------------------------------------------
# provision ubuntu 16.04 environment
# ----------------------------------------------------
# install unzip
sudo apt-get install unzip
# install, configure rclone (allows command-line access to Dropbox, Google Drive, etc.)
curl https://rclone.org/install.sh | sudo bash
echo "q" | rclone config --config=".rclone.conf"
# *** installing brew doesn't appear necessary in Ubuntu 16.04 case (based on testing with AWS image as of Apr 3 2018)
# # install brew (for Ubuntu; avoids password prompt)
# sudo apt-get install build-essential curl file git python-setuptools
# sudo apt install linuxbrew-wrapper
# test -d ~/.linuxbrew && PATH="$HOME/.linuxbrew/bin:$HOME/.linuxbrew/sbin:$PATH"
# test -d /home/linuxbrew/.linuxbrew && PATH="/home/linuxbrew/.linuxbrew/bin:/home/linuxbrew/.linuxbrew/sbin:$PATH"
# test -r ~/.bash_profile && echo "export PATH='$(brew --prefix)/bin:$(brew --prefix)/sbin'":'"$PATH"' >>~/.bash_profile
# echo "export PATH='$(brew --prefix)/bin:$(brew --prefix)/sbin'":'"$PATH"' >>~/.profile
# echo "export PATH='/home/linuxbrew/.linuxbrew/bin'":'"$PATH"'
# # install brew (for Linux, or Ubuntu if you know the root password)
# sh -c "$(curl -fsSL https://raw.githubusercontent.com/Linuxbrew/install/master/install.sh)"
# test -d ~/.linuxbrew && PATH="$HOME/.linuxbrew/bin:$HOME/.linuxbrew/sbin:$PATH"
# test -d /home/linuxbrew/.linuxbrew && PATH="/home/linuxbrew/.linuxbrew/bin:/home/linuxbrew/.linuxbrew/sbin:$PATH"
# test -r ~/.bash_profile && echo "export PATH='$(brew --prefix)/bin:$(brew --prefix)/sbin'":'"$PATH"' >>~/.bash_profile
# echo "export PATH='$(brew --prefix)/bin:$(brew --prefix)/sbin'":'"$PATH"' >>~/.profile
# echo "export PATH='/home/linuxbrew/.linuxbrew/bin'":'"$PATH"'