This script installs `qiime` following the instructions at http://qiime.org/install/install.html

install_qiime.sh

#!/bin/bash

# This script installs `qiime` following the instructions at http://qiime.org/install/install.html, creating a conda enviroment
# called `qiime1` 
# It also installs miniconda following the steps at https://conda.io/docs/install/quick.html, in case it's not found within
# the user's path

source activate qiime1 2> /dev/null
if [ $? -eq 0 ]; then
  echo "qiime is already installled. Use \`source activate qiime1i\` to activate its working environment"
  source deactivate
  exit 0
fi

command -v conda > /dev/null
if [ $? -ne 0 ]; then
  echo "Miniconda will be installed in order to provide your \`qiime\` environment. You should agree with its license. Write \`yes\` when asked"
  echo "\n"
  echo "You will also be asked for a location, just press ENTER to confirm the default one."
  echo "\n"
  echo "You will be finally asked to preppend Miniconda's path to your \`.bashrc\` file. Write \`yes\` then. In other case this installation may fail."
  echo "\n"
  read -p "Press ENTER to continue ..."
  wget https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh
  chmod +x Miniconda2-latest-Linux-x86_64.sh
  ./Miniconda2-latest-Linux-x86_64.sh
  source ~/.bashrc
  rm ./Miniconda2-latest-Linux-x86_64.sh
fi

conda create -y -n qiime1 python=2.7 qiime matplotlib=1.4.3 mock nose -c bioconda