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reorganize and new repo
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‎.gitignore

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containers.json
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.vagrant/**

‎LICENSE

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Copyright (c) 2013 by Preston Holmes
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Redistribution and use in source and binary forms of the software as well
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as documentation, with or without modification, are permitted provided
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that the following conditions are met:
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* Redistributions of source code must retain the above copyright
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notice, this list of conditions and the following disclaimer.
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* Redistributions in binary form must reproduce the above
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copyright notice, this list of conditions and the following
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disclaimer in the documentation and/or other materials provided
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with the distribution.
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* The names of the contributors may not be used to endorse or
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promote products derived from this software without specific
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prior written permission.
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THIS SOFTWARE AND DOCUMENTATION IS PROVIDED BY THE COPYRIGHT HOLDERS AND
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CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT
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NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
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A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER
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OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
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EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
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PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
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PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
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LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
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NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
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SOFTWARE AND DOCUMENTATION, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
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DAMAGE.
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‎README.rst

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JiffyLab
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========
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JiffyLab is a project to provide an entirely web based environment for the
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instruction, or lightweight use of, Python and UNIX shell environment with
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zero-configuration of the user's machine.
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Currently in early development status
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The Problem
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-----------
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Python is a wonderful first language, but sometimes introducing people to
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Python is bogged down by making sure that everyone has a usable development
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environment. This can often set a tone of frustration for beginners, as well as
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completely drain instructor and assistants time, instead of letting everyone
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"dive in".
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There are other advantages to having a standardized environment:
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* If the instructor is projecting the same thing as what the student sees, the
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student will be less likely to be thown off by inconsequential details such
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as differences in the shell prompt (> vs $ etc), different syntax
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highlighting colors, or use of some tool or feature not installed on the
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student's machine.
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* When all students are using the same exact setup, they are more likely to be
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capable of helping their neighbor, as if they got it working on their screen,
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they can probably get it working on their neigbor - peers can more
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effectively visually "diff" what might be different.
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* Even if the setup of a student machine goes smoothly at a technical level, it
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can still take time, especially if a significant number of material needs to
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be downloaded over slow links, or requires significant build time.
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Trade-offs
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----------
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Messing around with tools and your machine setup is of course part of being
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a developer - learning how to manage your system and Python 'PATH', learning an
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editor, virtualenvs, pip etc all need to happen. But not in your first hour as
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a new developer.
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Another reason to have students work through the challenge of getting
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a working dev environment on their own machines is so that they can continue to
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teach themselves and learn on their own once past the introduction. This is
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very important, and should be built into any worthwhile instruction, it just
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doesn't need to happen at the beginning. Once students have learned some
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material, they will have much more context to understand what it is they are
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setting up, and will potentially have a greater motivation for getting it all
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working. So in the end I believe this trade-off is a bit of a red herring, as
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it is not about "either or", but "which comes first".
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TODO Learn to work on a server
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Quickstart
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----------
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JiffyLab uses `Docker <http://docker.io>`_ which provides each student a
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sandboxed environment through the use of linux containers (think lightweight,
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process level virtual machines). Note that this technology is Linux specific,
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so does NOT run on Mac OS X. You can run this quite effectively inside a Linux
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virtual machine using `vagrant <http://vagrantup.com>`_ (in fact, this project
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was developed on a Mac).
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# notes
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vagrant virtualbox stall on raring box
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‎Vagrantfile

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# -*- mode: ruby -*-
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# vi: set ft=ruby :
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BOX_NAME = ENV['BOX_NAME'] || "raring"
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BOX_URI = ENV['BOX_URI'] || "http://files.vagrantup.com/precise64.box"
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AWS_REGION = ENV['AWS_REGION'] || "us-east-1"
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AWS_AMI = ENV['AWS_AMI'] || "ami-d0f89fb9"
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# Add X.org Ubuntu backported 3.8 kernel
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kernel_upgrade = "add-apt-repository -y ppa:ubuntu-x-swat/r-lts-backport; " \
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"apt-get update -qq; apt-get install -q -y linux-image-3.8.0-19-generic; shutdown -r +1;"
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Vagrant.configure("2") do |config|
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config.vm.provider :virtualbox do |vb, override|
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override.vm.box = 'raring'
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override.vm.box_url = 'http://cloud-images.ubuntu.com/raring/current/raring-server-cloudimg-vagrant-amd64-disk1.box'
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override.vm.network :private_network, ip:"10.10.10.10"
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vb_guest_install = "apt-get install -q -y linux-headers-3.8.0-19-generic dkms; " \
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"echo 'Downloading VBox Guest Additions...'; " \
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"wget -q http://dlc.sun.com.edgesuite.net/virtualbox/4.2.12/VBoxGuestAdditions_4.2.12.iso; "
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# Prepare the VM to add guest additions after reboot
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vb_guest_install << "echo -e 'mount -o loop,ro /home/vagrant/VBoxGuestAdditions_4.2.12.iso /mnt\n" \
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"echo yes | /mnt/VBoxLinuxAdditions.run\numount /mnt\n" \
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"rm /root/guest_additions.sh; ' > /root/guest_additions.sh; " \
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"chmod 700 /root/guest_additions.sh; " \
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"sed -i -E 's#^exit 0#[ -x /root/guest_additions.sh ] \\&\\& /root/guest_additions.sh#' /etc/rc.local; " \
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"echo 'Installation of VBox Guest Additions is proceeding in the background.'; " \
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"echo '\"vagrant reload\" can be used in about 2 minutes to activate the new guest additions.'; "
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override.vm.provision :shell, :path => "linux-setup.sh"
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end
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config.vm.provider :rackspace do |rs, override|
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override.vm.box = "dummy"
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override.ssh.private_key_path = ENV["RS_PRIVATE_KEY"]
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rs.username = ENV["RS_USERNAME"]
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rs.api_key = ENV["RS_API_KEY"]
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rs.public_key_path = ENV["RS_PUBLIC_KEY"]
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rs.flavor = /512MB/
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rs.image = /Raring/
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override.vm.provision :shell, :path => "linux-setup.sh"
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end
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end

‎docker-builds/anaconda/Dockerfile

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# Sets up a container for the web based lab login
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#
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# VERSION 0.0.1
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# At some point, more of this will be pushed into its own docker image
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FROM ubuntu
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MAINTAINER Preston Holmes "[email protected]"
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RUN apt-get update -qq
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RUN apt-get install -y -q python-dev python-dev-all
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# sshd
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RUN apt-get install -y -q openssh-server
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EXPOSE 22
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RUN apt-get install -y -q sudo gcc make nano sqlite3
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RUN apt-get install -y -q python-pip
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RUN pip install -U pip
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# git
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RUN apt-get install -y -q libcurl4-gnutls-dev libexpat1-dev gettext libz-dev libssl-dev
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RUN apt-get install -y -q git
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# TODO add git configs
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RUN
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RUN
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RUN
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RUN
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RUN
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‎docker-builds/anaconda/anaconda-install.sh

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#!/bin/bash
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# Copyright (c) 2012-2013 Continuum Analytics, Inc.
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# All rights reserved.
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#
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# NAME: Anaconda
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# VER: 1.5.0
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# PLAT: linux-64
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# DESCR: 1.4.0-888-g5c37ff3
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# BYTES: 321578266
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# LINES: 371
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# MD5: ef6521e88b7eeabd6b7bae1a41ad728e
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unset LD_LIBRARY_PATH
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THIS_DIR=$(cd $(dirname $0); pwd)
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THIS_FILE=$(basename $0)
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THIS_PATH="$THIS_DIR/$THIS_FILE"
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PREFIX=$HOME/anaconda
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BATCH=0
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# TODO check if exists and is the right size etc and only download if needed
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curl -O http://09c8d0b2229f813c1b93-c95ac804525aac4b6dba79b00b39d1d3.r79.cf1.rackcdn.com/Anaconda-1.5.0-Linux-x86_64.sh
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mkdir -p $PREFIX
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if (( $? )); then
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echo "ERROR: Could not create directory: $PREFIX" >&2
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exit 1
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fi
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PREFIX=$(cd $PREFIX; pwd)
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export PREFIX
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cd $PREFIX
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tail -n +371 "$THIS_DIR/Anaconda-1.5.0-Linux-x86_64.sh" | tar xf -
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install_dist()
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{
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echo "installing: $1 ..."
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DIST=$PREFIX/pkgs/$1
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mkdir -p $DIST
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tar xjf ${DIST}.tar.bz2 -C $DIST || exit 1
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rm -f ${DIST}.tar.bz2
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}
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install_dist python-2.7.4-0
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install_dist _license-1.1-py27_0
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install_dist astropy-0.2.1-np17py27_0
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install_dist atom-0.2.3-py27_0
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install_dist biopython-1.61-np17py27_0
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install_dist bitarray-0.8.1-py27_0
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install_dist boto-2.9.2-py27_0
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install_dist cairo-1.12.2-1
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install_dist casuarius-1.1-py27_0
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install_dist conda-1.5.2-py27_0
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install_dist cubes-0.10.2-py27_1
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install_dist curl-7.30.0-0
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install_dist cython-0.19-py27_0
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install_dist dateutil-2.1-py27_1
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install_dist disco-0.4.4-py27_0
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install_dist distribute-0.6.36-py27_1
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install_dist docutils-0.10-py27_0
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install_dist dynd-python-0.3.0-np17py27_0
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install_dist enaml-0.7.6-py27_0
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install_dist erlang-R15B01-0
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install_dist flask-0.9-py27_0
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install_dist freetype-2.4.10-0
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install_dist gevent-0.13.8-py27_0
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install_dist gevent-websocket-0.3.6-py27_2
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install_dist gevent_zeromq-0.2.5-py27_2
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install_dist greenlet-0.4.0-py27_0
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install_dist grin-1.2.1-py27_1
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install_dist h5py-2.1.1-np17py27_0
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install_dist hdf5-1.8.9-0
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install_dist imaging-1.1.7-py27_2
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install_dist ipython-0.13.2-py27_0
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install_dist jinja2-2.6-py27_0
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install_dist jpeg-8d-0
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install_dist libdynd-0.3.0-0
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install_dist libevent-2.0.20-0
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install_dist libnetcdf-4.2.1.1-1
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install_dist libpng-1.5.13-1
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install_dist libxml2-2.9.0-0
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install_dist libxslt-1.1.28-0
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install_dist llvm-3.2-0
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install_dist llvmpy-0.11.2-py27_0
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install_dist lxml-3.2.0-py27_0
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install_dist matplotlib-1.2.1-np17py27_1
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install_dist mdp-3.3-np17py27_0
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install_dist meta-0.4.2.dev-py27_0
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install_dist mpi4py-1.3-py27_0
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install_dist mpich2-1.4.1p1-0
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install_dist netcdf4-1.0.4-np17py27_0
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install_dist networkx-1.7-py27_0
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install_dist nltk-2.0.4-np17py27_0
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install_dist nose-1.3.0-py27_0
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install_dist numba-0.8.1-np17py27_0
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install_dist numexpr-2.0.1-np17py27_3
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install_dist numpy-1.7.1-py27_0
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install_dist opencv-2.4.2-np17py27_1
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install_dist openssl-1.0.1c-0
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install_dist pandas-0.11.0-np17py27_1
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install_dist pip-1.3.1-py27_1
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install_dist pixman-0.26.2-0
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install_dist ply-3.4-py27_0
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install_dist psutil-0.7.1-py27_0
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install_dist py-1.4.12-py27_0
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install_dist py2cairo-1.10.0-py27_1
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install_dist pycosat-0.6.0-py27_0
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install_dist pycparser-2.9.1-py27_0
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install_dist pycrypto-2.6-py27_0
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install_dist pycurl-7.19.0-py27_2
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install_dist pyflakes-0.7.2-py27_0
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install_dist pygments-1.6-py27_0
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install_dist pyparsing-1.5.6-py27_0
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install_dist pysal-1.5.0-np17py27_1
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install_dist pysam-0.6-py27_0
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install_dist pyside-1.1.2-py27_0
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install_dist pytables-2.4.0-np17py27_0
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install_dist pytest-2.3.4-py27_1
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install_dist pytz-2013b-py27_0
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install_dist pyyaml-3.10-py27_0
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install_dist pyzmq-2.2.0.1-py27_1
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install_dist qt-4.7.4-0
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install_dist readline-6.2-0
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install_dist redis-2.6.9-0
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install_dist redis-py-2.7.2-py27_0
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install_dist requests-1.2.0-py27_0
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install_dist rope-0.9.4-py27_0
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install_dist scikit-image-0.8.2-np17py27_1
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install_dist scikit-learn-0.13.1-np17py27_0
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install_dist scipy-0.12.0-np17py27_0
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install_dist shiboken-1.1.2-py27_0
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install_dist six-1.3.0-py27_0
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install_dist sphinx-1.1.3-py27_3
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install_dist spyder-2.2.0-py27_0
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install_dist sqlalchemy-0.8.1-py27_0
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install_dist sqlite-3.7.13-0
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install_dist statsmodels-0.4.3-np17py27_1
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install_dist sympy-0.7.2-py27_0
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install_dist system-5.8-1
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install_dist theano-0.5.0-np17py27_1
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install_dist tk-8.5.13-0
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install_dist tornado-3.0.1-py27_0
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install_dist util-linux-2.21-0
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install_dist werkzeug-0.8.3-py27_0
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install_dist xlrd-0.9.2-py27_0
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install_dist xlwt-0.7.5-py27_0
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install_dist yaml-0.1.4-0
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install_dist zeromq-2.2.0-1
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install_dist zlib-1.2.7-0
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install_dist anaconda-1.5.0-np17py27_0
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mkdir $PREFIX/envs
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mkdir $HOME/.continuum 2>/dev/null
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PYTHON="$PREFIX/pkgs/python-2.7.4-0/bin/python -E"
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$PYTHON -V
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if (( $? )); then
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echo "ERROR:
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cannot execute native linux-64 binary, output from 'uname -a' is:" >&2
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uname -a
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exit 1
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fi
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echo "creating default environment..."
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CONDA_INSTALL="$PREFIX/pkgs/conda-1.5.2-py27_0/lib/python2.7/site-packages/conda/install.py"
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$PYTHON $CONDA_INSTALL --prefix=$PREFIX --pkgs-dir=$PREFIX/pkgs --link-all || exit 1
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echo "installation finished."
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if [[ $PYTHONPATH != "" ]]; then
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echo "WARNING:
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You current have a PYTHONPATH environment variable set. This may cause
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unexpected behavior when running the Python interpreter in Anaconda.
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For best results, please verify that your PYTHONPATH only points to
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directories of packages that are compatible with the Python interpreter
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in Anaconda: $PREFIX"
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fi
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echo "
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# added by Anaconda 1.5.0 installer
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export PATH=\"$PREFIX/bin:\$PATH\"" >>$BASH_RC
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rm "$THIS_DIR/Anaconda-1.5.0-Linux-x86_64.sh"
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exit 0

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