This notebook was designed to run the QIIME Illumina Overview Tutorial on the QIIME 1.9.1 Amazon Web Services EC2 instance. You can find the AMI ID on the QIIME resources page. These steps covered here are important for having multiple users working on a single IPython Notebook server, but are a little bit of overkill if you're running this on your own AWS instance. If you're running this on your own instance, you should instead work with the IPython Notebook linked from here.
In [ ]:
from random import choice
from os import chdir, mkdir, makedirs
from os.path import join
from IPython.display import FileLinks, FileLink
from functools import partial
# to support running in a multi-user environment, each user will work in
# a temporary working directory with a randomly generated name
basedir = "temp"
choices = "ABCDEFGHIJKLMNOPQRSTUVWXYZ"
choices += choices.lower()
working_dir = join(basedir,''.join([choice(choices) for i in range(12)]))
print "Your working directory is %s" % working_dir
makedirs(working_dir)
chdir(working_dir)
!wget ftp://ftp.microbio.me/qiime/tutorial_files/moving_pictures_tutorial-1.9.0.tgz
!tar -xzf moving_pictures_tutorial-1.9.0.tgz
chdir('moving_pictures_tutorial-1.9.0/illumina')
FileLink = partial(FileLink, url_prefix=join(working_dir, 'moving_pictures_tutorial-1.9.0/illumina/'))
FileLinks = partial(FileLinks, url_prefix=join(working_dir, 'moving_pictures_tutorial-1.9.0/illumina/'))
You can now get started. Follow the steps found in the Illumina Overview Tutorial. You should begin with the steps under Check our mapping file for errors (the Getting Started steps have already been completed when you executed the steps above).
In [ ]: