Day 2 - installation instructions

(Instructions mostly copied from Short read quality and trimming!)

Use ami-05384865, with a 500 GB local disk (see: Start an Amazon Web Services computer:)

Make /mnt/ read/write:

sudo chmod a+rwxt /mnt

Run:

sudo apt-get -y update && \
sudo apt-get -y install trimmomatic fastqc python-pip \
   samtools zlib1g-dev ncurses-dev python-dev

Install anaconda:

curl -O https://repo.continuum.io/archive/Anaconda3-4.2.0-Linux-x86_64.sh
bash Anaconda3-4.2.0-Linux-x86_64.sh

Then update your environment and install khmer:

source ~/.bashrc

cd
git clone https://github.com/dib-lab/khmer.git
cd khmer
sudo python2 setup.py install

Running Jupyter Notebook

Let’s also run a Jupyter Notebook in /mnt. First, configure it a teensy bit more securely, and also have it run in the background.

Generate a config:

jupyter notebook --generate-config

Add a password, have it not run a browser, and put it on port 8000 by default:

cat >>/home/ubuntu/.jupyter/jupyter_notebook_config.py <<EOF
c = get_config()
c.NotebookApp.ip = '*'
c.NotebookApp.open_browser = False
c.NotebookApp.password = u'sha1:5d813e5d59a7:b4e430cf6dbd1aad04838c6e9cf684f4d76e245c'
c.NotebookApp.port = 8000

EOF

Now, run!

cd /mnt
jupyter notebook &

You should be able to visit port 8000 on your AWS computer and see the Jupyter console.

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