Looking at k-mer abundance distributionsΒΆ

Start up an Ubuntu 14.04 instance and run

sudo bash

apt-get update
apt-get -y install screen git curl gcc make g++ python-dev unzip \
        default-jre pkg-config libncurses5-dev r-base-core \
        r-cran-gplots python-matplotlib sysstat ipython-notebook

Install khmer:

cd /usr/local/share
git clone https://github.com/ged-lab/khmer.git
cd khmer
git checkout v1.1
make install

Download the notebook for today’s session:

cd /mnt
curl -O https://raw.githubusercontent.com/ngs-docs/angus/2014/files/kmer-abundance-distributions.ipynb

Run IPython Notebook:

ipython notebook --no-stdout --no-browser --ip='*' --port=80 --notebook-dir=/mnt

(Note: you can use:


instead if you want to store notebooks in your Dropbox.)

To connect to your notebook server, you need to enable inbound traffic on HTTP to your computer. Briefly, go to your instance and look at what security group you’re using (should be ‘launch-wizard-‘ something). On the left panel, under Network and Security, go into Security Groups. Select your security group, and select Inbound, and Edit. Click “Add rule”, and change “Custom TCP rule” to “http”. Then click “save”. Done!

Now, open your EC2 machine’s address in your Web browser.

LICENSE: This documentation and all textual/graphic site content is licensed under the Creative Commons - 0 License (CC0) -- fork @ github. Presentations (PPT/PDF) and PDFs are the property of their respective owners and are under the terms indicated within the presentation.
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