=================================
Day 2 - installation instructions
=================================

(Instructions mostly copied from :doc:`quality`!)

Use image "Ubuntu 14.04.3"

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 <http://khmer.readthedocs.io>`__
and `sourmash <http://sourmash.readthedocs.io/en/latest/>`__::

   source ~/.bashrc

   conda install -n root pip -y
   pip install https://github.com/dib-lab/khmer/archive/master.zip
   pip install https://github.com/dib-lab/sourmash/archive/2017-ucsc-metagenome.zip

(See `the sourmash docs for this workshop <sourmash.html>`__ for some
details on the sourmash install.)

Running Jupyter Notebook
------------------------

Let's also run a Jupyter Notebook in your home directory.  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 >> ~/.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! ::

  jupyter notebook &

This will output some stuff; to make the prompt appear again, hit ENTER
a few times.

You should now be able to visit port 8000 on your computer and see the
Jupyter console; to get the URL to Jupyter, run::

  echo http://$(hostname):8000/

.. note::

   If your network blocks port 8000 (e.g. cruznet at UCSC), you can run::

       ssh -N -f -L localhost:8000:localhost:8000 username@remotehost

   to tunnel the remote Jupyter notebook server over SSH.

We are now ready to `map and bin reads <https://2017-ucsc-metagenomics.readthedocs.io/en/latest/binning.html>`__ .