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tutorial.html
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tutorial.html
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<title>Running the khmer paper script pipeline</title>
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<div class="document" id="running-the-khmer-paper-script-pipeline">
<h1 class="title">Running the khmer paper script pipeline</h1>
<table class="docinfo" frame="void" rules="none">
<col class="docinfo-name" />
<col class="docinfo-content" />
<tbody valign="top">
<tr><th class="docinfo-name">Date:</th>
<td>June 20, 2013</td></tr>
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</table>
<p>Here are some brief notes on how to run the pipeline for our 2013
khmer counting paper on an Amazon EC2 rental instance. Using these
commands you should be able to completely recapitulate the paper.</p>
<p>The instructions below will reproduce all of the figures in the paper,
and will then compile the paper from scratch using the new figures.</p>
<p>(Note that you can also start with ami-61885608, which has all the
below software installed.) % not yet</p>
<div class="section" id="starting-up-a-machine-and-get-necessary-data-for-reproduction">
<h1>Starting up a machine and get necessary data for reproduction</h1>
<p>First, start up an EC2 instance using starcluster:</p>
<pre class="literal-block">
starcluster start -o -s 1 -i m2.2xlarge -n ami-999d49f0 pipeline
</pre>
<p>You can also do this via the AWS console; just use ami-999d49f0, and
start an instance with 30gb or more of memory.</p>
<p>Make sure that port 22 (SSH) and port 80 (HTTP) are open; you'll need
the first one to log in, and the second one to connect to the ipython
notebook.</p>
<p>Now, log in!</p>
<pre class="literal-block">
starcluster sshmaster pipeline
</pre>
<p>(or just ssh in however you would normally do it.)</p>
<p>First go to /mnt/ because we do not have enough space in home directory:</p>
<pre class="literal-block">
cd /mnt
</pre>
<p>Now, check out the source repository and grab the initial data
sets:</p>
<pre class="literal-block">
git clone https://github.com/ngs-docs/ngs-scripts
git clone https://github.com/ged-lab/2013-khmer-counting.git
cd 2013-khmer-counting
curl -O http://public.ged.msu.edu.s3.amazonaws.com/2013-khmer-counting/2013-khmer-counting-data.tar.gz
tar xzf 2013-khmer-counting-data.tar.gz
</pre>
</div>
<div class="section" id="installing-necessary-software">
<h1>Installing necessary software</h1>
<p>Before we get started, we need to install all the necessary software, including:</p>
<blockquote>
<ul class="simple">
<li>Tallymer</li>
<li>Jellyfish</li>
<li>DSK</li>
<li>ipython</li>
<li>LaTex</li>
<li>Velvet</li>
</ul>
</blockquote>
<p>To do so, run:</p>
<pre class="literal-block">
cd /mnt/2013-khmer-counting/pipeline
bash software_install.sh
</pre>
<!-- @CTB fix tags -->
<p>Next you'll need to install our packages 'screed' and 'khmer'.
In this case we're going to use the versions tagged for the paper</p>
<pre class="literal-block">
cd /usr/local/src
git clone git://github.com/ged-lab/screed.git
cd screed
git checkout 2013-khmer-counting
python setup.py install
cd ..
git clone http://github.com/ged-lab/khmer.git
cd khmer
git checkout 2013-khmer-counting
make test
cd ..
echo 'export PYTHONPATH=/usr/local/src/khmer/python' >> ~/.bashrc
echo 'export PATH=$PATH:/usr/local/src/khmer/scripts' >> ~/.bashrc
echo 'export PATH=$PATH:/usr/local/src/khmer/sandbox' >> ~/.bashrc
source ~/.bashrc
</pre>
<p>OK, now all your software is installed, hurrah!</p>
</div>
<div class="section" id="running-the-pipeline">
<h1>Running the pipeline</h1>
<p>Now go into the pipeline directory and run the pipeline. This will take a few
hours hours, so you might want to do it in 'screen' (see <a class="reference external" href="http://ged.msu.edu/angus/tutorials-2011/unix_long_jobs.html">"Running long jobs on
UNIX"</a>).</p>
<pre class="literal-block">
cd /mnt/2013-khmer-counting/pipeline
make KHMER=/usr/local/src/khmer
</pre>
<p>Once it successfully completes, copy the data over to the ../data/ directory:</p>
<pre class="literal-block">
make copydata
</pre>
<p>Run the ipython notebook server:</p>
<pre class="literal-block">
cd ../notebook
ipython notebook --pylab=inline --no-browser --ip=* --port=80 &
</pre>
<p>Connect into the ipython notebook (it will be running at '<a class="reference external" href="http:/">http:/</a>/<your EC2 hostname>'); if the above command succeeded but you can't connect in, you probably forgot to enable port 80 on your EC2 firewall.</p>
<p>Once you're connected in, select the 'khmer-counting' notebook (should be the
only one on the list) and open it. Once open, go to the 'Cell...' menu
and select 'Run all'.</p>
<p>Now go back to the command line and execute:</p>
<pre class="literal-block">
% cd ../
% make
</pre>
<p>and voila, 'khmer-counting.pdf' will contain the paper with the figures you just
created.</p>
</div>
</div>
</body>
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