https://github.com/heuermh/googlegenomics-mapreduce-java

Uses the Java MapReduce for Google App Engine to create a variant similarity matrix and run PCA.
https://github.com/heuermh/googlegenomics-mapreduce-java

Last synced: 9 days ago
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Uses the Java MapReduce for Google App Engine to create a variant similarity matrix and run PCA.

• Host: GitHub
• URL: https://github.com/heuermh/googlegenomics-mapreduce-java
• Owner: heuermh
• License: apache-2.0
• Created: 2014-04-30T22:00:49.000Z (over 10 years ago)
• Default Branch: master
• Last Pushed: 2014-09-29T16:32:29.000Z (about 10 years ago)
• Last Synced: 2024-05-02T00:30:09.604Z (6 months ago)
• Language: Java
• Homepage:
• Size: 279 KB
• Stars: 0
• Watchers: 3
• Forks: 1
• Open Issues: 0
• Metadata Files:
  • Readme: README.rst
  • Contributing: CONTRIBUTING.rst
  • License: LICENSE

Awesome Lists containing this project

README

        
mapreduce-java  |Build Status|_

==============================

.. |Build Status| image:: https://travis-ci.org/googlegenomics/mapreduce-java.png?branch=master

.. _Build Status: https://travis-ci.org/googlegenomics/mapreduce-java

Note: The mapreduce code in googlegenomics will be replaced by 

`Spark `_ and 

Dataflow examples. This code is deprecated.

Getting started

---------------

To use, you will need to download `Apache Maven `_. Then run a local server::

  cd mapreduce-java

  mvn appengine:devserver

(note: currently authentication fails when running locally. fix coming)

Before deploying, make sure the constants in `appengine-web.xml `_ 

are set to correct values (bucket-name, api-key, etc). The application tag also needs to be set to a valid

app engine project ID.

Once that's done, deploy with::

  mvn appengine:update

Code layout

-----------

`MainServlet.java `_:

    currently all of the mapreduce code is in this file.

    

`PcaServlet.java `_:

    takes the variant similarity data from the map reduce, runs a PCA analysis, and 

    outputs the result as JSON so that it can be graphed inside of ``index.html``.

`WEB-INF/appengine-web.xml `_:

    is the appengine specific config, make sure to replace the dummy app engine project ID with your own value.

`WEB-INF/web.xml `_

    sets up the 3 servlets used by this application. 2 are handled by common app engine code.

    

    

Project status

--------------

Goals

~~~~~

* Provide a real world MapReduce example that uses the Genomics API (in Java).

* Prove that a MapReduce is both feasible and a good idea for Genomics data. 

  The resulting analysis should be useful.

Current status

~~~~~~~~~~~~~~

Deprecated.