https://github.com/heuermh/googlegenomics-api-provider-local-java

Implements the Google Genomics API locally, reading its data from local BAM files.
https://github.com/heuermh/googlegenomics-api-provider-local-java

Last synced: 9 days ago
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Implements the Google Genomics API locally, reading its data from local BAM files.

• Host: GitHub
• URL: https://github.com/heuermh/googlegenomics-api-provider-local-java
• Owner: heuermh
• License: apache-2.0
• Created: 2014-04-30T22:01:32.000Z (over 10 years ago)
• Default Branch: master
• Last Pushed: 2014-09-08T16:09:06.000Z (about 10 years ago)
• Last Synced: 2024-05-02T00:30:09.553Z (6 months ago)
• Language: Java
• Homepage:
• Size: 1.01 MB
• Stars: 0
• Watchers: 3
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.rst
  • Contributing: CONTRIBUTING.rst
  • License: LICENSE

Awesome Lists containing this project

README

        
api-provider-local-java  |Build Status|_

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

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

.. _Build Status: https://travis-ci.org/googlegenomics/api-provider-local-java

Note: this repo supports v0.1 of the GA4GH APIs. There is a different 

`python server `_ that will support v0.5 

and will make this repo obsolete.

.....

Getting started  

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

To use, first build the code using `Apache Maven `_::

  cd api-provider-local-java

  mvn package

Once built, use the jar file to start a local server::

  java -cp target/api-provider-local-java-v1beta-jar-with-dependencies.jar com.google.cloud.genomics.localrepo.Server --dataset=testdata:testdata

There are two command line flags available:

``--port=``:

  Sets the port that the server listens on for incoming connections. If

  unspecified, the default is 5000.

``--dataset=:``:

  This flag can occur zero or more times. With each instance of this flag, you

  supply a dataset ID and a path to a directory on your local filesystem. When

  the server is started, each directory is recursively traversed, and all ``.bam``

  files with a corresponding sibling ``.bai`` file are included into the data

  with the given dataset ID. For example, if you have the following directory

  layout::

    my_directory/

      my_subdirectory/

        foo.bam

        foo.bam.bai

      another_subdirectory/

        bar.bam

      baz.bam

      baz.bam.bai

  and you passed the flag ``--dataset=my_data:/path/to/my_directory``, then

  ``my_directory/my_subdirectory/foo.bam`` and ``my_directory/baz.bam`` would be

  included into a dataset with ID ``my_data``, but

  ``my_directory/another_subdirectory/bar.bam`` would be excluded, due to not

  having its sibling ``.bai`` file.

Go to ``http://localhost:/datasets`` to see your data.  

Project status

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

This repository has been replaced by the work on `ga4gh/server `_.