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command line interface
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Availablility
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The source code for the command line tool is available in our GitHub repository (`repo <https://github.com/GoyalLab/singletCodeTools/>`_). You can clone the reposiory to access the code locally.

.. code-block:: bash

    git clone https://github.com/GoyalLab/singletCodeTools/

Using the interface
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Navigating to commandLineTools folder, you will find 3 files and you will need to run  singletCodeCommandLine.py. There are 2 modules available, one to run singletCode and the other to create a sample sheet if you have used Watermelon barcoding techmology using the fastq sequenced files from MISEQ.

Detailed information about the modules in the command line interface
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.. automodule:: source.commandLineTools.singletCodeCommandLine